diff --git a/mrdna/arbdmodel/LICENSE b/mrdna/arbdmodel/LICENSE
new file mode 120000
index 0000000000000000000000000000000000000000..ea5b60640b01f74e295037aa8a6b7d4ea278a739
--- /dev/null
+++ b/mrdna/arbdmodel/LICENSE
@@ -0,0 +1 @@
+../LICENSE
\ No newline at end of file
diff --git a/mrdna/arbdmodel/README.md b/mrdna/arbdmodel/README.md
new file mode 120000
index 0000000000000000000000000000000000000000..32d46ee883b58d6a383eed06eb98f33aa6530ded
--- /dev/null
+++ b/mrdna/arbdmodel/README.md
@@ -0,0 +1 @@
+../README.md
\ No newline at end of file
diff --git a/mrdna/arbdmodel/__init__.py b/mrdna/arbdmodel/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..17082119bd78e8b9a9e2e82a01972cc37f1b6339
--- /dev/null
+++ b/mrdna/arbdmodel/__init__.py
@@ -0,0 +1,1379 @@
+# -*- coding: utf-8 -*-
+from pathlib import Path
+
+from .version import get_version
+__version__ = get_version()
+
+import numpy as np
+from copy import copy, deepcopy
+from inspect import ismethod
+import os, sys, subprocess
+
+_RESOURCE_DIR = Path(__file__).parent / 'resources'
+def get_resource_path(relative_path):
+ return _RESOURCE_DIR / relative_path
+
+## Abstract classes
+class Transformable():
+ def __init__(self, position, orientation=None):
+ self.position = np.array(position)
+ if orientation is not None:
+ orientation = np.array(orientation)
+ self.orientation = orientation
+
+ def transform(self, R = ((1,0,0),(0,1,0),(0,0,1)),
+ center = (0,0,0), offset = (0,0,0)):
+
+ R,center,offset = [np.array(x) for x in (R,center,offset)]
+
+ self.position = R.dot(self.position-center)+center+offset
+
+ if self.orientation is not None:
+ ## TODO: what if self.orientation is taken from parent?!
+ self.orientation = self.orientation.dot(R)
+ ...
+
+ def collapsedPosition(self):
+ # print("collapsedPosition called", type(self), self.name)
+ if isinstance(self, Child):
+ # print(self.parent, isinstance(self.parent,Transformable))
+ if isinstance(self.parent, Transformable):
+ return self.applyOrientation(self.position) + self.parent.collapsedPosition()
+
+ # if self.parent.orientation is not None:
+ # return self.parent.collapsedOrientation().dot(self.position) + self.parent.collapsedPosition()
+ return np.array(self.position) # return a copy
+
+ def applyOrientation(self,obj):
+ # print("applyOrientation called", self.name, obj)
+ if isinstance(self, Child):
+ # print( self.orientation, self.orientation is not None, None is not None )
+ # if self.orientation is not None:
+ # # print("applyOrientation applying", self, self.name, self.orientation)
+ # obj = self.orientation.dot(obj)
+ if isinstance(self.parent, Transformable):
+ if self.parent.orientation is not None:
+ obj = self.parent.orientation.dot(obj)
+ obj = self.parent.applyOrientation(obj)
+ # print("applyOrientation returning", self.name, obj)
+ return obj
+
+class Parent():
+ def __init__(self, children=None, remove_duplicate_bonded_terms=False):
+ self.children = []
+ if children is not None:
+ for x in children:
+ self.add(x)
+
+ self.remove_duplicate_bonded_terms = remove_duplicate_bonded_terms
+ self.bonds = []
+ self.angles = []
+ self.dihedrals = []
+ self.impropers = []
+ self.exclusions = []
+
+ self.rigid = False
+
+ ## TODO: self.cacheInvalid = True # What will be in the cache?
+
+ def add(self,x):
+ ## TODO: check the parent-child tree to make sure there are no cycles
+ if not isinstance(x,Child):
+ raise Exception('Attempted to add an object to a group that does not inherit from the "Child" type')
+
+ if x.parent is not None and x.parent is not self:
+ raise Exception("Child {} already belongs to some group".format(x))
+ x.parent = self
+ self.children.append(x)
+
+ def insert(self,idx,x):
+ ## TODO: check the parent-child tree to make sure there are no cycles
+ if not isinstance(x,Child):
+ raise Exception('Attempted to add an object to a group that does not inherit from the "Child" type')
+
+ if x.parent is not None and x.parent is not self:
+ raise Exception("Child {} already belongs to some group".format(x))
+ x.parent = self
+ self.children.insert(idx,x)
+
+ def index(self, x):
+ return self.children.index(x)
+
+ def clear_all(self, keep_children=False):
+ if keep_children == False:
+ for x in self.children:
+ x.parent = None
+ self.children = []
+ self.bonds = []
+ self.angles = []
+ self.dihedrals = []
+ self.impropers = []
+ self.exclusions = []
+
+ def remove(self,x):
+ if x in self.children:
+ self.children.remove(x)
+ if x.parent is self:
+ x.parent = None
+
+ def add_bond(self, i,j, bond, exclude=False):
+ assert( i is not j )
+ ## TODO: how to handle duplicating and cloning bonds
+ # beads = [b for b in self]
+ # for b in (i,j): assert(b in beads)
+ self.bonds.append( (i,j, bond, exclude) )
+
+ def add_angle(self, i,j,k, angle):
+ assert( len(set((i,j,k))) == 3 )
+ # beads = [b for b in self]
+ # for b in (i,j,k): assert(b in beads)
+ self.angles.append( (i,j,k, angle) )
+
+ def add_dihedral(self, i,j,k,l, dihedral):
+ assert( len(set((i,j,k,l))) == 4 )
+
+ # beads = [b for b in self]
+ # for b in (i,j,k,l): assert(b in beads)
+ self.dihedrals.append( (i,j,k,l, dihedral) )
+
+ def add_improper(self, i,j,k,l, dihedral):
+ # beads = [b for b in self]
+ # for b in (i,j,k,l): assert(b in beads)
+ self.impropers.append( (i,j,k,l, dihedral) )
+
+ def add_exclusion(self, i,j):
+ ## TODO: how to handle duplicating and cloning bonds
+ ## TODO: perform following check elsewhere
+ # beads = [b for b in self]
+ # for b in (i,j): assert(b in beads)
+ self.exclusions.append( (i,j) )
+
+ def get_restraints(self):
+ ret = []
+ for c in self.children:
+ ret.extend( c.get_restraints() )
+ return ret
+
+ def get_bonds(self):
+ ret = self.bonds
+ for c in self.children:
+ if isinstance(c,Parent): ret.extend( c.get_bonds() )
+ if self.remove_duplicate_bonded_terms:
+ return list(set(ret))
+ else:
+ return ret
+
+
+ def get_angles(self):
+ ret = self.angles
+ for c in self.children:
+ if isinstance(c,Parent): ret.extend( c.get_angles() )
+ if self.remove_duplicate_bonded_terms:
+ return list(set(ret))
+ else:
+ return ret
+
+ def get_dihedrals(self):
+ ret = self.dihedrals
+ for c in self.children:
+ if isinstance(c,Parent): ret.extend( c.get_dihedrals() )
+ if self.remove_duplicate_bonded_terms:
+ return list(set(ret))
+ else:
+ return ret
+
+ def get_impropers(self):
+ ret = self.impropers
+ for c in self.children:
+ if isinstance(c,Parent): ret.extend( c.get_impropers() )
+ if self.remove_duplicate_bonded_terms:
+ return list(set(ret))
+ else:
+ return ret
+
+ def get_exclusions(self):
+ ret = self.exclusions
+ for c in self.children:
+ if isinstance(c,Parent): ret.extend( c.get_exclusions() )
+ if self.remove_duplicate_bonded_terms:
+ return list(set(ret))
+ else:
+ return ret
+
+ ## Removed because prohibitively slow
+ # def remove_duplicate_terms(self):
+ # for key in "bonds angles dihedrals impropers exclusions".split():
+ # self.remove_duplicate_item(key)
+
+ # def remove_duplicate_item(self, dict_key, existing=None):
+ # if existing is None: existing = []
+ # ret = [i for i in list(set(self.__dict__[dict_key])) if i not in existing]
+ # self.__dict__[dict_key] = ret
+ # existing.extend(ret)
+ # for c in self.children:
+ # if isinstance(c,Parent):
+ # ret = ret + c.remove_duplicate_item(dict_key, existing)
+ # return ret
+
+
+ def __iter__(self):
+ ## TODO: decide if this is the nicest way to do it!
+ """Depth-first iteration through tree"""
+ for x in self.children:
+ if isinstance(x,Parent):
+ if isinstance(x,Clone) and not isinstance(x.get_original_recursively(),Parent):
+ yield x
+ else:
+ for y in x:
+ yield y
+ else:
+ yield x
+
+ def __len__(self):
+ l = 0
+ for x in self.children:
+ if isinstance(x,Parent):
+ l += len(x)
+ else:
+ l += 1
+ return l
+
+ def __getitem__(self, i):
+ return self.children[i]
+
+ def __setitem__(self, i, val):
+ x = self.children[i]
+ x.parent = None
+ val.parent = self
+ self.children[i] = val
+
+class Child():
+ def __init__(self, parent=None):
+ self.parent = parent
+ if parent is not None:
+ assert( isinstance(parent, Parent) )
+ parent.children.append(self)
+
+ def __getattr__(self, name):
+ """
+ Try to get attribute from the parent
+
+ """
+ # if self.parent is not None:
+ if "parent" not in self.__dict__ or self.__dict__["parent"] is None or name is "children":
+ raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
+
+
+ excluded_attributes = ['parent','rigid']
+ if name in excluded_attributes:
+ raise AttributeError("'{}' object has no attribute '{}' and cannot look it up from the parent".format(type(self).__name__, name))
+
+ ## TODO: determine if there is a way to avoid __getattr__ if a method is being looked up
+ try:
+ ret = getattr(self.parent,name)
+ except:
+ raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
+ if ismethod(ret):
+ raise AttributeError("'{}' object has no method '{}'".format(type(self).__name__, name))
+ return ret
+
+
+ # def __getstate__(self):
+ # print("Child getstate called", self)
+ # print(self.__dict__)
+ # return (self.__dict__,)
+
+ # def __setstate__(self, state):
+ # self.__dict__, = state
+
+class Clone(Transformable, Parent, Child):
+ def __init__(self, original, parent=None,
+ position = None,
+ orientation = None):
+ if position is None and original.position is not None:
+ position = np.array( original.position )
+ if orientation is None and original.orientation is not None:
+ orientation = np.array( original.orientation )
+ if parent is None:
+ parent = original.parent
+ self.original = original
+ Child.__init__(self, parent)
+ Transformable.__init__(self, position, orientation)
+
+ ## TODO: keep own bond_list, etc, update when needed original changes
+
+ if "children" in original.__dict__ and len(original.children) > 0:
+ self.children = [Clone(c, parent = self) for c in original.children]
+ else:
+ self.children = []
+
+ def get_original_recursively(self):
+ if isinstance(self.original, Clone):
+ return self.original.get_original_recursively()
+ else:
+ return self.original
+
+ def __getattr__(self, name):
+ """
+ Try to get attribute from the original without descending the tree heirarchy, then look up parent
+
+ TODO: handle PointParticle lookups into ParticleType
+ """
+ # print("Clone getattr",name)
+ if name in self.original.__dict__:
+ return self.original.__dict__[name]
+ else:
+ if "parent" not in self.__dict__ or self.__dict__["parent"] is None:
+ raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
+ return getattr(self.parent, name)
+
+
+## Particle classes
+class ParticleType():
+ """Class that hold common attributes that particles can point to"""
+
+ excludedAttributes = ("idx","type_",
+ "position",
+ "children",
+ "parent", "excludedAttributes","rigid"
+ )
+
+ def __init__(self, name, charge=0, parent=None, **kargs):
+ """ Parent type is used to fall back on for nonbonded interactions if this type is not specifically referenced """
+
+ self.name = name
+ self.charge = charge
+ self.parent = parent
+
+ for key in ParticleType.excludedAttributes:
+ assert( key not in kargs )
+
+ for key,val in kargs.items():
+ self.__dict__[key] = val
+
+ def is_same_type(self, other):
+ assert(isinstance(other,ParticleType))
+ if self == other:
+ return True
+ elif self.parent is not None and self.parent == other:
+ return True
+ else:
+ return False
+
+ def __hash_key(self):
+ l = [self.name,self.charge]
+ for keyval in sorted(self.__dict__.items()):
+ if isinstance(keyval[1], list): keyval = (keyval[0],tuple(keyval[1]))
+ l.extend(keyval)
+ return tuple(l)
+
+ def __hash__(self):
+ return hash(self.__hash_key())
+
+ def _equal_check(a,b):
+ if a.name == b.name:
+ if a.__hash_key() != b.__hash_key():
+ raise Exception("Two different ParticleTypes have same 'name' attribute")
+
+ def __eq__(a,b):
+ a._equal_check(b)
+ return a.name == b.name
+ def __lt__(a,b):
+ a._equal_check(b)
+ return a.name < b.name
+ def __le__(a,b):
+ a._equal_check(b)
+ return a.name <= b.name
+ def __gt__(a,b):
+ a._equal_check(b)
+ return a.name > b.name
+ def __ge__(a,b):
+ a._equal_check(b)
+ return a.name >= b.name
+
+ def __repr__(self):
+ return '<{} {}{}>'.format( type(self), self.name, '[{}]'.format(self.parent) if self.parent is not None else '' )
+
+
+class PointParticle(Transformable, Child):
+ def __init__(self, type_, position, name="A", **kwargs):
+ parent = None
+ if 'parent' in kwargs:
+ parent = kwargs['parent']
+ Child.__init__(self, parent=parent)
+ Transformable.__init__(self,position)
+
+ self.type_ = type_
+ self.idx = None
+ self.name = name
+ self.counter = 0
+ self.restraints = []
+
+ for key,val in kwargs.items():
+ self.__dict__[key] = val
+
+ def add_restraint(self, restraint):
+ ## TODO: how to handle duplicating and cloning bonds
+ self.restraints.append( restraint )
+
+ def get_restraints(self):
+ return [(self,r) for r in self.restraints]
+
+ def duplicate(self):
+ new = deepcopy(self)
+ return new
+
+ def __getattr__(self, name):
+ """
+ First try to get attribute from the parent, then type_
+
+ Note that this data structure seems to be fragile, can result in stack overflow
+
+ """
+ # return Child.__getattr__(self,name)
+ try:
+ return Child.__getattr__(self,name)
+ except Exception as e:
+ if 'type_' in self.__dict__:
+ return getattr(self.type_, name)
+ else:
+ raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
+
+ def _get_psfpdb_dictionary(self):
+ p = self
+ try:
+ segname = p.segname
+ except:
+ segname = "A"
+ try:
+ chain = p.chain
+ except:
+ chain = "A"
+ try:
+ resname = p.resname
+ except:
+ resname = p.name[:3]
+ try:
+ resid = p.resid
+ except:
+ resid = p.idx+1
+ try:
+ mass = p.mass
+ except:
+ mass = 1
+
+ try:
+ occ = p.occupancy
+ except:
+ occ = 0
+ try:
+ beta = p.beta
+ except:
+ beta = 0
+
+ data = dict(segname = segname,
+ resname = resname,
+ name = str(p.name)[:4],
+ chain = chain[0],
+ resid = int(resid),
+ idx = p.idx+1,
+ type = p.type_.name[:7],
+ charge = p.charge,
+ mass = mass,
+ occupancy = occ,
+ beta = beta
+ )
+ return data
+
+
+class Group(Transformable, Parent, Child):
+
+ def __init__(self, name=None, children = None, parent=None,
+ position = np.array((0,0,0)),
+ orientation = np.array(((1,0,0),(0,1,0),(0,0,1))),
+ remove_duplicate_bonded_terms = False,
+ **kwargs):
+
+ Transformable.__init__(self, position, orientation)
+ Child.__init__(self, parent) # Initialize Child first
+ Parent.__init__(self, children, remove_duplicate_bonded_terms)
+ self.name = name
+ self.isClone = False
+
+ for key,val in kwargs.items():
+ self.__dict__[key] = val
+
+
+ def clone(self):
+ return Clone(self)
+ g = copy(self)
+ g.isClone = True # TODO: use?
+ g.children = [copy(c) for c in g.children]
+ for c in g.children:
+ c.parent = g
+ return g
+ g = Group(position = self.position,
+ orientation = self.orientation)
+ g.children = self.children # lists point to the same object
+
+ def duplicate(self):
+ new = deepcopy(self)
+ for c in new.children:
+ c.parent = new
+ return new
+ # Group(position = self.position,
+ # orientation = self.orientation)
+ # g.children = deepcopy self.children.deepcopy() # lists are the same object
+
+ ## TODO override deepcopy so parent can be excluded from copying?
+
+ # def __getstate__(self):
+ # return (self.children, self.parent, self.position, self.orientation)
+
+ # def __setstate__(self, state):
+ # self.children, self.parent, self.position, self.orientation = state
+
+
+class PdbModel(Transformable, Parent):
+
+ def __init__(self, children=None, dimensions=None, remove_duplicate_bonded_terms=False):
+ Transformable.__init__(self,(0,0,0))
+ Parent.__init__(self, children, remove_duplicate_bonded_terms)
+ self.dimensions = dimensions
+ self.particles = [p for p in self]
+ self.cacheInvalid = True
+
+ def _updateParticleOrder(self):
+ pass
+
+ def writePdb(self, filename, beta_from_fixed=False):
+ if self.cacheInvalid:
+ self._updateParticleOrder()
+ with open(filename,'w') as fh:
+ ## Write header
+ fh.write("CRYST1{:>9.3f}{:>9.3f}{:>9.3f} 90.00 90.00 90.00 P 1 1\n".format( *self.dimensions ))
+
+ ## Write coordinates
+ formatString = "ATOM {idx:>6.6s} {name:^4.4s} {resname:3.3s} {chain:1.1s}{resid:>5.5s} {x:8.8s}{y:8.8s}{z:8.8s}{occupancy:6.2f}{beta:6.2f} {charge:2d}{segname:>6s}\n"
+ for p in self.particles:
+ ## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
+ data = p._get_psfpdb_dictionary()
+ idx = data['idx']
+
+ if np.log10(idx) >= 5:
+ idx = " *****"
+ else:
+ idx = "{:>6d}".format(idx)
+ data['idx'] = idx
+
+ if beta_from_fixed:
+ data['beta'] = 1 if 'fixed' in p.__dict__ else 0
+
+ pos = p.collapsedPosition()
+ dig = [max(int(np.log10(np.abs(x)+1e-6)//1),0)+1 for x in pos]
+ for d in dig: assert( d <= 7 )
+ # assert( np.all(dig <= 7) )
+ fs = ["{: %d.%df}" % (8,7-d) for d in dig]
+ x,y,z = [f.format(x) for f,x in zip(fs,pos)]
+ data['x'] = x
+ data['y'] = y
+ data['z'] = z
+ assert(data['resid'] < 1e5)
+ data['charge'] = int(data['charge'])
+ data['resid'] = "{:<4d}".format(data['resid'])
+ fh.write( formatString.format(**data) )
+
+ return
+
+ def writePsf(self, filename):
+ if self.cacheUpToDate == False:
+ self._updateParticleOrder()
+ with open(filename,'w') as fh:
+ ## Write header
+ fh.write("PSF NAMD\n\n") # create NAMD formatted psf
+ fh.write("{:>8d} !NTITLE\n\n".format(0))
+
+ ## ATOMS section
+ fh.write("{:>8d} !NATOM\n".format(len(self.particles)))
+
+ ## From vmd/plugins/molfile_plugin/src/psfplugin.c
+ ## "%d %7s %10s %7s %7s %7s %f %f"
+ formatString = "{idx:>8d} {segname:7.7s} {resid:<10.10s} {resname:7.7s}" + \
+ " {name:7.7s} {type:7.7s} {charge:f} {mass:f}\n"
+ for p in self.particles:
+ data = p._get_psfpdb_dictionary()
+ data['resid'] = "%d%c%c" % (data['resid']," "," ") # TODO: work with large indices
+ fh.write( formatString.format(**data) )
+ fh.write("\n")
+
+ ## Write out bonds
+ bonds = self.get_bonds()
+ fh.write("{:>8d} !NBOND\n".format(len(bonds)))
+ counter = 0
+ for p1,p2,b,ex in bonds:
+ fh.write( "{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1) )
+ counter += 1
+ if counter == 4:
+ fh.write("\n")
+ counter = 0
+ else:
+ fh.write(" ")
+ fh.write("\n" if counter == 0 else "\n\n")
+
+ ## Write out angles
+ angles = self.get_angles()
+ fh.write("{:>8d} !NTHETA\n".format(len(angles)))
+ counter = 0
+ for p1,p2,p3,a in angles:
+ fh.write( "{:>8d}{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1,p3.idx+1) )
+ counter += 1
+ if counter == 3:
+ fh.write("\n")
+ counter = 0
+ else:
+ fh.write(" ")
+ fh.write("\n" if counter == 0 else "\n\n")
+
+ ## Write out dihedrals
+ dihedrals = self.get_dihedrals()
+ fh.write("{:>8d} !NPHI\n".format(len(dihedrals)))
+ counter = 0
+ for p1,p2,p3,p4,a in dihedrals:
+ fh.write( "{:>8d}{:>8d}{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1,p3.idx+1,p4.idx+1) )
+ counter += 1
+ if counter == 2:
+ fh.write("\n")
+ counter = 0
+ else:
+ fh.write(" ")
+ fh.write("\n" if counter == 0 else "\n\n")
+
+ ## Write out impropers
+ impropers = self.get_impropers()
+ fh.write("{:>8d} !NIMPHI\n".format(len(impropers)))
+ counter = 0
+ for p1,p2,p3,p4,a in impropers:
+ fh.write( "{:>8d}{:>8d}{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1,p3.idx+1,p4.idx+1) )
+ counter += 1
+ if counter == 2:
+ fh.write("\n")
+ counter = 0
+ else:
+ fh.write(" ")
+ fh.write("\n" if counter == 0 else "\n\n")
+
+ fh.write("\n{:>8d} !NDON: donors\n\n\n".format(0))
+ fh.write("\n{:>8d} !NACC: acceptors\n\n\n".format(0))
+ fh.write("\n 0 !NNB\n\n")
+ natoms = len(self.particles)
+ for i in range(natoms//8):
+ fh.write(" 0 0 0 0 0 0 0 0\n")
+ for i in range(natoms-8*(natoms//8)):
+ fh.write(" 0")
+ fh.write("\n\n 1 0 !NGRP\n\n")
+
+
+class ArbdModel(PdbModel):
+ def __init__(self, children, origin=None, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6,
+ particle_integrator = 'Brown',
+ cutoff=50, decomp_period=1000, pairlist_distance=None, nonbonded_resolution=0.1,
+ remove_duplicate_bonded_terms=True, extra_bd_file_lines=""):
+
+ PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms)
+ self.origin = origin
+ self.temperature = temperature
+
+ self.timestep = timestep
+ self.cutoff = cutoff
+
+ self.particle_integrator = particle_integrator
+
+ if pairlist_distance == None:
+ pairlist_distance = cutoff+30
+
+ self.decomp_period = decomp_period
+ self.pairlist_distance = pairlist_distance
+
+ self.extra_bd_file_lines = extra_bd_file_lines
+
+ self.numParticles = 0
+ self.particles = []
+ self.type_counts = None
+
+ self.nbSchemes = []
+ self._nbParamFiles = [] # This could be made more robust
+ self.nbResolution = 0.1
+
+ self._written_bond_files = dict()
+
+ self.cacheUpToDate = False
+
+ def clear_all(self, keep_children=False):
+ Parent.clear_all(self, keep_children=keep_children)
+ self.particles = []
+ self.numParticles = 0
+ self.type_counts = None
+ self._nbParamFiles = []
+ self._written_bond_files = dict()
+
+ def _getNbScheme(self, typeA, typeB):
+ scheme = None
+ for s,A,B in self.nbSchemes:
+ if A is None or B is None:
+ if A is None and B is None:
+ return s
+ elif A is None and typeB.is_same_type(B):
+ return s
+ elif B is None and typeA.is_same_type(A):
+ return s
+ elif typeA.is_same_type(A) and typeB.is_same_type(B):
+ return s
+ raise Exception("No nonbonded scheme found for %s and %s" % (typeA.name, typeB.name))
+
+ def _countParticleTypes(self):
+ ## TODO: check for modifications to particle that require
+ ## automatic generation of new particle type
+ type_counts = dict()
+ for p in self:
+ t = p.type_
+ if t in type_counts:
+ type_counts[t] += 1
+ else:
+ type_counts[t] = 1
+ self.type_counts = type_counts
+
+ def _updateParticleOrder(self):
+ ## Create ordered list
+ self.particles = [p for p in self]
+ # self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))
+
+ ## Update particle indices
+ for p,i in zip(self.particles,range(len(self.particles))):
+ p.idx = i
+
+ # self.initialCoords = np.array([p.initialPosition for p in self.particles])
+
+ def useNonbondedScheme(self, nbScheme, typeA=None, typeB=None):
+ self.add_nonbonded_scheme(nbScheme, typeA, typeB)
+
+ def add_nonbonded_scheme(self, nonbonded_scheme, typeA=None, typeB=None):
+ self.nbSchemes.append( (nonbonded_scheme, typeA, typeB) )
+ if typeA != typeB:
+ self.nbSchemes.append( (nonbonded_scheme, typeB, typeA) )
+
+ def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', restart_file=None, replicas=1, log_file=None, dry_run = False):
+ assert(type(gpu) is int)
+ num_steps = int(num_steps)
+
+ d_orig = os.getcwd()
+ try:
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ os.chdir(directory)
+
+ if timestep is not None:
+ self.timestep = timestep
+
+ if self.cacheUpToDate == False: # TODO: remove cache?
+ self._countParticleTypes()
+ self._updateParticleOrder()
+
+ if output_directory == '': output_directory='.'
+
+ if dry_run:
+ if arbd is None: arbd='arbd'
+ else:
+ if arbd is None:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ fname = os.path.join(path, "arbd")
+ if os.path.isfile(fname) and os.access(fname, os.X_OK):
+ arbd = fname
+ break
+
+ if arbd is None: raise Exception("ARBD was not found")
+
+ if not os.path.exists(arbd):
+ raise Exception("ARBD was not found")
+ if not os.path.isfile(arbd):
+ raise Exception("ARBD was not found")
+ if not os.access(arbd, os.X_OK):
+ raise Exception("ARBD is not executable")
+
+
+ if not os.path.exists(output_directory):
+ os.makedirs(output_directory)
+ elif not os.path.isdir(output_directory):
+ raise Exception("output_directory '%s' is not a directory!" % output_directory)
+
+
+ self.writePdb( output_name + ".pdb" )
+ self.writePsf( output_name + ".psf" )
+ self.writeArbdFiles( output_name, numSteps=num_steps, outputPeriod=output_period, restart_file=restart_file )
+ os.sync()
+
+ ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
+
+ cmd = [arbd, '-g', "%d" % gpu]
+ if replicas > 1:
+ cmd = cmd + ['-r',replicas]
+ cmd = cmd + ["%s.bd" % output_name, "%s/%s" % (output_directory, output_name)]
+ cmd = tuple(str(x) for x in cmd)
+
+ if dry_run:
+ print("Run with: %s" % " ".join(cmd))
+ else:
+ print("Running ARBD with: %s" % " ".join(cmd))
+ if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
+ fd = sys.stdout if log_file is None else log_file
+ process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for line in process.stdout:
+ fd.write(line)
+ fd.flush()
+ else:
+ with open(log_file,'w') as fd:
+ process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
+ process.communicate()
+
+ except:
+ raise
+ finally:
+ os.chdir(d_orig)
+
+
+ # -------------------------- #
+ # Methods for printing model #
+ # -------------------------- #
+
+ def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000, restart_file=None):
+ ## TODO: save and reference directories and prefixes using member data
+ d = self.potential_directory = "potentials"
+ if not os.path.exists(d):
+ os.makedirs(d)
+ self._restraint_filename = "%s/%s.restraint.txt" % (d, prefix)
+ self._bond_filename = "%s/%s.bonds.txt" % (d, prefix)
+ self._angle_filename = "%s/%s.angles.txt" % (d, prefix)
+ self._dihedral_filename = "%s/%s.dihedrals.txt" % (d, prefix)
+ self._exclusion_filename = "%s/%s.exculsions.txt" % (d, prefix)
+
+ # self._writeArbdCoordFile( prefix + ".coord.txt" )
+ self._writeArbdParticleFile( prefix + ".particles.txt" )
+ self._writeArbdRestraintFile()
+ self._writeArbdBondFile()
+ self._writeArbdAngleFile()
+ self._writeArbdDihedralFile()
+ self._writeArbdExclusionFile()
+ self._writeArbdPotentialFiles( prefix, directory = d )
+ self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod, restart_file=restart_file )
+
+ # def _writeArbdCoordFile(self, filename):
+ # with open(filename,'w') as fh:
+ # for p in self.particles:
+ # fh.write("%f %f %f\n" % tuple(x for x in p.collapsedPosition()))
+
+ def _writeArbdParticleFile(self, filename):
+ with open(filename,'w') as fh:
+ if self.particle_integrator == "Brown":
+ for p in self.particles:
+ data = tuple([p.idx,p.type_.name] + [x for x in p.collapsedPosition()])
+ fh.write("ATOM %d %s %f %f %f\n" % data)
+ else:
+ for p in self.particles:
+ data = [p.idx,p.type_.name] + [x for x in p.collapsedPosition()]
+ try:
+ data = data + p.momentum
+ except:
+ try:
+ data = data + p.velocity*p.mass
+ except:
+ data = data + [0,0,0]
+ fh.write("ATOM %d %s %f %f %f %f %f %f\n" % tuple(data))
+
+ def _write_rigid_group_file(self, filename, groups):
+ with open(filename,'w') as fh:
+ for g in groups:
+ fh.write("#Group\n")
+ try:
+ if len(g.trans_damping) != 3: raise
+ fh.write(" ".join(str(v) for v in g.trans_damping) + " ")
+ except:
+ raise ValueError("Group {} lacks 3-value 'trans_damping' attribute")
+ try:
+ if len(g.rot_damping) != 3: raise
+ fh.write(" ".join(str(v) for v in g.rot_damping) + " ")
+ except:
+ raise ValueError("Group {} lacks 3-value 'rot_damping' attribute")
+ fh.write("{}\n".format(len(g)))
+ particles = [p for p in g]
+
+ def chunks(l, n):
+ """Yield successive n-sized chunks from l."""
+ for i in range(0, len(l), n):
+ yield l[i:i + n]
+
+ for c in chunks(particles,8):
+ fh.write(" ".join(str(p.idx) for p in c) + "\n")
+
+
+ def _writeArbdConf(self, prefix, randomSeed=None, numSteps=100000000, outputPeriod=10000, restart_file=None):
+ ## TODO: raise exception if _writeArbdPotentialFiles has not been called
+ filename = "%s.bd" % prefix
+
+ ## Prepare a dictionary to fill in placeholders in the configuration file
+ params = self.__dict__.copy() # get parameters from System object
+
+ if randomSeed is None:
+ params['randomSeed'] = ""
+ else:
+ params['randomSeed'] = "seed %s" % randomSeed
+ params['numSteps'] = int(numSteps)
+
+ # params['coordinateFile'] = "%s.coord.txt" % prefix
+ params['particleFile'] = "%s.particles.txt" % prefix
+ if restart_file is None:
+ params['restartCoordinates'] = ""
+ else:
+ params['restartCoordinates'] = "restartCoordinates %s" % restart_file
+ params['outputPeriod'] = outputPeriod
+
+ for k,v in zip('XYZ', self.dimensions):
+ params['dim'+k] = v
+
+ if self.origin is None:
+ for k,v in zip('XYZ', self.dimensions):
+ params['origin'+k] = -v*0.5
+ else:
+ for k,v in zip('XYZ', self.origin):
+ params['origin'+k] = v
+
+ params['pairlist_distance'] -= params['cutoff']
+
+ """ Find rigid groups """
+ rigid_groups = []
+ def get_rigid_groups(parent):
+ ret_list = []
+ for c in parent.children:
+ is_rigid = c.rigid if 'rigid' in c.__dict__ else False
+ if is_rigid:
+ rigid_groups.append(c)
+ elif isinstance(c,Group):
+ get_rigid_groups(c)
+ get_rigid_groups(self)
+
+ if len(rigid_groups) > 0:
+ self.particle_integrator = 'FusDynamic'
+ rb_group_filename = "{}.rb-group.txt".format(prefix)
+ params['particle_integrator'] = """FusDynamics
+groupFileName {}
+scaleFactor 0.05""".format(rb_group_filename)
+ self._write_rigid_group_file(rb_group_filename, rigid_groups)
+
+ ## Actually write the file
+ with open(filename,'w') as fh:
+ fh.write("""{randomSeed}
+timestep {timestep}
+steps {numSteps}
+numberFluct 0 # deprecated
+
+interparticleForce 1 # other values deprecated
+fullLongRange 0 # deprecated
+temperature {temperature}
+ParticleDynamicType {particle_integrator}
+
+outputPeriod {outputPeriod}
+## Energy doesn't actually get printed!
+outputEnergyPeriod {outputPeriod}
+outputFormat dcd
+
+## Infrequent domain decomposition because this kernel is still very slow
+decompPeriod {decomp_period}
+cutoff {cutoff}
+pairlistDistance {pairlist_distance}
+
+origin {originX} {originY} {originZ}
+systemSize {dimX} {dimY} {dimZ}
+
+{extra_bd_file_lines}
+\n""".format(**params))
+
+ ## Write entries for each type of particle
+ for pt,num in self.getParticleTypesAndCounts():
+ ## TODO create new particle types if existing has grid
+ particleParams = pt.__dict__.copy()
+ particleParams['num'] = num
+ if self.particle_integrator in ('Brown','Brownian'):
+ try:
+ D = pt.diffusivity
+ except:
+ """ units "k K/(amu/ns)" "AA**2/ns" """
+ D = 831447.2 * self.temperature / (pt.mass * pt.damping_coefficient)
+ particleParams['dynamics'] = 'diffusion {D}'.format(D = D)
+ elif self.particle_integrator in ('Langevin','FusDynamic'):
+ try:
+ gamma = pt.damping_coefficient
+ except:
+ """ units "k K/(AA**2/ns)" "amu/ns" """
+ gamma = 831447.2 * self.temperature / (pt.mass*pt.diffusivity)
+ particleParams['dynamics'] = """mass {mass}
+transDamping {g} {g} {g}
+""".format(mass=pt.mass, g=gamma)
+ else:
+ raise ValueError("Unrecognized particle integrator '{}'".format(self.particle_integrator))
+ fh.write("""
+particle {name}
+num {num}
+{dynamics}
+""".format(**particleParams))
+ if 'grid' in particleParams:
+ if not isinstance(pt.grid, list): pt.grid = [pt.grid]
+ for g,s in pt.grid:
+ ## TODO, use Path.relative_to?
+ try:
+ fh.write("gridFile {}\n".format(g.relative_to(os.getcwd())))
+ except:
+ fh.write("gridFile {}\n".format(g))
+
+ fh.write("gridFileScale {}\n".format(s))
+
+ else:
+ fh.write("gridFile {}/null.dx\n".format(self.potential_directory))
+
+ ## Write coordinates and interactions
+ fh.write("""
+## Input coordinates
+inputParticles {particleFile}
+{restartCoordinates}
+
+## Interaction potentials
+tabulatedPotential 1
+## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file
+""".format(**params))
+ for pair,f in zip(self._particleTypePairIter(), self._nbParamFiles):
+ i,j,t1,t2 = pair
+ fh.write("tabulatedFile %d@%d@%s\n" % (i,j,f))
+
+ ## Bonded interactions
+ restraints = self.get_restraints()
+ bonds = self.get_bonds()
+ angles = self.get_angles()
+ dihedrals = self.get_dihedrals()
+ exclusions = self.get_exclusions()
+
+ if len(bonds) > 0:
+ for b in list(set([b for i,j,b,ex in bonds])):
+ fh.write("tabulatedBondFile %s\n" % b)
+
+ if len(angles) > 0:
+ for b in list(set([b for i,j,k,b in angles])):
+ fh.write("tabulatedAngleFile %s\n" % b)
+
+ if len(dihedrals) > 0:
+ for b in list(set([b for i,j,k,l,b in dihedrals])):
+ fh.write("tabulatedDihedralFile %s\n" % b)
+
+ if len(restraints) > 0:
+ fh.write("inputRestraints %s\n" % self._restraint_filename)
+ if len(bonds) > 0:
+ fh.write("inputBonds %s\n" % self._bond_filename)
+ if len(angles) > 0:
+ fh.write("inputAngles %s\n" % self._angle_filename)
+ if len(dihedrals) > 0:
+ fh.write("inputDihedrals %s\n" % self._dihedral_filename)
+ if len(exclusions) > 0:
+ fh.write("inputExcludes %s\n" % self._exclusion_filename)
+
+ write_null_dx = False
+ for pt,num in self.getParticleTypesAndCounts():
+ if "grid" not in pt.__dict__:
+ gridfile = "{}/null.dx".format(self.potential_directory)
+ with open(gridfile, 'w') as fh:
+ fh.write("""object 1 class gridpositions counts 2 2 2
+origin {originX} {originY} {originZ}
+delta {dimX} 0.000000 0.000000
+delta 0.000000 {dimY} 0.000000
+delta 0.000000 0.000000 {dimZ}
+object 2 class gridconnections counts 2 2 2
+object 3 class array type float rank 0 items 8 data follows
+0.0 0.0 0.0
+0.0 0.0 0.0
+0.0 0.0
+attribute "dep" string "positions"
+object "density" class field
+component "positions" value 1
+component "connections" value 2
+component "data" value 3
+""".format(**params))
+ break
+
+ def getParticleTypesAndCounts(self):
+ ## TODO: remove(?)
+ return sorted( self.type_counts.items(), key=lambda x: x[0] )
+
+ def _particleTypePairIter(self):
+ typesAndCounts = self.getParticleTypesAndCounts()
+ for i in range(len(typesAndCounts)):
+ t1 = typesAndCounts[i][0]
+ for j in range(i,len(typesAndCounts)):
+ t2 = typesAndCounts[j][0]
+ yield( (i,j,t1,t2) )
+
+ def _writeArbdPotentialFiles(self, prefix, directory = "potentials"):
+ try:
+ os.makedirs(directory)
+ except OSError:
+ if not os.path.isdir(directory):
+ raise
+
+ pathPrefix = "%s/%s" % (directory,prefix)
+ self._writeNonbondedParameterFiles( pathPrefix + "-nb" )
+ # self._writeBondParameterFiles( pathPrefix )
+ # self._writeAngleParameterFiles( pathPrefix )
+ # self._writeDihedralParameterFiles( pathPrefix )
+
+ def _writeNonbondedParameterFiles(self, prefix):
+ x = np.arange(0, self.cutoff, self.nbResolution)
+ for i,j,t1,t2 in self._particleTypePairIter():
+ f = "%s.%s-%s.dat" % (prefix, t1.name, t2.name)
+ scheme = self._getNbScheme(t1,t2)
+ scheme.write_file(f, t1, t2, rMax = self.cutoff)
+ self._nbParamFiles.append(f)
+
+ def _getNonbondedPotential(self,x,a,b):
+ return a*(np.exp(-x/b))
+
+ def _writeArbdRestraintFile( self ):
+ with open(self._restraint_filename,'w') as fh:
+ for i,restraint in self.get_restraints():
+ item = [i.idx]
+ if len(restraint) == 1:
+ item.append(restraint[0])
+ item.extend(i.get_collapsed_position())
+ elif len(restraint) == 2:
+ item.append(restraint[0])
+ item.extend(restraint[1])
+ elif len(restraint) == 5:
+ item.extend(restraint)
+ fh.write("RESTRAINT %d %f %f %f %f\n" % tuple(item))
+
+ def _writeArbdBondFile( self ):
+ for b in list( set( [b for i,j,b,ex in self.get_bonds()] ) ):
+ if type(b) is not str and not isinstance(b, Path):
+ b.write_file()
+
+ with open(self._bond_filename,'w') as fh:
+ for i,j,b,ex in self.get_bonds():
+ item = (i.idx, j.idx, str(b))
+ if ex:
+ fh.write("BOND REPLACE %d %d %s\n" % item)
+ else:
+ fh.write("BOND ADD %d %d %s\n" % item)
+
+ def _writeArbdAngleFile( self ):
+ for b in list( set( [b for i,j,k,b in self.get_angles()] ) ):
+ if type(b) is not str and not isinstance(b, Path):
+ b.write_file()
+
+ with open(self._angle_filename,'w') as fh:
+ for b in self.get_angles():
+ item = tuple([p.idx for p in b[:-1]] + [str(b[-1])])
+ fh.write("ANGLE %d %d %d %s\n" % item)
+
+ def _writeArbdDihedralFile( self ):
+ for b in list( set( [b for i,j,k,l,b in self.get_dihedrals()] ) ):
+ if type(b) is not str and not isinstance(b, Path):
+ b.write_file()
+
+ with open(self._dihedral_filename,'w') as fh:
+ for b in self.get_dihedrals():
+ item = tuple([p.idx for p in b[:-1]] + [str(b[-1])])
+ fh.write("DIHEDRAL %d %d %d %d %s\n" % item)
+
+ def _writeArbdExclusionFile( self ):
+ with open(self._exclusion_filename,'w') as fh:
+ for ex in self.get_exclusions():
+ item = tuple(int(p.idx) for p in ex)
+ fh.write("EXCLUDE %d %d\n" % item)
+
+ def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
+ ## TODO: cache coordinates using numpy arrays for quick min/max
+ raise(NotImplementedError)
+
+ def write_namd_configuration( self, output_name, num_steps = 1e6,
+ output_directory = 'output',
+ update_dimensions=True, extrabonds=True ):
+
+ format_data = self.__dict__.copy() # get parameters from System object
+
+ format_data['extrabonds'] = """extraBonds on
+extraBondsFile $prefix.exb
+""" if extrabonds else ""
+
+ if self.useTclForces:
+ format_data['margin'] = ""
+ format_data['tcl_forces'] = """tclForces on
+tclForcesScript $prefix.forces.tcl
+"""
+ else:
+ format_data['margin'] = """margin 30
+"""
+ format_data['tcl_forces'] = ""
+
+ if update_dimensions:
+ format_data['dimensions'] = self.dimensions_from_structure()
+
+ for k,v in zip('XYZ', format_data['dimensions']):
+ format_data['origin'+k] = -v*0.5
+ format_data['cell'+k] = v
+
+ format_data['prefix'] = output_name
+ format_data['num_steps'] = int(num_steps//12)*12
+ format_data['output_directory'] = output_directory
+ filename = '{}.namd'.format(output_name)
+
+ with open(filename,'w') as fh:
+ fh.write("""
+set prefix {prefix}
+set nLast 0; # increment when continueing a simulation
+set n [expr $nLast+1]
+set out {output_directory}/$prefix-$n
+set temperature {temperature}
+
+structure $prefix.psf
+coordinates $prefix.pdb
+
+outputName $out
+XSTfile $out.xst
+DCDfile $out.dcd
+
+#############################################################
+## SIMULATION PARAMETERS ##
+#############################################################
+
+# Input
+paraTypeCharmm on
+parameters charmm36.nbfix/par_all36_na.prm
+parameters charmm36.nbfix/par_water_ions_na.prm
+
+wrapAll off
+
+# Force-Field Parameters
+exclude scaled1-4
+1-4scaling 1.0
+switching on
+switchdist 8
+cutoff 10
+pairlistdist 12
+{margin}
+
+# Integrator Parameters
+timestep 2.0 ;# 2fs/step
+rigidBonds all ;# needed for 2fs steps
+nonbondedFreq 1
+fullElectFrequency 3
+stepspercycle 12
+
+# PME (for full-system periodic electrostatics)
+PME no
+PMEGridSpacing 1.2
+
+# Constant Temperature Control
+langevin on ;# do langevin dynamics
+# langevinDamping 1 ;# damping coefficient (gamma); used in original study
+langevinDamping 0.1 ;# less friction for faster relaxation
+langevinTemp $temperature
+langevinHydrogen off ;# don't couple langevin bath to hydrogens
+
+# output
+useGroupPressure yes
+xstFreq 4800
+outputEnergies 4800
+dcdfreq 4800
+restartfreq 48000
+
+#############################################################
+## EXTRA FORCES ##
+#############################################################
+
+# ENM and intrahelical extrabonds
+{extrabonds}
+{tcl_forces}
+
+#############################################################
+## RUN ##
+#############################################################
+
+# Continuing a job from the restart files
+cellBasisVector1 {cellX} 0 0
+cellBasisVector2 0 {cellY} 0
+cellBasisVector3 0 0 {cellZ}
+
+if {{$nLast == 0}} {{
+ temperature 300
+ fixedAtoms on
+ fixedAtomsForces on
+ fixedAtomsFile $prefix.fixed.pdb
+ fixedAtomsCol B
+ minimize 2400
+ fixedAtoms off
+ minimize 2400
+}} else {{
+ bincoordinates {output_directory}/$prefix-$nLast.restart.coor
+ binvelocities {output_directory}/$prefix-$nLast.restart.vel
+}}
+
+run {num_steps:d}
+""".format(**format_data))
+
+ def atomic_simulate(self, output_name, output_directory='output', dry_run = False, namd2=None, log_file=None, num_procs=None, gpu=None):
+ if self.cacheUpToDate == False: # TODO: remove cache?
+ self._countParticleTypes()
+ self._updateParticleOrder()
+
+ if output_directory == '': output_directory='.'
+ self.writePdb( output_name + ".pdb" )
+ self.writePdb( output_name + ".fixed.pdb", beta_from_fixed=True )
+ self.writePsf( output_name + ".psf" )
+ self.write_namd_configuration( output_name, output_directory = output_directory )
+ os.sync()
+
+ if not dry_run:
+ if namd2 is None:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ fname = os.path.join(path, "namd2")
+ if os.path.isfile(fname) and os.access(fname, os.X_OK):
+ namd2 = fname
+ break
+
+ if namd2 is None: raise Exception("NAMD2 was not found")
+
+ if not os.path.exists(namd2):
+ raise Exception("NAMD2 was not found")
+ if not os.path.isfile(namd2):
+ raise Exception("NAMD2 was not found")
+ if not os.access(namd2, os.X_OK):
+ raise Exception("NAMD2 is not executable")
+
+ if not os.path.exists(output_directory):
+ os.makedirs(output_directory)
+ elif not os.path.isdir(output_directory):
+ raise Exception("output_directory '%s' is not a directory!" % output_directory)
+
+ if num_procs is None:
+ import multiprocessing
+ num_procs = max(1,multiprocessing.cpu_count()-1)
+
+ cmd = [namd2, '+p{}'.format(num_procs), "%s.namd" % output_name]
+ cmd = tuple(str(x) for x in cmd)
+
+ print("Running NAMD2 with: %s" % " ".join(cmd))
+ if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
+ fd = sys.stdout if log_file is None else log_file
+ process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for line in process.stdout:
+ fd.write(line)
+ fd.flush()
+ else:
+ with open(log_file,'w') as fd:
+ process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
+ process.communicate()
diff --git a/mrdna/arbdmodel/abstract_polymer.py b/mrdna/arbdmodel/abstract_polymer.py
new file mode 100644
index 0000000000000000000000000000000000000000..732a9562645669297d7b4ea6b1218fe302815faa
--- /dev/null
+++ b/mrdna/arbdmodel/abstract_polymer.py
@@ -0,0 +1,548 @@
+from pathlib import Path
+from copy import copy, deepcopy
+
+import numpy as np
+from scipy import interpolate
+
+from . import ArbdModel
+from .coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
+
+
+
+"""
+TODO:
+ - test for large systems
+ - rework Location class
+ - remove recursive calls
+ - document
+ - develop unit test suite
+"""
+
+# class ParticleNotConnectedError(Exception):
+# pass
+
+class Location():
+ """ Site for connection within an object """
+ def __init__(self, parent, contour_position, type_, on_fwd_strand = True):
+ ## TODO: remove cyclic references(?)
+ assert( isinstance(parent, ConnectableElement) )
+ self.parent = parent
+ self.contour_position = contour_position # represents position along contour length in polymer
+ self.type_ = type_
+ # self.particle = None
+ self.connection = None
+
+ def get_connected_location(self):
+ if self.connection is None:
+ return None
+ else:
+ return self.connection.other(self)
+
+ def set_connection(self, connection):
+ self.connection = connection # TODO weakref?
+
+ def get_monomer_index(self):
+ try:
+ idx = self.parent.contour_to_monomer_index(self.contour_position, nearest_monomer=True)
+ except:
+ if self.contour_position == 0:
+ idx = 0
+ elif self.contour_position == 1:
+ idx = self.parent.num_monomers-1
+ else:
+ raise
+ return idx
+
+ def __repr__(self):
+ if self.on_fwd_strand:
+ on_fwd = "on_fwd_strand"
+ else:
+ on_fwd = "on_rev_strand"
+ return "<Location {}.{}[{:.2f},{:d}]>".format( self.parent.name, self.type_, self.contour_position, self.on_fwd_strand)
+
+class Connection():
+ """ Class for connecting two elements """
+ def __init__(self, A, B, type_ = None):
+ assert( isinstance(A,Location) )
+ assert( isinstance(B,Location) )
+ self.A = A
+ self.B = B
+ self.type_ = type_
+
+ def other(self, location):
+ if location is self.A:
+ return self.B
+ elif location is self.B:
+ return self.A
+ else:
+ raise ValueError
+
+ def delete(self):
+ self.A.parent.connections.remove(self)
+ if self.B.parent is not self.A.parent:
+ self.B.parent.connections.remove(self)
+ self.A.connection = None
+ self.B.connection = None
+
+ def __repr__(self):
+ return "<Connection {}--{}--{}]>".format( self.A, self.type_, self.B )
+
+class ConnectableElement():
+ """ Abstract base class """
+ def __init__(self, connection_locations=None, connections=None):
+ if connection_locations is None: connection_locations = []
+ if connections is None: connections = []
+
+ ## TODO decide on names
+ self.locations = self.connection_locations = connection_locations
+ self.connections = connections
+
+ def get_locations(self, type_=None, exclude=()):
+ locs = [l for l in self.connection_locations if (type_ is None or l.type_ == type_) and l.type_ not in exclude]
+ counter = dict()
+ for l in locs:
+ if l in counter:
+ counter[l] += 1
+ else:
+ counter[l] = 1
+ assert( np.all( [counter[l] == 1 for l in locs] ) )
+ return locs
+
+ def get_location_at(self, contour_position, on_fwd_strand=True, new_type="crossover"):
+ loc = None
+ if (self.num_monomers == 1):
+ ## Assumes that intrahelical connections have been made before crossovers
+ for l in self.locations:
+ if l.on_fwd_strand == on_fwd_strand and l.connection is None:
+ assert(loc is None)
+ loc = l
+ # assert( loc is not None )
+ else:
+ for l in self.locations:
+ if l.contour_position == contour_position and l.on_fwd_strand == on_fwd_strand:
+ assert(loc is None)
+ loc = l
+ if loc is None:
+ loc = Location( self, contour_position=contour_position, type_=new_type, on_fwd_strand=on_fwd_strand )
+ return loc
+
+ def get_connections_and_locations(self, connection_type=None, exclude=()):
+ """ Returns a list with each entry of the form:
+ connection, location_in_self, location_in_other """
+ type_ = connection_type
+ ret = []
+ for c in self.connections:
+ if (type_ is None or c.type_ == type_) and c.type_ not in exclude:
+ if c.A.parent is self:
+ ret.append( [c, c.A, c.B] )
+ elif c.B.parent is self:
+ ret.append( [c, c.B, c.A] )
+ else:
+ import pdb
+ pdb.set_trace()
+ raise Exception("Object contains connection that fails to refer to object")
+ return ret
+
+ def _connect(self, other, connection):
+ ## TODO fix circular references
+ A,B = [connection.A, connection.B]
+
+ A.connection = B.connection = connection
+ self.connections.append(connection)
+ if other is not self:
+ other.connections.append(connection)
+ else:
+ raise NotImplementedError("Objects cannot yet be connected to themselves; if you are attempting to make a circular object, try breaking the object into multiple components")
+ l = A.parent.locations
+ if A not in l: l.append(A)
+ l = B.parent.locations
+ if B not in l: l.append(B)
+
+
+class PolymerSection(ConnectableElement):
+ """ Base class that describes a linear section of a polymer """
+
+ def __init__(self, name, num_monomers,
+ monomer_length,
+ start_position = None,
+ end_position = None,
+ parent = None,
+ **kwargs):
+
+ ConnectableElement.__init__(self, connection_locations=[], connections=[])
+
+ if 'segname' not in kwargs:
+ self.segname = name
+
+ for key,val in kwargs.items():
+ self.__dict__[key] = val
+
+ self.num_monomers = int(num_monomers)
+ self.monomer_length = monomer_length
+
+ if start_position is None: start_position = np.array((0,0,0))
+
+ if end_position is None:
+ end_position = np.array((0,0,self.monomer_length*num_monomers)) + start_position
+ self.start_position = start_position
+ self.end_position = end_position
+
+ self.start_orientation = None
+
+ ## Set up interpolation for positions
+ self._set_splines_from_ends()
+
+ # self.sequence = None
+
+ def __repr__(self):
+ return "<{} {}[{:d}]>".format( type(self), self.name, self.num_monomers )
+
+ def set_splines(self, contours, coords):
+ tck, u = interpolate.splprep( coords.T, u=contours, s=0, k=1)
+ self.position_spline_params = (tck,u)
+
+ def set_orientation_splines(self, contours, quaternions):
+ tck, u = interpolate.splprep( quaternions.T, u=contours, s=0, k=1)
+ self.quaternion_spline_params = (tck,u)
+
+ def get_center(self):
+ tck, u = self.position_spline_params
+ return np.mean(self.contour_to_position(u), axis=0)
+
+ def _get_location_positions(self):
+ return [self.contour_to_monomer_index(l.contour_position) for l in self.locations]
+
+ def insert_monomers(self, at_monomer: int, num_monomer: int, seq=tuple()):
+ assert(np.isclose(np.around(num_monomer),num_monomer))
+ if at_monomer < 0:
+ raise ValueError("Attempted to insert DNA into {} at a negative location".format(self))
+ if at_monomer > self.num_monomer-1:
+ raise ValueError("Attempted to insert DNA into {} at beyond the end of the Polymer".format(self))
+ if num_monomers < 0:
+ raise ValueError("Attempted to insert DNA a negative amount of DNA into {}".format(self))
+
+ num_monomers = np.around(num_monomer)
+ monomer_positions = self._get_location_positions()
+ new_monomer_positions = [p if p <= at_monomer else p+num_monomers for p in monomer_positions]
+
+ ## TODO: handle sequence
+
+ self.num_monomers = self.num_monomer+num_monomer
+
+ for l,p in zip(self.locations, new_monomer_positions):
+ l.contour_position = self.monomer_index_to_contour(p)
+
+ def remove_monomers(self, first_monomer: int, last_monomer: int):
+ """ Removes nucleotides between first_monomer and last_monomer, inclusive """
+ assert(np.isclose(np.around(first_monomer),first_monomer))
+ assert(np.isclose(np.around(last_monomer),last_monomer))
+ tmp = min((first_monomer,last_monomer))
+ last_monomer = max((first_monomer,last_monomer))
+ fist_monomer = tmp
+
+ if first_monomer < 0 or first_monomer > self.num_monomer-2:
+ raise ValueError("Attempted to remove DNA from {} starting at an invalid location {}".format(self, first_monomer))
+ if last_monomer < 1 or last_monomer > self.num_monomer-1:
+ raise ValueError("Attempted to remove DNA from {} ending at an invalid location {}".format(self, last_monomer))
+ if first_monomer == last_monomer:
+ return
+
+ first_monomer = np.around(first_monomer)
+ last_monomer = np.around(last_monomer)
+
+ monomer_positions = self._get_location_positions()
+
+ bad_locations = list(filter(lambda p: p >= first_monomer and p <= last_monomer, monomer_positions))
+ if len(bad_locations) > 0:
+ raise Exception("Attempted to remove DNA containing locations {} from {} between {} and {}".format(bad_locations,self,first_monomer,last_monomer))
+
+ removed_monomer = last_monomer-first_monomer+1
+ new_monomer_positions = [p if p <= last_monomer else p-removed_monomer for p in monomer_positions]
+ num_monomers = self.num_monomer-removed_monomer
+
+ if self.sequence is not None and len(self.sequence) == self.num_monomer:
+ self.sequence = [s for s,i in zip(self.sequence,range(self.num_monomer))
+ if i < first_monomer or i > last_monomer]
+ assert( len(self.sequence) == num_monomers )
+
+ self.num_monomers = num_monomers
+
+ for l,p in zip(self.locations, new_monomer_positions):
+ l.contour_position = self.monomer_position_to_contour(p)
+
+ def __filter_contours(contours, positions, position_filter, contour_filter):
+ u = contours
+ r = positions
+
+ ## Filter
+ ids = list(range(len(u)))
+ if contour_filter is not None:
+ ids = list(filter(lambda i: contour_filter(u[i]), ids))
+ if position_filter is not None:
+ ids = list(filter(lambda i: position_filter(r[i,:]), ids))
+ return ids
+
+ def translate(self, translation_vector, position_filter=None, contour_filter=None):
+ dr = np.array(translation_vector)
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = PolymerSection.__filter_contours(u, r, position_filter, contour_filter)
+ if len(ids) == 0: return
+
+ ## Translate
+ r[ids,:] = r[ids,:] + dr[np.newaxis,:]
+ self.set_splines(u,r)
+
+ def rotate(self, rotation_matrix, about=None, position_filter=None, contour_filter=None):
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = PolymerSection.__filter_contours(u, r, position_filter, contour_filter)
+ if len(ids) == 0: return
+
+ if about is None:
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in ids])
+ else:
+ dr = np.array(about)
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in ids])
+
+ self.set_splines(u,r)
+
+ if self.quaternion_spline_params is not None:
+ ## TODO: performance: don't shift between quaternion and matrix representations so much
+ tck, u = self.quaternion_spline_params
+ orientations = [self.contour_to_orientation(v) for v in u]
+ for i in ids:
+ orientations[i,:] = rotation_matrix.dot(orientations[i])
+ quats = [quaternion_from_matrix(o) for o in orientations]
+ self.set_orientation_splines(u, quats)
+
+ def _set_splines_from_ends(self, resolution=4):
+ self.quaternion_spline_params = None
+ r0 = np.array(self.start_position)[np.newaxis,:]
+ r1 = np.array(self.end_position)[np.newaxis,:]
+ u = np.linspace(0,1, max(3,self.num_monomers//int(resolution)))
+ s = u[:,np.newaxis]
+ coords = (1-s)*r0 + s*r1
+ self.set_splines(u, coords)
+
+ def contour_to_monomer_index(self, contour_pos, nearest_monomer=False):
+ idx = contour_pos*(self.num_monomer) - 0.5
+ if nearest_monomer:
+ assert( np.isclose(np.around(idx),idx) )
+ idx = np.around(idx)
+ return idx
+
+ def monomer_index_to_contour(self,monomer_pos):
+ return (monomer_pos+0.5)/(self.num_monomers)
+
+ def contour_to_position(self,s):
+ p = interpolate.splev( s, self.position_spline_params[0] )
+ if len(p) > 1: p = np.array(p).T
+ return p
+
+ def contour_to_tangent(self,s):
+ t = interpolate.splev( s, self.position_spline_params[0], der=1 )
+ t = (t / np.linalg.norm(t,axis=0))
+ return t.T
+
+
+ def contour_to_orientation(self,s):
+ assert( isinstance(s,float) or isinstance(s,int) or len(s) == 1 ) # TODO make vectorized version
+
+ if self.quaternion_spline_params is None:
+ axis = self.contour_to_tangent(s)
+ axis = axis / np.linalg.norm(axis)
+ rotAxis = np.cross(axis,np.array((0,0,1)))
+ rotAxisL = np.linalg.norm(rotAxis)
+ zAxis = np.array((0,0,1))
+
+ if rotAxisL > 0.001:
+ theta = np.arcsin(rotAxisL) * 180/np.pi
+ if axis.dot(zAxis) < 0: theta = 180-theta
+ orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta, normalizeAxis=False ).T
+ else:
+ orientation0 = np.eye(3) if axis.dot(zAxis) > 0 else \
+ rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
+ if self.start_orientation is not None:
+ orientation0 = orientation0.dot(self.start_orientation)
+
+ # orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_monomer_index(s), normalizeAxis=False )
+ # orientation = orientation.dot(orientation0)
+ orientation = orientation0
+ else:
+ q = interpolate.splev( s, self.quaternion_spline_params[0] )
+ if len(q) > 1: q = np.array(q).T # TODO: is this needed?
+ orientation = quaternion_to_matrix(q)
+
+ return orientation
+
+ def get_contour_sorted_connections_and_locations(self,type_):
+ sort_fn = lambda c: c[1].contour_position
+ cl = self.get_connections_and_locations(type_)
+ return sorted(cl, key=sort_fn)
+
+ def add_location(self, nt, type_, on_fwd_strand=True):
+ ## Create location if needed, add to polymer
+ c = self.monomer_index_to_contour(nt)
+ assert(c >= 0 and c <= 1)
+ # TODO? loc = self.Location( contour_position=c, type_=type_, on_fwd_strand=is_fwd )
+ loc = Location( self, contour_position=c, type_=type_, on_fwd_strand=on_fwd_strand )
+ self.locations.append(loc)
+
+ def iterate_connections_and_locations(self, reverse=False):
+ ## connections to other polymers
+ cl = self.get_contour_sorted_connections_and_locations()
+ if reverse:
+ cl = cl[::-1]
+
+ for c in cl:
+ yield c
+
+class AbstractPolymerGroup():
+ def __init__(self, polymers=[],
+ **kwargs):
+
+ """ Simulation system parameters """
+ ## TODO decide whether to move these elsewhere
+ # self.dimensions = dimensions
+ # self.temperature = temperature
+ # self.timestep = timestep
+ # self.cutoff = cutoff
+ # self.decomposition_period = decomposition_period
+ # self.pairlist_distance = pairlist_distance
+ # self.nonbonded_resolution = nonbonded_resolution
+ self.polymers = polymers
+
+ self.grid_potentials = []
+
+ # self.useNonbondedScheme( nbDnaScheme )
+
+ def get_connections(self,type_=None,exclude=()):
+ """ Find all connections in model, without double-counting """
+ added=set()
+ ret=[]
+ for s in self.polymers:
+ items = [e for e in s.get_connections_and_locations(type_,exclude=exclude) if e[0] not in added]
+ added.update([e[0] for e in items])
+ ret.extend( list(sorted(items,key=lambda x: x[1].contour_position)) )
+ return ret
+
+ def extend(self, other, copy=True, include_strands=False):
+ assert( isinstance(other, PolymerSectionModel) )
+ if copy:
+ for s in other.polymers:
+ self.polymers.append(deepcopy(s))
+ if include_strands:
+ for s in other.strands:
+ self.strands.append(deepcopy(s))
+ else:
+ for s in other.polymers:
+ self.polymers.append(s)
+ if include_strands:
+ for s in other.strands:
+ self.strands.append(s)
+ self._clear_beads()
+
+ def update(self, polymer , copy=False):
+ assert( isinstance(polymer, PolymerSection) )
+ if copy:
+ polymer = deepcopy(polymer)
+ self.polymers.append(polymer)
+
+ """ Operations on spline coordinates """
+ def translate(self, translation_vector, position_filter=None):
+ for s in self.polymers:
+ s.translate(translation_vector, position_filter=position_filter)
+
+ def rotate(self, rotation_matrix, about=None, position_filter=None):
+ for s in self.polymers:
+ s.rotate(rotation_matrix, about=about, position_filter=position_filter)
+
+ def get_center(self, include_ssdna=False):
+ if include_ssdna:
+ polymers = self.polymers
+ else:
+ polymers = list(filter(lambda s: isinstance(s,DoubleStrandedPolymerSection),
+ self.polymers))
+ centers = [s.get_center() for s in polymers]
+ weights = [s.num_monomers*2 if isinstance(s,DoubleStrandedPolymerSection) else s.num_monomers for s in polymers]
+ # centers,weights = [np.array(a) for a in (centers,weights)]
+ return np.average( centers, axis=0, weights=weights)
+
+ def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
+ positions = []
+ for s in self.polymers:
+ positions.append(s.contour_to_position(0))
+ positions.append(s.contour_to_position(0.5))
+ positions.append(s.contour_to_position(1))
+ positions = np.array(positions)
+ dx,dy,dz = [(np.max(positions[:,i])-np.min(positions[:,i])+30)*padding_factor for i in range(3)]
+ if isotropic:
+ dx = dy = dz = max((dx,dy,dz))
+ return [dx,dy,dz]
+
+ def add_grid_potential(self, grid_file, scale=1, per_monomer=True):
+ grid_file = Path(grid_file)
+ if not grid_file.is_file():
+ raise ValueError("Grid file {} does not exist".format(grid_file))
+ if not grid_file.is_absolute():
+ grid_file = Path.cwd() / grid_file
+ self.grid_potentials.append((grid_file,scale,per_,pmp,er))
+
+ def vmd_tube_tcl(self, file_name="drawTubes.tcl", radius=5):
+ with open(file_name, 'w') as tclFile:
+ tclFile.write("## beginning TCL script \n")
+
+ def draw_tube(polymer,radius_value=10, color="cyan", resolution=5):
+ tclFile.write("## Tube being drawn... \n")
+
+ contours = np.linspace(0,1, max(2,1+polymer.num_monomers//resolution) )
+ rs = [polymer.contour_to_position(c) for c in contours]
+
+ radius_value = str(radius_value)
+ tclFile.write("graphics top color {} \n".format(str(color)))
+ for i in range(len(rs)-2):
+ r0 = rs[i]
+ r1 = rs[i+1]
+ filled = "yes" if i in (0,len(rs)-2) else "no"
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled {} \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value), filled))
+ tclFile.write("graphics top sphere {{ {} {} {} }} radius {} resolution 30\n".format(r1[0], r1[1], r1[2], str(radius_value)))
+ r0 = rs[-2]
+ r0 = rs[-1]
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value)))
+
+ ## material
+ tclFile.write("graphics top materials on \n")
+ tclFile.write("graphics top material AOEdgy \n")
+
+ ## iterate through the model polymers
+ for s in self.polymers:
+ draw_tube(s,radius,"cyan")
+
+
+ def vmd_cylinder_tcl(self, file_name="drawCylinders.tcl", radius=5):
+
+ with open(file_name, 'w') as tclFile:
+ tclFile.write("## beginning TCL script \n")
+ def draw_cylinder(polymer,radius_value=10,color="cyan"):
+ tclFile.write("## cylinder being drawn... \n")
+ r0 = polymer.contour_to_position(0)
+ r1 = polymer.contour_to_position(1)
+
+ radius_value = str(radius_value)
+ color = str(color)
+
+ tclFile.write("graphics top color {} \n".format(color))
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], radius_value))
+
+ ## material
+ tclFile.write("graphics top materials on \n")
+ tclFile.write("graphics top material AOEdgy \n")
+
+ ## iterate through the model polymers
+ for s in self.polymers:
+ draw_cylinder(s,radius,"cyan")
diff --git a/mrdna/arbdmodel/coords.py b/mrdna/arbdmodel/coords.py
new file mode 100644
index 0000000000000000000000000000000000000000..41628e83501c17098094fc12b7d4d4e6594ebcb6
--- /dev/null
+++ b/mrdna/arbdmodel/coords.py
@@ -0,0 +1,204 @@
+import numpy as np
+from scipy.optimize import newton
+
+def minimizeRmsd(coordsB, coordsA, weights=None, maxIter=100):
+ ## Going through many iterations wasn't really needed
+ tol = 1
+ count = 0
+
+ R = np.eye(3)
+ comB = np.zeros([3,])
+ cNext = coordsB
+
+ while tol > 1e-6:
+ q,cB,comA = _minimizeRmsd(cNext,coordsA, weights)
+ R = R.dot(quaternion_to_matrix(q))
+ assert( np.all(np.isreal( R )) )
+
+ comB += cB
+ cLast = cNext
+ cNext = (coordsB-comB).dot(R)
+
+ tol = np.sum(((cNext-cLast)**2)[:]) / np.max(np.shape(coordsB))
+ if count > maxIter:
+ Exception("Exceeded maxIter (%d)" % maxIter)
+ count += 1
+
+ print("%d iterations",count)
+ return R, comB, comA
+
+
+def minimizeRmsd(coordsB, coordsA, weights=None):
+ q,comA,comB = _minimizeRmsd(coordsB, coordsA, weights)
+ assert( np.all(np.isreal( q )) )
+ return quaternion_to_matrix(q),comA,comB
+
+
+## http://onlinelibrary.wiley.com/doi/10.1002/jcc.21439/full
+def _minimizeRmsd(coordsB, coordsA, weights=None):
+ A = coordsA
+ B = coordsB
+
+ shapeA,shapeB = [np.shape(X) for X in (A,B)]
+ for s in (shapeA,shapeB): assert( len(s) == 2 )
+
+ A,B = [X.T if s[1] > s[0] else X for X,s in zip([A,B],(shapeA,shapeB))] # TODO: print warning
+
+ shapeA,shapeB = [np.shape(X) for X in (A,B)]
+ assert( shapeA == shapeB )
+ for X,s in zip((A,B),(shapeA,shapeB)):
+ assert( s[1] == 3 and s[0] >= s[1] )
+
+ # if weights is None: weights = np.ones(len(A))
+ if weights is None:
+ comA,comB = [np.mean( X, axis=0 ) for X in (A,B)]
+ else:
+ assert( len(weights[:]) == len(B) )
+ W = np.diag(weights)
+ comA,comB = [np.sum( W.dot(X), axis=0 ) / np.sum(W) for X in (A,B)]
+
+ A = np.array( A-comA )
+ B = np.array( B-comB )
+
+ if weights is None:
+ s = A.T.dot(B)
+ else:
+ s = A.T.dot(W.dot(B))
+
+ sxx,sxy,sxz = s[0,:]
+ syx,syy,syz = s[1,:]
+ szx,szy,szz = s[2,:]
+
+ K = [[ sxx+syy+szz, syz-szy, szx-sxz, sxy-syx],
+ [syz-szy, sxx-syy-szz, sxy+syx, sxz+szx],
+ [szx-sxz, sxy+syx, -sxx+syy-szz, syz+szy],
+ [sxy-syx, sxz+szx, syz+szy, -sxx-syy+szz]]
+ K = np.array(K)
+
+ # GA = np.trace( A.T.dot(W.dot(A)) )
+ # GB = np.trace( B.T.dot(W.dot(B)) )
+
+ ## Finding GA/GB can be done more quickly
+ # I = np.eye(4)
+ # x0 = (GA+GB)*0.5
+ # vals = newtoon(lambda x: np.det(K-x*I), x0 = x0)
+
+ vals, vecs = np.linalg.eig(K)
+ i = np.argmax(vals)
+ q = vecs[:,i]
+
+ # RMSD = np.sqrt( (GA+GB-2*vals[i]) / len(A) )
+ # print("CHECK:", K.dot(q)-vals[i]*q )
+ return q, comB, comA
+
+def quaternion_to_matrix(q):
+ assert(len(q) == 4)
+
+ ## It looks like the wikipedia article I used employed a less common convention for q (see below
+ ## http://en.wikipedia.org/wiki/Rotation_formalisms_in_three_dimensions#Rotation_matrix_.E2.86.94_quaternion
+ # q1,q2,q3,q4 = q
+ # R = [[1-2*(q2*q2 + q3*q3), 2*(q1*q2 - q3*q4), 2*(q1*q3 + q2*q4)],
+ # [ 2*(q1*q2 + q3*q4), 1-2*(q1*q1 + q3*q3), 2*(q2*q3 - q1*q4)],
+ # [ 2*(q1*q3 - q2*q4), 2*(q1*q4 + q2*q3), 1-2*(q2*q2 + q1*q1)]]
+
+ q = q / np.linalg.norm(q)
+ q0,q1,q2,q3 = q
+ R = [[1-2*(q2*q2 + q3*q3), 2*(q1*q2 - q3*q0), 2*(q1*q3 + q2*q0)],
+ [ 2*(q1*q2 + q3*q0), 1-2*(q1*q1 + q3*q3), 2*(q2*q3 - q1*q0)],
+ [ 2*(q1*q3 - q2*q0), 2*(q1*q0 + q2*q3), 1-2*(q2*q2 + q1*q1)]]
+
+ return np.array(R)
+
+def quaternion_from_matrix( R ):
+ e1 = R[0]
+ e2 = R[1]
+ e3 = R[2]
+
+ # d1 = 0.5 * np.sqrt( 1+R[0,0]+R[1,1]+R[2,2] )
+ # d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
+ # d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
+ # d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
+
+ d1 = 1+R[0,0]+R[1,1]+R[2,2]
+ d2 = 1+R[0,0]-R[1,1]-R[2,2]
+ d3 = 1-R[0,0]+R[1,1]-R[2,2]
+ d4 = 1-R[0,0]-R[1,1]+R[2,2]
+
+ maxD = max((d1,d2,d3,d4))
+ d = 0.5 / np.sqrt(maxD)
+
+ if d1 == maxD:
+ return np.array(( 1.0/(4*d),
+ d * (R[2,1]-R[1,2]),
+ d * (R[0,2]-R[2,0]),
+ d * (R[1,0]-R[0,1]) ))
+ elif d2 == maxD:
+ return np.array(( d * (R[2,1]-R[1,2]),
+ 1.0/(4*d),
+ d * (R[0,1]+R[1,0]),
+ d * (R[0,2]+R[2,0]) ))
+ elif d3 == maxD:
+ return np.array(( d * (R[0,2]-R[2,0]),
+ d * (R[0,1]+R[1,0]),
+ 1.0/(4*d),
+ d * (R[1,2]+R[2,1]) ))
+ elif d4 == maxD:
+ return np.array(( d * (R[1,0]-R[0,1]),
+ d * (R[0,2]+R[2,0]),
+ d * (R[1,2]+R[2,1]),
+ 1.0/(4*d) ))
+
+def rotationAboutAxis(axis,angle, normalizeAxis=True):
+ if normalizeAxis: axis = axis / np.linalg.norm(axis)
+ angle = angle * 0.5 * np.pi/180
+ cos = np.cos( angle )
+ sin = np.sin( angle )
+ q = [cos] + [sin*x for x in axis]
+ return quaternion_to_matrix(q)
+
+def readArbdCoords(fname):
+ coords = []
+ with open(fname) as fh:
+ for line in fh:
+ coords.append([float(x) for x in line.split()[1:]])
+ return np.array(coords)
+
+def readAvgArbdCoords(psf,pdb,dcd,rmsdThreshold=3.5):
+ import MDAnalysis as mda
+
+ usel = mda.Universe(psf, dcd)
+ sel = usel.select_atoms("name D*")
+
+ # r0 = ref.xyz[0,ids,:]
+ ts = usel.trajectory[-1]
+ r0 = sel.positions
+ pos = []
+ for t in range(ts.frame-1,-1,-1):
+ usel.trajectory[t]
+ R,comA,comB = minimizeRmsd(sel.positions,r0)
+ r = np.array( [(r-comA).dot(R)+comB for r in sel.positions] )
+ rmsd = np.mean( (r-r0)**2 )
+ r = np.array( [(r-comA).dot(R)+comB for r in usel.atoms.positions] )
+ pos.append( r )
+ if rmsd > rmsdThreshold**2:
+ break
+ t0=t+1
+ print( "Averaging coordinates in %s after frame %d" % (dcd, t0) )
+
+ pos = np.mean(pos, axis=0)
+ return pos
+
+def unit_quat_conversions():
+ for axis in [[0,0,1],[1,1,1],[1,0,0],[-1,-2,0]]:
+ for angle in np.linspace(-180,180,10):
+ R = rotationAboutAxis(axis, angle)
+ R2 = quaternion_to_matrix( quaternion_from_matrix( R ) )
+ if not np.all( np.abs(R-R2) < 0.01 ):
+ import pdb
+ pdb.set_trace()
+ quaternion_to_matrix( quaternion_from_matrix( R ) )
+
+
+if __name__ == "__main__":
+ unit_quat_conversions()
+
diff --git a/mrdna/arbdmodel/fjc_polymer_model.py b/mrdna/arbdmodel/fjc_polymer_model.py
new file mode 100644
index 0000000000000000000000000000000000000000..cec6a939b5aa454659ba2611f00e301fdb03a3d9
--- /dev/null
+++ b/mrdna/arbdmodel/fjc_polymer_model.py
@@ -0,0 +1,160 @@
+# -*- coding: utf-8 -*-
+## Test with `python -m arbdmodel.hps_polymer_model`
+
+import numpy as np
+import sys
+
+
+## Local imports
+from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path
+from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .interactions import NonbondedScheme, HarmonicBond, HarmonicPotential
+from .coords import quaternion_to_matrix
+
+
+"""Define particle types"""
+type_ = ParticleType("X",
+ damping_coefficient = 40.9,
+ mass=120
+)
+
+## Bonded potentials
+class FjcNonbonded(NonbondedScheme):
+ def __init__(self, resolution=0.1, rMin=0):
+ NonbondedScheme.__init__(self, typesA=None, typesB=None, resolution=resolution, rMin=rMin)
+
+ def potential(self, r, typeA, typeB):
+ """ Constant force excluded volume """
+ force = 10 # kcal_mol/AA
+ radius = 6
+
+ u = np.zeros(r.shape)
+ # s = r < 2*radius
+ # u[s] = (2*radius - r[s]) * force
+ return u
+
+class FjcBeadsFromPolymer(Group):
+
+ def __init__(self, polymer, sequence=None,
+ rest_length = 3.8, spring_constant = 25,
+ **kwargs):
+
+ # if sequence is None:
+ # raise NotImplementedError
+ # # ... set random sequence
+
+ self.polymer = polymer
+ self.sequence = sequence
+ self.spring_constant = 25
+ self.rest_length = 3.8
+
+ for prop in ('segname','chain'):
+ if prop not in kwargs:
+ # import pdb
+ # pdb.set_trace()
+ try:
+ self.__dict__[prop] = polymer.__dict__[prop]
+ except:
+ pass
+
+ # if len(sequence) != polymer.num_monomers:
+ # raise ValueError("Length of sequence does not match length of polymer")
+ Group.__init__(self, **kwargs)
+
+
+ def _clear_beads(self):
+ ...
+
+ def _generate_beads(self):
+ # beads = self.children
+ nb = self.polymer.num_monomers
+
+ for i in range(nb):
+ c = self.polymer.monomer_index_to_contour(i)
+ r = self.polymer.contour_to_position(c)
+
+ bead = PointParticle(type_, r,
+ resid = i+1)
+ self.add(bead)
+
+ ## Two consecutive nts
+ for i in range(len(self.children)-1):
+ b1 = self.children[i]
+ b2 = self.children[i+1]
+ """ units "10 kJ/N_A" kcal_mol """
+ bond = HarmonicBond(k = self.spring_constant,
+ r0 = self.rest_length,
+ rRange = (0,500),
+ resolution = 0.01,
+ maxForce = 50)
+ self.add_bond( i=b1, j=b2, bond = bond, exclude=True )
+
+class FjcModel(ArbdModel):
+ def __init__(self, polymers,
+ sequences = None,
+ rest_length = 3.8,
+ spring_constant = 25,
+ damping_coefficient = 40.9,
+ DEBUG=False,
+ **kwargs):
+
+ """
+ [damping_coefficient]: ns
+ """
+
+ print("WARNING: diffusion coefficient arbitrarily set to 100 AA**2/ns in FjcModel")
+
+ kwargs['timestep'] = 50e-6
+ kwargs['cutoff'] = 10
+
+ if 'decompPeriod' not in kwargs:
+ kwargs['decompPeriod'] = 100000
+
+ """ Assign sequences """
+ if sequences is None:
+ # raise NotImplementedError("HpsModel must be provided a sequences argument")
+ sequences = [None for i in range(len(polymers))]
+
+ self.polymer_group = AbstractPolymerGroup(polymers)
+ self.sequences = sequences
+ self.rest_length = rest_length
+ self.spring_constant = spring_constant
+ ArbdModel.__init__(self, [], **kwargs)
+
+ """ Update type diffusion coefficients """
+ self.set_damping_coefficient( damping_coefficient )
+
+ """ Set up nonbonded interactions """
+ nonbonded = FjcNonbonded()
+ self.useNonbondedScheme( nonbonded, typeA=type_, typeB=type_ )
+
+ """ Generate beads """
+ self.generate_beads()
+
+ def update_splines(self, coords):
+ i = 0
+ for p,c in zip(self.polymer_group.polymers,self.children):
+ n = len(c.children)
+ p.set_splines(np.linspace(0,1,n), coords[i:i+n])
+ i += n
+
+ self.clear_all()
+ self.generate_beads()
+ ## TODO Apply restraints, etc
+
+ def generate_beads(self):
+ self.peptides = [FjcBeadsFromPolymer(p,s, rest_length = self.rest_length,
+ spring_constant = self.spring_constant )
+ for p,s in zip(self.polymer_group.polymers,self.sequences)]
+
+ for s in self.peptides:
+ self.add(s)
+ s._generate_beads()
+
+ def set_damping_coefficient(self, damping_coefficient):
+ for t in [type_]:
+ t.damping_coefficient = damping_coefficient
+ # t.diffusivity = 831447.2 * temperature / (t.mass * damping_coefficient)
+
+if __name__ == "__main__":
+ pass
diff --git a/mrdna/arbdmodel/hps_polymer_model.py b/mrdna/arbdmodel/hps_polymer_model.py
new file mode 100644
index 0000000000000000000000000000000000000000..f56d43ba7ff9cdb0a480500be686b05eeb906b09
--- /dev/null
+++ b/mrdna/arbdmodel/hps_polymer_model.py
@@ -0,0 +1,313 @@
+# -*- coding: utf-8 -*-
+## Test with `python -m arbdmodel.hps_polymer_model`
+
+import numpy as np
+import sys
+
+
+## Local imports
+from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path
+from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .interactions import NonbondedScheme, HarmonicBond, HarmonicAngle, HarmonicDihedral
+from .coords import quaternion_to_matrix
+
+"""Define particle types"""
+_types = dict(
+ A = ParticleType("ALA",
+ mass = 71.08,
+ charge = 0,
+ sigma = 5.04,
+ lambda_ = 0.72973,
+ ),
+ R = ParticleType("ARG",
+ mass = 156.2,
+ charge = 1,
+ sigma = 6.56,
+ lambda_ = 0.0,
+ ),
+ N = ParticleType("ASN",
+ mass = 114.1,
+ charge = 0,
+ sigma = 5.68,
+ lambda_ = 0.432432,
+ ),
+ D = ParticleType("ASP",
+ mass = 115.1,
+ charge = -1,
+ sigma = 5.58,
+ lambda_ = 0.378378,
+ ),
+ C = ParticleType("CYS",
+ mass = 103.1,
+ charge = 0,
+ sigma = 5.48,
+ lambda_ = 0.594595,
+ ),
+ Q = ParticleType("GLN",
+ mass = 128.1,
+ charge = 0,
+ sigma = 6.02,
+ lambda_ = 0.513514,
+ ),
+ E = ParticleType("GLU",
+ mass = 129.1,
+ charge = -1,
+ sigma = 5.92,
+ lambda_ = 0.459459,
+ ),
+ G = ParticleType("GLY",
+ mass = 57.05,
+ charge = 0,
+ sigma = 4.5,
+ lambda_ = 0.648649,
+ ),
+ H = ParticleType("HIS",
+ mass = 137.1,
+ charge = 0.5,
+ sigma = 6.08,
+ lambda_ = 0.513514,
+ ),
+ I = ParticleType("ILE",
+ mass = 113.2,
+ charge = 0,
+ sigma = 6.18,
+ lambda_ = 0.972973,
+ ),
+ L = ParticleType("LEU",
+ mass = 113.2,
+ charge = 0,
+ sigma = 6.18,
+ lambda_ = 0.972973,
+ ),
+ K = ParticleType("LYS",
+ mass = 128.2,
+ charge = 1,
+ sigma = 6.36,
+ lambda_ = 0.513514,
+ ),
+ M = ParticleType("MET",
+ mass = 131.2,
+ charge = 0,
+ sigma = 6.18,
+ lambda_ = 0.837838,
+ ),
+ F = ParticleType("PHE",
+ mass = 147.2,
+ charge = 0,
+ sigma = 6.36,
+ lambda_ = 1.0,
+ ),
+ P = ParticleType("PRO",
+ mass = 97.12,
+ charge = 0,
+ sigma = 5.56,
+ lambda_ = 1.0,
+ ),
+ S = ParticleType("SER",
+ mass = 87.08,
+ charge = 0,
+ sigma = 5.18,
+ lambda_ = 0.594595,
+ ),
+ T = ParticleType("THR",
+ mass = 101.1,
+ charge = 0,
+ sigma = 5.62,
+ lambda_ = 0.675676,
+ ),
+ W = ParticleType("TRP",
+ mass = 186.2,
+ charge = 0,
+ sigma = 6.78,
+ lambda_ = 0.945946,
+ ),
+ Y = ParticleType("TYR",
+ mass = 163.2,
+ charge = 0,
+ sigma = 6.46,
+ lambda_ = 0.864865,
+ ),
+ V = ParticleType("VAL",
+ mass = 99.07,
+ charge = 0,
+ sigma = 5.86,
+ lambda_ = 0.891892,
+ )
+)
+for k,t in _types.items():
+ t.resname = t.name
+
+class HpsNonbonded(NonbondedScheme):
+ def __init__(self, debye_length=10, resolution=0.1, rMin=0):
+ NonbondedScheme.__init__(self, typesA=None, typesB=None, resolution=resolution, rMin=rMin)
+ self.debye_length = debye_length
+ self.maxForce = 50
+
+ def potential(self, r, typeA, typeB):
+ """ Electrostatics """
+ ld = self.debye_length
+ q1 = typeA.charge
+ q2 = typeB.charge
+ D = 80 # dielectric of water
+ ## units "e**2 / (4 * pi * epsilon0 AA)" kcal_mol
+ A = 332.06371
+ u_elec = (A*q1*q2/D)*np.exp(-r/ld) / r
+
+ """ Hydrophobicity scale model """
+ lambda_ = 0.5 * (typeA.lambda_ + typeB.lambda_)
+ sigma = 0.5 * (typeA.sigma + typeB.sigma)
+ epsilon = 0.2
+
+ r6 = (sigma/r)**6
+ r12 = r6**2
+ u_lj = 4 * epsilon * (r12-r6)
+ u_hps = lambda_ * np.array(u_lj)
+ s = r<=sigma*2**(1/6)
+ u_hps[s] = u_lj[s] + (1-lambda_) * epsilon
+
+ u = u_elec + u_hps
+ u[0] = u[1] # Remove NaN
+
+ maxForce = self.maxForce
+ if maxForce is not None:
+ assert(maxForce > 0)
+ f = np.diff(u)/np.diff(r)
+ f[f>maxForce] = maxForce
+ f[f<-maxForce] = -maxForce
+ u[0] = 0
+ u[1:] = np.cumsum(f*np.diff(r))
+
+ u = u-u[-1]
+
+ return u
+
+class HpsBeadsFromPolymer(Group):
+ # p = PointParticle(_P, (0,0,0), "P")
+ # b = PointParticle(_B, (3,0,1), "B")
+ # nt = Group( name = "nt", children = [p,b])
+ # nt.add_bond( i=p, j=b, bond = get_resource_path('two_bead_model/BPB.dat') )
+
+ def __init__(self, polymer, sequence=None, **kwargs):
+
+ if sequence is None:
+ raise NotImplementedError
+ # ... set random sequence
+
+ self.polymer = polymer
+ self.sequence = sequence
+
+ for prop in ('segname','chain'):
+ if prop not in kwargs:
+ # import pdb
+ # pdb.set_trace()
+ try:
+ self.__dict__[prop] = polymer.__dict__[prop]
+ except:
+ pass
+
+ if len(sequence) != polymer.num_monomers:
+ raise ValueError("Length of sequence does not match length of polymer")
+ Group.__init__(self, **kwargs)
+
+ def _clear_beads(self):
+ ...
+
+ def _generate_beads(self):
+ # beads = self.children
+
+ for i in range(self.polymer.num_monomers):
+ c = self.polymer.monomer_index_to_contour(i)
+ r = self.polymer.contour_to_position(c)
+ s = self.sequence[i]
+
+ bead = PointParticle(_types[s], r,
+ name = s,
+ resid = i+1)
+ self.add(bead)
+ # import pdb
+ # pdb.set_trace()
+ # continue
+
+ ## Two consecutive nts
+ for i in range(len(self.children)-1):
+ b1 = self.children[i]
+ b2 = self.children[i+1]
+ """ units "10 kJ/N_A" kcal_mol """
+ bond = HarmonicBond(k = 2.3900574,
+ r0 = 3.8,
+ rRange = (0,500),
+ resolution = 0.01,
+ maxForce = 10)
+ self.add_bond( i=b1, j=b2, bond = bond, exclude=True )
+
+
+class HpsModel(ArbdModel):
+ def __init__(self, polymers,
+ sequences = None,
+ debye_length = 10,
+ damping_coefficient = 10,
+ DEBUG=False,
+ **kwargs):
+
+ """
+ [debye_length]: angstroms
+ [damping_coefficient]: ns
+ """
+ kwargs['timestep'] = 10e-6
+ kwargs['cutoff'] = max(4*debye_length,20)
+
+ if 'decompPeriod' not in kwargs:
+ kwargs['decompPeriod'] = 1000
+
+ """ Assign sequences """
+ if sequences is None:
+ raise NotImplementedError("HpsModel must be provided a sequences argument")
+
+ self.polymer_group = AbstractPolymerGroup(polymers)
+ self.sequences = sequences
+ ArbdModel.__init__(self, [], **kwargs)
+
+ """ Update type diffusion coefficients """
+ self.types = all_types = [t for key,t in _types.items()]
+ self.set_damping_coefficient( damping_coefficient )
+
+ """ Set up nonbonded interactions """
+ nonbonded = HpsNonbonded(debye_length)
+ for i in range(len(all_types)):
+ t1 = all_types[i]
+ for j in range(i,len(all_types)):
+ t2 = all_types[j]
+ self.useNonbondedScheme( nonbonded, typeA=t1, typeB=t2 )
+
+ """ Generate beads """
+ self.generate_beads()
+
+ def update_splines(self, coords):
+ i = 0
+ for p in self.polymer_group.polymers:
+ n = p.num_monomers
+ p.set_splines(np.linspace(0,1,n), coords[i:i+n])
+ i += n
+
+ self.clear_all()
+ self.generate_beads()
+ ## TODO Apply restraints, etc
+
+ def generate_beads(self):
+ self.peptides = [HpsBeadsFromPolymer(p,s)
+ for p,s in zip(self.polymer_group.polymers,self.sequences)]
+
+ for s in self.peptides:
+ self.add(s)
+ s._generate_beads()
+
+ def set_damping_coefficient(self, damping_coefficient):
+ for t in self.types:
+ t.damping_coefficient = damping_coefficient
+ # t.diffusivity = 831447.2 * temperature / (t.mass * damping_coefficient)
+
+if __name__ == "__main__":
+
+ print("TYPES")
+ for n,t in _types.items():
+ print("{}\t{}\t{}\t{}\t{}".format(t.name, t.mass, t.charge, t.sigma, t.lambda_))
diff --git a/mrdna/arbdmodel/interactions.py b/mrdna/arbdmodel/interactions.py
new file mode 100644
index 0000000000000000000000000000000000000000..1c4b9b6c7276d5368a01fa6a24731c9a0abb37a3
--- /dev/null
+++ b/mrdna/arbdmodel/interactions.py
@@ -0,0 +1,154 @@
+from shutil import copyfile
+import os, sys
+import numpy as np
+
+class NonbondedScheme():
+ """ Abstract class for writing nonbonded interactions """
+
+ def __init__(self, typesA=None, typesB=None, resolution=0.1, rMin=0):
+ """If typesA is None, and typesB is None, then """
+ self.resolution = resolution
+ self.rMin = rMin
+
+ def add_sim_system(self, simSystem):
+ self.rMax = simSystem.cutoff
+ self.r = np.arange(rMin,rMax,resolution)
+
+ def potential(self, r, typeA, typeB):
+ raise NotImplementedError
+
+ def write_file(self, filename, typeA, typeB, rMax):
+ r = np.arange(self.rMin, rMax+self.resolution, self.resolution)
+ u = self.potential(r, typeA, typeB)
+ np.savetxt(filename, np.array([r,u]).T)
+
+
+class LennardJones(NonbondedScheme):
+ def potential(self, r, typeA, typeB):
+ epsilon = np.sqrt( typeA.epsilon**2 + typeB.epsilon**2 )
+ r0 = 0.5 * (typeA.radius + typeB.radius)
+ r6 = (r0/r)**6
+ r12 = r6**2
+ u = epsilon * (r12-2*r6)
+ u[0] = u[1] # Remove NaN
+ return u
+# LennardJones = LennardJones()
+
+class HalfHarmonic(NonbondedScheme):
+ def potential(self, r, typeA, typeB):
+ k = 10 # kcal/mol AA**2
+ r0 = (typeA.radius + typeB.radius)
+ u = 0.5 * k * (r-r0)**2
+ u[r > r0] = np.zeros( np.shape(u[r > r0]) )
+ return u
+# HalfHarmonic = HalfHarmonic()
+
+class TabulatedPotential(NonbondedScheme):
+ def __init__(self, tableFile, typesA=None, typesB=None, resolution=0.1, rMin=0):
+ """If typesA is None, and typesB is None, then """
+ self.tableFile = tableFile
+ # self.resolution = resolution
+ # self.rMin = rMin
+
+ ## TODO: check that tableFile exists and is regular file
+
+ def write_file(self, filename, typeA, typeB, rMax):
+ if filename != self.tableFile:
+ copyfile(self.tableFile, filename)
+
+## Bonded potentials
+class HarmonicPotential():
+ def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
+ self.k = k
+ self.r0 = r0
+ self.rRange = rRange
+ self.resolution = 0.1
+ self.maxForce = maxForce
+ self.prefix = prefix
+ self.periodic = False
+ self.type_ = "None"
+ self.max_potential = max_potential
+ self.kscale_ = None # only used for
+
+ def filename(self):
+ # raise NotImplementedError("Not implemented")
+ return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
+ self.k*self.kscale_, self.r0)
+
+ def __str__(self):
+ return self.filename()
+
+ def potential(self, dr):
+ return 0.5*self.k*dr**2
+
+ def write_file(self):
+ r = np.arange( self.rRange[0],
+ self.rRange[1]+self.resolution,
+ self.resolution )
+ dr = r-self.r0
+
+ if self.periodic == True:
+ rSpan = self.rRange[1]-self.rRange[0]
+ assert(rSpan > 0)
+ dr = np.mod( dr+0.5*rSpan, rSpan) - 0.5*rSpan
+
+ u = self.potential(dr)
+
+ maxForce = self.maxForce
+ if maxForce is not None:
+ assert(maxForce > 0)
+ f = np.diff(u)/np.diff(r)
+ f[f>maxForce] = maxForce
+ f[f<-maxForce] = -maxForce
+ u[0] = 0
+ u[1:] = np.cumsum(f*np.diff(r))
+
+ if self.max_potential is not None:
+ f = np.diff(u)/np.diff(r)
+ ids = np.where( 0.5*(u[1:]+u[:-1]) > self.max_potential )[0]
+
+ w = np.sqrt(2*self.max_potential/self.k)
+ drAvg = 0.5*(np.abs(dr[ids]) + np.abs(dr[ids+1]))
+
+ f[ids] = f[ids] * np.exp(-(drAvg-w)/(w))
+ u[0] = 0
+ u[1:] = np.cumsum(f*np.diff(r))
+
+ u = u - np.min(u)
+
+ np.savetxt( self.filename(), np.array([r, u]).T, fmt="%f" )
+
+ def __hash__(self):
+ assert(self.type_ != "None")
+ return hash((self.type_, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
+
+ def __eq__(self, other):
+ for a in ("type_", "k", "r0", "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
+ if self.__dict__[a] != other.__dict__[a]:
+ return False
+ return True
+
+# class NonBonded(HarmonicPotential):
+# def _init_hook(self):
+# self.type = "nonbonded"
+# self.kscale_ = 1.0
+
+class HarmonicBond(HarmonicPotential):
+ def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ self.type_ = "bond"
+ self.kscale_ = 1.0
+
+class HarmonicAngle(HarmonicPotential):
+ def __init__(self, k, r0, rRange=(0,181), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ self.type_ = "angle"
+ self.kscale_ = (180.0/np.pi)**2
+
+class HarmonicDihedral(HarmonicPotential):
+ def __init__(self, k, r0, rRange=(-180,180), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ self.periodic = True
+ self.type_ = "dihedral"
+ self.kscale_ = (180.0/np.pi)**2
+
diff --git a/mrdna/arbdmodel/kh_polymer_model.py b/mrdna/arbdmodel/kh_polymer_model.py
new file mode 100644
index 0000000000000000000000000000000000000000..4d732a08e3044c9b73e499f087945c960a4c5ab3
--- /dev/null
+++ b/mrdna/arbdmodel/kh_polymer_model.py
@@ -0,0 +1,313 @@
+# -*- coding: utf-8 -*-
+## Test with `python -m arbdmodel.kh_polymer_model`
+
+import numpy as np
+import sys
+
+## Local imports
+from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path
+from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .interactions import NonbondedScheme, HarmonicBond, HarmonicAngle, HarmonicDihedral
+from .coords import quaternion_to_matrix
+from .kh_polymer_model_pair_epsilon import epsilon_mj
+
+"""Define particle types"""
+_types = dict(
+ A = ParticleType("ALA",
+ mass = 71.08,
+ charge = 0,
+ sigma = 5.04,
+ ),
+ R = ParticleType("ARG",
+ mass = 156.2,
+ charge = 1,
+ sigma = 6.56,
+ ),
+ N = ParticleType("ASN",
+ mass = 114.1,
+ charge = 0,
+ sigma = 5.68,
+ ),
+ D = ParticleType("ASP",
+ mass = 115.1,
+ charge = -1,
+ sigma = 5.58,
+ ),
+ C = ParticleType("CYS",
+ mass = 103.1,
+ charge = 0,
+ sigma = 5.48,
+ ),
+ Q = ParticleType("GLN",
+ mass = 128.1,
+ charge = 0,
+ sigma = 6.02,
+ ),
+ E = ParticleType("GLU",
+ mass = 129.1,
+ charge = -1,
+ sigma = 5.92,
+ ),
+ G = ParticleType("GLY",
+ mass = 57.05,
+ charge = 0,
+ sigma = 4.5,
+ ),
+ H = ParticleType("HIS",
+ mass = 137.1,
+ charge = 0.5,
+ sigma = 6.08,
+ ),
+ I = ParticleType("ILE",
+ mass = 113.2,
+ charge = 0,
+ sigma = 6.18,
+ ),
+ L = ParticleType("LEU",
+ mass = 113.2,
+ charge = 0,
+ sigma = 6.18,
+ ),
+ K = ParticleType("LYS",
+ mass = 128.2,
+ charge = 1,
+ sigma = 6.36,
+ ),
+ M = ParticleType("MET",
+ mass = 131.2,
+ charge = 0,
+ sigma = 6.18,
+ ),
+ F = ParticleType("PHE",
+ mass = 147.2,
+ charge = 0,
+ sigma = 6.36,
+ ),
+ P = ParticleType("PRO",
+ mass = 97.12,
+ charge = 0,
+ sigma = 5.56,
+ ),
+ S = ParticleType("SER",
+ mass = 87.08,
+ charge = 0,
+ sigma = 5.18,
+ ),
+ T = ParticleType("THR",
+ mass = 101.1,
+ charge = 0,
+ sigma = 5.62,
+ ),
+ W = ParticleType("TRP",
+ mass = 186.2,
+ charge = 0,
+ sigma = 6.78,
+ ),
+ Y = ParticleType("TYR",
+ mass = 163.2,
+ charge = 0,
+ sigma = 6.46,
+ ),
+ V = ParticleType("VAL",
+ mass = 99.07,
+ charge = 0,
+ sigma = 5.86,
+ )
+)
+for k,t in _types.items():
+ t.resname = t.name
+
+class KhNonbonded(NonbondedScheme):
+ def __init__(self, debye_length=10, resolution=0.1, rMin=0):
+ NonbondedScheme.__init__(self, typesA=None, typesB=None, resolution=resolution, rMin=rMin)
+ self.debye_length = debye_length
+ self.maxForce = 50
+
+ def potential(self, r, typeA, typeB):
+ """ Electrostatics """
+ ld = self.debye_length
+ q1 = typeA.charge
+ q2 = typeB.charge
+ D = 80 # dielectric of water
+ ## units "e**2 / (4 * pi * epsilon0 AA)" kcal_mol
+ A = 332.06371
+ u_elec = (A*q1*q2/D)*np.exp(-r/ld) / r
+
+ """ KH scale model """
+ # alpha = 0.228
+ # epsilon0 = -1.0
+ # e_mj = epsilon_mj[(typeA.name,typeB.name)]
+ # epsilon = alpha * np.abs( e_mj - epsilon0 )
+ epsilon = epsilon_mj[(typeA.name,typeB.name)]
+ lambda_ = -1 if epsilon > 0 else 1
+ epsilon = np.abs(epsilon)
+
+ sigma = 0.5 * (typeA.sigma + typeB.sigma)
+
+ r6 = (sigma/r)**6
+ r12 = r6**2
+ u_lj = 4 * epsilon * (r12-r6)
+ u_hps = lambda_ * np.array(u_lj)
+ s = r<=sigma*2**(1/6)
+ u_hps[s] = u_lj[s] + (1-lambda_) * epsilon
+
+ u = u_elec + u_hps
+ u[0] = u[1] # Remove NaN
+
+ maxForce = self.maxForce
+ if maxForce is not None:
+ assert(maxForce > 0)
+ f = np.diff(u)/np.diff(r)
+ f[f>maxForce] = maxForce
+ f[f<-maxForce] = -maxForce
+ u[0] = 0
+ u[1:] = np.cumsum(f*np.diff(r))
+
+ u = u-u[-1]
+
+ return u
+
+class KhBeadsFromPolymer(Group):
+ # p = PointParticle(_P, (0,0,0), "P")
+ # b = PointParticle(_B, (3,0,1), "B")
+ # nt = Group( name = "nt", children = [p,b])
+ # nt.add_bond( i=p, j=b, bond = get_resource_path('two_bead_model/BPB.dat') )
+
+ def __init__(self, polymer, sequence=None, **kwargs):
+
+ if sequence is None:
+ raise NotImplementedError
+ # ... set random sequence
+
+ self.polymer = polymer
+ self.sequence = sequence
+
+ for prop in ('segname','chain'):
+ if prop not in kwargs:
+ # import pdb
+ # pdb.set_trace()
+ try:
+ self.__dict__[prop] = polymer.__dict__[prop]
+ except:
+ pass
+
+ if len(sequence) != polymer.num_monomers:
+ raise ValueError("Length of sequence does not match length of polymer")
+ Group.__init__(self, **kwargs)
+
+ def _clear_beads(self):
+ ...
+
+ def _generate_beads(self):
+ # beads = self.children
+
+ for i in range(self.polymer.num_monomers):
+ c = self.polymer.monomer_index_to_contour(i)
+ r = self.polymer.contour_to_position(c)
+ s = self.sequence[i]
+
+ bead = PointParticle(_types[s], r,
+ name = s,
+ resid = i+1)
+ self.add(bead)
+ # import pdb
+ # pdb.set_trace()
+ # continue
+
+ ## Two consecutive nts
+ for i in range(len(self.children)-1):
+ b1 = self.children[i]
+ b2 = self.children[i+1]
+ """ units "10 kJ/N_A" kcal_mol """
+ bond = HarmonicBond(k = 2.3900574,
+ r0 = 3.8,
+ rRange = (0,500),
+ resolution = 0.01,
+ maxForce = 10)
+ self.add_bond( i=b1, j=b2, bond = bond, exclude=True )
+
+
+class KhModel(ArbdModel):
+ def __init__(self, polymers,
+ sequences = None,
+ debye_length = 10,
+ damping_coefficient = 10,
+ DEBUG=False,
+ **kwargs):
+
+ """
+ [debye_length]: angstroms
+ [damping_coefficient]: ns
+ """
+ kwargs['timestep'] = 10e-6
+ kwargs['cutoff'] = max(4*debye_length,20)
+
+ if 'decompPeriod' not in kwargs:
+ kwargs['decompPeriod'] = 1000
+
+ """ Assign sequences """
+ if sequences is None:
+ raise NotImplementedError("KhModel must be provided a sequences argument")
+
+ self.polymer_group = AbstractPolymerGroup(polymers)
+ self.sequences = sequences
+ ArbdModel.__init__(self, [], **kwargs)
+
+ """ Update type diffusion coefficients """
+ self.types = all_types = [t for key,t in _types.items()]
+ self.set_damping_coefficient( damping_coefficient )
+
+ """ Set up nonbonded interactions """
+ nonbonded = KhNonbonded(debye_length)
+ for i in range(len(all_types)):
+ t1 = all_types[i]
+ for j in range(i,len(all_types)):
+ t2 = all_types[j]
+ self.useNonbondedScheme( nonbonded, typeA=t1, typeB=t2 )
+
+ """ Generate beads """
+ self.generate_beads()
+
+ def update_splines(self, coords):
+ i = 0
+ for p in self.polymer_group.polymers:
+ n = p.num_monomers
+ p.set_splines(np.linspace(0,1,n), coords[i:i+n])
+ i += n
+
+ self.clear_all()
+ self.generate_beads()
+ ## TODO Apply restraints, etc
+
+ def generate_beads(self):
+ self.peptides = [KhBeadsFromPolymer(p,s)
+ for p,s in zip(self.polymer_group.polymers,self.sequences)]
+
+ for s in self.peptides:
+ self.add(s)
+ s._generate_beads()
+
+ def set_damping_coefficient(self, damping_coefficient):
+ for t in self.types:
+ t.damping_coefficient = damping_coefficient
+ # t.diffusivity = 831447.2 * temperature / (t.mass * damping_coefficient)
+
+if __name__ == "__main__":
+
+ from matplotlib import pyplot as plt
+ nt = len(_types)
+ # print("TYPES")
+ # for n,t in _types.items():
+ # print("{}\t{}\t{}\t{}\t{}".format(t.name, t.mass, t.charge, t.sigma, t.lambda_))
+ type_string = 'WYFMLIVAPGCQNTSEDKHR'
+ d = np.zeros([nt,nt])
+ for i in range(nt):
+ n1 = type_string[i]
+ t1 = _types[n1]
+ for j in range(nt):
+ n2 = type_string[j]
+ t2 = _types[n2]
+ d[nt-i-1,j] = epsilon_mj[(t1.name,t2.name)]
+
+ plt.imshow(d.T)
+ plt.show()
diff --git a/mrdna/arbdmodel/kh_polymer_model_pair_epsilon.py b/mrdna/arbdmodel/kh_polymer_model_pair_epsilon.py
new file mode 100644
index 0000000000000000000000000000000000000000..e696b2c2d2ba7bd4b9f500cfd039add279d8ea0f
--- /dev/null
+++ b/mrdna/arbdmodel/kh_polymer_model_pair_epsilon.py
@@ -0,0 +1,229 @@
+
+_txtdata = """CYS CYS -0.509719
+CYS MET -0.448877
+MET MET -0.512423
+CYS PHE -0.558393
+MET PHE -0.661148
+PHE PHE -0.755790
+CYS ILE -0.517831
+MET ILE -0.588137
+PHE ILE -0.699005
+ILE ILE -0.658443
+CYS LEU -0.562449
+MET LEU -0.640867
+PHE LEU -0.758494
+ILE LEU -0.726045
+LEU LEU -0.770663
+CYS VAL -0.444821
+MET VAL -0.493495
+PHE VAL -0.624642
+ILE VAL -0.592194
+LEU VAL -0.650331
+VAL VAL -0.520535
+CYS TRP -0.443469
+MET TRP -0.524592
+PHE TRP -0.607066
+ILE TRP -0.555688
+LEU TRP -0.604362
+VAL TRP -0.474566
+TRP TRP -0.458342
+CYS TYR -0.336658
+MET TYR -0.438061
+PHE TYR -0.539464
+ILE TYR -0.484030
+LEU TYR -0.540816
+VAL TYR -0.398852
+TRP TYR -0.404260
+TYR TYR -0.338010
+CYS ALA -0.256888
+MET ALA -0.306913
+PHE ALA -0.424541
+ILE ALA -0.393444
+LEU ALA -0.438061
+VAL ALA -0.320433
+TRP ALA -0.290689
+TYR ALA -0.228495
+ALA ALA -0.141964
+CYS GLY -0.201454
+MET GLY -0.232551
+PHE GLY -0.332602
+ILE GLY -0.285280
+LEU GLY -0.336658
+VAL GLY -0.231199
+TRP GLY -0.236607
+TYR GLY -0.181173
+ALA GLY -0.086531
+GLY GLY -0.077066
+CYS THR -0.194694
+MET THR -0.248775
+PHE THR -0.352882
+ILE THR -0.319081
+LEU THR -0.360995
+VAL THR -0.242015
+TRP THR -0.209566
+TYR THR -0.181173
+ALA THR -0.087883
+GLY THR -0.055434
+THR THR -0.060842
+CYS SER -0.160893
+MET SER -0.183877
+PHE SER -0.317729
+ILE SER -0.250127
+LEU SER -0.304209
+VAL SER -0.186582
+TRP SER -0.178469
+TYR SER -0.150076
+ALA SER -0.045969
+GLY SER -0.020281
+THR SER -0.039209
+SER SER 0.000000
+CYS ASN -0.124388
+MET ASN -0.173061
+PHE ASN -0.281224
+ILE ASN -0.212270
+LEU ASN -0.279872
+VAL ASN -0.156837
+TRP ASN -0.189286
+TYR ASN -0.147372
+ALA ASN -0.022985
+GLY ASN -0.009464
+THR ASN -0.028393
+SER ASN 0.012168
+ASN ASN -0.001352
+CYS GLN -0.159541
+MET GLN -0.220383
+PHE GLN -0.328546
+ILE GLN -0.270408
+LEU GLN -0.320433
+VAL GLN -0.189286
+TRP GLN -0.194694
+TYR GLN -0.175765
+ALA GLN -0.029745
+GLY GLN 0.001352
+THR GLN -0.031097
+SER GLN 0.024337
+ASN GLN -0.005408
+GLN GLN 0.017577
+CYS ASP -0.100051
+MET ASP -0.121684
+PHE ASP -0.244719
+ILE ASP -0.202806
+LEU ASP -0.233903
+VAL ASP -0.109515
+TRP ASP -0.158189
+TYR ASP -0.147372
+ALA ASP -0.004056
+GLY ASP 0.010816
+THR ASP -0.017577
+SER ASP 0.005408
+ASN ASP -0.001352
+GLN ASP 0.028393
+ASP ASP 0.062194
+CYS GLU -0.081122
+MET GLU -0.164949
+PHE GLU -0.255536
+ILE GLU -0.216326
+LEU GLU -0.259592
+VAL GLU -0.135204
+TRP GLU -0.178469
+TYR GLU -0.151428
+ALA GLU 0.021633
+GLY GLU 0.060842
+THR GLU -0.009464
+SER GLU 0.025689
+ASN GLU 0.021633
+GLN GLU 0.033801
+ASP GLU 0.087883
+GLU GLU 0.102755
+CYS HIS -0.260944
+MET HIS -0.312321
+PHE HIS -0.419132
+ILE HIS -0.333954
+LEU HIS -0.388035
+VAL HIS -0.258240
+TRP HIS -0.312321
+TYR HIS -0.250127
+ALA HIS -0.100051
+GLY HIS -0.064898
+THR HIS -0.101403
+SER HIS -0.059490
+ASN HIS -0.055434
+GLN HIS -0.041913
+ASP HIS -0.087883
+GLU HIS -0.064898
+HIS HIS -0.186582
+CYS ARG -0.121684
+MET ARG -0.196046
+PHE ARG -0.312321
+ILE ARG -0.265000
+LEU ARG -0.319081
+VAL ARG -0.189286
+TRP ARG -0.235255
+TYR ARG -0.201454
+ALA ARG -0.021633
+GLY ARG -0.006760
+THR ARG -0.031097
+SER ARG 0.006760
+ASN ARG 0.004056
+GLN ARG -0.017577
+ASP ARG -0.083826
+GLU ARG -0.081122
+HIS ARG -0.066250
+ARG ARG 0.016224
+CYS LYS -0.037857
+MET LYS -0.109515
+PHE LYS -0.228495
+ILE LYS -0.181173
+LEU LYS -0.229847
+VAL LYS -0.110867
+TRP LYS -0.137908
+TYR LYS -0.125740
+ALA LYS 0.048673
+GLY LYS 0.070306
+THR LYS 0.048673
+SER LYS 0.083826
+ASN LYS 0.062194
+GLN LYS 0.051378
+ASP LYS -0.001352
+GLU LYS -0.017577
+HIS LYS 0.043265
+ARG LYS 0.146020
+LYS LYS 0.209566
+CYS PRO -0.189286
+MET PRO -0.240663
+PHE PRO -0.348826
+ILE PRO -0.282576
+LEU PRO -0.342066
+VAL PRO -0.223087
+TRP PRO -0.278520
+TYR PRO -0.205510
+ALA PRO -0.048673
+GLY PRO -0.027041
+THR PRO -0.031097
+SER PRO 0.013520
+ASN PRO 0.018929
+GLN PRO -0.008112
+ASP PRO 0.045969
+GLU PRO 0.055434
+HIS PRO -0.078418
+ARG PRO -0.004056
+LYS PRO 0.094643
+PRO PRO -0.010816"""
+
+epsilon_mj = dict()
+
+def __add_value(key,v):
+ if key not in epsilon_mj:
+ epsilon_mj[key] = v
+ else:
+ assert(epsilon_mj[key] == v)
+
+for line in _txtdata.split('\n'):
+ n1,n2,v = line.split()
+ v = float(v)
+
+ __add_value((n1,n2), v)
+ __add_value((n2,n1), v)
+
+if __name__ == '__main__':
+ print(epsilon_mj)
diff --git a/mrdna/arbdmodel/nonbonded.py b/mrdna/arbdmodel/nonbonded.py
new file mode 100644
index 0000000000000000000000000000000000000000..35ed22113877774093d143dc748c6a7dc20995b9
--- /dev/null
+++ b/mrdna/arbdmodel/nonbonded.py
@@ -0,0 +1,241 @@
+from shutil import copyfile
+import os, sys
+import numpy as np
+
+class NonbondedScheme():
+ """ Abstract class for writing nonbonded interactions """
+
+ def __init__(self, typesA=None, typesB=None, resolution=0.1, rMin=0):
+ """If typesA is None, and typesB is None, then """
+ self.resolution = resolution
+ self.rMin = rMin
+
+ def add_sim_system(self, simSystem):
+ self.rMax = simSystem.cutoff
+ self.r = np.arange(rMin,rMax,resolution)
+
+ def potential(self, r, typeA, typeB):
+ raise NotImplementedError
+
+ def write_file(self, filename, typeA, typeB, rMax):
+ r = np.arange(self.rMin, rMax+self.resolution, self.resolution)
+ u = self.potential(r, typeA, typeB)
+ np.savetxt(filename, np.array([r,u]).T)
+
+
+class LennardJones(NonbondedScheme):
+ def potential(self, r, typeA, typeB):
+ epsilon = sqrt( typeA.epsilon**2 + typeB.epsilon**2 )
+ r0 = 0.5 * (typeA.radius + typeB.radius)
+ r6 = (r0/r)**6
+ r12 = r6**2
+ u = epsilon * (r12-2*r6)
+ u[0] = u[1] # Remove NaN
+ return u
+LennardJones = LennardJones()
+
+class HalfHarmonic(NonbondedScheme):
+ def potential(self, r, typeA, typeB):
+ k = 10 # kcal/mol AA**2
+ r0 = (typeA.radius + typeB.radius)
+ u = 0.5 * k * (r-r0)**2
+ u[r > r0] = np.zeros( np.shape(u[r > r0]) )
+ return u
+HalfHarmonic = HalfHarmonic()
+
+class TabulatedPotential(NonbondedScheme):
+ def __init__(self, tableFile, typesA=None, typesB=None, resolution=0.1, rMin=0):
+ """If typesA is None, and typesB is None, then """
+ self.tableFile = tableFile
+ # self.resolution = resolution
+ # self.rMin = rMin
+
+ ## TODO: check that tableFile exists and is regular file
+
+ def write_file(self, filename, typeA, typeB, rMax):
+ if filename != self.tableFile:
+ copyfile(self.tableFile, filename)
+
+## Bonded potentials
+class BasePotential():
+ def __init__(self, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
+ self.r0 = r0
+ self.rRange = rRange
+ self.resolution = resolution
+ self.maxForce = maxForce
+ self.prefix = prefix
+ self.periodic = False
+ self.type_ = "None"
+ self.max_potential = max_potential
+ self.kscale_ = None # only used for
+
+ def filename(self):
+ raise NotImplementedError("Not implemented")
+
+ def potential(self,dr):
+ raise NotImplementedError("Not implemented")
+
+ def __str__(self):
+ return self.filename()
+
+ def write_file(self):
+ r = np.arange( self.rRange[0],
+ self.rRange[1]+self.resolution,
+ self.resolution )
+ dr = r-self.r0
+
+ if self.periodic == True:
+ rSpan = self.rRange[1]-self.rRange[0]
+ assert(rSpan > 0)
+ dr = np.mod( dr+0.5*rSpan, rSpan) - 0.5*rSpan
+
+ u = self.potential(dr)
+
+ maxForce = self.maxForce
+ if maxForce is not None:
+ assert(maxForce > 0)
+ f = np.diff(u)/np.diff(r)
+ f[f>maxForce] = maxForce
+ f[f<-maxForce] = -maxForce
+ u[0] = 0
+ u[1:] = np.cumsum(f*np.diff(r))
+
+ if self.max_potential is not None:
+ f = np.diff(u)/np.diff(r)
+ ids = np.where( 0.5*(u[1:]+u[:-1]) > self.max_potential )[0]
+
+ w = np.sqrt(2*self.max_potential/self.k)
+ drAvg = 0.5*(np.abs(dr[ids]) + np.abs(dr[ids+1]))
+
+ f[ids] = f[ids] * np.exp(-(drAvg-w)/(w))
+ u[0] = 0
+ u[1:] = np.cumsum(f*np.diff(r))
+
+ u = u - np.min(u)
+
+ np.savetxt( self.filename(), np.array([r, u]).T, fmt="%f" )
+
+class HarmonicPotential(BasePotential):
+ def __init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix, correct_geometry=False):
+ self.k = k
+ self.kscale_ = None
+ BasePotential.__init__(self, r0, rRange, resolution, maxForce, max_potential, prefix)
+
+ def filename(self):
+ return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
+ self.k*self.kscale_, self.r0)
+ def potential(self,dr):
+ return 0.5*self.k*dr**2
+
+ def __hash__(self):
+ assert(self.type_ != "None")
+ return hash((self.type_, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
+
+ def __eq__(self, other):
+ for a in ("type_", "k", "r0", "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
+ if self.__dict__[a] != other.__dict__[a]:
+ return False
+ return True
+
+# class NonBonded(HarmonicPotential):
+# def _init_hook(self):
+# self.type = "nonbonded"
+# self.kscale_ = 1.0
+
+class HarmonicBond(HarmonicPotential):
+ def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/", correct_geometry=False, temperature=295):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ self.type_ = "gbond" if correct_geometry else "bond"
+ self.kscale_ = 1.0
+ self.correct_geometry = correct_geometry
+ self.temperature = temperature
+
+ def potential(self,dr):
+ u = HarmonicPotential.potential(self,dr)
+ if self.correct_geometry:
+ with np.errstate(divide='ignore',invalid='ignore'):
+ du = 2*0.58622592*np.log(dr+self.r0) * self.temperature/295
+ du[np.logical_not(np.isfinite(du))] = 0
+ u = u-du
+ return u
+
+
+class HarmonicAngle(HarmonicPotential):
+ def __init__(self, k, r0, rRange=(0,181), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ self.type_ = "angle"
+ self.kscale_ = (180.0/np.pi)**2
+
+class HarmonicDihedral(HarmonicPotential):
+ def __init__(self, k, r0, rRange=(-180,180), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
+ HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
+ self.periodic = True
+ self.type_ = "dihedral"
+ self.kscale_ = (180.0/np.pi)**2
+
+class WLCSKBond(BasePotential):
+ """ ## https://aip.scitation.org/doi/full/10.1063/1.4968020 """
+ def __init__(self, d, lp, kT, rRange=(0,50), resolution=0.02, maxForce=100, max_potential=None, prefix="potentials/"):
+ BasePotential.__init__(self, 0, rRange, resolution, maxForce, max_potential, prefix)
+ self.type_ = "wlcbond"
+ self.d = d # separation
+ self.lp = lp # persistence length
+ self.kT = kT
+
+ def filename(self):
+ return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
+ self.d, self.lp)
+ def potential(self, dr):
+ nk = self.d / (2*self.lp)
+ q2 = (dr / self.d)**2
+ a1,a2 = 1, -7.0/(2*nk)
+ a3 = 3.0/32 - 3.0/(8*nk) - 6.0/(4*nk**2)
+ p0,p1,p2,p3,p4 = 13.0/32, 3.4719,2.5064,-1.2906,0.6482
+ a4 = (p0 + p1/(2*nk) + p2*(2*nk)**-2) / (1+p3/(2*nk)+p4*(2*nk)**-2)
+ with np.errstate(divide='ignore',invalid='ignore'):
+ u = self.kT * nk * ( a1/(1-q2) - a2*np.log(1-q2) + a3*q2 - 0.5*a4*q2*(q2-2) )
+ max_force = np.diff(u[q2<1][-2:]) / np.diff(dr).mean()
+ max_u = u[q2<1][-1]
+ max_dr = dr[q2<1][-2]
+ assert( max_force >= 0 )
+ u[q2>=1] = (dr[q2>=1]-max_dr)*max_force + max_u
+ return u
+
+ def __hash__(self):
+ assert(self.type_ != "None")
+ return hash((self.type_, self.d, self.lp, self.kT, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
+
+ def __eq__(self, other):
+ for a in ("type_", "d", "lp", "kT" "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
+ if self.__dict__[a] != other.__dict__[a]:
+ return False
+ return True
+
+class WLCSKAngle(BasePotential):
+ ## https://aip.scitation.org/doi/full/10.1063/1.4968020
+ def __init__(self, d, lp, kT, rRange=(0,181), resolution=0.5, maxForce=None, max_potential=None, prefix="potentials/"):
+ BasePotential.__init__(self, 180, rRange, resolution, maxForce, max_potential, prefix)
+ self.type_ = "wlcangle"
+ self.d = d # separation
+ self.lp = lp # persistence length
+ self.kT = kT
+
+ def filename(self):
+ return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
+ self.d, self.lp)
+ def potential(self,dr):
+ nk = self.d / (2*self.lp)
+ p1,p2,p3,p4 = -1.237, 0.8105, -1.0243, 0.4595
+ C = (1 + p1*(2*nk) + p2*(2*nk)**2) / (2*nk+p3*(2*nk)**2+p4*(2*nk)**3)
+ u = self.kT * C * (1-np.cos(dr * np.pi / 180))
+ return u
+
+ def __hash__(self):
+ assert(self.type_ != "None")
+ return hash((self.type_, self.d, self.lp, self.kT, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
+
+ def __eq__(self, other):
+ for a in ("type_", "d", "lp", "kT" "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
+ if self.__dict__[a] != other.__dict__[a]:
+ return False
+ return True
diff --git a/mrdna/arbdmodel/onck_polymer_model.py b/mrdna/arbdmodel/onck_polymer_model.py
new file mode 100644
index 0000000000000000000000000000000000000000..861f90d64dee96f83483264026d38b2b55c1000d
--- /dev/null
+++ b/mrdna/arbdmodel/onck_polymer_model.py
@@ -0,0 +1,327 @@
+# -*- coding: utf-8 -*-
+## Test with `python -m arbdmodel.onck_polymer_model`
+
+import numpy as np
+import sys
+
+
+## Local imports
+from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path
+from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .interactions import NonbondedScheme, HarmonicBond, HarmonicAngle, HarmonicDihedral
+from .coords import quaternion_to_matrix
+
+"""Define particle types"""
+_types = dict(
+ A = ParticleType("ALA",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.7,
+ lambda_ = 0.72973,
+ ),
+ R = ParticleType("ARG",
+ mass = 120,
+ charge = 1,
+ epsilon = 0.0,
+ lambda_ = 0.0,
+ ),
+ N = ParticleType("ASN",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.33,
+ lambda_ = 0.432432,
+ ),
+ D = ParticleType("ASP",
+ mass = 120,
+ charge = -1,
+ epsilon = 0.0005,
+ ),
+ C = ParticleType("CYS",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.68,
+ ),
+ Q = ParticleType("GLN",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.64,
+ ),
+ E = ParticleType("GLU",
+ mass = 120,
+ charge = -1,
+ epsilon = 0.0005,
+ ),
+ G = ParticleType("GLY",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.41,
+ ),
+ H = ParticleType("HIS",
+ mass = 120,
+ charge = 0.0,
+ epsilon = 0.53,
+ ),
+ I = ParticleType("ILE",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.98,
+ ),
+ L = ParticleType("LEU",
+ mass = 120,
+ charge = 0,
+ epsilon = 1.0,
+ ),
+ K = ParticleType("LYS",
+ mass = 120,
+ charge = 1,
+ epsilon = 0.0005,
+ ),
+ M = ParticleType("MET",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.78,
+ ),
+ F = ParticleType("PHE",
+ mass = 120,
+ charge = 0,
+ epsilon = 1.0,
+ ),
+ P = ParticleType("PRO",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.65,
+ ),
+ S = ParticleType("SER",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.45,
+ ),
+ T = ParticleType("THR",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.51,
+ ),
+ W = ParticleType("TRP",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.96,
+ ),
+ Y = ParticleType("TYR",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.82,
+ ),
+ V = ParticleType("VAL",
+ mass = 120,
+ charge = 0,
+ epsilon = 0.94,
+ )
+)
+for k,t in _types.items():
+ t.resname = t.name
+
+class OnckNonbonded(NonbondedScheme):
+ def __init__(self, debye_length=10, resolution=0.1, rMin=0):
+ NonbondedScheme.__init__(self, typesA=None, typesB=None,
+ resolution=resolution, rMin=rMin)
+ self.debye_length = debye_length
+ self.maxForce = 50
+ # self.maxForce = 100
+ # self.maxForce = None
+
+ def potential(self, r, typeA, typeB):
+ """ Electrostatics """
+ ld = self.debye_length
+ q1 = typeA.charge
+ q2 = typeB.charge
+ D = 80 # dielectric of water
+ _z = 2.5
+ D = 80 * (1- (r/_z)**2 * np.exp(r/_z)/(np.exp(r/_z)-1)**2)
+ ## units "e**2 / (4 * pi * epsilon0 AA)" kcal_mol
+ A = 332.06371
+ u_elec = (A*q1*q2/D)*np.exp(-r/ld) / r
+
+ """ LJ-type term """
+ alpha = 0.27
+ epsilon_hp = 3.1070746 # units "13 kJ/N_A" kcal_mol
+ epsilon_rep = 2.3900574 # units "10 kJ/N_A" kcal_mol
+
+ sigma = 6.0
+ epsilon = epsilon_hp*np.sqrt( (typeA.epsilon*typeB.epsilon)**alpha )
+
+ r6 = (sigma/r)**6
+ r8 = (sigma/r)**8
+ u_lj = (epsilon_rep-epsilon) * r8
+ s = r<=sigma
+ u_lj[s] = epsilon_rep*r8[s] - epsilon*(4*r6[s]-1)/3
+ u_lj[r>25] = 0
+
+
+ u = u_elec + u_lj
+ u[0] = u[1] # Remove NaN
+
+ maxForce = self.maxForce
+ if maxForce is not None:
+ assert(maxForce > 0)
+ f = np.diff(u)/np.diff(r)
+ f[f>maxForce] = maxForce
+ f[f<-maxForce] = -maxForce
+ u[0] = 0
+ u[1:] = np.cumsum(f*np.diff(r))
+
+ u = u-u[-1]
+
+ return u
+
+class OnckBeadsFromPolymer(Group):
+ """ units "8038 kJ / (N_A nm**2)" "0.5 * kcal_mol/AA**2" """
+ peptide_bond = HarmonicBond(k = 38.422562,
+ r0 = 3.8,
+ rRange = (0,500),
+ resolution = 0.01,
+ maxForce = 10)
+
+ def __init__(self, polymer, sequence=None, **kwargs):
+
+ if sequence is None:
+ raise NotImplementedError
+ # ... set random sequence
+
+ self.polymer = polymer
+ self.sequence = sequence
+
+ for prop in ('segname','chain'):
+ if prop not in kwargs:
+ # import pdb
+ # pdb.set_trace()
+ try:
+ self.__dict__[prop] = polymer.__dict__[prop]
+ except:
+ pass
+
+ if len(sequence) != polymer.num_monomers:
+ raise ValueError("Length of sequence does not match length of polymer")
+ Group.__init__(self, **kwargs)
+
+ def _clear_beads(self):
+ ...
+
+ def _generate_beads(self):
+ for i in range(self.polymer.num_monomers):
+ c = self.polymer.monomer_index_to_contour(i)
+ r = self.polymer.contour_to_position(c)
+ s = self.sequence[i]
+
+ bead = PointParticle(_types[s], r,
+ name = s,
+ resid = i+1)
+ self.add(bead)
+
+ ## Two consecutive monomers
+ for i in range(len(self.children)-1):
+ b1,b2 = [self.children[i+j] for j in range(2)]
+ bond = OnckBeadsFromPolymer.peptide_bond
+ self.add_bond( i=b1, j=b2, bond = bond, exclude=True )
+
+ def bead_to_type(bead):
+ if bead.type_.name == 'PRO':
+ return 'P'
+ elif bead.type_.name == 'GLY':
+ return 'G'
+ else:
+ return 'X'
+
+ ## Three consecutive monomers
+ for i in range(len(self.children)-2):
+ b1,b2,b3 = [self.children[i+j] for j in range(3)]
+ t1,t2,t3 = ([bead_to_type(b) for b in (b1,b2,b3)])
+
+ filename = 'onck_model_potentials/bend_O{}{}.txt'.format(
+ t2,'P' if t3 == 'P' else 'Y' )
+ self.add_angle( i=b1, j=b2, k=b3,
+ angle = get_resource_path(filename) )
+ self.add_exclusion( i=b1, j=b3 )
+
+ ## Four consecutive monomers
+ for i in range(len(self.children)-3):
+ b1,b2,b3,b4 = [self.children[i+j] for j in range(4)]
+ t1,t2,t3,t4 = ([bead_to_type(b) for b in (b1,b2,b3,b4)])
+
+ filename = 'onck_model_potentials/dih_{}{}.txt'.format(t2,t3)
+ self.add_dihedral( i=b1, j=b2, k=b3, l=b4,
+ dihedral = get_resource_path(filename) )
+ self.add_exclusion( i=b1, j=b4 )
+
+class OnckModel(ArbdModel):
+ def __init__(self, polymers,
+ sequences = None,
+ debye_length = 10,
+ damping_coefficient = 50e3,
+ DEBUG=False,
+ **kwargs):
+
+ """
+ [debye_length]: angstroms
+ [damping_coefficient]: ns
+ """
+ if debye_length != 10:
+ print("""WARNING: you are deviated from the model published by Onck by choosing a debye length != 1 nm.
+ Be advised that the non-bonded cutoff is simply set to 5 * debye_length, but this is not necessarily prescribed by the model.""")
+ kwargs['timestep'] = 20e-6
+ kwargs['cutoff'] = max(5*debye_length,25)
+
+ if 'decompPeriod' not in kwargs:
+ kwargs['decompPeriod'] = 1000
+
+ """ Assign sequences """
+ if sequences is None:
+ raise NotImplementedError("OnckModel must be provided a sequences argument")
+
+ self.polymer_group = AbstractPolymerGroup(polymers)
+ self.sequences = sequences
+ ArbdModel.__init__(self, [], **kwargs)
+
+ """ Update type diffusion coefficients """
+ self.types = all_types = [t for key,t in _types.items()]
+ self.set_damping_coefficient( damping_coefficient )
+
+ """ Set up nonbonded interactions """
+ nonbonded = OnckNonbonded(debye_length)
+ for i in range(len(all_types)):
+ t1 = all_types[i]
+ for j in range(i,len(all_types)):
+ t2 = all_types[j]
+ self.useNonbondedScheme( nonbonded, typeA=t1, typeB=t2 )
+
+ """ Generate beads """
+ self.generate_beads()
+
+ def update_splines(self, coords):
+ i = 0
+ for p in self.polymer_group.polymers:
+ n = p.num_monomers
+ p.set_splines(np.linspace(0,1,n), coords[i:i+n])
+ i += n
+
+ self.clear_all()
+ self.generate_beads()
+ ## TODO Apply restraints, etc
+
+ def generate_beads(self):
+ self.peptides = [OnckBeadsFromPolymer(p,s)
+ for p,s in zip(self.polymer_group.polymers,self.sequences)]
+
+ for s in self.peptides:
+ self.add(s)
+ s._generate_beads()
+
+ def set_damping_coefficient(self, damping_coefficient):
+ for t in self.types:
+ t.damping_coefficient = damping_coefficient
+ # t.diffusivity = 831447.2 * temperature / (t.mass * damping_coefficient)
+
+if __name__ == "__main__":
+
+ print("TYPES")
+ for n,t in _types.items():
+ print("{}\t{}\t{}\t{}\t{}".format(n, t.name, t.mass, t.charge, t.epsilon))
diff --git a/mrdna/arbdmodel/resources/two_bead_model/BBP.dat b/mrdna/arbdmodel/resources/two_bead_model/BBP.dat
new file mode 100644
index 0000000000000000000000000000000000000000..65eb64969b2499842c9653e22f9639996551ccaf
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/BBP.dat
@@ -0,0 +1,2500 @@
+0.000000 40.295654
+0.020000 40.092237
+0.040000 39.889282
+0.060000 39.686791
+0.080000 39.484761
+0.100000 39.283195
+0.120000 39.082091
+0.140000 38.881449
+0.160000 38.681270
+0.180000 38.481554
+0.200000 38.282301
+0.220000 38.083510
+0.240000 37.885182
+0.260000 37.687316
+0.280000 37.489913
+0.300000 37.292972
+0.320000 37.096495
+0.340000 36.900479
+0.360000 36.704927
+0.380000 36.509837
+0.400000 36.315209
+0.420000 36.121045
+0.440000 35.927343
+0.460000 35.734103
+0.480000 35.541326
+0.500000 35.349012
+0.520000 35.157161
+0.540000 34.965772
+0.560000 34.774845
+0.580000 34.584382
+0.600000 34.394380
+0.620000 34.204842
+0.640000 34.015766
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/BPB.dat b/mrdna/arbdmodel/resources/two_bead_model/BPB.dat
new file mode 100644
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/BPP.dat b/mrdna/arbdmodel/resources/two_bead_model/BPP.dat
new file mode 100644
index 0000000000000000000000000000000000000000..bd174f4dd843301b9b0e64003296ea81e4af7283
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/NBBB.dat b/mrdna/arbdmodel/resources/two_bead_model/NBBB.dat
new file mode 100644
index 0000000000000000000000000000000000000000..369ec1bf5dc25fb1f4fa63ac261ed8f5064dc524
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/NBPB.dat b/mrdna/arbdmodel/resources/two_bead_model/NBPB.dat
new file mode 100644
index 0000000000000000000000000000000000000000..cb0898738463385f18ddfc0deb210637b41837ef
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/NBPB.dat
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/NBPP.dat b/mrdna/arbdmodel/resources/two_bead_model/NBPP.dat
new file mode 100644
index 0000000000000000000000000000000000000000..256d384afb42bc4fc277ce05c965d7662b640a56
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/NBPP.dat
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/b1p1p2b2.dat b/mrdna/arbdmodel/resources/two_bead_model/b1p1p2b2.dat
new file mode 100644
index 0000000000000000000000000000000000000000..2de9010d7eae2a28a49fc3f4cc4d5836369c67b8
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/b1p1p2b2.dat
@@ -0,0 +1,180 @@
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-pri.bea b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-pri.bea
new file mode 100644
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-pri.vrml b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-pri.vrml
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+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.14615E+00 0.13759E+00 0.16219E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.99249E-01 -0.35207E+00 -0.75146E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.15180E+00 0.60146E+00 0.42776E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.42013E-01 0.10435E+01 0.13816E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.69385E+00 0.53262E+00 -0.19950E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.96370E+00 0.51111E-01 -0.33400E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.14501E+01 0.44458E-01 0.50102E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.63121E+00 -0.41294E+00 -0.11540E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.87832E+00 -0.95904E+00 -0.15844E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.99025E+00 -0.32059E+00 0.36061E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.71657E+00 -0.54383E+00 0.63269E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-res.txt b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-res.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5e9c255a081dc9fc427de93fc4d9d78441e2188
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-res.txt
@@ -0,0 +1,190 @@
+ ------------------------------------------------------------
+ HYDROPRO, Version 10, September 2011
+ A. Ortega, D. Amoros, J. Garcia de la Torre,
+ "Prediction of hydrodynamic and other solution properties of
+ rigid proteins from atomic- and residue-level models"
+ Biophys. J. 101, 892-898 (2011).
+ ------------------------------------------------------------
+
+
+ SUMMARY OF DATA AND RESULTS
+
+ This file : b-bead.hydropro-res.txt
+ Case : b !Name
+ Structural file : b-bead.pdb
+
+ Radius of elements in primary model : 2.90 Angs.
+ Type of hydropro calculation : 1
+
+ Temperature: 22.0 centigrade
+ Solvent viscosity: 0.01000 poise
+ Molecular weight: 181. Da
+ Solute partial specific volume: 1.000 cm^3/g
+ Solution density: 1.000 g/cm^3
+
+ Translational diffusion coefficient: 4.137E-06 cm^2/s
+ Radius of gyration: 4.262E-08 cm
+ Volume: 4.295E-22 cm^3
+ Rotational diffusion coefficient: 1.302E+09 s^-1
+ Relaxation time (1): 1.890E-10 s
+ Relaxation time (2): 1.765E-10 s
+ Relaxation time (3): 1.743E-10 s
+ Relaxation time (4): 1.424E-10 s
+ Relaxation time (5): 1.430E-10 s
+ Harmonic mean (correlation) time: 1.628E-10 s
+ Intrinsic viscosity: 5.274E+00 cm^3/g
+ Sedimentation coefficient: 0.000E+00 Svedberg
+
+
+
+ Center of diffusion (x): 5.113E-08 cm
+ Center of diffusion (x): 6.380E-08 cm
+ Center of diffusion (x): 3.871E-08 cm
+
+ Generalized (6x6) diffusion matrix: (Dtt Dtr)
+
+ (Drt Drr)
+
+
+ 4.334E-06 1.273E-09 -3.350E-08 4.491E-01 -1.381E-01 -1.107E-01
+ 1.261E-09 4.555E-06 -8.120E-08 -1.380E-01 -3.259E-01 2.473E-01
+ -3.347E-08 -8.122E-08 4.229E-06 -1.108E-01 2.471E-01 -2.012E-01
+
+
+ 4.491E-01 -1.380E-01 -1.108E-01 1.211E+09 -2.254E+07 -1.629E+07
+ -1.381E-01 -3.259E-01 2.471E-01 -2.254E+07 1.561E+09 -9.402E+07
+ -1.107E-01 2.473E-01 -2.012E-01 -1.629E+07 -9.402E+07 1.133E+09
+
+ List of equivalent radii
+
+ Translational: 5.225E-08
+ Gyration : 5.502E-08
+ Volume : 4.680E-08
+ Rotation (1): 5.686E-08
+ Rotation (2): 5.558E-08
+ Rotation (3): 5.535E-08
+ Rotation (4): 5.174E-08
+ Rotation (5): 5.181E-08
+ Rotation (h): 5.083E-08
+ Intrinsic viscosity: 5.329E-08
+ Longest distance: 6.342E-08
+
+ Longest distance : 1.268E-07 cm
+
+
+
+ Calculation of scattering form factor, P vs h
+ h P(h)
+ 0.00E+00 1.04E+00
+ 3.51E+06 1.03E+00
+ 7.02E+06 1.02E+00
+ 1.05E+07 9.94E-01
+ 1.40E+07 9.64E-01
+ 1.76E+07 9.26E-01
+ 2.11E+07 8.81E-01
+ 2.46E+07 8.31E-01
+ 2.81E+07 7.78E-01
+ 3.16E+07 7.21E-01
+ 3.51E+07 6.62E-01
+ 3.86E+07 6.03E-01
+ 4.21E+07 5.45E-01
+ 4.56E+07 4.88E-01
+ 4.91E+07 4.33E-01
+ 5.27E+07 3.82E-01
+ 5.62E+07 3.34E-01
+ 5.97E+07 2.90E-01
+ 6.32E+07 2.50E-01
+ 6.67E+07 2.14E-01
+ 7.02E+07 1.83E-01
+ 7.37E+07 1.55E-01
+ 7.72E+07 1.31E-01
+ 8.07E+07 1.11E-01
+ 8.42E+07 9.39E-02
+ 8.78E+07 7.95E-02
+ 9.13E+07 6.75E-02
+ 9.48E+07 5.75E-02
+ 9.83E+07 4.94E-02
+ 1.02E+08 4.27E-02
+ 1.05E+08 3.72E-02
+ 1.09E+08 3.28E-02
+ 1.12E+08 2.91E-02
+ 1.16E+08 2.60E-02
+ 1.19E+08 2.35E-02
+ 1.23E+08 2.14E-02
+ 1.26E+08 1.97E-02
+ 1.30E+08 1.82E-02
+ 1.33E+08 1.70E-02
+ 1.37E+08 1.59E-02
+ 1.40E+08 1.50E-02
+ 1.44E+08 1.42E-02
+ 1.47E+08 1.35E-02
+ 1.51E+08 1.29E-02
+ 1.54E+08 1.24E-02
+ 1.58E+08 1.20E-02
+ 1.61E+08 1.15E-02
+ 1.65E+08 1.11E-02
+ 1.68E+08 1.08E-02
+ 1.72E+08 1.04E-02
+ 1.76E+08 1.01E-02
+
+
+ Distribution of distances
+
+ 50 intervals between RMIN and RMAX centered at R;
+ Values of p(R)
+
+
+ RMIN(cm) RMAX(cm) R(cm) p(R)(cm^(-1))
+ 0.000E+00 2.537E-09 1.268E-09 4.271E+05
+ 2.537E-09 5.074E-09 3.805E-09 1.509E+06
+ 5.074E-09 7.611E-09 6.342E-09 2.871E+06
+ 7.611E-09 1.015E-08 8.879E-09 4.478E+06
+ 1.015E-08 1.268E-08 1.142E-08 6.284E+06
+ 1.268E-08 1.522E-08 1.395E-08 8.228E+06
+ 1.522E-08 1.776E-08 1.649E-08 1.024E+07
+ 1.776E-08 2.029E-08 1.903E-08 1.227E+07
+ 2.029E-08 2.283E-08 2.156E-08 1.423E+07
+ 2.283E-08 2.537E-08 2.410E-08 1.606E+07
+ 2.537E-08 2.791E-08 2.664E-08 1.770E+07
+ 2.791E-08 3.044E-08 2.917E-08 1.908E+07
+ 3.044E-08 3.298E-08 3.171E-08 2.017E+07
+ 3.298E-08 3.552E-08 3.425E-08 2.093E+07
+ 3.552E-08 3.805E-08 3.678E-08 2.135E+07
+ 3.805E-08 4.059E-08 3.932E-08 2.141E+07
+ 4.059E-08 4.313E-08 4.186E-08 2.113E+07
+ 4.313E-08 4.566E-08 4.439E-08 2.052E+07
+ 4.566E-08 4.820E-08 4.693E-08 1.963E+07
+ 4.820E-08 5.074E-08 4.947E-08 1.850E+07
+ 5.074E-08 5.327E-08 5.201E-08 1.720E+07
+ 5.327E-08 5.581E-08 5.454E-08 1.580E+07
+ 5.581E-08 5.835E-08 5.708E-08 1.439E+07
+ 5.835E-08 6.088E-08 5.962E-08 1.302E+07
+ 6.088E-08 6.342E-08 6.215E-08 1.163E+07
+ 6.342E-08 6.596E-08 6.469E-08 1.026E+07
+ 6.596E-08 6.850E-08 6.723E-08 8.950E+06
+ 6.850E-08 7.103E-08 6.976E-08 7.711E+06
+ 7.103E-08 7.357E-08 7.230E-08 6.558E+06
+ 7.357E-08 7.611E-08 7.484E-08 5.501E+06
+ 7.611E-08 7.864E-08 7.737E-08 4.552E+06
+ 7.864E-08 8.118E-08 7.991E-08 3.718E+06
+ 8.118E-08 8.372E-08 8.245E-08 2.992E+06
+ 8.372E-08 8.625E-08 8.498E-08 2.363E+06
+ 8.625E-08 8.879E-08 8.752E-08 1.826E+06
+ 8.879E-08 9.133E-08 9.006E-08 1.380E+06
+ 9.133E-08 9.386E-08 9.260E-08 1.019E+06
+ 9.386E-08 9.640E-08 9.513E-08 7.328E+05
+ 9.640E-08 9.894E-08 9.767E-08 5.114E+05
+ 9.894E-08 1.015E-07 1.002E-07 3.460E+05
+ 1.015E-07 1.040E-07 1.027E-07 2.263E+05
+ 1.040E-07 1.065E-07 1.053E-07 1.422E+05
+ 1.065E-07 1.091E-07 1.078E-07 8.510E+04
+ 1.091E-07 1.116E-07 1.104E-07 4.817E+04
+ 1.116E-07 1.142E-07 1.129E-07 2.595E+04
+ 1.142E-07 1.167E-07 1.154E-07 1.309E+04
+ 1.167E-07 1.192E-07 1.180E-07 5.789E+03
+ 1.192E-07 1.218E-07 1.205E-07 2.157E+03
+ 1.218E-07 1.243E-07 1.230E-07 4.983E+02
+ 1.243E-07 1.268E-07 1.256E-07 1.970E+01
+
+ Check for normalization:
+ (RMAX-RMIN)*SUM(p(R))= 1.035E+00 SHOULD BE= 1
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-sol.txt b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-sol.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9602628134bfd86b723bd1c7a6e4457c58beb233
Binary files /dev/null and b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-sol.txt differ
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.pdb b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..dd4e2acadd5947cdafc10716d6c70805e01ff701
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.pdb
@@ -0,0 +1,24 @@
+CRYST1 394.970 493.874 795.001 90.00 90.00 90.00 P 1 1
+ATOM 1 C4' THY S 16 1.387 -0.487 -77.056 0.00 0.00 S101
+ATOM 2 H4' THY S 16 1.453 -1.596 -77.013 0.00 0.00 S101
+ATOM 3 O4' THY S 16 2.736 0.086 -77.219 0.00 0.00 S101
+ATOM 4 C1' THY S 16 2.946 1.123 -76.275 0.00 0.00 S101
+ATOM 5 H1' THY S 16 4.009 1.037 -75.963 0.00 0.00 S101
+ATOM 6 N1 THY S 16 2.682 2.456 -76.875 0.00 0.00 S101
+ATOM 7 C6 THY S 16 1.430 3.039 -76.789 0.00 0.00 S101
+ATOM 8 H6 THY S 16 0.588 2.368 -76.622 0.00 0.00 S101
+ATOM 9 C2 THY S 16 3.729 3.125 -77.465 0.00 0.00 S101
+ATOM 10 O2 THY S 16 4.867 2.674 -77.534 0.00 0.00 S101
+ATOM 11 N3 THY S 16 3.427 4.381 -77.923 0.00 0.00 S101
+ATOM 12 H3 THY S 16 4.197 4.890 -78.333 0.00 0.00 S101
+ATOM 13 C4 THY S 16 2.263 5.077 -77.691 0.00 0.00 S101
+ATOM 14 O4 THY S 16 2.250 6.297 -77.847 0.00 0.00 S101
+ATOM 15 C5 THY S 16 1.169 4.286 -77.198 0.00 0.00 S101
+ATOM 16 C5M THY S 16 -0.168 4.915 -76.954 0.00 0.00 S101
+ATOM 17 H51 THY S 16 -0.985 4.177 -77.103 0.00 0.00 S101
+ATOM 18 H52 THY S 16 -0.357 5.760 -77.650 0.00 0.00 S101
+ATOM 19 H53 THY S 16 -0.240 5.295 -75.913 0.00 0.00 S101
+ATOM 20 C2' THY S 16 2.081 0.750 -75.088 0.00 0.00 S101
+ATOM 21 H2'' THY S 16 1.779 1.626 -74.475 0.00 0.00 S101
+ATOM 22 H2' THY S 16 2.651 0.047 -74.443 0.00 0.00 S101
+END
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/b.hydropro.dat b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b.hydropro.dat
new file mode 100644
index 0000000000000000000000000000000000000000..3788e9929348c88ce1b626dda0859af7521e46d9
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b.hydropro.dat
@@ -0,0 +1,18 @@
+b !Name of molecule
+b-bead.hydropro !Name for output file
+b-bead.pdb !Strucutural (PBD) file
+1 !Type of calculation
+2.9, !AER, hydrodynamic radius of primary elements
+6, !NSIG
+1.2, !Minimum radius of beads in the shell (SIGMIN)
+2.0, !Maximum radius of beads in the shell (SIGMAX)
+22., !T (temperature, centigrade)
+0.01, !ETA (Viscosity of the solvent in poises)
+181, !RM (Molecular weight)
+1.0, !Partial specific volume, cm3/g
+1.0, !Solvent density, g/cm3
+-1 !Number of values of Q
+-1 !Number of intervals
+0, !Number of trials for MC calculation of covolume
+1 !IDIF=1 (yes) for full diffusion tensors
+*
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro-fit.txt b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro-fit.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00827c1204e06695c25a7630d8523dabcd21a7a8
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro-fit.txt
@@ -0,0 +1,2 @@
+b 2.95E+02 1.00E-02 1.81E+02 1.00E+00 2.95E+02 1.00E-02 1.00E+00 4.14E-06 4.26E-08 4.29E-22 1.89E-10 1.77E-10 1.74E-10 1.42E-10 1.43E-10 5.27E+00 1.27E-07 0.00E+00
+b 2.95E+02 1.00E-02 1.81E+02 1.00E+00 2.95E+02 1.00E-02 1.00E+00 5.23E-08 5.50E-08 4.68E-08 5.69E-08 5.56E-08 5.54E-08 5.17E-08 5.18E-08 5.33E-08 6.34E-08 -1.00E+00
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro-sum.txt b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro-sum.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2892a63b5f92cc384bd49710c53f5ac8ef2a821e
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro-sum.txt
@@ -0,0 +1 @@
+b 4.14E-06 4.26E-08 4.29E-22 1.89E-10 1.77E-10 1.74E-10 1.42E-10 1.43E-10 5.27E+00 0.00E+00 1.27E-07 0.00E+00 5.10E+01 1.76E+08 1.04E+00 1.03E+00 1.02E+00 9.94E-01 9.64E-01 9.26E-01 8.81E-01 8.31E-01 7.78E-01 7.21E-01 6.62E-01 6.03E-01 5.45E-01 4.88E-01 4.33E-01 3.82E-01 3.34E-01 2.90E-01 2.50E-01 2.14E-01 1.83E-01 1.55E-01 1.31E-01 1.11E-01 9.39E-02 7.95E-02 6.75E-02 5.75E-02 4.94E-02 4.27E-02 3.72E-02 3.28E-02 2.91E-02 2.60E-02 2.35E-02 2.14E-02 1.97E-02 1.82E-02 1.70E-02 1.59E-02 1.50E-02 1.42E-02 1.35E-02 1.29E-02 1.24E-02 1.20E-02 1.15E-02 1.11E-02 1.08E-02 1.04E-02 1.01E-02 5.00E+01 1.27E-07 4.27E+05 1.51E+06 2.87E+06 4.48E+06 6.28E+06 8.23E+06 1.02E+07 1.23E+07 1.42E+07 1.61E+07 1.77E+07 1.91E+07 2.02E+07 2.09E+07 2.13E+07 2.14E+07 2.11E+07 2.05E+07 1.96E+07 1.85E+07 1.72E+07 1.58E+07 1.44E+07 1.30E+07 1.16E+07 1.03E+07 8.95E+06 7.71E+06 6.56E+06 5.50E+06 4.55E+06 3.72E+06 2.99E+06 2.36E+06 1.83E+06 1.38E+06 1.02E+06 7.33E+05 5.11E+05 3.46E+05 2.26E+05 1.42E+05 8.51E+04 4.82E+04 2.60E+04 1.31E+04 5.79E+03 2.16E+03 4.98E+02 1.97E+01
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro.dat b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro.dat
new file mode 100644
index 0000000000000000000000000000000000000000..3788e9929348c88ce1b626dda0859af7521e46d9
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro.dat
@@ -0,0 +1,18 @@
+b !Name of molecule
+b-bead.hydropro !Name for output file
+b-bead.pdb !Strucutural (PBD) file
+1 !Type of calculation
+2.9, !AER, hydrodynamic radius of primary elements
+6, !NSIG
+1.2, !Minimum radius of beads in the shell (SIGMIN)
+2.0, !Maximum radius of beads in the shell (SIGMAX)
+22., !T (temperature, centigrade)
+0.01, !ETA (Viscosity of the solvent in poises)
+181, !RM (Molecular weight)
+1.0, !Partial specific volume, cm3/g
+1.0, !Solvent density, g/cm3
+-1 !Number of values of Q
+-1 !Number of intervals
+0, !Number of trials for MC calculation of covolume
+1 !IDIF=1 (yes) for full diffusion tensors
+*
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro10-lnx.exe b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro10-lnx.exe
new file mode 120000
index 0000000000000000000000000000000000000000..a9bf1107c28369cdeec95b978f5831e4f22fe026
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/hydropro10-lnx.exe
@@ -0,0 +1 @@
+/home/cmaffeo2/Public/hydropro10-lnx.exe
\ No newline at end of file
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-pri.bea b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-pri.bea
new file mode 100644
index 0000000000000000000000000000000000000000..f46a0c639e7f694559353d7cfe2c80bf6b893c2b
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-pri.bea
@@ -0,0 +1,8 @@
+ATOM 1 O -0.288 0.686 -39.332
+ATOM 2 O -0.585 0.233 -38.897
+ATOM 3 O -0.815 0.458 -38.197
+ATOM 4 O -1.508 0.309 -38.114
+ATOM 5 O -0.601 1.131 -38.071
+ATOM 6 O -0.406 0.005 -37.723
+ATOM 7 O 0.286 -0.017 -37.797
+ATOM 8 O 0.412 -0.347 -38.201
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-pri.vrml b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-pri.vrml
new file mode 100644
index 0000000000000000000000000000000000000000..2dfa5a517fc50506248ff839740bae70562c1b2d
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-pri.vrml
@@ -0,0 +1,73 @@
+#VRML V2.0 utf8
+Transform {
+ translation -0.45362E+00 -0.11172E+01 0.60272E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.30105E+00 -0.50216E+00 -0.34204E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.37239E+00 0.25315E+00 0.60709E-03
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.85319E+00 0.68340E+00 -0.42082E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.51600E+00 0.19023E+00 0.75918E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.39776E+00 0.56724E+00 -0.69582E-01
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.97636E+00 0.16692E+00 0.19842E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation 0.11221E+01 -0.24157E+00 -0.18605E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.15123E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-res.txt b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-res.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5fa34c66ecc60d17b15e8876ac040ad43a9a209
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-res.txt
@@ -0,0 +1,190 @@
+ ------------------------------------------------------------
+ HYDROPRO, Version 10, September 2011
+ A. Ortega, D. Amoros, J. Garcia de la Torre,
+ "Prediction of hydrodynamic and other solution properties of
+ rigid proteins from atomic- and residue-level models"
+ Biophys. J. 101, 892-898 (2011).
+ ------------------------------------------------------------
+
+
+ SUMMARY OF DATA AND RESULTS
+
+ This file : p-bead.hydropro-res.txt
+ Case : P !Name
+ Structural file : p-bead.pdb
+
+ Radius of elements in primary model : 2.90 Angs.
+ Type of hydropro calculation : 1
+
+ Temperature: 22.0 centigrade
+ Solvent viscosity: 0.01000 poise
+ Molecular weight: 122. Da
+ Solute partial specific volume: 1.000 cm^3/g
+ Solution density: 1.000 g/cm^3
+
+ Translational diffusion coefficient: 4.225E-06 cm^2/s
+ Radius of gyration: 3.977E-08 cm
+ Volume: 4.737E-22 cm^3
+ Rotational diffusion coefficient: 1.989E+09 s^-1
+ Relaxation time (1): 1.360E-10 s
+ Relaxation time (2): 1.370E-10 s
+ Relaxation time (3): 1.407E-10 s
+ Relaxation time (4): 1.442E-10 s
+ Relaxation time (5): 1.442E-10 s
+ Harmonic mean (correlation) time: 1.403E-10 s
+ Intrinsic viscosity: 7.327E+00 cm^3/g
+ Sedimentation coefficient: 0.000E+00 Svedberg
+
+
+
+ Center of diffusion (x): 5.120E-08 cm
+ Center of diffusion (x): 4.284E-08 cm
+ Center of diffusion (x): 4.957E-08 cm
+
+ Generalized (6x6) diffusion matrix: (Dtt Dtr)
+
+ (Drt Drr)
+
+
+ 5.135E-06 -8.539E-08 -8.050E-10 1.991E-01 -3.158E-01 -5.231E-01
+ -8.543E-08 4.878E-06 -3.549E-08 -3.160E-01 -1.947E-01 2.990E-01
+ -7.718E-10 -3.553E-08 5.027E-06 -5.231E-01 2.992E-01 4.199E-02
+
+
+ 1.991E-01 -3.160E-01 -5.231E-01 2.160E+09 -1.170E+08 8.446E+06
+ -3.158E-01 -1.947E-01 2.992E-01 -1.170E+08 1.835E+09 -3.214E+07
+ -5.231E-01 2.990E-01 4.199E-02 8.451E+06 -3.214E+07 1.971E+09
+
+ List of equivalent radii
+
+ Translational: 5.116E-08
+ Gyration : 5.135E-08
+ Volume : 4.836E-08
+ Rotation (1): 5.095E-08
+ Rotation (2): 5.107E-08
+ Rotation (3): 5.153E-08
+ Rotation (4): 5.196E-08
+ Rotation (5): 5.196E-08
+ Rotation (h): 4.411E-08
+ Intrinsic viscosity: 5.214E-08
+ Longest distance: 5.003E-08
+
+ Longest distance : 1.001E-07 cm
+
+
+
+ Calculation of scattering form factor, P vs h
+ h P(h)
+ 0.00E+00 1.05E+00
+ 4.10E+06 1.04E+00
+ 8.19E+06 1.03E+00
+ 1.23E+07 1.00E+00
+ 1.64E+07 9.73E-01
+ 2.05E+07 9.34E-01
+ 2.46E+07 8.89E-01
+ 2.87E+07 8.38E-01
+ 3.28E+07 7.83E-01
+ 3.69E+07 7.24E-01
+ 4.10E+07 6.64E-01
+ 4.51E+07 6.03E-01
+ 4.92E+07 5.43E-01
+ 5.33E+07 4.84E-01
+ 5.74E+07 4.28E-01
+ 6.15E+07 3.74E-01
+ 6.56E+07 3.25E-01
+ 6.97E+07 2.79E-01
+ 7.37E+07 2.38E-01
+ 7.78E+07 2.01E-01
+ 8.19E+07 1.69E-01
+ 8.60E+07 1.41E-01
+ 9.01E+07 1.17E-01
+ 9.42E+07 9.71E-02
+ 9.83E+07 8.04E-02
+ 1.02E+08 6.67E-02
+ 1.07E+08 5.56E-02
+ 1.11E+08 4.68E-02
+ 1.15E+08 3.97E-02
+ 1.19E+08 3.42E-02
+ 1.23E+08 3.00E-02
+ 1.27E+08 2.66E-02
+ 1.31E+08 2.41E-02
+ 1.35E+08 2.20E-02
+ 1.39E+08 2.04E-02
+ 1.43E+08 1.91E-02
+ 1.47E+08 1.81E-02
+ 1.52E+08 1.72E-02
+ 1.56E+08 1.64E-02
+ 1.60E+08 1.57E-02
+ 1.64E+08 1.51E-02
+ 1.68E+08 1.45E-02
+ 1.72E+08 1.40E-02
+ 1.76E+08 1.35E-02
+ 1.80E+08 1.30E-02
+ 1.84E+08 1.26E-02
+ 1.88E+08 1.21E-02
+ 1.93E+08 1.17E-02
+ 1.97E+08 1.13E-02
+ 2.01E+08 1.09E-02
+ 2.05E+08 1.05E-02
+
+
+ Distribution of distances
+
+ 50 intervals between RMIN and RMAX centered at R;
+ Values of p(R)
+
+
+ RMIN(cm) RMAX(cm) R(cm) p(R)(cm^(-1))
+ 0.000E+00 2.001E-09 1.001E-09 4.429E+05
+ 2.001E-09 4.003E-09 3.002E-09 1.534E+06
+ 4.003E-09 6.004E-09 5.003E-09 2.880E+06
+ 6.004E-09 8.005E-09 7.005E-09 4.452E+06
+ 8.005E-09 1.001E-08 9.006E-09 6.214E+06
+ 1.001E-08 1.201E-08 1.101E-08 8.128E+06
+ 1.201E-08 1.401E-08 1.301E-08 1.015E+07
+ 1.401E-08 1.601E-08 1.501E-08 1.222E+07
+ 1.601E-08 1.801E-08 1.701E-08 1.429E+07
+ 1.801E-08 2.001E-08 1.901E-08 1.631E+07
+ 2.001E-08 2.201E-08 2.101E-08 1.824E+07
+ 2.201E-08 2.402E-08 2.302E-08 2.001E+07
+ 2.402E-08 2.602E-08 2.502E-08 2.159E+07
+ 2.602E-08 2.802E-08 2.702E-08 2.294E+07
+ 2.802E-08 3.002E-08 2.902E-08 2.401E+07
+ 3.002E-08 3.202E-08 3.102E-08 2.477E+07
+ 3.202E-08 3.402E-08 3.302E-08 2.523E+07
+ 3.402E-08 3.602E-08 3.502E-08 2.535E+07
+ 3.602E-08 3.803E-08 3.702E-08 2.515E+07
+ 3.803E-08 4.003E-08 3.903E-08 2.463E+07
+ 4.003E-08 4.203E-08 4.103E-08 2.382E+07
+ 4.203E-08 4.403E-08 4.303E-08 2.273E+07
+ 4.403E-08 4.603E-08 4.503E-08 2.141E+07
+ 4.603E-08 4.803E-08 4.703E-08 1.989E+07
+ 4.803E-08 5.003E-08 4.903E-08 1.824E+07
+ 5.003E-08 5.203E-08 5.103E-08 1.651E+07
+ 5.203E-08 5.404E-08 5.303E-08 1.475E+07
+ 5.404E-08 5.604E-08 5.504E-08 1.303E+07
+ 5.604E-08 5.804E-08 5.704E-08 1.143E+07
+ 5.804E-08 6.004E-08 5.904E-08 9.980E+06
+ 6.004E-08 6.204E-08 6.104E-08 8.605E+06
+ 6.204E-08 6.404E-08 6.304E-08 7.304E+06
+ 6.404E-08 6.604E-08 6.504E-08 6.101E+06
+ 6.604E-08 6.804E-08 6.704E-08 5.011E+06
+ 6.804E-08 7.005E-08 6.905E-08 4.043E+06
+ 7.005E-08 7.205E-08 7.105E-08 3.197E+06
+ 7.205E-08 7.405E-08 7.305E-08 2.471E+06
+ 7.405E-08 7.605E-08 7.505E-08 1.856E+06
+ 7.605E-08 7.805E-08 7.705E-08 1.351E+06
+ 7.805E-08 8.005E-08 7.905E-08 9.519E+05
+ 8.005E-08 8.205E-08 8.105E-08 6.488E+05
+ 8.205E-08 8.406E-08 8.305E-08 4.270E+05
+ 8.406E-08 8.606E-08 8.506E-08 2.669E+05
+ 8.606E-08 8.806E-08 8.706E-08 1.548E+05
+ 8.806E-08 9.006E-08 8.906E-08 8.041E+04
+ 9.006E-08 9.206E-08 9.106E-08 3.566E+04
+ 9.206E-08 9.406E-08 9.306E-08 1.332E+04
+ 9.406E-08 9.606E-08 9.506E-08 4.376E+03
+ 9.606E-08 9.806E-08 9.706E-08 9.813E+02
+ 9.806E-08 1.001E-07 9.907E-08 3.842E+01
+
+ Check for normalization:
+ (RMAX-RMIN)*SUM(p(R))= 1.046E+00 SHOULD BE= 1
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-sol.txt b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-sol.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b6091af3e9c4eef5cb5be4ccf2f1ca2eb1e58fa
Binary files /dev/null and b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.hydropro-sol.txt differ
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.pdb b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..d936bd8aa1e3d8604c4c87b735b3816c1d6fa407
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p-bead.pdb
@@ -0,0 +1,12 @@
+CRYST1 394.970 493.874 795.001 90.00 90.00 90.00 P 1 1
+ATOM 1 C3' GUA S 15 -0.596 1.421 -81.474 0.00 0.00 S101
+ATOM 2 H3' GUA S 15 -1.199 2.342 -81.620 0.00 0.00 S101
+ATOM 3 O3' GUA S 15 -1.211 0.482 -80.573 0.00 0.00 S101
+ATOM 4 P THY S 16 -1.688 0.949 -79.123 0.00 0.00 S101
+ATOM 5 O1P THY S 16 -3.123 0.641 -78.951 0.00 0.00 S101
+ATOM 6 O2P THY S 16 -1.244 2.342 -78.861 0.00 0.00 S101
+ATOM 7 O5' THY S 16 -0.842 0.010 -78.141 0.00 0.00 S101
+ATOM 8 C5' THY S 16 0.593 -0.035 -78.293 0.00 0.00 S101
+ATOM 9 H5' THY S 16 0.970 0.981 -78.535 0.00 0.00 S101
+ATOM 10 H5'' THY S 16 0.854 -0.718 -79.130 0.00 0.00 S101
+END
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/p.hydropro.dat b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p.hydropro.dat
new file mode 100644
index 0000000000000000000000000000000000000000..aac57039c7c014fbbec297fd2e2cdf898fa3365e
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/p.hydropro.dat
@@ -0,0 +1,18 @@
+P !Name of molecule
+p-bead.hydropro !Name for output file
+p-bead.pdb !Strucutural (PBD) file
+1 !Type of calculation
+2.9, !AER, hydrodynamic radius of primary elements
+6, !NSIG
+1.2, !Minimum radius of beads in the shell (SIGMIN)
+2.0, !Maximum radius of beads in the shell (SIGMAX)
+22., !T (temperature, centigrade)
+0.01, !ETA (Viscosity of the solvent in poises)
+122, !RM (Molecular weight)
+1.0, !Partial specific volume, cm3/g
+1.0, !Solvent density, g/cm3
+-1 !Number of values of Q
+-1 !Number of intervals
+0, !Number of trials for MC calculation of covolume
+1 !IDIF=1 (yes) for full diffusion tensors
+*
diff --git a/mrdna/arbdmodel/resources/two_bead_model/diffusion/run.sh b/mrdna/arbdmodel/resources/two_bead_model/diffusion/run.sh
new file mode 100644
index 0000000000000000000000000000000000000000..f1932c0965b10c08d2c8145ffcccddbe92486adf
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/run.sh
@@ -0,0 +1,5 @@
+
+for i in p b; do
+ cp -f $i.hydropro.dat hydropro.dat
+ ./hydropro10-lnx.exe
+done
diff --git a/mrdna/arbdmodel/resources/two_bead_model/p0p1p2p3.dat b/mrdna/arbdmodel/resources/two_bead_model/p0p1p2p3.dat
new file mode 100644
index 0000000000000000000000000000000000000000..42b5d892dda2ad1250ee4fff8576eab06de6085c
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/p0p1p2p3.dat
@@ -0,0 +1,180 @@
+-180 0.331491
+-178 0.340033
+-176 0.366540
+-174 0.371105
+-172 0.368259
+-170 0.359652
+-168 0.373302
+-166 0.378814
+-164 0.388061
+-162 0.379878
+-160 0.392574
+-158 0.397884
+-156 0.392854
+-154 0.385870
+-152 0.384760
+-150 0.391249
+-148 0.397294
+-146 0.394862
+-144 0.400624
+-142 0.395834
+-140 0.401573
+-138 0.399388
+-136 0.404732
+-134 0.399077
+-132 0.402104
+-130 0.401334
+-128 0.402310
+-126 0.406637
+-124 0.401189
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+-8 0.019798
+-6 0.012138
+-4 0.015972
+-2 0.000000
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/p1p2b2.dat b/mrdna/arbdmodel/resources/two_bead_model/p1p2b2.dat
new file mode 100644
index 0000000000000000000000000000000000000000..bfdd772908388f4f5f9d3b37de6eb5d9c10e53e6
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/p1p2b2.dat
@@ -0,0 +1,181 @@
+0.000000 15.810857
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+2.000000 14.941069
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+4.000000 14.096983
+5.000000 13.684578
+6.000000 13.278598
+7.000000 12.879043
+8.000000 12.485914
+9.000000 12.099210
+10.000000 11.718931
+11.000000 11.345078
+12.000000 10.977650
+13.000000 10.616647
+14.000000 10.262070
+15.000000 9.913918
+16.000000 9.572191
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+18.000000 8.908013
+19.000000 8.585562
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index 0000000000000000000000000000000000000000..ac28356a540f10fc966d31a31308715d618150ef
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new file mode 100644
index 0000000000000000000000000000000000000000..f86c33577de28cafde51c0e67b8a146578a409c3
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/zeroBPB.dat b/mrdna/arbdmodel/resources/two_bead_model/zeroBPB.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f86c33577de28cafde51c0e67b8a146578a409c3
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/zeroBPB.dat
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/zeroBPP.dat b/mrdna/arbdmodel/resources/two_bead_model/zeroBPP.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f86c33577de28cafde51c0e67b8a146578a409c3
--- /dev/null
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/zeroNBBB.dat b/mrdna/arbdmodel/resources/two_bead_model/zeroNBBB.dat
new file mode 100644
index 0000000000000000000000000000000000000000..d7795c1ea21660a51ec08be06eaf8b440021d158
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/zeroNBBB.dat
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/zeroNBPB.dat b/mrdna/arbdmodel/resources/two_bead_model/zeroNBPB.dat
new file mode 100644
index 0000000000000000000000000000000000000000..d7795c1ea21660a51ec08be06eaf8b440021d158
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/zeroNBPB.dat
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diff --git a/mrdna/arbdmodel/resources/two_bead_model/zeroNBPP.dat b/mrdna/arbdmodel/resources/two_bead_model/zeroNBPP.dat
new file mode 100644
index 0000000000000000000000000000000000000000..d7795c1ea21660a51ec08be06eaf8b440021d158
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/zeroNBPP.dat
@@ -0,0 +1,720 @@
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diff --git a/mrdna/arbdmodel/segmentmodel.py b/mrdna/arbdmodel/segmentmodel.py
new file mode 100644
index 0000000000000000000000000000000000000000..3a45e74697b56bb89a5610e59823b972b52b093e
--- /dev/null
+++ b/mrdna/arbdmodel/segmentmodel.py
@@ -0,0 +1,3090 @@
+import pdb
+from pathlib import Path
+import numpy as np
+import random
+from .model.arbdmodel import PointParticle, ParticleType, Group, ArbdModel
+from .coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
+from .model.nonbonded import *
+from copy import copy, deepcopy
+from .model.nbPot import nbDnaScheme
+
+from scipy.special import erf
+import scipy.optimize as opt
+from scipy import interpolate
+
+from .model.CanonicalNucleotideAtoms import canonicalNtFwd, canonicalNtRev, seqComplement
+from .model.CanonicalNucleotideAtoms import enmTemplateHC, enmTemplateSQ, enmCorrectionsHC
+
+from .model.spring_from_lp import k_angle as angle_spring_from_lp
+
+# import pdb
+"""
+TODO:
+ + fix handling of crossovers for atomic representation
+ + map to atomic representation
+ + add nicks
+ + transform ssDNA nucleotides
+ - shrink ssDNA
+ + shrink dsDNA backbone
+ + make orientation continuous
+ + sequence
+ + handle circular dna
+ + ensure crossover bead potentials aren't applied twice
+ + remove performance bottlenecks
+ - test for large systems
+ + assign sequence
+ + ENM
+ - rework Location class
+ - remove recursive calls
+ - document
+ - develop unit test suite
+"""
+class CircularDnaError(Exception):
+ pass
+
+class ParticleNotConnectedError(Exception):
+ pass
+
+class Location():
+ """ Site for connection within an object """
+ def __init__(self, container, address, type_, on_fwd_strand = True):
+ ## TODO: remove cyclic references(?)
+ self.container = container
+ self.address = address # represents position along contour length in segment
+ # assert( type_ in ("end3","end5") ) # TODO remove or make conditional
+ self.on_fwd_strand = on_fwd_strand
+ self.type_ = type_
+ self.particle = None
+ self.connection = None
+ self.is_3prime_side_of_connection = None
+
+ self.prev_in_strand = None
+ self.next_in_strand = None
+
+ self.combine = None # some locations might be combined in bead model
+
+ def get_connected_location(self):
+ if self.connection is None:
+ return None
+ else:
+ return self.connection.other(self)
+
+ def set_connection(self, connection, is_3prime_side_of_connection):
+ self.connection = connection # TODO weakref?
+ self.is_3prime_side_of_connection = is_3prime_side_of_connection
+
+ def get_nt_pos(self):
+ try:
+ pos = self.container.contour_to_nt_pos(self.address, round_nt=True)
+ except:
+ if self.address == 0:
+ pos = 0
+ elif self.address == 1:
+ pos = self.container.num_nt-1
+ else:
+ raise
+ return pos
+
+ def __repr__(self):
+ if self.on_fwd_strand:
+ on_fwd = "on_fwd_strand"
+ else:
+ on_fwd = "on_rev_strand"
+ return "<Location {}.{}[{:.2f},{:d}]>".format( self.container.name, self.type_, self.address, self.on_fwd_strand)
+
+class Connection():
+ """ Abstract base class for connection between two elements """
+ def __init__(self, A, B, type_ = None):
+ assert( isinstance(A,Location) )
+ assert( isinstance(B,Location) )
+ self.A = A
+ self.B = B
+ self.type_ = type_
+
+ def other(self, location):
+ if location is self.A:
+ return self.B
+ elif location is self.B:
+ return self.A
+ else:
+ raise Exception("OutOfBoundsError")
+
+ def delete(self):
+ self.A.container.connections.remove(self)
+ if self.B.container is not self.A.container:
+ self.B.container.connections.remove(self)
+ self.A.connection = None
+ self.B.connection = None
+
+ def __repr__(self):
+ return "<Connection {}--{}--{}]>".format( self.A, self.type_, self.B )
+
+
+
+# class ConnectableElement(Transformable):
+class ConnectableElement():
+ """ Abstract base class """
+ def __init__(self, connection_locations=None, connections=None):
+ if connection_locations is None: connection_locations = []
+ if connections is None: connections = []
+
+ ## TODO decide on names
+ self.locations = self.connection_locations = connection_locations
+ self.connections = connections
+
+ def get_locations(self, type_=None, exclude=()):
+ locs = [l for l in self.connection_locations if (type_ is None or l.type_ == type_) and l.type_ not in exclude]
+ counter = dict()
+ for l in locs:
+ if l in counter:
+ counter[l] += 1
+ else:
+ counter[l] = 1
+ assert( np.all( [counter[l] == 1 for l in locs] ) )
+ return locs
+
+ def get_location_at(self, address, on_fwd_strand=True, new_type="crossover"):
+ loc = None
+ if (self.num_nt == 1):
+ # import pdb
+ # pdb.set_trace()
+ ## Assumes that intrahelical connections have been made before crossovers
+ for l in self.locations:
+ if l.on_fwd_strand == on_fwd_strand and l.connection is None:
+ assert(loc is None)
+ loc = l
+ # assert( loc is not None )
+ else:
+ for l in self.locations:
+ if l.address == address and l.on_fwd_strand == on_fwd_strand:
+ assert(loc is None)
+ loc = l
+ if loc is None:
+ loc = Location( self, address=address, type_=new_type, on_fwd_strand=on_fwd_strand )
+ return loc
+
+ def get_connections_and_locations(self, connection_type=None, exclude=()):
+ """ Returns a list with each entry of the form:
+ connection, location_in_self, location_in_other """
+ type_ = connection_type
+ ret = []
+ for c in self.connections:
+ if (type_ is None or c.type_ == type_) and c.type_ not in exclude:
+ if c.A.container is self:
+ ret.append( [c, c.A, c.B] )
+ elif c.B.container is self:
+ ret.append( [c, c.B, c.A] )
+ else:
+ import pdb
+ pdb.set_trace()
+ raise Exception("Object contains connection that fails to refer to object")
+ return ret
+
+ def _connect(self, other, connection, in_3prime_direction=None):
+ ## TODO fix circular references
+ A,B = [connection.A, connection.B]
+ if in_3prime_direction is not None:
+ A.is_3prime_side_of_connection = not in_3prime_direction
+ B.is_3prime_side_of_connection = in_3prime_direction
+
+ A.connection = B.connection = connection
+ self.connections.append(connection)
+ if other is not self:
+ other.connections.append(connection)
+ else:
+ raise NotImplementedError("Segments cannot yet be connected to themselves; if you are attempting to make a circular object, try breaking the object into multiple segments")
+ l = A.container.locations
+ if A not in l: l.append(A)
+ l = B.container.locations
+ if B not in l: l.append(B)
+
+
+ # def _find_connections(self, loc):
+ # return [c for c in self.connections if c.A == loc or c.B == loc]
+
+class SegmentParticle(PointParticle):
+ def __init__(self, type_, position, name="A", **kwargs):
+ self.name = name
+ self.contour_position = None
+ PointParticle.__init__(self, type_, position, name=name, **kwargs)
+ self.intrahelical_neighbors = []
+ self.other_neighbors = []
+ self.locations = []
+
+ def get_intrahelical_above(self):
+ """ Returns bead directly above self """
+ # assert( len(self.intrahelical_neighbors) <= 2 )
+ for b in self.intrahelical_neighbors:
+ if b.get_contour_position(self.parent, self.contour_position) > self.contour_position:
+ return b
+
+ def get_intrahelical_below(self):
+ """ Returns bead directly below self """
+ # assert( len(self.intrahelical_neighbors) <= 2 )
+ for b in self.intrahelical_neighbors:
+ if b.get_contour_position(self.parent, self.contour_position) < self.contour_position:
+ return b
+
+ def _neighbor_should_be_added(self,b):
+ if type(self.parent) != type(b.parent):
+ return True
+
+ c1 = self.contour_position
+ c2 = b.get_contour_position(self.parent,c1)
+ if c2 < c1:
+ b0 = self.get_intrahelical_below()
+ else:
+ b0 = self.get_intrahelical_above()
+
+ if b0 is not None:
+ c0 = b0.get_contour_position(self.parent,c1)
+ if np.abs(c2-c1) < np.abs(c0-c1):
+ ## remove b0
+ self.intrahelical_neighbors.remove(b0)
+ b0.intrahelical_neighbors.remove(self)
+ return True
+ else:
+ return False
+ return True
+
+ def make_intrahelical_neighbor(self,b):
+ add1 = self._neighbor_should_be_added(b)
+ add2 = b._neighbor_should_be_added(self)
+ if add1 and add2:
+ # assert(len(b.intrahelical_neighbors) <= 1)
+ # assert(len(self.intrahelical_neighbors) <= 1)
+ self.intrahelical_neighbors.append(b)
+ b.intrahelical_neighbors.append(self)
+
+ def conceptual_get_position(self, context):
+ """
+ context: object
+
+Q: does this function do too much?
+Danger of mixing return values
+
+Q: does context describe the system or present an argument?
+ """
+
+ ## Validate Inputs
+ ...
+
+ ## Algorithm
+ """
+context specifies:
+ - kind of output: real space, nt within segment, fraction of segment
+ - absolute or relative
+ - constraints: e.g. if passing through
+ """
+ """
+given context, provide the position
+ input
+"""
+
+ def get_nt_position(self, seg, near_address=None):
+ """ Returns the "address" of the nucleotide relative to seg in
+ nucleotides, taking the shortest (intrahelical) contour length route to seg
+ """
+ if seg == self.parent:
+ pos = self.contour_position
+ else:
+ pos = self.get_contour_position(seg,near_address)
+ return seg.contour_to_nt_pos(pos)
+
+ def get_contour_position(self,seg, address = None):
+ """ TODO: fix paradigm where a bead maps to exactly one location in a polymer
+ - One way: modify get_contour_position to take an optional argument that indicates where in the polymer you are looking from
+ """
+
+ if seg == self.parent:
+ return self.contour_position
+ else:
+ cutoff = 30*3
+ target_seg = seg
+
+ ## depth-first search
+ ## TODO cache distances to nearby locations?
+ def descend_search_tree(seg, contour_in_seg, distance=0, visited_segs=None):
+ nonlocal cutoff
+ if visited_segs is None: visited_segs = []
+
+ if seg == target_seg:
+ # pdb.set_trace()
+ ## Found a segment in our target
+ sign = 1 if contour_in_seg == 1 else -1
+ if sign == -1: assert( contour_in_seg == 0 )
+ if distance < cutoff: # TODO: check if this does anything
+ cutoff = distance
+ return [[distance, contour_in_seg+sign*seg.nt_pos_to_contour(distance)]], [(seg, contour_in_seg, distance)]
+ if distance > cutoff:
+ return None,None
+
+ ret_list = []
+ hist_list = []
+ ## Find intrahelical locations in seg that we might pass through
+ conn_locs = seg.get_connections_and_locations("intrahelical")
+ if isinstance(target_seg, SingleStrandedSegment):
+ tmp = seg.get_connections_and_locations("sscrossover")
+ conn_locs = conn_locs + list(filter(lambda x: x[2].container == target_seg, tmp))
+ for c,A,B in conn_locs:
+ if B.container in visited_segs: continue
+ dx = seg.contour_to_nt_pos( A.address, round_nt=False ) - seg.contour_to_nt_pos( contour_in_seg, round_nt=False)
+ dx = np.abs(dx)
+ results,history = descend_search_tree( B.container, B.address,
+ distance+dx, visited_segs + [seg] )
+ if results is not None:
+ ret_list.extend( results )
+ hist_list.extend( history )
+ return ret_list,hist_list
+
+ results,history = descend_search_tree(self.parent, self.contour_position)
+ if results is None or len(results) == 0:
+ raise Exception("Could not find location in segment") # TODO better error
+ if address is not None:
+ return sorted(results,key=lambda x:(x[0],(x[1]-address)**2))[0][1]
+ else:
+ return sorted(results,key=lambda x:x[0])[0][1]
+ # nt_pos = self.get_nt_position(seg)
+ # return seg.nt_pos_to_contour(nt_pos)
+
+ def update_position(self, contour_position):
+ self.contour_position = contour_position
+ self.position = self.parent.contour_to_position(contour_position)
+ if 'orientation_bead' in self.__dict__:
+ o = self.orientation_bead
+ o.contour_position = contour_position
+ orientation = self.parent.contour_to_orientation(contour_position)
+ if orientation is None:
+ print("WARNING: local_twist is True, but orientation is None; using identity")
+ orientation = np.eye(3)
+ o.position = self.position + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
+
+ def __repr__(self):
+ return "<SegmentParticle {} on {}[{:.2f}]>".format( self.name, self.parent, self.contour_position)
+
+
+## TODO break this class into smaller, better encapsulated pieces
+class Segment(ConnectableElement, Group):
+
+ """ Base class that describes a segment of DNA. When built from
+ cadnano models, should not span helices """
+
+ """Define basic particle types"""
+ dsDNA_particle = ParticleType("D",
+ diffusivity = 43.5,
+ mass = 300,
+ radius = 3,
+ )
+ orientation_particle = ParticleType("O",
+ diffusivity = 100,
+ mass = 300,
+ radius = 1,
+ )
+
+ # orientation_bond = HarmonicBond(10,2)
+ orientation_bond = HarmonicBond(30,1.5, rRange = (0,500) )
+
+ ssDNA_particle = ParticleType("S",
+ diffusivity = 43.5,
+ mass = 150,
+ radius = 3,
+ )
+
+ def __init__(self, name, num_nt,
+ start_position = None,
+ end_position = None,
+ segment_model = None,
+ **kwargs):
+
+ if start_position is None: start_position = np.array((0,0,0))
+
+ Group.__init__(self, name, children=[], **kwargs)
+ ConnectableElement.__init__(self, connection_locations=[], connections=[])
+
+ if 'segname' not in kwargs:
+ self.segname = name
+ # self.resname = name
+ self.start_orientation = None
+ self.twist_per_nt = 0
+
+ self.beads = [c for c in self.children] # self.beads will not contain orientation beads
+
+ self._bead_model_generation = 0 # TODO: remove?
+ self.segment_model = segment_model # TODO: remove?
+
+ self.strand_pieces = dict()
+ for d in ('fwd','rev'):
+ self.strand_pieces[d] = []
+
+ self.num_nt = int(num_nt)
+ if end_position is None:
+ end_position = np.array((0,0,self.distance_per_nt*num_nt)) + start_position
+ self.start_position = start_position
+ self.end_position = end_position
+
+ ## Used to assign cadnano names to beads
+ self._generate_bead_callbacks = []
+ self._generate_nucleotide_callbacks = []
+
+ ## Set up interpolation for positions
+ self._set_splines_from_ends()
+
+ self.sequence = None
+
+ def __repr__(self):
+ return "<{} {}[{:d}]>".format( type(self), self.name, self.num_nt )
+
+ def set_splines(self, contours, coords):
+ tck, u = interpolate.splprep( coords.T, u=contours, s=0, k=1)
+ self.position_spline_params = (tck,u)
+
+ def set_orientation_splines(self, contours, quaternions):
+ tck, u = interpolate.splprep( quaternions.T, u=contours, s=0, k=1)
+ self.quaternion_spline_params = (tck,u)
+
+ def get_center(self):
+ tck, u = self.position_spline_params
+ return np.mean(self.contour_to_position(u), axis=0)
+
+ def _get_location_positions(self):
+ return [self.contour_to_nt_pos(l.address) for l in self.locations]
+
+ def insert_dna(self, at_nt: int, num_nt: int, seq=tuple()):
+ assert(np.isclose(np.around(num_nt),num_nt))
+ if at_nt < 0:
+ raise ValueError("Attempted to insert DNA into {} at a negative location".format(self))
+ if at_nt > self.num_nt-1:
+ raise ValueError("Attempted to insert DNA into {} at beyond the end of the Segment".format(self))
+ if num_nt < 0:
+ raise ValueError("Attempted to insert DNA a negative amount of DNA into {}".format(self))
+
+ num_nt = np.around(num_nt)
+ nt_positions = self._get_location_positions()
+ new_nt_positions = [p if p <= at_nt else p+num_nt for p in nt_positions]
+
+ ## TODO: handle sequence
+
+ self.num_nt = self.num_nt+num_nt
+
+ for l,p in zip(self.locations, new_nt_positions):
+ l.address = self.nt_pos_to_contour(p)
+
+ def remove_dna(self, first_nt: int, last_nt: int):
+ """ Removes nucleotides between first_nt and last_nt, inclusive """
+ assert(np.isclose(np.around(first_nt),first_nt))
+ assert(np.isclose(np.around(last_nt),last_nt))
+ tmp = min((first_nt,last_nt))
+ last_nt = max((first_nt,last_nt))
+ fist_nt = tmp
+
+ if first_nt < 0 or first_nt > self.num_nt-2:
+ raise ValueError("Attempted to remove DNA from {} starting at an invalid location {}".format(self, first_nt))
+ if last_nt < 1 or last_nt > self.num_nt-1:
+ raise ValueError("Attempted to remove DNA from {} ending at an invalid location {}".format(self, last_nt))
+ if first_nt == last_nt:
+ return
+
+ first_nt = np.around(first_nt)
+ last_nt = np.around(last_nt)
+
+ nt_positions = self._get_location_positions()
+
+ bad_locations = list(filter(lambda p: p >= first_nt and p <= last_nt, nt_positions))
+ if len(bad_locations) > 0:
+ raise Exception("Attempted to remove DNA containing locations {} from {} between {} and {}".format(bad_locations,self,first_nt,last_nt))
+
+ removed_nt = last_nt-first_nt+1
+ new_nt_positions = [p if p <= last_nt else p-removed_nt for p in nt_positions]
+ num_nt = self.num_nt-removed_nt
+
+ if self.sequence is not None and len(self.sequence) == self.num_nt:
+ self.sequence = [s for s,i in zip(self.sequence,range(self.num_nt))
+ if i < first_nt or i > last_nt]
+ assert( len(self.sequence) == num_nt )
+
+ self.num_nt = num_nt
+
+ for l,p in zip(self.locations, new_nt_positions):
+ l.address = self.nt_pos_to_contour(p)
+
+ def __filter_contours(contours, positions, position_filter, contour_filter):
+ u = contours
+ r = positions
+
+ ## Filter
+ ids = list(range(len(u)))
+ if contour_filter is not None:
+ ids = list(filter(lambda i: contour_filter(u[i]), ids))
+ if position_filter is not None:
+ ids = list(filter(lambda i: position_filter(r[i,:]), ids))
+ return ids
+
+ def translate(self, translation_vector, position_filter=None, contour_filter=None):
+ dr = np.array(translation_vector)
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = Segment.__filter_contours(u, r, position_filter, contour_filter)
+ if len(ids) == 0: return
+
+ ## Translate
+ r[ids,:] = r[ids,:] + dr[np.newaxis,:]
+ self.set_splines(u,r)
+
+ def rotate(self, rotation_matrix, about=None, position_filter=None, contour_filter=None):
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = Segment.__filter_contours(u, r, position_filter, contour_filter)
+ if len(ids) == 0: return
+
+ if about is None:
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in ids])
+ else:
+ dr = np.array(about)
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in ids])
+
+ self.set_splines(u,r)
+
+ if self.quaternion_spline_params is not None:
+ ## TODO: performance: don't shift between quaternion and matrix representations so much
+ tck, u = self.quaternion_spline_params
+ orientations = [self.contour_to_orientation(v) for v in u]
+ for i in ids:
+ orientations[i,:] = rotation_matrix.dot(orientations[i])
+ quats = [quaternion_from_matrix(o) for o in orientations]
+ self.set_orientation_splines(u, quats)
+
+ def _set_splines_from_ends(self, resolution=4):
+ self.quaternion_spline_params = None
+ r0 = np.array(self.start_position)[np.newaxis,:]
+ r1 = np.array(self.end_position)[np.newaxis,:]
+ u = np.linspace(0,1, max(3,self.num_nt//int(resolution)))
+ s = u[:,np.newaxis]
+ coords = (1-s)*r0 + s*r1
+ self.set_splines(u, coords)
+
+ def clear_all(self):
+ Group.clear_all(self) # TODO: use super?
+ self.beads = []
+ # for c,loc,other in self.get_connections_and_locations():
+ # loc.particle = None
+ # other.particle = None
+ for l in self.locations:
+ l.particle = None
+
+ def contour_to_nt_pos(self, contour_pos, round_nt=False):
+ nt = contour_pos*(self.num_nt) - 0.5
+ if round_nt:
+ assert( np.isclose(np.around(nt),nt) )
+ nt = np.around(nt)
+ return nt
+
+ def nt_pos_to_contour(self,nt_pos):
+ return (nt_pos+0.5)/(self.num_nt)
+
+ def contour_to_position(self,s):
+ p = interpolate.splev( s, self.position_spline_params[0] )
+ if len(p) > 1: p = np.array(p).T
+ return p
+
+ def contour_to_tangent(self,s):
+ t = interpolate.splev( s, self.position_spline_params[0], der=1 )
+ t = (t / np.linalg.norm(t,axis=0))
+ return t.T
+
+
+ def contour_to_orientation(self,s):
+ assert( isinstance(s,float) or isinstance(s,int) or len(s) == 1 ) # TODO make vectorized version
+
+ if self.quaternion_spline_params is None:
+ axis = self.contour_to_tangent(s)
+ axis = axis / np.linalg.norm(axis)
+ rotAxis = np.cross(axis,np.array((0,0,1)))
+ rotAxisL = np.linalg.norm(rotAxis)
+ zAxis = np.array((0,0,1))
+
+ if rotAxisL > 0.001:
+ theta = np.arcsin(rotAxisL) * 180/np.pi
+ if axis.dot(zAxis) < 0: theta = 180-theta
+ orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta, normalizeAxis=False ).T
+ else:
+ orientation0 = np.eye(3) if axis.dot(zAxis) > 0 else \
+ rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
+ if self.start_orientation is not None:
+ orientation0 = orientation0.dot(self.start_orientation)
+
+ orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
+ orientation = orientation.dot(orientation0)
+ else:
+ q = interpolate.splev( s, self.quaternion_spline_params[0] )
+ if len(q) > 1: q = np.array(q).T # TODO: is this needed?
+ orientation = quaternion_to_matrix(q)
+
+ return orientation
+
+ def get_contour_sorted_connections_and_locations(self,type_):
+ sort_fn = lambda c: c[1].address
+ cl = self.get_connections_and_locations(type_)
+ return sorted(cl, key=sort_fn)
+
+ def randomize_unset_sequence(self):
+ bases = list(seqComplement.keys())
+ # bases = ['T'] ## FOR DEBUG
+ if self.sequence is None:
+ self.sequence = [random.choice(bases) for i in range(self.num_nt)]
+ else:
+ assert(len(self.sequence) == self.num_nt) # TODO move
+ for i in range(len(self.sequence)):
+ if self.sequence[i] is None:
+ self.sequence[i] = random.choice(bases)
+
+ def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead ):
+ raise NotImplementedError
+
+ def _generate_one_bead(self, contour_position, nts):
+ raise NotImplementedError
+
+ def _generate_atomic_nucleotide(self, contour_position, is_fwd, seq, scale, strand_segment):
+ """ Seq should include modifications like 5T, T3 Tsinglet; direction matters too """
+
+ # print("Generating nucleotide at {}".format(contour_position))
+
+ pos = self.contour_to_position(contour_position)
+ orientation = self.contour_to_orientation(contour_position)
+
+ """ deleteme
+ ## TODO: move this code (?)
+ if orientation is None:
+ import pdb
+ pdb.set_trace()
+ axis = self.contour_to_tangent(contour_position)
+ angleVec = np.array([1,0,0])
+ if axis.dot(angleVec) > 0.9: angleVec = np.array([0,1,0])
+ angleVec = angleVec - angleVec.dot(axis)*axis
+ angleVec = angleVec/np.linalg.norm(angleVec)
+ y = np.cross(axis,angleVec)
+ orientation = np.array([angleVec,y,axis]).T
+ ## TODO: improve placement of ssDNA
+ # rot = rotationAboutAxis( axis, contour_position*self.twist_per_nt*self.num_nt, normalizeAxis=True )
+ # orientation = rot.dot(orientation)
+ else:
+ orientation = orientation
+ """
+ key = seq
+ nt_dict = canonicalNtFwd if is_fwd else canonicalNtRev
+
+ atoms = nt_dict[ key ].generate() # TODO: clone?
+ atoms.orientation = orientation.dot(atoms.orientation)
+ if isinstance(self, SingleStrandedSegment):
+ if scale is not None and scale != 1:
+ for a in atoms:
+ a.position = scale*a.position
+ atoms.position = pos - atoms.atoms_by_name["C1'"].collapsedPosition()
+ else:
+ if scale is not None and scale != 1:
+ if atoms.sequence in ("A","G"):
+ r0 = atoms.atoms_by_name["N9"].position
+ else:
+ r0 = atoms.atoms_by_name["N1"].position
+ for a in atoms:
+ if a.name[-1] in ("'","P","T"):
+ a.position = scale*(a.position-r0) + r0
+ else:
+ a.fixed = 1
+ atoms.position = pos
+
+ atoms.contour_position = contour_position
+ strand_segment.add(atoms)
+
+ for callback in self._generate_nucleotide_callbacks:
+ callback(atoms)
+
+ return atoms
+
+ def add_location(self, nt, type_, on_fwd_strand=True):
+ ## Create location if needed, add to segment
+ c = self.nt_pos_to_contour(nt)
+ assert(c >= 0 and c <= 1)
+ # TODO? loc = self.Location( address=c, type_=type_, on_fwd_strand=is_fwd )
+ loc = Location( self, address=c, type_=type_, on_fwd_strand=on_fwd_strand )
+ self.locations.append(loc)
+
+ ## TODO? Replace with abstract strand-based model?
+
+ def add_nick(self, nt, on_fwd_strand=True):
+ self.add_3prime(nt,on_fwd_strand)
+ self.add_5prime(nt+1,on_fwd_strand)
+
+ def add_5prime(self, nt, on_fwd_strand=True):
+ if isinstance(self,SingleStrandedSegment):
+ on_fwd_strand = True
+ self.add_location(nt,"5prime",on_fwd_strand)
+
+ def add_3prime(self, nt, on_fwd_strand=True):
+ if isinstance(self,SingleStrandedSegment):
+ on_fwd_strand = True
+ self.add_location(nt,"3prime",on_fwd_strand)
+
+ def get_3prime_locations(self):
+ return sorted(self.get_locations("3prime"),key=lambda x: x.address)
+
+ def get_5prime_locations(self):
+ ## TODO? ensure that data is consistent before _build_model calls
+ return sorted(self.get_locations("5prime"),key=lambda x: x.address)
+
+ def iterate_connections_and_locations(self, reverse=False):
+ ## connections to other segments
+ cl = self.get_contour_sorted_connections_and_locations()
+ if reverse:
+ cl = cl[::-1]
+
+ for c in cl:
+ yield c
+
+ ## TODO rename
+ def _add_strand_piece(self, strand_piece):
+ """ Registers a strand segment within this object """
+
+ ## TODO use weakref
+ d = 'fwd' if strand_piece.is_fwd else 'rev'
+
+ ## Validate strand_piece (ensure no clashes)
+ for s in self.strand_pieces[d]:
+ l,h = sorted((s.start,s.end))
+ for value in (strand_piece.start,strand_piece.end):
+ assert( value < l or value > h )
+
+ ## Add strand_piece in correct order
+ self.strand_pieces[d].append(strand_piece)
+ self.strand_pieces[d] = sorted(self.strand_pieces[d],
+ key = lambda x: x.start)
+
+ ## TODO rename
+ def get_strand_segment(self, nt_pos, is_fwd, move_at_least=0.5):
+ """ Walks through locations, checking for crossovers """
+ # if self.name in ("6-1","1-1"):
+ # import pdb
+ # pdb.set_trace()
+ move_at_least = 0
+
+ ## Iterate through locations
+ # locations = sorted(self.locations, key=lambda l:(l.address,not l.on_fwd_strand), reverse=(not is_fwd))
+ def loc_rank(l):
+ nt = l.get_nt_pos()
+ ## optionally add logic about type of connection
+ return (nt, not l.on_fwd_strand)
+ # locations = sorted(self.locations, key=lambda l:(l.address,not l.on_fwd_strand), reverse=(not is_fwd))
+ locations = sorted(self.locations, key=loc_rank, reverse=(not is_fwd))
+ # print(locations)
+
+ for l in locations:
+ # TODOTODO probably okay
+ if l.address == 0:
+ pos = 0.0
+ elif l.address == 1:
+ pos = self.num_nt-1
+ else:
+ pos = self.contour_to_nt_pos(l.address, round_nt=True)
+
+ ## DEBUG
+
+
+ ## Skip locations encountered before our strand
+ # tol = 0.1
+ # if is_fwd:
+ # if pos-nt_pos <= tol: continue
+ # elif nt_pos-pos <= tol: continue
+ if (pos-nt_pos)*(2*is_fwd-1) < move_at_least: continue
+ ## TODO: remove move_at_least
+ if np.isclose(pos,nt_pos):
+ if l.is_3prime_side_of_connection: continue
+
+ ## Stop if we found the 3prime end
+ if l.on_fwd_strand == is_fwd and l.type_ == "3prime" and l.connection is None:
+ # print(" found end at",l)
+ return pos, None, None, None, None
+
+ ## Check location connections
+ c = l.connection
+ if c is None: continue
+ B = c.other(l)
+
+ ## Found a location on the same strand?
+ if l.on_fwd_strand == is_fwd:
+ # print(" passing through",l)
+ # print("from {}, connection {} to {}".format(nt_pos,l,B))
+ Bpos = B.get_nt_pos()
+ return pos, B.container, Bpos, B.on_fwd_strand, 0.5
+
+ ## Stop at other strand crossovers so basepairs line up
+ elif c.type_ == "crossover":
+ if nt_pos == pos: continue
+ # print(" pausing at",l)
+ return pos, l.container, pos+(2*is_fwd-1), is_fwd, 0
+
+ raise Exception("Shouldn't be here")
+ # print("Shouldn't be here")
+ ## Made it to the end of the segment without finding a connection
+ return 1*is_fwd, None, None, None
+
+ def get_nearest_bead(self, contour_position):
+ if len(self.beads) < 1: return None
+ cs = np.array([b.contour_position for b in self.beads]) # TODO: cache
+ # TODO: include beads in connections?
+ i = np.argmin((cs - contour_position)**2)
+
+ return self.beads[i]
+
+ def _get_atomic_nucleotide(self, nucleotide_idx, is_fwd=True):
+ d = 'fwd' if is_fwd else 'rev'
+ for s in self.strand_pieces[d]:
+ try:
+ return s.get_nucleotide(nucleotide_idx)
+ except:
+ pass
+ raise Exception("Could not find nucleotide in {} at {}.{}".format( self, nucleotide_idx, d ))
+
+ def get_all_consecutive_beads(self, number):
+ assert(number >= 1)
+ ## Assume that consecutive beads in self.beads are bonded
+ ret = []
+ for i in range(len(self.beads)-number+1):
+ tmp = [self.beads[i+j] for j in range(0,number)]
+ ret.append( tmp )
+ return ret
+
+ def _add_bead(self,b):
+
+ # assert(b.parent is None)
+ if b.parent is not None:
+ b.parent.children.remove(b)
+ self.add(b)
+ self.beads.append(b) # don't add orientation bead
+ if "orientation_bead" in b.__dict__: # TODO: think of a cleaner approach
+ o = b.orientation_bead
+ o.contour_position = b.contour_position
+ if o.parent is not None:
+ o.parent.children.remove(o)
+ self.add(o)
+ self.add_bond(b,o, Segment.orientation_bond, exclude=True)
+
+ def _rebuild_children(self, new_children):
+ # print("_rebuild_children on %s" % self.name)
+ old_children = self.children
+ old_beads = self.beads
+ self.children = []
+ self.beads = []
+
+ if True:
+ ## TODO: remove this if duplicates are never found
+ # print("Searching for duplicate particles...")
+ ## Remove duplicates, preserving order
+ tmp = []
+ for c in new_children:
+ if c not in tmp:
+ tmp.append(c)
+ else:
+ print(" DUPLICATE PARTICLE FOUND!")
+ new_children = tmp
+
+ for b in new_children:
+ self.beads.append(b)
+ self.children.append(b)
+ if "orientation_bead" in b.__dict__: # TODO: think of a cleaner approach
+ self.children.append(b.orientation_bead)
+
+ # tmp = [c for c in self.children if c not in old_children]
+ # assert(len(tmp) == 0)
+ # tmp = [c for c in old_children if c not in self.children]
+ # assert(len(tmp) == 0)
+ assert(len(old_children) == len(self.children))
+ assert(len(old_beads) == len(self.beads))
+
+
+ def _generate_beads(self, bead_model, max_basepairs_per_bead, max_nucleotides_per_bead):
+
+ """ Generate beads (positions, types, etc) and bonds, angles, dihedrals, exclusions """
+ ## TODO: decide whether to remove bead_model argument
+ ## (currently unused)
+
+ ## First find points between-which beads must be generated
+ # conn_locs = self.get_contour_sorted_connections_and_locations()
+ # locs = [A for c,A,B in conn_locs]
+ # existing_beads = [l.particle for l in locs if l.particle is not None]
+ # if self.name == "S001":
+ # pdb.set_trace()
+
+ # pdb.set_trace()
+ existing_beads0 = { (l.particle, l.particle.get_contour_position(self,l.address))
+ for l in self.locations if l.particle is not None }
+ existing_beads = sorted( list(existing_beads0), key=lambda bc: bc[1] )
+
+ # if self.num_nt == 1 and all([l.particle is not None for l in self.locations]):
+ # pdb.set_trace()
+ # return
+
+ for b,c in existing_beads:
+ assert(b.parent is not None)
+
+ ## Add ends if they don't exist yet
+ ## TODOTODO: test 1 nt segments?
+ if len(existing_beads) == 0 or existing_beads[0][0].get_nt_position(self,0) >= 0.5:
+ # if len(existing_beads) > 0:
+ # assert(existing_beads[0].get_nt_position(self) >= 0.5)
+ b = self._generate_one_bead( self.nt_pos_to_contour(0), 0)
+ existing_beads = (b,0) + existing_beads
+
+ if existing_beads[-1][0].get_nt_position(self,1)-(self.num_nt-1) < -0.5 or len(existing_beads)==1:
+ b = self._generate_one_bead( self.nt_pos_to_contour(self.num_nt-1), 0)
+ existing_beads.append( (b,1) )
+ assert(len(existing_beads) > 1)
+
+ ## Walk through existing_beads, add beads between
+ tmp_children = [] # build list of children in nice order
+ last = None
+
+ for I in range(len(existing_beads)-1):
+ eb1,eb2 = [existing_beads[i][0] for i in (I,I+1)]
+ ec1,ec2 = [existing_beads[i][1] for i in (I,I+1)]
+ assert( (eb1,ec1) is not (eb2,ec2) )
+
+ # if np.isclose(eb1.position[2], eb2.position[2]):
+ # import pdb
+ # pdb.set_trace()
+
+ # print(" %s working on %d to %d" % (self.name, eb1.position[2], eb2.position[2]))
+ e_ds = ec2-ec1
+ num_beads = self._get_num_beads( e_ds, max_basepairs_per_bead, max_nucleotides_per_bead )
+
+ ## Ensure there is a ssDNA bead between dsDNA beads
+ if num_beads == 0 and isinstance(self,SingleStrandedSegment) and isinstance(eb1.parent,DoubleStrandedSegment) and isinstance(eb2.parent,DoubleStrandedSegment):
+ num_beads = 1
+ ## TODO similarly ensure there is a dsDNA bead between ssDNA beads
+
+ ds = e_ds / (num_beads+1)
+ nts = ds*self.num_nt
+ eb1.num_nt += 0.5*nts
+ eb2.num_nt += 0.5*nts
+
+ ## Add beads
+ if eb1.parent == self:
+ tmp_children.append(eb1)
+
+ s0 = ec1
+ if last is not None:
+ last.make_intrahelical_neighbor(eb1)
+ last = eb1
+ for j in range(num_beads):
+ s = ds*(j+1) + s0
+ # if self.name in ("51-2","51-3"):
+ # if self.name in ("31-2",):
+ # print(" adding bead at {}".format(s))
+ b = self._generate_one_bead(s,nts)
+
+ last.make_intrahelical_neighbor(b)
+ last = b
+ tmp_children.append(b)
+
+ last.make_intrahelical_neighbor(eb2)
+
+ if eb2.parent == self:
+ tmp_children.append(eb2)
+ # if self.name in ("31-2",):
+ # pdb.set_trace()
+ self._rebuild_children(tmp_children)
+
+ for callback in self._generate_bead_callbacks:
+ callback(self)
+
+ def _regenerate_beads(self, max_nts_per_bead=4, ):
+ ...
+
+
+class DoubleStrandedSegment(Segment):
+
+ """ Class that describes a segment of ssDNA. When built from
+ cadnano models, should not span helices """
+
+ def __init__(self, name, num_bp, start_position = np.array((0,0,0)),
+ end_position = None,
+ segment_model = None,
+ local_twist = False,
+ num_turns = None,
+ start_orientation = None,
+ twist_persistence_length = 90,
+ **kwargs):
+
+ self.helical_rise = 10.44
+ self.distance_per_nt = 3.4
+ Segment.__init__(self, name, num_bp,
+ start_position,
+ end_position,
+ segment_model,
+ **kwargs)
+ self.num_bp = self.num_nt
+
+ self.local_twist = local_twist
+ if num_turns is None:
+ num_turns = float(num_bp) / self.helical_rise
+ self.twist_per_nt = float(360 * num_turns) / num_bp
+
+ if start_orientation is None:
+ start_orientation = np.eye(3) # np.array(((1,0,0),(0,1,0),(0,0,1)))
+ self.start_orientation = start_orientation
+ self.twist_persistence_length = twist_persistence_length
+
+ self.nicks = []
+
+ self.start = self.start5 = Location( self, address=0, type_= "end5" )
+ self.start3 = Location( self, address=0, type_ = "end3", on_fwd_strand=False )
+
+ self.end = self.end3 = Location( self, address=1, type_ = "end3" )
+ self.end5 = Location( self, address=1, type_= "end5", on_fwd_strand=False )
+ # for l in (self.start5,self.start3,self.end3,self.end5):
+ # self.locations.append(l)
+
+ ## TODO: initialize sensible spline for orientation
+
+ ## Convenience methods
+ ## TODO: add errors if unrealistic connections are made
+ ## TODO: make connections automatically between unconnected strands
+ def connect_start5(self, end3, type_="intrahelical", force_connection=False):
+ if isinstance(end3, SingleStrandedSegment):
+ end3 = end3.end3
+ self._connect_ends( self.start5, end3, type_, force_connection = force_connection )
+ def connect_start3(self, end5, type_="intrahelical", force_connection=False):
+ if isinstance(end5, SingleStrandedSegment):
+ end5 = end5.start5
+ self._connect_ends( self.start3, end5, type_, force_connection = force_connection )
+ def connect_end3(self, end5, type_="intrahelical", force_connection=False):
+ if isinstance(end5, SingleStrandedSegment):
+ end5 = end5.start5
+ self._connect_ends( self.end3, end5, type_, force_connection = force_connection )
+ def connect_end5(self, end3, type_="intrahelical", force_connection=False):
+ if isinstance(end3, SingleStrandedSegment):
+ end3 = end3.end3
+ self._connect_ends( self.end5, end3, type_, force_connection = force_connection )
+
+ def add_crossover(self, nt, other, other_nt, strands_fwd=(True,False), nt_on_5prime=True, type_="crossover"):
+ """ Add a crossover between two helices """
+ ## Validate other, nt, other_nt
+ ## TODO
+
+ if isinstance(other,SingleStrandedSegment):
+ other.add_crossover(other_nt, self, nt, strands_fwd[::-1], not nt_on_5prime)
+ else:
+
+ ## Create locations, connections and add to segments
+ c = self.nt_pos_to_contour(nt)
+ assert(c >= 0 and c <= 1)
+
+ loc = self.get_location_at(c, strands_fwd[0])
+
+ c = other.nt_pos_to_contour(other_nt)
+ # TODOTODO: may need to subtract or add a little depending on 3prime/5prime
+ assert(c >= 0 and c <= 1)
+ other_loc = other.get_location_at(c, strands_fwd[1])
+ self._connect(other, Connection( loc, other_loc, type_=type_ ))
+ if nt_on_5prime:
+ loc.is_3prime_side_of_connection = False
+ other_loc.is_3prime_side_of_connection = True
+ else:
+ loc.is_3prime_side_of_connection = True
+ other_loc.is_3prime_side_of_connection = False
+
+ ## Real work
+ def _connect_ends(self, end1, end2, type_, force_connection):
+ debug = False
+ ## TODO remove self?
+ ## validate the input
+ for end in (end1, end2):
+ assert( isinstance(end, Location) )
+ assert( end.type_ in ("end3","end5") )
+ assert( end1.type_ != end2.type_ )
+
+ ## Remove other connections involving these points
+ if end1.connection is not None:
+ if debug: print("WARNING: reconnecting {}".format(end1))
+ end1.connection.delete()
+ if end2.connection is not None:
+ if debug: print("WARNING: reconnecting {}".format(end2))
+ end2.connection.delete()
+
+ ## Create and add connection
+ if end2.type_ == "end5":
+ end1.container._connect( end2.container, Connection( end1, end2, type_=type_ ), in_3prime_direction=True )
+ else:
+ end2.container._connect( end1.container, Connection( end2, end1, type_=type_ ), in_3prime_direction=True )
+ def _get_num_beads(self, contour, max_basepairs_per_bead, max_nucleotides_per_bead):
+ # return int(contour*self.num_nt // max_basepairs_per_bead)
+ return int(contour*(self.num_nt**2/(self.num_nt+1)) // max_basepairs_per_bead)
+
+ def _generate_one_bead(self, contour_position, nts):
+ pos = self.contour_to_position(contour_position)
+ if self.local_twist:
+ orientation = self.contour_to_orientation(contour_position)
+ if orientation is None:
+ print("WARNING: local_twist is True, but orientation is None; using identity")
+ orientation = np.eye(3)
+ opos = pos + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
+ # if np.linalg.norm(pos) > 1e3:
+ # pdb.set_trace()
+ assert(np.linalg.norm(opos-pos) < 10 )
+ o = SegmentParticle( Segment.orientation_particle, opos, name="O",
+ contour_position = contour_position,
+ num_nt=nts, parent=self )
+ bead = SegmentParticle( Segment.dsDNA_particle, pos, name="DNA",
+ num_nt=nts, parent=self,
+ orientation_bead=o,
+ contour_position=contour_position )
+
+ else:
+ bead = SegmentParticle( Segment.dsDNA_particle, pos, name="DNA",
+ num_nt=nts, parent=self,
+ contour_position=contour_position )
+ self._add_bead(bead)
+ return bead
+
+class SingleStrandedSegment(Segment):
+
+ """ Class that describes a segment of ssDNA. When built from
+ cadnano models, should not span helices """
+
+ def __init__(self, name, num_nt, start_position = None,
+ end_position = None,
+ segment_model = None,
+ **kwargs):
+
+ if start_position is None: start_position = np.array((0,0,0))
+ self.distance_per_nt = 5
+ Segment.__init__(self, name, num_nt,
+ start_position,
+ end_position,
+ segment_model,
+ **kwargs)
+
+ self.start = self.start5 = Location( self, address=0, type_= "end5" ) # TODO change type_?
+ self.end = self.end3 = Location( self, address=1, type_ = "end3" )
+ # for l in (self.start5,self.end3):
+ # self.locations.append(l)
+
+ def connect_end3(self, end5, force_connection=False):
+ self._connect_end( end5, _5_to_3 = True, force_connection = force_connection )
+
+ def connect_start5(self, end3, force_connection=False):
+ self._connect_end( end3, _5_to_3 = False, force_connection = force_connection )
+
+ def connect_5end(self, end3, force_connection=False): # TODO: change name or possibly deprecate
+ print("WARNING: 'connect_5end' will be deprecated")
+ return self.connect_start5( end3, force_connection=False)
+
+ def _connect_end(self, other, _5_to_3, force_connection):
+ assert( isinstance(other, Location) )
+ if _5_to_3 == True:
+ seg1 = self
+ seg2 = other.container
+ end1 = self.end3
+ end2 = other
+ assert(other.type_ != "end3")
+ # if (other.type_ is not "end5"):
+ # print("WARNING: code does not prevent connecting 3prime to 3prime, etc")
+ else:
+ seg1 = other.container
+ seg2 = self
+ end1 = other
+ end2 = self.start
+ assert(other.type_ != "end5")
+ # if (other.type_ is not "end3"):
+ # print("WARNING: code does not prevent connecting 3prime to 3prime, etc")
+
+ ## Remove other connections involving these points
+ if end1.connection is not None:
+ print("WARNING: reconnecting {}".format(end1))
+ end1.connection.delete()
+ if end2.connection is not None:
+ print("WARNING: reconnecting {}".format(end2))
+ end2.connection.delete()
+
+ conn = Connection( end1, end2, type_="intrahelical" )
+ seg1._connect( seg2, conn, in_3prime_direction=True )
+
+
+ def add_crossover(self, nt, other, other_nt, strands_fwd=(True,False), nt_on_5prime=True, type_='sscrossover'):
+ """ Add a crossover between two helices """
+ ## TODO Validate other, nt, other_nt
+
+ assert(nt < self.num_nt)
+ assert(other_nt < other.num_nt)
+ if nt in (0,1,self.num_nt-1) and other_nt in (0,1,other.num_nt-1):
+ if nt_on_5prime == True:
+ other_end = other.start5 if strands_fwd[1] else other.end5
+ self.connect_end3( other_end )
+ else:
+ other_end = other.end3 if strands_fwd[1] else other.start3
+ self.connect_start5( other_end )
+ return
+
+ # c1 = self.nt_pos_to_contour(nt)
+ # # TODOTODO
+ # ## Ensure connections occur at ends, otherwise the structure doesn't make sense
+ # # assert(np.isclose(c1,0) or np.isclose(c1,1))
+ # assert(np.isclose(nt,0) or np.isclose(nt,self.num_nt-1))
+ if nt == 0 and (self.num_nt > 1 or not nt_on_5prime):
+ c1 = 0
+ elif nt == self.num_nt-1:
+ c1 = 1
+ else:
+ raise Exception("Crossovers can only be at the ends of an ssDNA segment")
+ loc = self.get_location_at(c1, True)
+
+ if other_nt == 0:
+ c2 = 0
+ elif other_nt == other.num_nt-1:
+ c2 = 1
+ else:
+ c2 = other.nt_pos_to_contour(other_nt)
+
+ if isinstance(other,SingleStrandedSegment):
+ ## Ensure connections occur at opposing ends
+ assert(np.isclose(other_nt,0) or np.isclose(other_nt,self.num_nt-1))
+ other_loc = other.get_location_at( c2, True )
+ # if ("22-2" in (self.name, other.name)):
+ # pdb.set_trace()
+ if nt_on_5prime:
+ self.connect_end3( other_loc )
+ else:
+ other.connect_end3( self )
+
+ else:
+ assert(c2 >= 0 and c2 <= 1)
+ other_loc = other.get_location_at( c2, strands_fwd[1] )
+ if nt_on_5prime:
+ self._connect(other, Connection( loc, other_loc, type_="sscrossover" ), in_3prime_direction=True )
+ else:
+ other._connect(self, Connection( other_loc, loc, type_="sscrossover" ), in_3prime_direction=True )
+
+ def _get_num_beads(self, contour, max_basepairs_per_bead, max_nucleotides_per_bead):
+ return int(contour*(self.num_nt**2/(self.num_nt+1)) // max_basepairs_per_bead)
+ # return int(contour*self.num_nt // max_nucleotides_per_bead)
+
+ def _generate_one_bead(self, contour_position, nts):
+ pos = self.contour_to_position(contour_position)
+ b = SegmentParticle( Segment.ssDNA_particle, pos,
+ name="NAS",
+ num_nt=nts, parent=self,
+ contour_position=contour_position )
+ self._add_bead(b)
+ return b
+
+class StrandInSegment(Group):
+ """ Represents a piece of an ssDNA strand within a segment """
+
+ def __init__(self, segment, start, end, is_fwd):
+ """ start/end should be provided expressed in nt coordinates, is_fwd tuples """
+ Group.__init__(self)
+ self.num_nt = 0
+ # self.sequence = []
+ self.segment = segment
+ self.start = start
+ self.end = end
+ self.is_fwd = is_fwd
+
+ nts = np.abs(end-start)+1
+ self.num_nt = int(round(nts))
+ assert( np.isclose(self.num_nt,nts) )
+ segment._add_strand_piece(self)
+
+ def _nucleotide_ids(self):
+ nt0 = self.start # seg.contour_to_nt_pos(self.start)
+ assert( np.abs(nt0 - round(nt0)) < 1e-5 )
+ nt0 = int(round(nt0))
+ assert( (self.end-self.start) >= 0 or not self.is_fwd )
+
+ direction = (2*self.is_fwd-1)
+ return range(nt0,nt0 + direction*self.num_nt, direction)
+
+ def get_sequence(self):
+ """ return 5-to-3 """
+ # TODOTODO test
+ seg = self.segment
+ if self.is_fwd:
+ return [seg.sequence[nt] for nt in self._nucleotide_ids()]
+ else:
+ return [seqComplement[seg.sequence[nt]] for nt in self._nucleotide_ids()]
+
+ def get_contour_points(self):
+ c0,c1 = [self.segment.nt_pos_to_contour(p) for p in (self.start,self.end)]
+ return np.linspace(c0,c1,self.num_nt)
+
+ def get_nucleotide(self, idx):
+ """ idx expressed as nt coordinate within segment """
+
+ lo,hi = sorted((self.start,self.end))
+ if self.is_fwd:
+ idx_in_strand = idx - lo
+ else:
+ idx_in_strand = hi - idx
+ assert( np.isclose( idx_in_strand , int(round(idx_in_strand)) ) )
+ assert(idx_in_strand >= 0)
+ return self.children[int(round(idx_in_strand))]
+ def __repr__(self):
+ return "<StrandInSegment {}{}[{:.2f}-{:.2f},{:d}]>".format( self.parent.segname, self.segment.name, self.start, self.end, self.is_fwd)
+
+
+class Strand(Group):
+ """ Represents an entire ssDNA strand from 5' to 3' as it routes through segments """
+ def __init__(self, segname = None, is_circular = False):
+ Group.__init__(self)
+ self.num_nt = 0
+ self.children = self.strand_segments = []
+ self.segname = segname
+ self.is_circular = is_circular
+ self.debug = False
+
+ def __repr__(self):
+ return "<Strand {}({})>".format( self.segname, self.num_nt )
+
+ ## TODO disambiguate names of functions
+ def add_dna(self, segment, start, end, is_fwd):
+ """ start/end are given as nt """
+ if np.abs(start-end) <= 0.9:
+ if self.debug:
+ print( "WARNING: segment constructed with a very small number of nts ({})".format(np.abs(start-end)) )
+ # import pdb
+ # pdb.set_trace()
+ for s in self.strand_segments:
+ if s.segment == segment and s.is_fwd == is_fwd:
+ # assert( s.start not in (start,end) )
+ # assert( s.end not in (start,end) )
+ if s.start in (start,end) or s.end in (start,end):
+ raise CircularDnaError("Found circular DNA")
+
+ s = StrandInSegment( segment, start, end, is_fwd )
+ self.add( s )
+ self.num_nt += s.num_nt
+
+ def set_sequence(self,sequence): # , set_complement=True):
+ ## validate input
+ assert( len(sequence) >= self.num_nt )
+ assert( np.all( [i in ('A','T','C','G') for i in sequence] ) )
+
+ seq_idx = 0
+ ## set sequence on each segment
+ for s in self.children:
+ seg = s.segment
+ if seg.sequence is None:
+ seg.sequence = [None for i in range(seg.num_nt)]
+
+ if s.is_fwd:
+ for nt in s._nucleotide_ids():
+ seg.sequence[nt] = sequence[seq_idx]
+ seq_idx += 1
+ else:
+ for nt in s._nucleotide_ids():
+ seg.sequence[nt] = seqComplement[sequence[seq_idx]]
+ seq_idx += 1
+
+ # def get_sequence(self):
+ # sequence = []
+ # for ss in self.strand_segments:
+ # sequence.extend( ss.get_sequence() )
+
+ # assert( len(sequence) >= self.num_nt )
+ # ret = ["5"+sequence[0]] +\
+ # sequence[1:-1] +\
+ # [sequence[-1]+"3"]
+ # assert( len(ret) == self.num_nt )
+ # return ret
+
+ def link_nucleotides(self, nt5, nt3):
+ parent = nt5.parent if nt5.parent is nt3.parent else self
+ o3,c3,c4,c2,h3 = [nt5.atoms_by_name[n]
+ for n in ("O3'","C3'","C4'","C2'","H3'")]
+ p,o5,o1,o2,c5 = [nt3.atoms_by_name[n]
+ for n in ("P","O5'","O1P","O2P","C5'")]
+ parent.add_bond( o3, p, None )
+ parent.add_angle( c3, o3, p, None )
+ for x in (o5,o1,o2):
+ parent.add_angle( o3, p, x, None )
+ parent.add_dihedral(c3, o3, p, x, None )
+ for x in (c4,c2,h3):
+ parent.add_dihedral(x, c3, o3, p, None )
+ parent.add_dihedral(o3, p, o5, c5, None)
+
+ def generate_atomic_model(self, scale, first_atomic_index):
+ last = None
+ resid = 1
+ ## TODO relabel "strand_segment"
+ strand_segment_count = 0
+ for s in self.strand_segments:
+ strand_segment_count += 1
+ seg = s.segment
+ contour = s.get_contour_points()
+ # if s.end == s.start:
+ # pdb.set_trace()
+ # assert(s.end != s.start)
+ assert( s.num_nt == 1 or (np.linalg.norm( seg.contour_to_position(contour[-1]) - seg.contour_to_position(contour[0]) ) > 0.1) )
+ nucleotide_count = 0
+ for c,seq in zip(contour,s.get_sequence()):
+ nucleotide_count += 1
+ if last is None and not self.is_circular:
+ seq = "5"+seq
+ if strand_segment_count == len(s.strand_segments) and nucleotide_count == s.num_nt and not self.is_circular:
+ seq = seq+"3"
+
+ nt = seg._generate_atomic_nucleotide( c, s.is_fwd, seq, scale, s )
+
+ ## Join last basepairs
+ if last is not None:
+ self.link_nucleotides(last,nt)
+
+ nt.__dict__['resid'] = resid
+ resid += 1
+ last = nt
+ nt._first_atomic_index = first_atomic_index
+ first_atomic_index += len(nt.children)
+
+ if self.is_circular:
+ self.link_nucleotides(last,self.strand_segments[0].children[0])
+
+ return first_atomic_index
+
+ def update_atomic_orientations(self,default_orientation):
+ last = None
+ resid = 1
+ for s in self.strand_segments:
+ seg = s.segment
+ contour = s.get_contour_points()
+ for c,seq,nt in zip(contour,s.get_sequence(),s.children):
+
+ orientation = seg.contour_to_orientation(c)
+ ## TODO: move this code (?)
+ if orientation is None:
+ axis = seg.contour_to_tangent(c)
+ angleVec = np.array([1,0,0])
+ if axis.dot(angleVec) > 0.9: angleVec = np.array([0,1,0])
+ angleVec = angleVec - angleVec.dot(axis)*axis
+ angleVec = angleVec/np.linalg.norm(angleVec)
+ y = np.cross(axis,angleVec)
+ orientation = np.array([angleVec,y,axis]).T
+
+ nt.orientation = orientation.dot(default_orientation) # this one should be correct
+
+class SegmentModel(ArbdModel):
+ def __init__(self, segments=[], local_twist=True, escapable_twist=True,
+ max_basepairs_per_bead=7,
+ max_nucleotides_per_bead=4,
+ dimensions=(1000,1000,1000), temperature=291,
+ timestep=50e-6, cutoff=50,
+ decompPeriod=10000, pairlistDistance=None,
+ nonbondedResolution=0,DEBUG=0):
+ self.DEBUG = DEBUG
+ if DEBUG > 0: print("Building ARBD Model")
+ ArbdModel.__init__(self,segments,
+ dimensions, temperature, timestep, cutoff,
+ decompPeriod, pairlistDistance=None,
+ nonbondedResolution=0)
+
+ # self.max_basepairs_per_bead = max_basepairs_per_bead # dsDNA
+ # self.max_nucleotides_per_bead = max_nucleotides_per_bead # ssDNA
+ self.children = self.segments = segments
+
+ self._bonded_potential = dict() # cache for bonded potentials
+ self._generate_strands()
+ self.grid_potentials = []
+ self._generate_bead_model( max_basepairs_per_bead, max_nucleotides_per_bead, local_twist, escapable_twist)
+
+ self.useNonbondedScheme( nbDnaScheme )
+ self.useTclForces = False
+
+ def get_connections(self,type_=None,exclude=()):
+ """ Find all connections in model, without double-counting """
+ added=set()
+ ret=[]
+ for s in self.segments:
+ items = [e for e in s.get_connections_and_locations(type_,exclude=exclude) if e[0] not in added]
+ added.update([e[0] for e in items])
+ ret.extend( list(sorted(items,key=lambda x: x[1].address)) )
+ return ret
+
+ def _recursively_get_beads_within_bonds(self,b1,bonds,done=()):
+ ret = []
+ done = list(done)
+ done.append(b1)
+ if bonds == 0:
+ return [[]]
+
+ for b2 in b1.intrahelical_neighbors:
+ if b2 in done: continue
+ for tmp in self._recursively_get_beads_within_bonds(b2, bonds-1, done):
+ ret.append( [b2]+tmp )
+ return ret
+
+ def _get_intrahelical_beads(self,num=2):
+ ## TODO: add check that this is not called before adding intrahelical_neighbors in _generate_bead_model
+
+ assert(num >= 2)
+
+ ret = []
+ for s in self.segments:
+ for b1 in s.beads:
+ for bead_list in self._recursively_get_beads_within_bonds(b1, num-1):
+ assert(len(bead_list) == num-1)
+ if b1.idx < bead_list[-1].idx: # avoid double-counting
+ ret.append([b1]+bead_list)
+ return ret
+
+
+ def _get_intrahelical_angle_beads(self):
+ return self._get_intrahelical_beads(num=3)
+
+ def _get_potential(self, type_, kSpring, d, max_potential = None):
+ key = (type_, kSpring, d, max_potential)
+ if key not in self._bonded_potential:
+ assert( kSpring >= 0 )
+ if type_ == "bond":
+ self._bonded_potential[key] = HarmonicBond(kSpring,d, rRange=(0,1200), max_potential=max_potential)
+ elif type_ == "angle":
+ self._bonded_potential[key] = HarmonicAngle(kSpring,d, max_potential=max_potential)
+ # , resolution = 1, maxForce=0.1)
+ elif type_ == "dihedral":
+ self._bonded_potential[key] = HarmonicDihedral(kSpring,d, max_potential=max_potential)
+ else:
+ raise Exception("Unhandled potential type '%s'" % type_)
+ return self._bonded_potential[key]
+ def get_bond_potential(self, kSpring, d):
+ assert( d > 0.2 )
+ return self._get_potential("bond", kSpring, d)
+ def get_angle_potential(self, kSpring, d):
+ return self._get_potential("angle", kSpring, d)
+ def get_dihedral_potential(self, kSpring, d, max_potential=None):
+ while d > 180: d-=360
+ while d < -180: d+=360
+ return self._get_potential("dihedral", kSpring, d, max_potential)
+
+
+ def _getParent(self, *beads ):
+ if np.all( [b1.parent == b2.parent
+ for b1,b2 in zip(beads[:-1],beads[1:])] ):
+ return beads[0].parent
+ else:
+ return self
+
+ def _get_twist_spring_constant(self, sep):
+ """ sep in nt """
+ kT = 0.58622522 # kcal/mol
+ twist_persistence_length = 90 # set semi-arbitrarily as there is a large spread in literature
+ ## <cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
+ ## Assume A is small
+ ## int[B_] := Normal[Integrate[ Series[Cos[x] Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]/
+ ## Integrate[Series[Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]]
+
+ ## Actually, without assumptions I get fitFun below
+ ## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
+ ## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
+ Lp = twist_persistence_length/0.34
+
+ fitFun = lambda x: np.real(erf( (4*np.pi*x + 1j)/(2*np.sqrt(x)) )) * np.exp(-1/(4*x)) / erf(2*np.sqrt(x)*np.pi) - np.exp(-sep/Lp)
+ k = opt.leastsq( fitFun, x0=np.exp(-sep/Lp) )
+ return k[0][0] * 2*kT*0.00030461742
+
+ def extend(self, other, copy=True, include_strands=False):
+ assert( isinstance(other, SegmentModel) )
+ if copy:
+ for s in other.segments:
+ self.segments.append(deepcopy(s))
+ if include_strands:
+ for s in other.strands:
+ self.strands.append(deepcopy(s))
+ else:
+ for s in other.segments:
+ self.segments.append(s)
+ if include_strands:
+ for s in other.strands:
+ self.strands.append(s)
+ self._clear_beads()
+
+ def update(self, segment , copy=False):
+ assert( isinstance(segment, Segment) )
+ if copy:
+ segment = deepcopy(segment)
+ self.segments.append(segment)
+ self._clear_beads()
+
+ """ Mapping between different resolution models """
+ def clear_atomic(self):
+ for strand in self.strands:
+ for s in strand.children:
+ s.clear_all()
+ for seg in self.segments:
+ for d in ('fwd','rev'):
+ seg.strand_pieces[d] = []
+ self._generate_strands()
+ ## Clear sequence if needed
+ for seg in self.segments:
+ if seg.sequence is not None and len(seg.sequence) != seg.num_nt:
+ seg.sequence = None
+
+ def clear_beads(self):
+ return self._clear_beads()
+
+ def _clear_beads(self):
+ ## TODO: deprecate
+ for s in self.segments:
+ try:
+ s.clear_all()
+ except:
+ ...
+ self.clear_all(keep_children=True)
+
+ try:
+ if len(self.strands[0].children[0].children) > 0:
+ self.clear_atomic()
+ except:
+ ...
+
+ ## Check that it worked
+ assert( len([b for b in self]) == 0 )
+ locParticles = []
+ for s in self.segments:
+ for c,A,B in s.get_connections_and_locations():
+ for l in (A,B):
+ if l.particle is not None:
+ locParticles.append(l.particle)
+ assert( len(locParticles) == 0 )
+ assert( len([b for s in self.segments for b in s.beads]) == 0 )
+
+ def _update_segment_positions(self, bead_coordinates):
+ print("WARNING: called deprecated command '_update_segment_positions; use 'update_splines' instead")
+ return self.update_splines(bead_coordinates)
+
+ ## Operations on spline coordinates
+ def translate(self, translation_vector, position_filter=None):
+ for s in self.segments:
+ s.translate(translation_vector, position_filter=position_filter)
+
+ def rotate(self, rotation_matrix, about=None, position_filter=None):
+ for s in self.segments:
+ s.rotate(rotation_matrix, about=about, position_filter=position_filter)
+
+ def get_center(self, include_ssdna=False):
+ if include_ssdna:
+ segments = self.segments
+ else:
+ segments = list(filter(lambda s: isinstance(s,DoubleStrandedSegment),
+ self.segments))
+ centers = [s.get_center() for s in segments]
+ weights = [s.num_nt*2 if isinstance(s,DoubleStrandedSegment) else s.num_nt for s in segments]
+ # centers,weights = [np.array(a) for a in (centers,weights)]
+ return np.average( centers, axis=0, weights=weights)
+
+ def update_splines(self, bead_coordinates):
+ """ Set new function for each segments functions
+ contour_to_position and contour_to_orientation """
+
+ for s in self.segments:
+ # if s.name == "61-1":
+ # pdb.set_trace()
+
+ cabs = s.get_connections_and_locations("intrahelical")
+ if isinstance(s,SingleStrandedSegment):
+ cabs = cabs + [[c,A,B] for c,A,B in s.get_connections_and_locations("sscrossover") if A.address == 0 or A.address == 1]
+ if np.any( [B.particle is None for c,A,B in cabs] ):
+ print( "WARNING: none type found in connection, skipping" )
+ cabs = [e for e in cabs if e[2].particle is not None]
+
+ def get_beads_and_contour_positions(s):
+ ret_list = []
+ def zip_bead_contour(beads,address=None):
+ if isinstance(address,list):
+ assert(False)
+ for b,a in zip(beads,address):
+ if b is None: continue
+ try:
+ ret_list.append((b, b.get_contour_position(s,a)))
+ except:
+ ...
+ else:
+ for b in beads:
+ if b is None: continue
+ try:
+ ret_list.append((b, b.get_contour_position(s,address)))
+ except:
+ ...
+ return ret_list
+
+ ## Add beads from segment s
+ beads_contours = zip_bead_contour(s.beads)
+ beads_contours.extend( zip_bead_contour([A.particle for c,A,B in cabs]) )
+ beads = set([b for b,c in beads_contours])
+
+ ## Add nearby beads
+ for c,A,B in cabs:
+ ## TODOTODO test?
+ filter_fn = lambda x: x is not None and x not in beads
+ bs = list( filter( filter_fn, B.particle.intrahelical_neighbors ) )
+ beads_contours.extend( zip_bead_contour( bs, A.address ) )
+ beads.update(bs)
+ for i in range(3):
+ bs = list( filter( filter_fn, [n for b in bs for n in b.intrahelical_neighbors] ) )
+ beads_contours.extend( zip_bead_contour( bs, A.address ) )
+ beads.update(bs)
+
+ beads_contours = list(set(beads_contours))
+ beads = list(beads)
+
+ ## Skip beads that are None (some locations were not assigned a particle to avoid double-counting)
+ # beads = [b for b in beads if b is not None]
+ assert( np.any([b is None for b,c in beads_contours]) == False )
+ # beads = list(filter(lambda x: x[0] is not None, beads))
+
+ if isinstance(s, DoubleStrandedSegment):
+ beads_contours = list(filter(lambda x: x[0].type_.name[0] == "D", beads_contours))
+ return beads_contours
+
+ beads_contours = get_beads_and_contour_positions(s)
+ contours = [c for b,c in beads_contours]
+ contours = np.array(contours, dtype=np.float16) # deliberately use low precision
+ contours,ids1 = np.unique(contours, return_index=True)
+ beads_contours = [beads_contours[i] for i in ids1]
+
+ assert( np.any( (contours[:-1] - contours[1:])**2 >= 1e-8 ) )
+
+ ## TODO: keep closest beads beyond +-1.5 if there are fewer than 2 beads
+ tmp = []
+ dist = 1
+ while len(tmp) < 5 and dist < 3:
+ tmp = list(filter(lambda bc: np.abs(bc[1]-0.5) < dist, beads_contours))
+ dist += 0.1
+
+ if len(tmp) <= 1:
+ raise Exception("Failed to fit spline into segment {}".format(s))
+
+ beads = [b for b,c in tmp]
+ contours = [c for b,c in tmp]
+ ids = [b.idx for b in beads]
+
+ if len(beads) <= 1:
+ pdb.set_trace()
+
+
+ """ Get positions """
+ positions = bead_coordinates[ids,:].T
+
+ # print("BEADS NOT IN {}:".format(s))
+ # for b,c in filter(lambda z: z[0] not in s.beads, zip(beads,contours)):
+ # print(" {}[{:03f}]: {:0.3f}".format(b.parent.name, b.contour_position, c) )
+
+
+ tck, u = interpolate.splprep( positions, u=contours, s=0, k=1 )
+
+ # if len(beads) < 8:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+
+ # else:
+ # try:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=3, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+ # except:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+
+ s.position_spline_params = (tck,u)
+
+ """ Get orientation """
+ def get_orientation_vector(bead,tangent):
+ if 'orientation_bead' in bead.__dict__:
+ o = bead.orientation_bead
+ oVec = bead_coordinates[o.idx,:] - bead_coordinates[bead.idx,:]
+ oVec = oVec - oVec.dot(tangent)*tangent
+ oVec = oVec/np.linalg.norm(oVec)
+ else:
+ oVec = None
+ return oVec
+
+ def remove_tangential_projection(vector, tangent):
+ """ Assume tangent is normalized """
+ v = vector - vector.dot(tangent)*tangent
+ return v/np.linalg.norm(v)
+
+ def get_orientation_vector(bead,tangent):
+ if 'orientation_bead' in bead.__dict__:
+ o = bead.orientation_bead
+ oVec = bead_coordinates[o.idx,:] - bead_coordinates[bead.idx,:]
+ oVec = remove_tangential_projection(oVec,tangent)
+ else:
+ oVec = None
+ return oVec
+
+
+ def get_previous_idx_if_none(list_):
+ previous = None
+ result = []
+ i = 0
+ for e in list_:
+ if e is None:
+ result.append(previous)
+ else:
+ previous = i
+ i+=1
+ return result
+ def get_next_idx_if_none(list_):
+ tmp = get_previous_idx_if_none(list_[::-1])[::-1]
+ return [ len(list_)-1-idx if idx is not None else idx for idx in tmp ]
+
+ def fill_in_orientation_vectors(contours,orientation_vectors,tangents):
+ result = []
+ last_idx = get_previous_idx_if_none( orientation_vectors )
+ next_idx = get_next_idx_if_none( orientation_vectors )
+ none_idx = 0
+ for c,ov,t in zip(contours,orientation_vectors,tangents):
+ if ov is not None:
+ result.append(ov)
+ else:
+ p = last_idx[none_idx]
+ n = next_idx[none_idx]
+ none_idx += 1
+ if p is None:
+ if n is None:
+ ## Should be quite rare; give something random if it happens
+ print("WARNING: unable to interpolate orientation")
+ o = np.array((1,0,0))
+ result.append( remove_tangential_projection(o,t) )
+ else:
+ o = orientation_vectors[n]
+ result.append( remove_tangential_projection(o,t) )
+ else:
+ if n is None:
+ o = orientation_vectors[p]
+ result.append( remove_tangential_projection(o,t) )
+ else:
+ cp,cn = [contours[i] for i in (p,n)]
+ op,on = [orientation_vectors[i] for i in (p,n)]
+ if (cn-cp) > 1e-6:
+ o = ((cn-c)*op+(c-cp)*on)/(cn-cp)
+ else:
+ o = op+on
+ result.append( remove_tangential_projection(o,t) )
+ return result
+
+ tangents = s.contour_to_tangent(contours)
+ orientation_vectors = [get_orientation_vector(b,t) for b,t in zip(beads,tangents)]
+ if len(beads) > 3 and any([e is not None for e in orientation_vectors] ):
+ orientation_vectors = fill_in_orientation_vectors(contours, orientation_vectors, tangents)
+
+ quats = []
+ lastq = None
+ for b,t,oVec in zip(beads,tangents,orientation_vectors):
+ y = np.cross(t,oVec)
+ assert( np.abs(np.linalg.norm(y) - 1) < 1e-2 )
+ q = quaternion_from_matrix( np.array([oVec,y,t]).T)
+
+ if lastq is not None:
+ if q.dot(lastq) < 0:
+ q = -q
+ quats.append( q )
+ lastq = q
+
+ # pdb.set_trace()
+ quats = np.array(quats)
+ # tck, u = interpolate.splprep( quats.T, u=contours, s=3, k=3 ) ;# cubic spline not as good
+ tck, u = interpolate.splprep( quats.T, u=contours, s=0, k=1 )
+ s.quaternion_spline_params = (tck,u)
+
+ def _generate_bead_model(self,
+ max_basepairs_per_bead = 7,
+ max_nucleotides_per_bead = 4,
+ local_twist=False,
+ escapable_twist=True):
+ ## TODO: deprecate
+ self.generate_bead_model( max_basepairs_per_bead = max_basepairs_per_bead,
+ max_nucleotides_per_bead = max_nucleotides_per_bead,
+ local_twist=local_twist,
+ escapable_twist=escapable_twist)
+
+ def generate_bead_model(self,
+ max_basepairs_per_bead = 7,
+ max_nucleotides_per_bead = 4,
+ local_twist=False,
+ escapable_twist=True):
+
+ self.children = self.segments # is this okay?
+ self.clear_beads()
+
+ segments = self.segments
+ for s in segments:
+ s.local_twist = local_twist
+
+ """ Simplify connections """
+ # d_nt = dict() #
+ # for s in segments:
+ # d_nt[s] = 1.5/(s.num_nt-1)
+ # for s in segments:
+ # ## replace consecutive crossovers with
+ # cl = sorted( s.get_connections_and_locations("crossover"), key=lambda x: x[1].address )
+ # last = None
+ # for entry in cl:
+ # c,A,B = entry
+ # if last is not None and \
+ # (A.address - last[1].address) < d_nt[s]:
+ # same_type = c.type_ == last[0].type_
+ # same_dest_seg = B.container == last[2].container
+ # if same_type and same_dest_seg:
+ # if np.abs(B.address - last[2].address) < d_nt[B.container]:
+ # ## combine
+ # A.combine = last[1]
+ # B.combine = last[2]
+
+ # ...
+ # # if last is not None:
+ # # s.bead_locations.append(last)
+ # ...
+ # last = entry
+ # del d_nt
+
+ """ Generate beads at intrahelical junctions """
+ if self.DEBUG: print( "Adding intrahelical beads at junctions" )
+
+ ## Loop through all connections, generating beads at appropriate locations
+ for c,A,B in self.get_connections("intrahelical"):
+ s1,s2 = [l.container for l in (A,B)]
+
+ assert( A.particle is None )
+ assert( B.particle is None )
+
+ ## TODO: offload the work here to s1
+ # TODOTODO
+ a1,a2 = [l.address for l in (A,B)]
+ for a in (a1,a2):
+ assert( np.isclose(a,0) or np.isclose(a,1) )
+
+ ## TODO improve this for combinations of ssDNA and dsDNA (maybe a1/a2 should be calculated differently)
+ """ Search to see whether bead at location is already found """
+ b = None
+ if isinstance(s1,DoubleStrandedSegment):
+ b = s1.get_nearest_bead(a1)
+ if b is not None:
+ assert( b.parent is s1 )
+ """ if above assertion is true, no problem here """
+ if np.abs(b.get_nt_position(s1) - s1.contour_to_nt_pos(a1)) > 0.5:
+ b = None
+ if b is None and isinstance(s2,DoubleStrandedSegment):
+ b = s2.get_nearest_bead(a2)
+ if b is not None:
+ if np.abs(b.get_nt_position(s2) - s2.contour_to_nt_pos(a2)) > 0.5:
+ b = None
+
+
+ if b is not None and b.parent not in (s1,s2):
+ b = None
+
+ if b is None:
+ ## need to generate a bead
+ if isinstance(s2,DoubleStrandedSegment):
+ b = s2._generate_one_bead(a2,0)
+ else:
+ b = s1._generate_one_bead(a1,0)
+ A.particle = B.particle = b
+ b.is_intrahelical = True
+ b.locations.extend([A,B])
+
+ # pdb.set_trace()
+
+ """ Generate beads at other junctions """
+ for c,A,B in self.get_connections(exclude="intrahelical"):
+ s1,s2 = [l.container for l in (A,B)]
+ if A.particle is not None and B.particle is not None:
+ continue
+ # assert( A.particle is None )
+ # assert( B.particle is None )
+
+ ## TODO: offload the work here to s1/s2 (?)
+ a1,a2 = [l.address for l in (A,B)]
+
+ def maybe_add_bead(location, seg, address, ):
+ if location.particle is None:
+ b = seg.get_nearest_bead(address)
+ try:
+ distance = seg.contour_to_nt_pos(np.abs(b.contour_position-address))
+ max_distance = min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
+ if "is_intrahelical" in b.__dict__:
+ max_distance = 0.5
+ if distance >= max_distance:
+ raise Exception("except")
+
+ ## combine beads
+ b.update_position( 0.5*(b.contour_position + address) ) # avg position
+ except:
+ b = seg._generate_one_bead(address,0)
+ location.particle = b
+ b.locations.append(location)
+
+ maybe_add_bead(A,s1,a1)
+ maybe_add_bead(B,s2,a2)
+
+ """ Some tests """
+ for c,A,B in self.get_connections("intrahelical"):
+ for l in (A,B):
+ if l.particle is None: continue
+ assert( l.particle.parent is not None )
+
+ """ Generate beads in between """
+ if self.DEBUG: print("Generating beads")
+ for s in segments:
+ s._generate_beads( self, max_basepairs_per_bead, max_nucleotides_per_bead )
+
+ # """ Combine beads at junctions as needed """
+ # for c,A,B in self.get_connections():
+ # ...
+
+ # ## Debug
+ # all_beads = [b for s in segments for b in s.beads]
+ # positions = np.array([b.position for b in all_beads])
+ # dists = positions[:,np.newaxis,:] - positions[np.newaxis,:,:]
+ # ids = np.where( np.sum(dists**2,axis=-1) + 0.02**2*np.eye(len(dists)) < 0.02**2 )
+ # print( ids )
+ # pdb.set_trace()
+
+ """ Add intrahelical neighbors at connections """
+
+ for c,A,B in self.get_connections("intrahelical"):
+ b1,b2 = [l.particle for l in (A,B)]
+ if b1 is b2:
+ ## already handled by Segment._generate_beads
+ pass
+ else:
+ for b in (b1,b2): assert( b is not None )
+ b1.make_intrahelical_neighbor(b2)
+
+ """ Reassign bead types """
+ if self.DEBUG: print("Assigning bead types")
+ beadtype_s = dict()
+ beadtype_count = dict(D=0,O=0,S=0)
+
+ def _assign_bead_type(bead, num_nt, decimals):
+ num_nt0 = bead.num_nt
+ bead.num_nt = np.around( np.float32(num_nt), decimals=decimals )
+ char = bead.type_.name[0].upper()
+ key = (char, bead.num_nt)
+ if key in beadtype_s:
+ bead.type_ = beadtype_s[key]
+ else:
+ t = deepcopy(bead.type_)
+ t.__dict__["nts"] = bead.num_nt*2 if char in ("D","O") else bead.num_nt
+ # t.name = t.name + "%03d" % (t.nts*10**decimals)
+ t.name = char + "%03d" % (beadtype_count[char])
+ t.mass = t.nts * 150
+ t.diffusivity = 150 if t.nts == 0 else min( 50 / np.sqrt(t.nts/5), 150)
+ beadtype_count[char] += 1
+ if self.DEBUG: print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
+ beadtype_s[key] = bead.type_ = t
+
+ # (cluster_size[c-1])
+
+
+ import scipy.cluster.hierarchy as hcluster
+ beads = [b for s in segments for b in s if b.type_.name[0].upper() in ("D","O")]
+ data = np.array([b.num_nt for b in beads])[:,np.newaxis]
+ order = int(2-np.log10(2*max_basepairs_per_bead)//1)
+ try:
+ clusters = hcluster.fclusterdata(data, float(max_basepairs_per_bead)/500, criterion="distance")
+ cluster_size = [np.mean(data[clusters == i]) for i in np.unique(clusters)]
+ except:
+ clusters = np.arange(len(data))+1
+ cluster_size = data.flatten()
+ for b,c in zip(beads,clusters):
+ _assign_bead_type(b, cluster_size[c-1], decimals=order)
+
+ beads = [b for s in segments for b in s if b.type_.name[0].upper() in ("S")]
+ data = np.array([b.num_nt for b in beads])[:,np.newaxis]
+ order = int(2-np.log10(max_nucleotides_per_bead)//1)
+ try:
+ clusters = hcluster.fclusterdata(data, float(max_nucleotides_per_bead)/500, criterion="distance")
+ cluster_size = [np.mean(data[clusters == i]) for i in np.unique(clusters)]
+ except:
+ clusters = np.arange(len(data))+1
+ cluster_size = data.flatten()
+ for b,c in zip(beads,clusters):
+ _assign_bead_type(b, cluster_size[c-1], decimals=order)
+
+ self._apply_grid_potentials_to_beads(beadtype_s)
+
+ # for bead in [b for s in segments for b in s]:
+ # num_nt0 = bead.num_nt
+ # # bead.num_nt = np.around( np.float32(num_nt), decimals=decimals )
+ # key = (bead.type_.name[0].upper(), bead.num_nt)
+ # if key in beadtype_s:
+ # bead.type_ = beadtype_s[key]
+ # else:
+ # t = deepcopy(bead.type_)
+ # t.__dict__["nts"] = bead.num_nt*2 if t.name[0].upper() in ("D","O") else bead.num_nt
+ # # t.name = t.name + "%03d" % (t.nts*10**decimals)
+ # t.name = t.name + "%.16f" % (t.nts)
+ # print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
+ # beadtype_s[key] = bead.type_ = t
+
+
+ """ Update bead indices """
+ self._countParticleTypes() # probably not needed here
+ self._updateParticleOrder()
+
+ """ Add intrahelical bond potentials """
+ if self.DEBUG: print("Adding intrahelical bond potentials")
+ dists = dict() # intrahelical distances built for later use
+ intra_beads = self._get_intrahelical_beads()
+ if self.DEBUG: print(" Adding %d bonds" % len(intra_beads))
+ for b1,b2 in intra_beads:
+ # assert( not np.isclose( np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()), 0 ) )
+ if np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()) < 1:
+ # print("WARNING: some beads are very close")
+ ...
+
+ parent = self._getParent(b1,b2)
+
+ ## TODO: could be sligtly smarter about sep
+ sep = 0.5*(b1.num_nt+b2.num_nt)
+
+ conversion = 0.014393265 # units "pN/AA" kcal_mol/AA^2
+ if b1.type_.name[0] == "D" and b2.type_.name[0] == "D":
+ elastic_modulus_times_area = 1000 # pN http://markolab.bmbcb.northwestern.edu/marko/Cocco.CRP.02.pdf
+ d = 3.4*sep
+ k = conversion*elastic_modulus_times_area/d
+ else:
+ ## TODO: get better numbers our ssDNA model
+ elastic_modulus_times_area = 800 # pN http://markolab.bmbcb.northwestern.edu/marko/Cocco.CRP.02.pdf
+ d = 5*sep
+ k = conversion*elastic_modulus_times_area/d
+ # print(sep,d,k)
+
+ if b1 not in dists:
+ dists[b1] = dict()
+ if b2 not in dists:
+ dists[b2] = dict()
+ # dists[b1].append([b2,sep])
+ # dists[b2].append([b1,sep])
+ dists[b1][b2] = sep
+ dists[b2][b1] = sep
+
+ if b1 is b2: continue
+
+ # dists[[b1,b2]] = dists[[b2,b1]] = sep
+ bond = self.get_bond_potential(k,d)
+ parent.add_bond( b1, b2, bond, exclude=True )
+
+ # for s in self.segments:
+ # sepsum = 0
+ # beadsum = 0
+ # for b1 in s.beads:
+ # beadsum += b1.num_nt
+ # for bead_list in self._recursively_get_beads_within_bonds(b1, 1):
+ # assert(len(bead_list) == 1)
+ # if b1.idx < bead_list[-1].idx: # avoid double-counting
+ # for b2 in bead_list:
+ # if b2.parent == b1.parent:
+ # sepsum += dists[b1][b2]
+ # sepsum += sep
+ # print("Helix {}: bps {}, beads {}, separation {}".format(s.name, s.num_nt, beadsum, sepsum))
+
+ """ Add intrahelical angle potentials """
+ def get_effective_dsDNA_Lp(sep):
+
+ """ The persistence length of our model was found to be a
+ little off (probably due to NB interactions). This
+ attempts to compensate """
+
+ ## For 1 bp, Lp=559, for 25 Lp = 524
+ beads_per_bp = sep/2
+ Lp0 = 147
+ # return 0.93457944*Lp0 ;# factor1
+ return 0.97*Lp0 ;# factor2
+ # factor = bead_per_bp * (0.954-0.8944
+ # return Lp0 * bead_per_bp
+
+ empirical_compensation_factor = max_basepairs_per_bead
+
+ if self.DEBUG: print("Adding intrahelical angle potentials")
+ for b1,b2,b3 in self._get_intrahelical_angle_beads():
+ ## TODO: could be slightly smarter about sep
+ sep = 0.5*(0.5*b1.num_nt+b2.num_nt+0.5*b3.num_nt)
+ parent = self._getParent(b1,b2,b3)
+
+ kT = 0.58622522 # kcal/mol
+ if b1.type_.name[0] == "D" and b2.type_.name[0] == "D" and b3.type_.name[0] == "D":
+ Lp = get_effective_dsDNA_Lp(sep)
+ k = angle_spring_from_lp(sep,Lp)
+ if local_twist:
+ k_dihed = 0.25*k
+ k *= 0.75 # reduce because orientation beads impose similar springs
+ dihed = self.get_dihedral_potential(k_dihed,180)
+ parent.add_dihedral(b1,b2,b2.orientation_bead,b3, dihed)
+
+
+ else:
+ ## TODO: get correct number from ssDNA model
+ k = angle_spring_from_lp(sep,2)
+
+ angle = self.get_angle_potential(k,180)
+ parent.add_angle( b1, b2, b3, angle )
+
+ """ Add intrahelical exclusions """
+ if self.DEBUG: print("Adding intrahelical exclusions")
+ beads = dists.keys()
+ def _recursively_get_beads_within(b1,d,done=()):
+ ret = []
+ for b2,sep in dists[b1].items():
+ if b2 in done: continue
+ if sep < d:
+ ret.append( b2 )
+ done.append( b2 )
+ tmp = _recursively_get_beads_within(b2, d-sep, done)
+ if len(tmp) > 0: ret.extend(tmp)
+ return ret
+
+ exclusions = set()
+ for b1 in beads:
+ exclusions.update( [(b1,b) for b in _recursively_get_beads_within(b1, 20, done=[b1])] )
+
+ if self.DEBUG: print("Adding %d exclusions" % len(exclusions))
+ for b1,b2 in exclusions:
+ parent = self._getParent(b1,b2)
+ parent.add_exclusion( b1, b2 )
+
+ """ Twist potentials """
+ if local_twist:
+ if self.DEBUG: print("Adding twist potentials")
+
+ for b1 in beads:
+ if "orientation_bead" not in b1.__dict__: continue
+ for b2,sep in dists[b1].items():
+ if "orientation_bead" not in b2.__dict__: continue
+ if b2.idx < b1.idx: continue # Don't double-count
+
+ p1,p2 = [b.parent for b in (b1,b2)]
+ o1,o2 = [b.orientation_bead for b in (b1,b2)]
+
+ parent = self._getParent( b1, b2 )
+
+ """ Add heuristic 90 degree potential to keep orientation bead orthogonal """
+ Lp = get_effective_dsDNA_Lp(sep)
+ k = 0.5*angle_spring_from_lp(sep,Lp)
+ pot = self.get_angle_potential(k,90)
+ parent.add_angle(o1,b1,b2, pot)
+ parent.add_angle(b1,b2,o2, pot)
+
+ ## TODO: improve this
+ twist_per_nt = 0.5 * (p1.twist_per_nt + p2.twist_per_nt)
+ angle = sep*twist_per_nt
+ if angle > 360 or angle < -360:
+ print("WARNING: twist angle out of normal range... proceeding anyway")
+ # raise Exception("The twist between beads is too large")
+
+ k = self._get_twist_spring_constant(sep)
+ if escapable_twist:
+ pot = self.get_dihedral_potential(k,angle,max_potential=1)
+ else:
+ pot = self.get_dihedral_potential(k,angle)
+ parent.add_dihedral(o1,b1,b2,o2, pot)
+
+ def k_angle(sep):
+ return 0.5*angle_spring_from_lp(sep,147)
+
+ def k_xover_angle(sep):
+ return 0.5 * k_angle(sep)
+
+ def add_local_crossover_orientation_potential(b1,b2,is_parallel=True):
+ u1,u2 = [b.get_intrahelical_above() for b in (b1,b2)]
+ d1,d2 = [b.get_intrahelical_below() for b in (b1,b2)]
+
+ k = k_xover_angle(sep=1)
+ pot = self.get_angle_potential(k,120)
+
+ if 'orientation_bead' in b1.__dict__:
+ o = b1.orientation_bead
+ self.add_angle( o,b1,b2, pot )
+ if 'orientation_bead' in b2.__dict__:
+ o = b2.orientation_bead
+ self.add_angle( b1,b2,o, pot )
+
+ if 'orientation_bead' in b1.__dict__:
+ t0 = -90 if A.on_fwd_strand else 90
+ if not is_parallel: t0 *= -1
+
+ o1 = b1.orientation_bead
+ if u2 is not None and isinstance(u2.parent,DoubleStrandedSegment):
+ k = k_xover_angle( dists[b2][u2] )
+ pot = self.get_dihedral_potential(k,t0)
+ self.add_dihedral( o1,b1,b2,u2, pot )
+ elif d2 is not None and isinstance(d2.parent,DoubleStrandedSegment):
+ k = k_xover_angle( dists[b2][d2] )
+ pot = self.get_dihedral_potential(k,-t0)
+ self.add_dihedral( o1,b1,b2,d2, pot )
+ if 'orientation_bead' in b2.__dict__:
+ t0 = -90 if B.on_fwd_strand else 90
+ if not is_parallel: t0 *= -1
+
+ o2 = b2.orientation_bead
+ if u1 is not None and isinstance(u1.parent,DoubleStrandedSegment):
+ k = k_xover_angle( dists[b1][u1] )
+ pot = self.get_dihedral_potential(k,t0)
+ self.add_dihedral( o2,b2,b1,u1, pot )
+ elif d1 is not None and isinstance(d1.parent,DoubleStrandedSegment):
+ k = k_xover_angle( dists[b1][d1] )
+ pot = self.get_dihedral_potential(k,-t0)
+ self.add_dihedral( o2,b2,b1,d1, pot )
+
+
+ """ Add connection potentials """
+ for c,A,B in self.get_connections("terminal_crossover"):
+ ## TODO: use a better description here
+ b1,b2 = [loc.particle for loc in (c.A,c.B)]
+ # pot = self.get_bond_potential(4,18.5)
+ pot = self.get_bond_potential(4,12)
+ self.add_bond(b1,b2, pot)
+
+ dotProduct = b1.parent.contour_to_tangent(b1.contour_position).dot(
+ b2.parent.contour_to_tangent(b2.contour_position) )
+
+ ## Add potential to provide a particular orinetation
+ if local_twist:
+ add_local_crossover_orientation_potential(b1,b2, is_parallel=dotProduct > 0)
+
+
+ """ Add connection potentials """
+ for c,A,B in self.get_connections("sscrossover"):
+ b1,b2 = [loc.particle for loc in (c.A,c.B)]
+ ## TODO: improve parameters
+ pot = self.get_bond_potential(4,6)
+ self.add_bond(b1,b2, pot)
+
+ ## Add potentials to provide a sensible orientation
+ ## TODO refine potentials against all-atom simulation data
+ """
+ u1,u2 = [b.get_intrahelical_above() for b in (b1,b2)]
+ d1,d2 = [b.get_intrahelical_below() for b in (b1,b2)]
+ k_fn = k_angle
+ if isinstance(b1.parent,DoubleStrandedSegment):
+ a,b,c = (d1,b1,b2) if d1.parent is b1.parent else (u1,b1,b2)
+ else:
+ a,b,c = (d2,b2,b1) if d2.parent is b2.parent else (u2,b2,b1)
+ """
+
+ # pot = self.get_angle_potential( k_fn(dists[a][b]), 120 ) # a little taller than 90 degrees
+ # self.add_angle( a,b,c, pot )
+ # o = b.orientation_bead
+ # angle=3
+ # pot = self.get_angle_potential( 1, 0 ) # a little taller than 90 degrees
+ # self.add_angle( a,b,c, pot )
+
+ dotProduct = b1.parent.contour_to_tangent(b1.contour_position).dot(
+ b2.parent.contour_to_tangent(b2.contour_position) )
+
+ if local_twist:
+ add_local_crossover_orientation_potential(b1,b2, is_parallel=dotProduct > 0)
+
+
+ crossover_bead_pots = set()
+ for c,A,B in self.get_connections("crossover"):
+ b1,b2 = [loc.particle for loc in (A,B)]
+
+ ## Avoid double-counting
+ if (b1,b2,A.on_fwd_strand,B.on_fwd_strand) in crossover_bead_pots: continue
+ crossover_bead_pots.add((b1,b2,A.on_fwd_strand,B.on_fwd_strand))
+ crossover_bead_pots.add((b2,b1,B.on_fwd_strand,A.on_fwd_strand))
+
+ pot = self.get_bond_potential(4,18.5)
+ self.add_bond(b1,b2, pot)
+
+ ## Get beads above and below
+ u1,u2 = [b.get_intrahelical_above() for b in (b1,b2)]
+ d1,d2 = [b.get_intrahelical_below() for b in (b1,b2)]
+ dotProduct = b1.parent.contour_to_tangent(b1.contour_position).dot(
+ b2.parent.contour_to_tangent(b2.contour_position) )
+ if dotProduct < 0:
+ tmp = d2
+ d2 = u2
+ u2 = tmp
+
+ a = None
+ if u1 is not None and u2 is not None:
+ t0 = 0
+ a,b,c,d = (u1,b1,b2,u2)
+ elif d1 is not None and d2 is not None:
+ t0 = 0
+ a,b,c,d = (d1,b1,b2,d2 )
+ elif d1 is not None and u2 is not None:
+ t0 = 180
+ a,b,c,d = (d1,b1,b2,u2)
+ elif u1 is not None and d2 is not None:
+ t0 = 180
+ a,b,c,d = (u1,b1,b2,d2)
+
+ if a is not None:
+ k = k_xover_angle( dists[b][a]+dists[c][d] )
+ pot = self.get_dihedral_potential(k,t0)
+ self.add_dihedral( a,b,c,d, pot )
+
+ if local_twist:
+ add_local_crossover_orientation_potential(b1,b2, is_parallel=dotProduct > 0)
+
+
+ ## TODOTODO check that this works
+ for crossovers in self.get_consecutive_crossovers():
+ if local_twist: break
+ ## filter crossovers
+ for i in range(len(crossovers)-2):
+ c1,A1,B1,dir1 = crossovers[i]
+ c2,A2,B2,dir2 = crossovers[i+1]
+ s1,s2 = [l.container for l in (A1,A2)]
+ sep = A1.particle.get_nt_position(s1,near_address=A1.address) - A2.particle.get_nt_position(s2,near_address=A2.address)
+ sep = np.abs(sep)
+
+ assert(sep >= 0)
+
+ n1,n2,n3,n4 = (B1.particle, A1.particle, A2.particle, B2.particle)
+
+ """
+ <cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
+ """
+
+ ## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
+ ## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
+ Lp = s1.twist_persistence_length/0.34 # set semi-arbitrarily as there is a large spread in literature
+
+ def get_spring(sep):
+ fitFun = lambda x: np.real(erf( (4*np.pi*x + 1j)/(2*np.sqrt(x)) )) * np.exp(-1/(4*x)) / erf(2*np.sqrt(x)*np.pi) - np.exp(-sep/Lp)
+ k = opt.leastsq( fitFun, x0=np.exp(-sep/Lp) )
+ return k[0][0] * 2*kT*0.00030461742
+
+ k = get_spring( max(sep,2) )
+ t0 = sep*s1.twist_per_nt # TODO weighted avg between s1 and s2
+
+ # pdb.set_trace()
+ if A1.on_fwd_strand: t0 -= 120
+ if dir1 != dir2:
+ A2_on_fwd = not A2.on_fwd_strand
+ else:
+ A2_on_fwd = A2.on_fwd_strand
+ if A2_on_fwd: t0 += 120
+
+ # t0 = (t0 % 360
+
+ # if n2.idx == 0:
+ # print( n1.idx,n2.idx,n3.idx,n4.idx,k,t0,sep )
+ if sep == 0 and n1 is not n4:
+ # pot = self.get_angle_potential(k,t0)
+ # self.add_angle( n1,n2,n4, pot )
+ pass
+ else:
+ pot = self.get_dihedral_potential(k,t0)
+ self.add_dihedral( n1,n2,n3,n4, pot )
+
+ # ## remove duplicate potentials; ## TODO ensure that they aren't added twice in the first place?
+ # self.remove_duplicate_terms()
+
+ def walk_through_helices(segment, direction=1, processed_segments=None):
+ """
+
+ First and last segment should be same for circular helices
+ """
+
+ assert( direction in (1,-1) )
+ if processed_segments == None:
+ processed_segments = set()
+
+ def segment_is_new_helix(s):
+ return isinstance(s,DoubleStrandedSegment) and s not in processed_segments
+
+ new_s = None
+ s = segment
+ ## iterate intrahelically connected dsDNA segments
+ while segment_is_new_helix(s):
+ conn_locs = s.get_contour_sorted_connections_and_locations("intrahelical")[::direction]
+ processed_segments.add(new_s)
+ new_s = None
+ new_dir = None
+ for i in range(len(conn_locs)):
+ c,A,B = conn_locs[i]
+ ## TODO: handle change of direction
+ # TODOTODO
+ address = 1*(direction==-1)
+ if A.address == address and segment_is_new_helix(B.container):
+ new_s = B.container
+ assert(B.address in (0,1))
+ new_dir = 2*(B.address == 0) - 1
+ break
+
+ yield s,direction
+ s = new_s # will break if None
+ direction = new_dir
+
+ # if new_s is None:
+ # break
+ # else:
+ # s = new_s
+ # yield s
+ ## return s
+
+
+ def get_consecutive_crossovers(self):
+ ## TODOTODO TEST
+ crossovers = []
+ processed_segments = set()
+ for s1 in self.segments:
+ if not isinstance(s1,DoubleStrandedSegment):
+ continue
+ if s1 in processed_segments: continue
+
+ s0,d0 = list(SegmentModel.walk_through_helices(s1,direction=-1))[-1]
+
+ # s,direction = get_start_of_helices()
+ tmp = []
+ for s,d in SegmentModel.walk_through_helices(s0,-d0):
+ if s == s0 and len(tmp) > 0:
+ ## end of circular helix, only add first crossover
+ cl_list = s.get_contour_sorted_connections_and_locations("crossover")
+ if len(cl_list) > 0:
+ tmp.append( cl_list[::d][0] + [d] )
+ else:
+ tmp.extend( [cl + [d] for cl in s.get_contour_sorted_connections_and_locations("crossover")[::d]] )
+ processed_segments.add(s)
+ crossovers.append(tmp)
+ return crossovers
+
+ def set_sequence(self, sequence, force=True):
+ if force:
+ self.strands[0].set_sequence(sequence)
+ else:
+ try:
+ self.strands[0].set_sequence(sequence)
+ except:
+ ...
+ for s in self.segments:
+ s.randomize_unset_sequence()
+
+ def _generate_strands(self):
+ ## clear strands
+ try:
+ for s in self.strands:
+ self.children.remove(s)
+ for seg in self.segments:
+ for d in ('fwd','rev'):
+ seg.strand_pieces[d] = []
+ except:
+ pass
+ self.strands = strands = []
+
+ """ Ensure unconnected ends have 5prime Location objects """
+ for seg in self.segments:
+ ## TODO move into Segment calls
+ five_prime_locs = sum([seg.get_locations(s) for s in ("5prime","crossover","terminal_crossover")],[])
+ three_prime_locs = sum([seg.get_locations(s) for s in ("3prime","crossover","terminal_crossover")],[])
+
+ def is_start_5prime(l):
+ return l.get_nt_pos() < 1 and l.on_fwd_strand
+ def is_end_5prime(l):
+ return l.get_nt_pos() > seg.num_nt-2 and not l.on_fwd_strand
+ def is_start_3prime(l):
+ return l.get_nt_pos() < 1 and not l.on_fwd_strand
+ def is_end_3prime(l):
+ return l.get_nt_pos() > seg.num_nt-2 and l.on_fwd_strand
+
+ if seg.start5.connection is None:
+ if len(list(filter( is_start_5prime, five_prime_locs ))) == 0:
+ seg.add_5prime(0) # TODO ensure this is the same place
+
+ if 'end5' in seg.__dict__ and seg.end5.connection is None:
+ if len(list(filter( is_end_5prime, five_prime_locs ))) == 0:
+ seg.add_5prime(seg.num_nt-1,on_fwd_strand=False)
+
+ if 'start3' in seg.__dict__ and seg.start3.connection is None:
+ if len(list(filter( is_start_3prime, three_prime_locs ))) == 0:
+ seg.add_3prime(0,on_fwd_strand=False)
+
+ if seg.end3.connection is None:
+ if len(list(filter( is_end_3prime, three_prime_locs ))) == 0:
+ seg.add_3prime(seg.num_nt-1)
+
+ # print( [(l,l.get_connected_location()) for l in seg.locations] )
+ # addresses = np.array([l.address for l in seg.get_locations("5prime")])
+ # if not np.any( addresses == 0 ):
+ # ## check if end is connected
+ # for c,l,B in self.get_connections_and_locations():
+ # if c[0]
+
+ """ Build strands from connectivity of helices """
+ def _recursively_build_strand(strand, segment, pos, is_fwd, mycounter=0, move_at_least=0.5):
+ seg = segment
+ history = []
+ while True:
+ mycounter+=1
+ if mycounter > 10000:
+ raise Exception("Too many iterations")
+
+ #if seg.name == "22-1" and pos > 140:
+ # if seg.name == "22-2":
+ # import pdb
+ # pdb.set_trace()
+
+ end_pos, next_seg, next_pos, next_dir, move_at_least = seg.get_strand_segment(pos, is_fwd, move_at_least)
+ history.append((seg,pos,end_pos,is_fwd))
+ try:
+ strand.add_dna(seg, pos, end_pos, is_fwd)
+ except CircularDnaError:
+ ## Circular DNA was found
+ break
+ except:
+ print("Unexpected error:", sys.exc_info()[0])
+ # import pdb
+ # pdb.set_trace()
+ # seg.get_strand_segment(pos, is_fwd, move_at_least)
+ # strand.add_dna(seg, pos, end_pos, is_fwd)
+ raise
+
+ if next_seg is None:
+ break
+ else:
+ seg,pos,is_fwd = (next_seg, next_pos, next_dir)
+ strand.history = list(history)
+ return history
+
+ strand_counter = 0
+ history = []
+ for seg in self.segments:
+ locs = filter(lambda l: l.connection is None, seg.get_5prime_locations())
+ if locs is None: continue
+ # for pos, is_fwd in locs:
+ for l in locs:
+ # print("Tracing",l)
+ # TODOTODO
+ pos = seg.contour_to_nt_pos(l.address, round_nt=True)
+ is_fwd = l.on_fwd_strand
+ s = Strand(segname="S{:03d}".format(len(strands)))
+ strand_history = _recursively_build_strand(s, seg, pos, is_fwd)
+ history.append((l,strand_history))
+ # print("{} {}".format(seg.name,s.num_nt))
+ strands.append(s)
+
+ ## Trace circular DNA
+ def strands_cover_segment(segment, is_fwd=True):
+ direction = 'fwd' if is_fwd else 'rev'
+ nt = 0
+ for sp in segment.strand_pieces[direction]:
+ nt += sp.num_nt
+ return nt == segment.num_nt
+
+ def find_nt_not_in_strand(segment, is_fwd=True):
+ fwd_str = 'fwd' if is_fwd else 'rev'
+
+ def check(val):
+ assert(val >= 0 and val < segment.num_nt)
+ # print("find_nt_not_in_strand({},{}) returning {}".format(
+ # segment, is_fwd, val))
+ return val
+
+ if is_fwd:
+ last = -1
+ for sp in segment.strand_pieces[fwd_str]:
+ if sp.start-last > 1:
+ return check(last+1)
+ last = sp.end
+ return check(last+1)
+ else:
+ last = segment.num_nt
+ for sp in segment.strand_pieces[fwd_str]:
+ if last-sp.end > 1:
+ return check(last-1)
+ last = sp.start
+ return check(last-1)
+
+ def add_strand_if_needed(seg,is_fwd):
+ history = []
+ if not strands_cover_segment(seg, is_fwd):
+ pos = nt = find_nt_not_in_strand(seg, is_fwd)
+ s = Strand(is_circular = True)
+ history = _recursively_build_strand(s, seg, pos, is_fwd)
+ strands.append(s)
+ return history
+
+ for seg in self.segments:
+ add_strand_if_needed(seg,True)
+ if isinstance(seg, DoubleStrandedSegment):
+ add_strand_if_needed(seg,False)
+
+ self.strands = sorted(strands, key=lambda s:s.num_nt)[::-1]
+ def check_strands():
+ dsdna = filter(lambda s: isinstance(s,DoubleStrandedSegment), self.segments)
+ for s in dsdna:
+ nt_fwd = nt_rev = 0
+ for sp in s.strand_pieces['fwd']:
+ nt_fwd += sp.num_nt
+ for sp in s.strand_pieces['rev']:
+ nt_rev += sp.num_nt
+ assert( nt_fwd == s.num_nt and nt_rev == s.num_nt )
+ # print("{}: {},{} (fwd,rev)".format(s.name, nt_fwd/s.num_nt,nt_rev/s.num_nt))
+ check_strands()
+
+ ## relabel segname
+ counter = 0
+ for s in self.strands:
+ if s.segname is None:
+ s.segname = "D%03d" % counter
+ counter += 1
+
+ def _assign_basepairs(self):
+ ## Assign basepairs
+ for seg in self.segments:
+ if isinstance(seg, DoubleStrandedSegment):
+ strands1 = seg.strand_pieces['fwd'] # already sorted
+ strands2 = seg.strand_pieces['rev']
+
+ nts1 = [nt for s in strands1 for nt in s.children]
+ nts2 = [nt for s in strands2 for nt in s.children[::-1]]
+ assert(len(nts1) == len(nts2))
+ for nt1,nt2 in zip(nts1,nts2):
+ ## TODO weakref
+ nt1.basepair = nt2
+ nt2.basepair = nt1
+
+ def _update_orientations(self,orientation):
+ for s in self.strands:
+ s.update_atomic_orientations(orientation)
+
+ def write_atomic_ENM(self, output_name, lattice_type=None):
+ ## TODO: ensure atomic model was generated already
+ if lattice_type is None:
+ try:
+ lattice_type = self.lattice_type
+ except:
+ lattice_type = "square"
+ else:
+ try:
+ if lattice_type != self.lattice_type:
+ print("WARNING: printing ENM with a lattice type ({}) that differs from model's lattice type ({})".format(lattice_type,self.lattice_type))
+ except:
+ pass
+
+ if lattice_type == "square":
+ enmTemplate = enmTemplateSQ
+ elif lattice_type == "honeycomb":
+ enmTemplate = enmTemplateHC
+ else:
+ raise Exception("Lattice type '%s' not supported" % self.latticeType)
+
+ ## TODO: allow ENM to be created without first building atomic model
+ noStackPrime = 0
+ noBasepair = 0
+ with open("%s.exb" % output_name,'w') as fh:
+ # natoms=0
+
+ for seg in self.segments:
+ ## Continue unless dsDNA
+ if not isinstance(seg,DoubleStrandedSegment): continue
+ for strand_piece in seg.strand_pieces['fwd'] + seg.strand_pieces['rev']:
+ for nt1 in strand_piece.children:
+ other = []
+ nt2 = nt1.basepair
+ if strand_piece.is_fwd:
+ other.append((nt2,'pair'))
+
+ nt2 = nt2.get_intrahelical_above()
+ if nt2 is not None and strand_piece.is_fwd:
+ ## TODO: check if this already exists
+ other.append((nt2,'paircross'))
+
+ nt2 = nt1.get_intrahelical_above()
+ if nt2 is not None:
+ other.append((nt2,'stack'))
+ nt2 = nt2.basepair
+ if nt2 is not None and strand_piece.is_fwd:
+ other.append((nt2,'cross'))
+
+ for nt2,key in other:
+ """
+ if np.linalg.norm(nt2.position-nt1.position) > 7:
+ import pdb
+ pdb.set_trace()
+ """
+ key = ','.join((key,nt1.sequence[0],nt2.sequence[0]))
+ for n1, n2, d in enmTemplate[key]:
+ d = float(d)
+ k = 0.1
+ if lattice_type == 'honeycomb':
+ correctionKey = ','.join((key,n1,n2))
+ assert(correctionKey in enmCorrectionsHC)
+ dk,dr = enmCorrectionsHC[correctionKey]
+ k = float(dk)
+ d += float(dr)
+
+ i = nt1._get_atomic_index(name=n1)
+ j = nt2._get_atomic_index(name=n2)
+ fh.write("bond %d %d %f %.2f\n" % (i,j,k,d))
+
+ # print("NO STACKS found for:", noStackPrime)
+ # print("NO BASEPAIRS found for:", noBasepair)
+
+ ## Loop dsDNA regions
+ push_bonds = []
+ processed_segs = set()
+ ## TODO possibly merge some of this code with SegmentModel.get_consecutive_crossovers()
+ for segI in self.segments: # TODOTODO: generalize through some abstract intrahelical interface that effectively joins "segments", for now interhelical bonds that cross intrahelically-connected segments are ignored
+ if not isinstance(segI,DoubleStrandedSegment): continue
+
+ ## Loop over dsDNA regions connected by crossovers
+ conn_locs = segI.get_contour_sorted_connections_and_locations("crossover")
+ other_segs = list(set([B.container for c,A,B in conn_locs]))
+ for segJ in other_segs:
+ if (segI,segJ) in processed_segs:
+ continue
+ processed_segs.add((segI,segJ))
+ processed_segs.add((segJ,segI))
+
+ ## TODO perhaps handle ends that are not between crossovers
+
+ ## Loop over ordered pairs of crossovers between the two
+ cls = filter(lambda x: x[-1].container == segJ, conn_locs)
+ cls = sorted( cls, key=lambda x: x[1].get_nt_pos() )
+ for cl1,cl2 in zip(cls[:-1],cls[1:]):
+ c1,A1,B1 = cl1
+ c2,A2,B2 = cl2
+
+ ntsI1,ntsI2 = [segI.contour_to_nt_pos(A.address) for A in (A1,A2)]
+ ntsJ1,ntsJ2 = [segJ.contour_to_nt_pos(B.address) for B in (B1,B2)]
+ ntsI = ntsI2-ntsI1+1
+ ntsJ = ntsJ2-ntsJ1+1
+ assert( np.isclose( ntsI, int(round(ntsI)) ) )
+ assert( np.isclose( ntsJ, int(round(ntsJ)) ) )
+ ntsI,ntsJ = [int(round(i)) for i in (ntsI,ntsJ)]
+
+ ## Find if dsDNA "segments" are pointing in same direction
+ ## could move this block out of the loop
+ tangentA = segI.contour_to_tangent(A1.address)
+ tangentB = segJ.contour_to_tangent(B1.address)
+ dot1 = tangentA.dot(tangentB)
+ tangentA = segI.contour_to_tangent(A2.address)
+ tangentB = segJ.contour_to_tangent(B2.address)
+ dot2 = tangentA.dot(tangentB)
+
+ if dot1 > 0.5 and dot2 > 0.5:
+ ...
+ elif dot1 < -0.5 and dot2 < -0.5:
+ ## TODO, reverse
+ ...
+ # print("Warning: {} and {} are on antiparallel helices (not yet implemented)... skipping".format(A1,B1))
+ continue
+ else:
+ # print("Warning: {} and {} are on helices that do not point in similar direction... skipping".format(A1,B1))
+ continue
+
+ ## Go through each nucleotide between the two
+ for ijmin in range(min(ntsI,ntsJ)):
+ i=j=ijmin
+ if ntsI < ntsJ:
+ j = int(round(float(ntsJ*i)/ntsI))
+ elif ntsJ < ntsI:
+ i = int(round(float(ntsI*j)/ntsJ))
+ ntI_idx = int(round(ntsI1+i))
+ ntJ_idx = int(round(ntsJ1+j))
+
+ ## Skip nucleotides that are too close to crossovers
+ if i < 11 or j < 11: continue
+ if ntsI2-ntI_idx < 11 or ntsJ2-ntJ_idx < 11: continue
+
+ ## Find phosphates at ntI/ntJ
+ for direction in [True,False]:
+ try:
+ i = segI._get_atomic_nucleotide(ntI_idx, direction)._get_atomic_index(name="P")
+ j = segJ._get_atomic_nucleotide(ntJ_idx, direction)._get_atomic_index(name="P")
+ push_bonds.append((i,j))
+ except:
+ # print("WARNING: could not find 'P' atom in {}:{} or {}:{}".format( segI, ntI_idx, segJ, ntJ_idx ))
+ ...
+
+ # print("PUSH BONDS:", len(push_bonds))
+
+ if not self.useTclForces:
+ with open("%s.exb" % output_name, 'a') as fh:
+ for i,j in push_bonds:
+ fh.write("bond %d %d %f %.2f\n" % (i,j,1.0,31))
+ else:
+ flat_push_bonds = list(sum(push_bonds))
+ atomList = list(set( flat_push_bonds ))
+ with open("%s.forces.tcl" % output_name,'w') as fh:
+ fh.write("set atomList {%s}\n\n" %
+ " ".join([str(x-1) for x in atomList]) )
+ fh.write("set bonds {%s}\n" %
+ " ".join([str(x-1) for x in flat_push_bonds]) )
+ fh.write("""
+foreach atom $atomList {
+ addatom $atom
+}
+
+proc calcforces {} {
+ global atomList bonds
+ loadcoords rv
+
+ foreach i $atomList {
+ set force($i) {0 0 0}
+ }
+
+ foreach {i j} $bonds {
+ set rvec [vecsub $rv($j) $rv($i)]
+ # lassign $rvec x y z
+ # set r [expr {sqrt($x*$x+$y*$y+$z*$z)}]
+ set r [getbond $rv($j) $rv($i)]
+ set f [expr {2*($r-31.0)/$r}]
+ vecadd $force($i) [vecscale $f $rvec]
+ vecadd $force($j) [vecscale [expr {-1.0*$f}] $rvec]
+ }
+
+ foreach i $atomList {
+ addforce $i $force($i)
+ }
+
+}
+""")
+
+ def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
+ positions = []
+ for s in self.segments:
+ positions.append(s.contour_to_position(0))
+ positions.append(s.contour_to_position(0.5))
+ positions.append(s.contour_to_position(1))
+ positions = np.array(positions)
+ dx,dy,dz = [(np.max(positions[:,i])-np.min(positions[:,i])+30)*padding_factor for i in range(3)]
+ if isotropic:
+ dx = dy = dz = max((dx,dy,dz))
+ return [dx,dy,dz]
+
+ def add_grid_potential(self, grid_file, scale=1, per_nucleotide=True):
+ grid_file = Path(grid_file)
+ if not grid_file.is_file():
+ raise ValueError("Grid file {} does not exist".format(grid_file))
+ if not grid_file.is_absolute():
+ grid_file = Path.cwd() / grid_file
+ self.grid_potentials.append((grid_file,scale,per_nucleotide))
+
+ def _apply_grid_potentials_to_beads(self, bead_type_dict):
+ if len(self.grid_potentials) > 1:
+ raise NotImplementedError("Multiple grid potentials are not yet supported")
+
+ for grid_file, scale, per_nucleotide in self.grid_potentials:
+ for key,particle_type in bead_type_dict.items():
+ if particle_type.name[0] == "O": continue
+ s = scale*particle_type.nts if per_nucleotide else scale
+ try:
+ particle_type.grid = particle_type.grid + (grid_file, s)
+ except:
+ particle_type.grid = tuple((grid_file, s))
+
+ def _generate_atomic_model(self, scale=1):
+ ## TODO: deprecate
+ self.generate_atomic_model(scale=scale)
+
+ def generate_atomic_model(self, scale=1):
+ self.clear_beads()
+ self.children = self.strands # TODO: is this going to be okay? probably
+ first_atomic_index = 0
+ for s in self.strands:
+ first_atomic_index = s.generate_atomic_model(scale,first_atomic_index)
+ self._assign_basepairs()
+ return
+
+ ## Angle optimization
+ angles = np.linspace(-180,180,180)
+ score = []
+ for a in angles:
+ o = rotationAboutAxis([0,0,1], a)
+ sum2 = count = 0
+ for s in self.strands:
+ s.update_atomic_orientations(o)
+ for s1,s2 in zip(s.strand_segments[:-1],s.strand_segments[1:]):
+ nt1 = s1.children[-1]
+ nt2 = s2.children[0]
+ o3 = nt1.atoms_by_name["O3'"]
+ p = nt2.atoms_by_name["P"]
+ sum2 += np.sum((p.collapsedPosition()-o3.collapsedPosition())**2)
+ count += 1
+ score.append(sum2/count)
+ print(angles[np.argmin(score)])
+ print(score)
+
+ def vmd_tube_tcl(self, file_name="drawTubes.tcl"):
+ with open(file_name, 'w') as tclFile:
+ tclFile.write("## beginning TCL script \n")
+
+ def draw_tube(segment,radius_value=10, color="cyan", resolution=5):
+ tclFile.write("## Tube being drawn... \n")
+
+ contours = np.linspace(0,1, max(2,1+segment.num_nt//resolution) )
+ rs = [segment.contour_to_position(c) for c in contours]
+
+ radius_value = str(radius_value)
+ tclFile.write("graphics top color {} \n".format(str(color)))
+ for i in range(len(rs)-2):
+ r0 = rs[i]
+ r1 = rs[i+1]
+ filled = "yes" if i in (0,len(rs)-2) else "no"
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled {} \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value), filled))
+ tclFile.write("graphics top sphere {{ {} {} {} }} radius {} resolution 30\n".format(r1[0], r1[1], r1[2], str(radius_value)))
+ r0 = rs[-2]
+ r0 = rs[-1]
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value)))
+
+ ## material
+ tclFile.write("graphics top materials on \n")
+ tclFile.write("graphics top material AOEdgy \n")
+
+ ## iterate through the model segments
+ for s in self.segments:
+ if isinstance(s,DoubleStrandedSegment):
+ tclFile.write("## dsDNA! \n")
+ draw_tube(s,10,"cyan")
+ elif isinstance(s,SingleStrandedSegment):
+ tclFile.write("## ssDNA! \n")
+ draw_tube(s,3,"orange",resolution=1.5)
+ else:
+ raise Exception ("your model includes beads that are neither ssDNA nor dsDNA")
+ ## tclFile complete
+ tclFile.close()
+
+ def vmd_cylinder_tcl(self, file_name="drawCylinders.tcl"):
+ #raise NotImplementedError
+ with open(file_name, 'w') as tclFile:
+ tclFile.write("## beginning TCL script \n")
+ def draw_cylinder(segment,radius_value=10,color="cyan"):
+ tclFile.write("## cylinder being drawn... \n")
+ r0 = segment.contour_to_position(0)
+ r1 = segment.contour_to_position(1)
+
+ radius_value = str(radius_value)
+ color = str(color)
+
+ tclFile.write("graphics top color {} \n".format(color))
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], radius_value))
+
+ ## material
+ tclFile.write("graphics top materials on \n")
+ tclFile.write("graphics top material AOEdgy \n")
+
+ ## iterate through the model segments
+ for s in self.segments:
+ if isinstance(s,DoubleStrandedSegment):
+ tclFile.write("## dsDNA! \n")
+ draw_cylinder(s,10,"cyan")
+ elif isinstance(s,SingleStrandedSegment):
+ tclFile.write("## ssDNA! \n")
+ draw_cylinder(s,3,"orange")
+ else:
+ raise Exception ("your model includes beads that are neither ssDNA nor dsDNA")
+ ## tclFile complete
+ tclFile.close()
diff --git a/mrdna/arbdmodel/ssdna_two_bead.py b/mrdna/arbdmodel/ssdna_two_bead.py
new file mode 100644
index 0000000000000000000000000000000000000000..40fb40e5537ac389048f6b81e72468b7b5987ffd
--- /dev/null
+++ b/mrdna/arbdmodel/ssdna_two_bead.py
@@ -0,0 +1,200 @@
+# -*- coding: utf-8 -*-
+import numpy as np
+import sys
+
+## Local imports
+from . import ArbdModel, ParticleType, PointParticle, Group, get_resource_path
+from .abstract_polymer import PolymerSection, AbstractPolymerGroup
+from .interactions import TabulatedPotential, HarmonicBond, HarmonicAngle, HarmonicDihedral
+from .coords import quaternion_to_matrix
+
+"""Define particle types"""
+
+## units "295 k K/(160 amu * 1.24/ps)" "AA**2/ns"
+## units "295 k K/(180 amu * 1.24/ps)" "AA**2/ns"
+_P = ParticleType("P",
+ diffusivity = 1621,
+ mass = 121,
+ radius = 5,
+ nts = 0.5 # made compatible with nbPot
+)
+
+_B = ParticleType("B",
+ diffusivity = 1093,
+ mass = 181, # thymine
+ radius = 3,
+ nts = 0.5 # made compatible with nbPot
+)
+
+class DnaStrandFromPolymer(Group):
+ p = PointParticle(_P, (0,0,0), "P")
+ b = PointParticle(_B, (3,0,1), "B")
+ nt = Group( name = "nt", children = [p,b])
+ nt.add_bond( i=p, j=b, bond = get_resource_path('two_bead_model/BPB.dat'), exclude = True )
+
+ def __init__(self, polymer, **kwargs):
+ self.polymer = polymer
+ Group.__init__(self, **kwargs)
+
+ def _clear_beads(self):
+ ...
+
+ def _generate_beads(self):
+ nts = self.nts = self.children
+
+ for i in range(self.polymer.num_monomers):
+ c = self.polymer.monomer_index_to_contour(i)
+ r = self.polymer.contour_to_position(c)
+ o = self.polymer.contour_to_orientation(c)
+
+ new = DnaStrandFromPolymer.nt.duplicate()
+ new.orientation = o
+ new.position = r
+ self.add(new)
+
+ ## Two consecutive nts
+ for i in range(len(nts)-1):
+ p1,b1 = nts[i].children
+ p2,b2 = nts[i+1].children
+ self.add_bond( i=b1, j=p2, bond = get_resource_path('two_bead_model/BBP.dat'), exclude=True )
+ self.add_bond( i=p1, j=p2, bond = get_resource_path('two_bead_model/BPP.dat'), exclude=True )
+ self.add_angle( i=p1, j=p2, k=b2, angle = get_resource_path('two_bead_model/p1p2b2.dat') )
+ self.add_angle( i=b1, j=p2, k=b2, angle = get_resource_path('two_bead_model/b1p2b2.dat') )
+ self.add_dihedral( i=b1, j=p1, k=p2, l=b2, dihedral = get_resource_path('two_bead_model/b1p1p2b2.dat') )
+ self.add_exclusion( i=b1, j=b2 )
+ self.add_exclusion( i=p1, j=b2 )
+
+ ## Three consecutive nts
+ for i in range(len(nts)-2):
+ p1,b1 = nts[i].children
+ p2,b2 = nts[i+1].children
+ p3,b3 = nts[i+2].children
+ self.add_angle( i=p1, j=p2, k=p3, angle = get_resource_path('two_bead_model/p1p2p3.dat') )
+ self.add_angle( i=b1, j=p2, k=p3, angle = get_resource_path('two_bead_model/b1p2p3.dat') )
+ self.add_dihedral( i=b1, j=p2, k=p3, l=b3, dihedral = get_resource_path('two_bead_model/b1p2p3b3.dat') )
+ self.add_exclusion( i=p1, j=p3 )
+ self.add_exclusion( i=b1, j=p3 )
+
+ ## Four consecutive nts
+ for i in range(len(nts)-3):
+ p1,b1 = nts[i].children
+ p2,b2 = nts[i+1].children
+ p3,b3 = nts[i+2].children
+ p4,b4 = nts[i+3].children
+ self.add_dihedral( i=p1, j=p2, k=p3, l=p4, dihedral = get_resource_path('two_bead_model/p0p1p2p3.dat') )
+
+# def hybridize(strand1, strand2, parent=None, num_bp=None, start1=None, end2=None):
+
+# """ hybridize num_bp basepairs between strand1 and strand2,
+# starting with nt at start1 and ending with nucleotide and end2 """
+
+# num_nt1 = len(strand1.children)
+# num_nt2 = len(strand2.children)
+
+# if parent is None:
+# assert(strand1.parent == strand2.parent)
+# parent = strand1.parent
+
+# if start1 is None:
+# start1 = 0
+# if end2 is None:
+# end2 = num_nt2
+
+# assert(start1 >= 0)
+# assert(end2 > 0)
+# assert(start1 < num_nt1)
+# assert(end2 <= num_nt2)
+
+# if num_bp is None:
+# num_bp = min(num_nt1-start1, end2)
+
+# if num_bp > num_nt1-start1:
+# raise ValueError("Attempted to hybridize too many basepairs ({}) for strand1 ({})".format(num_bp,num_nt1-start1))
+# if num_bp > end2:
+# raise ValueError("Attempted to hybridize too many basepairs ({}) for strand1 ({})".format(num_bp,end2))
+
+# nts1 = strand1.children[start1:start1+num_bp]
+# nts2 = strand2.children[end2-num_bp:end2][::-1]
+# assert( len(nts1) == len(nts2) )
+
+# kAngle = 0.0274155 # 90 kcal_mol per radian**2
+
+# ## every bp
+# for i in range(num_bp):
+# p11,b11 = nts1[i].children
+# p21,b21 = nts2[i].children
+# parent.add_bond( i=b11, j=b21, bond=HarmonicBond(10,7.835) )
+# parent.add_angle( i=p11, j=b11, k=b21, angle=HarmonicAngle(kAngle,162.0) )
+# parent.add_angle( i=p21, j=b21, k=b11, angle=HarmonicAngle(kAngle,162.0) )
+
+# ## every 2 bp
+# for i in range(num_bp-1):
+# p11,b11 = nts1[i].children
+# p12,b12 = nts1[i+1].children
+# p21,b21 = nts2[i].children
+# p22,b22 = nts2[i+1].children
+
+# parent.add_bond( i=b11, j=b22, bond=HarmonicBond(1,8.41) )
+# parent.add_bond( i=b12, j=b21, bond=HarmonicBond(1,7.96) )
+# parent.add_angle( i=p11, j=p12, k=b12, angle=HarmonicAngle(kAngle,87.0) )
+# parent.add_angle( i=p22, j=p21, k=b11, angle=HarmonicAngle(kAngle,87.0) )
+
+# ## every 3 bp
+# for i in range(num_bp-2):
+# p11,b11 = nts1[i].children
+# p12,b12 = nts1[i+1].children
+# p13,b13 = nts1[i+2].children
+# p21,b21 = nts2[i].children
+# p22,b22 = nts2[i+1].children
+# p23,b23 = nts2[i+2].children
+
+# parent.add_angle( i=p11, j=p12, k=p13, angle=HarmonicAngle(kAngle,150.0) )
+# parent.add_angle( i=p21, j=p22, k=p23, angle=HarmonicAngle(kAngle,150.0) )
+
+class DnaModel(ArbdModel):
+ def __init__(self, polymers,
+ DEBUG=False,
+ **kwargs):
+
+ kwargs['timestep'] = 20e-6
+ kwargs['cutoff'] = 35
+
+ self.polymer_group = AbstractPolymerGroup(polymers)
+ self.strands = [DnaStrandFromPolymer(p) for p in self.polymer_group.polymers]
+
+ ArbdModel.__init__(self, self.strands, **kwargs)
+
+ self.useNonbondedScheme( TabulatedPotential(get_resource_path('two_bead_model/NBBB.dat')), typeA=_B, typeB=_B )
+ self.useNonbondedScheme( TabulatedPotential(get_resource_path('two_bead_model/NBPB.dat')), typeA=_P, typeB=_B )
+ self.useNonbondedScheme( TabulatedPotential(get_resource_path('two_bead_model/NBPP.dat')), typeA=_P, typeB=_P )
+
+ self.generate_beads()
+
+ def generate_beads(self):
+ for s in self.strands:
+ s._generate_beads()
+
+
+
+if __name__ == "__main__":
+ strands = []
+ for i in range(5,60,5):
+
+ strands.extend( [strand.duplicate() for j in range(int(round(600/i**1.2)))] )
+
+ ## Randomly place strands through system
+ model = ArbdModel( strands, dimensions=(200, 200, 200) )
+
+ old_schemes = model.nbSchemes
+ model.nbSchemes = []
+ model.useNonbondedScheme( TabulatedPotential(get_resource_path('two_bead_model/NBBB.dat')), typeA=B, typeB=B )
+ model.useNonbondedScheme( TabulatedPotential(get_resource_path('two_bead_model/NBPB.dat')), typeA=P, typeB=B )
+ model.useNonbondedScheme( TabulatedPotential(get_resource_path('two_bead_model/NBPP.dat')), typeA=P, typeB=P )
+ model.nbSchemes.extend(old_schemes)
+
+ for s in strands:
+ s.orientation = randomOrientation()
+ s.position = np.array( [(a-0.5)*b for a,b in
+ zip( np.random.uniform(size=3), model.dimensions )] )
+
+ model.simulate( output_name = 'many-strands', output_period=1e4, num_steps=1e6 )
diff --git a/mrdna/arbdmodel/version.py b/mrdna/arbdmodel/version.py
new file mode 100644
index 0000000000000000000000000000000000000000..4a416a5aee20abe72870b8e585b402974d223eea
--- /dev/null
+++ b/mrdna/arbdmodel/version.py
@@ -0,0 +1,150 @@
+# -*- coding: utf-8 -*-
+# Author: Douglas Creager <dcreager@dcreager.net>
+# This file is placed into the public domain.
+
+# Calculates the current version number. If possible, this is the
+# output of “git describeâ€, modified to conform to the versioning
+# scheme that setuptools uses. If “git describe†returns an error
+# (most likely because we're in an unpacked copy of a release tarball,
+# rather than in a git working copy), then we fall back on reading the
+# contents of the RELEASE-VERSION file.
+#
+# To use this script, simply import it your setup.py file, and use the
+# results of get_git_version() as your package version:
+#
+# from version import *
+#
+# setup(
+# version=get_git_version(),
+# .
+# .
+# .
+# )
+#
+#
+# This will automatically update the RELEASE-VERSION file, if
+# necessary. Note that the RELEASE-VERSION file should *not* be
+# checked into git; please add it to your top-level .gitignore file.
+#
+# You'll probably want to distribute the RELEASE-VERSION file in your
+# sdist tarballs; to do this, just create a MANIFEST.in file that
+# contains the following line:
+#
+# include RELEASE-VERSION
+
+__all__ = ("get_version")
+
+from pathlib import Path
+import subprocess
+from subprocess import Popen, PIPE
+
+_version_file = Path(__file__).parent / "RELEASE-VERSION"
+
+
+def check_git_repository():
+ try:
+ remotes = subprocess.check_output(['git', 'remote', '-v'], stderr=subprocess.STDOUT)
+ return b'arbdmodel.git' in remotes
+ except:
+ return False
+
+def call_git_describe(abbrev):
+ try:
+ p = Popen(['git', 'describe', '--tags', '--abbrev=%d' % abbrev],
+ stdout=PIPE, stderr=PIPE)
+ p.stderr.close()
+ line = p.stdout.readlines()[0]
+ return line.strip().decode('utf-8')
+
+ except:
+ return None
+
+
+def is_dirty():
+ try:
+ p = Popen(["git", "diff-index", "--name-only", "HEAD"],
+ stdout=PIPE, stderr=PIPE)
+ p.stderr.close()
+ lines = p.stdout.readlines()
+ return len(lines) > 0
+ except:
+ return False
+
+
+def read_release_version():
+ try:
+ f = open(_version_file, "r")
+
+ try:
+ version = f.readlines()[0]
+ return version.strip()
+
+ finally:
+ f.close()
+
+ except:
+ return None
+
+
+def write_release_version(version):
+ f = open(_version_file, "w")
+ f.write("%s\n" % version)
+ f.close()
+
+def get_version(abbrev=7):
+ # Read in the version that's currently in RELEASE-VERSION.
+
+
+ release_version = read_release_version()
+
+ if not check_git_repository():
+ return release_version
+ # raise Exception(__function__ +" called from outside a version controlled source repository")
+
+
+ # First try to get the current version using “git describeâ€.
+
+ split_version = call_git_describe(abbrev).split("-")
+ version = split_version[0]
+ if len(split_version) > 1 and int(split_version[-2]) > 0:
+ version += ".dev{}".format(int(split_version[-2]))
+
+
+ # If that doesn't work, fall back on the value that's in
+ # RELEASE-VERSION.
+
+ if version is None:
+ version = release_version
+
+ # If we still don't have anything, that's an error.
+
+ if version is None:
+ raise ValueError("Cannot find the version number!")
+
+ # If the current version is different from what's in the
+ # RELEASE-VERSION file, update the file to be current.
+
+ if version != release_version:
+ write_release_version(version)
+
+ # Finally, return the current version.
+
+ return version
+
+
+if __name__ == "__main__":
+ print( get_version() )
+
+def read_version_file(filename):
+ with open(filename) as fh:
+ version = fh.readlines()[0].strip()
+ return version
+
+
+try:
+ version = read_version_file(_version_file)
+except:
+ try:
+ version = read_version_file(_version_file)
+ except:
+ version = "Unknown"
diff --git a/mrdna/coords.py b/mrdna/coords.py
index 41628e83501c17098094fc12b7d4d4e6594ebcb6..363ab96a158c1f90b3a8590ee49947089a8fecf1 100644
--- a/mrdna/coords.py
+++ b/mrdna/coords.py
@@ -1,204 +1,4 @@
-import numpy as np
-from scipy.optimize import newton
+from .arbdmodel.coords import *
-def minimizeRmsd(coordsB, coordsA, weights=None, maxIter=100):
- ## Going through many iterations wasn't really needed
- tol = 1
- count = 0
-
- R = np.eye(3)
- comB = np.zeros([3,])
- cNext = coordsB
-
- while tol > 1e-6:
- q,cB,comA = _minimizeRmsd(cNext,coordsA, weights)
- R = R.dot(quaternion_to_matrix(q))
- assert( np.all(np.isreal( R )) )
-
- comB += cB
- cLast = cNext
- cNext = (coordsB-comB).dot(R)
-
- tol = np.sum(((cNext-cLast)**2)[:]) / np.max(np.shape(coordsB))
- if count > maxIter:
- Exception("Exceeded maxIter (%d)" % maxIter)
- count += 1
-
- print("%d iterations",count)
- return R, comB, comA
-
-
-def minimizeRmsd(coordsB, coordsA, weights=None):
- q,comA,comB = _minimizeRmsd(coordsB, coordsA, weights)
- assert( np.all(np.isreal( q )) )
- return quaternion_to_matrix(q),comA,comB
-
-
-## http://onlinelibrary.wiley.com/doi/10.1002/jcc.21439/full
-def _minimizeRmsd(coordsB, coordsA, weights=None):
- A = coordsA
- B = coordsB
-
- shapeA,shapeB = [np.shape(X) for X in (A,B)]
- for s in (shapeA,shapeB): assert( len(s) == 2 )
-
- A,B = [X.T if s[1] > s[0] else X for X,s in zip([A,B],(shapeA,shapeB))] # TODO: print warning
-
- shapeA,shapeB = [np.shape(X) for X in (A,B)]
- assert( shapeA == shapeB )
- for X,s in zip((A,B),(shapeA,shapeB)):
- assert( s[1] == 3 and s[0] >= s[1] )
-
- # if weights is None: weights = np.ones(len(A))
- if weights is None:
- comA,comB = [np.mean( X, axis=0 ) for X in (A,B)]
- else:
- assert( len(weights[:]) == len(B) )
- W = np.diag(weights)
- comA,comB = [np.sum( W.dot(X), axis=0 ) / np.sum(W) for X in (A,B)]
-
- A = np.array( A-comA )
- B = np.array( B-comB )
-
- if weights is None:
- s = A.T.dot(B)
- else:
- s = A.T.dot(W.dot(B))
-
- sxx,sxy,sxz = s[0,:]
- syx,syy,syz = s[1,:]
- szx,szy,szz = s[2,:]
-
- K = [[ sxx+syy+szz, syz-szy, szx-sxz, sxy-syx],
- [syz-szy, sxx-syy-szz, sxy+syx, sxz+szx],
- [szx-sxz, sxy+syx, -sxx+syy-szz, syz+szy],
- [sxy-syx, sxz+szx, syz+szy, -sxx-syy+szz]]
- K = np.array(K)
-
- # GA = np.trace( A.T.dot(W.dot(A)) )
- # GB = np.trace( B.T.dot(W.dot(B)) )
-
- ## Finding GA/GB can be done more quickly
- # I = np.eye(4)
- # x0 = (GA+GB)*0.5
- # vals = newtoon(lambda x: np.det(K-x*I), x0 = x0)
-
- vals, vecs = np.linalg.eig(K)
- i = np.argmax(vals)
- q = vecs[:,i]
-
- # RMSD = np.sqrt( (GA+GB-2*vals[i]) / len(A) )
- # print("CHECK:", K.dot(q)-vals[i]*q )
- return q, comB, comA
-
-def quaternion_to_matrix(q):
- assert(len(q) == 4)
-
- ## It looks like the wikipedia article I used employed a less common convention for q (see below
- ## http://en.wikipedia.org/wiki/Rotation_formalisms_in_three_dimensions#Rotation_matrix_.E2.86.94_quaternion
- # q1,q2,q3,q4 = q
- # R = [[1-2*(q2*q2 + q3*q3), 2*(q1*q2 - q3*q4), 2*(q1*q3 + q2*q4)],
- # [ 2*(q1*q2 + q3*q4), 1-2*(q1*q1 + q3*q3), 2*(q2*q3 - q1*q4)],
- # [ 2*(q1*q3 - q2*q4), 2*(q1*q4 + q2*q3), 1-2*(q2*q2 + q1*q1)]]
-
- q = q / np.linalg.norm(q)
- q0,q1,q2,q3 = q
- R = [[1-2*(q2*q2 + q3*q3), 2*(q1*q2 - q3*q0), 2*(q1*q3 + q2*q0)],
- [ 2*(q1*q2 + q3*q0), 1-2*(q1*q1 + q3*q3), 2*(q2*q3 - q1*q0)],
- [ 2*(q1*q3 - q2*q0), 2*(q1*q0 + q2*q3), 1-2*(q2*q2 + q1*q1)]]
-
- return np.array(R)
-
-def quaternion_from_matrix( R ):
- e1 = R[0]
- e2 = R[1]
- e3 = R[2]
-
- # d1 = 0.5 * np.sqrt( 1+R[0,0]+R[1,1]+R[2,2] )
- # d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
- # d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
- # d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
-
- d1 = 1+R[0,0]+R[1,1]+R[2,2]
- d2 = 1+R[0,0]-R[1,1]-R[2,2]
- d3 = 1-R[0,0]+R[1,1]-R[2,2]
- d4 = 1-R[0,0]-R[1,1]+R[2,2]
-
- maxD = max((d1,d2,d3,d4))
- d = 0.5 / np.sqrt(maxD)
-
- if d1 == maxD:
- return np.array(( 1.0/(4*d),
- d * (R[2,1]-R[1,2]),
- d * (R[0,2]-R[2,0]),
- d * (R[1,0]-R[0,1]) ))
- elif d2 == maxD:
- return np.array(( d * (R[2,1]-R[1,2]),
- 1.0/(4*d),
- d * (R[0,1]+R[1,0]),
- d * (R[0,2]+R[2,0]) ))
- elif d3 == maxD:
- return np.array(( d * (R[0,2]-R[2,0]),
- d * (R[0,1]+R[1,0]),
- 1.0/(4*d),
- d * (R[1,2]+R[2,1]) ))
- elif d4 == maxD:
- return np.array(( d * (R[1,0]-R[0,1]),
- d * (R[0,2]+R[2,0]),
- d * (R[1,2]+R[2,1]),
- 1.0/(4*d) ))
-
-def rotationAboutAxis(axis,angle, normalizeAxis=True):
- if normalizeAxis: axis = axis / np.linalg.norm(axis)
- angle = angle * 0.5 * np.pi/180
- cos = np.cos( angle )
- sin = np.sin( angle )
- q = [cos] + [sin*x for x in axis]
- return quaternion_to_matrix(q)
-
-def readArbdCoords(fname):
- coords = []
- with open(fname) as fh:
- for line in fh:
- coords.append([float(x) for x in line.split()[1:]])
- return np.array(coords)
-
-def readAvgArbdCoords(psf,pdb,dcd,rmsdThreshold=3.5):
- import MDAnalysis as mda
-
- usel = mda.Universe(psf, dcd)
- sel = usel.select_atoms("name D*")
-
- # r0 = ref.xyz[0,ids,:]
- ts = usel.trajectory[-1]
- r0 = sel.positions
- pos = []
- for t in range(ts.frame-1,-1,-1):
- usel.trajectory[t]
- R,comA,comB = minimizeRmsd(sel.positions,r0)
- r = np.array( [(r-comA).dot(R)+comB for r in sel.positions] )
- rmsd = np.mean( (r-r0)**2 )
- r = np.array( [(r-comA).dot(R)+comB for r in usel.atoms.positions] )
- pos.append( r )
- if rmsd > rmsdThreshold**2:
- break
- t0=t+1
- print( "Averaging coordinates in %s after frame %d" % (dcd, t0) )
-
- pos = np.mean(pos, axis=0)
- return pos
-
-def unit_quat_conversions():
- for axis in [[0,0,1],[1,1,1],[1,0,0],[-1,-2,0]]:
- for angle in np.linspace(-180,180,10):
- R = rotationAboutAxis(axis, angle)
- R2 = quaternion_to_matrix( quaternion_from_matrix( R ) )
- if not np.all( np.abs(R-R2) < 0.01 ):
- import pdb
- pdb.set_trace()
- quaternion_to_matrix( quaternion_from_matrix( R ) )
-
-
-if __name__ == "__main__":
- unit_quat_conversions()
-
+from sys import stderr
+stderr.write("WARNING: the module 'mrdna.coords' has been deprecated. Please change your scripts to use 'mrdna.arbdmodel.coords'\n")
diff --git a/mrdna/model/CanonicalNucleotideAtoms.py b/mrdna/model/CanonicalNucleotideAtoms.py
index fa0a2e98ca6bbe1ca19c1f84acd3858216058e52..7b2dcdce5f172e80aad27eeaa926ed9e17bf51ff 100644
--- a/mrdna/model/CanonicalNucleotideAtoms.py
+++ b/mrdna/model/CanonicalNucleotideAtoms.py
@@ -1,8 +1,8 @@
import json
import numpy as np
import copy
-from ..coords import rotationAboutAxis
-from .arbdmodel import Group, PointParticle, ParticleType
+from ..arbdmodel.coords import rotationAboutAxis
+from ..arbdmodel import Group, PointParticle, ParticleType
from .. import get_resource_path
seqComplement = dict(A='T',G='C')
diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py
index 0a358264035998e34dc0ebbd7d07fe1a7cdf11ab..8219ed633b23f07b79959f0bb812f2a772a91eaf 100644
--- a/mrdna/model/arbdmodel.py
+++ b/mrdna/model/arbdmodel.py
@@ -1,1499 +1,5 @@
-# -*- coding: utf-8 -*-
-from pathlib import Path
-import numpy as np
-from copy import copy, deepcopy
-from inspect import ismethod
+from ..arbdmodel import *
-# from datetime import datetime
-# from math import pi,sqrt,exp,floor
-# from scipy.special import erf
-# import scipy.optimize as opt
-import os, sys, subprocess
+from sys import stderr
+stderr.write("WARNING: the module 'mrdna.model.arbdmodel' has been deprecated. Please change your scripts to use 'mrdna.arbdmodel'\n")
-
-## Abstract classes
-class Transformable():
- def __init__(self, position, orientation=None):
- self.position = np.array(position)
- if orientation is not None:
- orientation = np.array(orientation)
- self.orientation = orientation
-
- def transform(self, R = ((1,0,0),(0,1,0),(0,0,1)),
- center = (0,0,0), offset = (0,0,0)):
-
- R,center,offset = [np.array(x) for x in (R,center,offset)]
-
- self.position = R.dot(self.position-center)+center+offset
-
- if self.orientation is not None:
- ## TODO: what if self.orientation is taken from parent?!
- self.orientation = self.orientation.dot(R)
- ...
-
- def collapsedPosition(self):
- # print("collapsedPosition called", type(self), self.name)
- if isinstance(self, Child):
- # print(self.parent, isinstance(self.parent,Transformable))
- if isinstance(self.parent, Transformable):
- return self.applyOrientation(self.position) + self.parent.collapsedPosition()
-
- # if self.parent.orientation is not None:
- # return self.parent.collapsedOrientation().dot(self.position) + self.parent.collapsedPosition()
- return np.array(self.position) # return a copy
-
- def applyOrientation(self,obj):
- # print("applyOrientation called", self.name, obj)
- if isinstance(self, Child):
- # print( self.orientation, self.orientation is not None, None is not None )
- # if self.orientation is not None:
- # # print("applyOrientation applying", self, self.name, self.orientation)
- # obj = self.orientation.dot(obj)
- if isinstance(self.parent, Transformable):
- if self.parent.orientation is not None:
- obj = self.parent.orientation.dot(obj)
- obj = self.parent.applyOrientation(obj)
- # print("applyOrientation returning", self.name, obj)
- return obj
-
-class Parent():
- def __init__(self, children=None, remove_duplicate_bonded_terms=False):
- self.children = []
- if children is not None:
- for x in children:
- self.add(x)
-
- self.remove_duplicate_bonded_terms = remove_duplicate_bonded_terms
- self.bonds = []
- self.angles = []
- self.dihedrals = []
- self.impropers = []
- self.exclusions = []
-
- ## TODO: self.cacheInvalid = True # What will be in the cache?
-
-
- def add(self,x):
- ## TODO: check the parent-child tree to make sure there are no cycles
- if not isinstance(x,Child):
- raise Exception('Attempted to add an object to a group that does not inherit from the "Child" type')
-
- if x.parent is not None and x.parent is not self:
- raise Exception("Child {} already belongs to some group".format(x))
- x.parent = self
- self.children.append(x)
-
- def clear_all(self, keep_children=False):
- if keep_children == False:
- for x in self.children:
- x.parent = None
- self.children = []
- self.bonds = []
- self.angles = []
- self.dihedrals = []
- self.impropers = []
- self.exclusions = []
-
- def remove(self,x):
- if x in self.children:
- self.children.remove(x)
- x.parent = None
-
- def add_bond(self, i,j, bond, exclude=False):
- assert( i is not j )
- ## TODO: how to handle duplicating and cloning bonds
- # beads = [b for b in self]
- # for b in (i,j): assert(b in beads)
- self.bonds.append( (i,j, bond, exclude) )
-
- def add_angle(self, i,j,k, angle):
- assert( len(set((i,j,k))) == 3 )
- # beads = [b for b in self]
- # for b in (i,j,k): assert(b in beads)
- self.angles.append( (i,j,k, angle) )
-
- def add_dihedral(self, i,j,k,l, dihedral):
- assert( len(set((i,j,k,l))) == 4 )
-
- # beads = [b for b in self]
- # for b in (i,j,k,l): assert(b in beads)
- self.dihedrals.append( (i,j,k,l, dihedral) )
-
- def add_improper(self, i,j,k,l, dihedral):
- # beads = [b for b in self]
- # for b in (i,j,k,l): assert(b in beads)
- self.impropers.append( (i,j,k,l, dihedral) )
-
- def add_exclusion(self, i,j):
- ## TODO: how to handle duplicating and cloning bonds
- ## TODO: perform following check elsewhere
- # beads = [b for b in self]
- # for b in (i,j): assert(b in beads)
- self.exclusions.append( (i,j) )
-
- def get_restraints(self):
- ret = []
- for c in self.children:
- ret.extend( c.get_restraints() )
- return ret
-
- def get_bonds(self):
- ret = self.bonds
- for c in self.children:
- if isinstance(c,Parent): ret.extend( c.get_bonds() )
- if self.remove_duplicate_bonded_terms:
- return list(set(ret))
- else:
- return ret
-
-
- def get_angles(self):
- ret = self.angles
- for c in self.children:
- if isinstance(c,Parent): ret.extend( c.get_angles() )
- if self.remove_duplicate_bonded_terms:
- return list(set(ret))
- else:
- return ret
-
- def get_dihedrals(self):
- ret = self.dihedrals
- for c in self.children:
- if isinstance(c,Parent): ret.extend( c.get_dihedrals() )
- if self.remove_duplicate_bonded_terms:
- return list(set(ret))
- else:
- return ret
-
- def get_impropers(self):
- ret = self.impropers
- for c in self.children:
- if isinstance(c,Parent): ret.extend( c.get_impropers() )
- if self.remove_duplicate_bonded_terms:
- return list(set(ret))
- else:
- return ret
-
- def get_exclusions(self):
- ret = self.exclusions
- for c in self.children:
- if isinstance(c,Parent): ret.extend( c.get_exclusions() )
- if self.remove_duplicate_bonded_terms:
- return list(set(ret))
- else:
- return ret
-
- ## Removed because prohibitively slow
- # def remove_duplicate_terms(self):
- # for key in "bonds angles dihedrals impropers exclusions".split():
- # self.remove_duplicate_item(key)
-
- # def remove_duplicate_item(self, dict_key, existing=None):
- # if existing is None: existing = []
- # ret = [i for i in list(set(self.__dict__[dict_key])) if i not in existing]
- # self.__dict__[dict_key] = ret
- # existing.extend(ret)
- # for c in self.children:
- # if isinstance(c,Parent):
- # ret = ret + c.remove_duplicate_item(dict_key, existing)
- # return ret
-
-
- def __iter__(self):
- ## TODO: decide if this is the nicest way to do it!
- """Depth-first iteration through tree"""
- for x in self.children:
- if isinstance(x,Parent):
- if isinstance(x,Clone) and not isinstance(x.get_original_recursively(),Parent):
- yield x
- else:
- for y in x:
- yield y
- else:
- yield x
-
- def __len__(self):
- l = 0
- for x in self.children:
- if isinstance(x,Parent):
- l += len(x)
- else:
- l += 1
- return l
-
- def __getitem__(self, i):
- return self.children[i]
-
- def __setitem__(self, i, val):
- x = self.children[i]
- x.parent = None
- val.parent = self
- self.children[i] = val
-
-class Child():
- def __init__(self, parent=None):
- self.parent = parent
- if parent is not None:
- assert( isinstance(parent, Parent) )
- parent.children.append(self)
-
- def __getattr__(self, name):
- """
- Try to get attribute from the parent
- """
- # if self.parent is not None:
- if "parent" not in self.__dict__ or self.__dict__["parent"] is None or name is "children":
- raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
-
- ## TODO: determine if there is a way to avoid __getattr__ if a method is being looked up
- try:
- ret = getattr(self.parent,name)
- except:
- raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
- if ismethod(ret):
- raise AttributeError("'{}' object has no method '{}'".format(type(self).__name__, name))
- return ret
-
-
- # def __getstate__(self):
- # print("Child getstate called", self)
- # print(self.__dict__)
- # return (self.__dict__,)
-
- # def __setstate__(self, state):
- # self.__dict__, = state
-
-class Clone(Transformable, Parent, Child):
- def __init__(self, original, parent=None,
- position = None,
- orientation = None):
- if position is None and original.position is not None:
- position = np.array( original.position )
- if orientation is None and original.orientation is not None:
- orientation = np.array( original.orientation )
- if parent is None:
- parent = original.parent
- self.original = original
- Child.__init__(self, parent)
- Transformable.__init__(self, position, orientation)
-
- ## TODO: keep own bond_list, etc, update when needed original changes
-
- if "children" in original.__dict__ and len(original.children) > 0:
- self.children = [Clone(c, parent = self) for c in original.children]
- else:
- self.children = []
-
- def get_original_recursively(self):
- if isinstance(self.original, Clone):
- return self.original.get_original_recursively()
- else:
- return self.original
-
- def __getattr__(self, name):
- """
- Try to get attribute from the original without descending the tree heirarchy, then look up parent
-
- TODO: handle PointParticle lookups into ParticleType
- """
- # print("Clone getattr",name)
- if name in self.original.__dict__:
- return self.original.__dict__[name]
- else:
- if "parent" not in self.__dict__ or self.__dict__["parent"] is None:
- raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
- return getattr(self.parent, name)
-
-
-## Particle classes
-class ParticleType():
- """Class that hold common attributes that particles can point to"""
-
- excludedAttributes = ("idx","type_",
- "position",
- "children",
- "parent", "excludedAttributes",
- )
-
- def __init__(self, name, charge=0, **kargs):
- # parent = None
- # if "parent" in kargs: parent = kargs["parent"]
- # Child.__init__(self, parent)
-
- self.name = name
- self.charge = charge
- for key in ParticleType.excludedAttributes:
- assert( key not in kargs )
-
- for key,val in kargs.items():
- self.__dict__[key] = val
-
- def __hash_key(self):
- l = [self.name,self.charge]
- for keyval in sorted(self.__dict__.items()):
- if isinstance(keyval[1], list): keyval = (keyval[0],tuple(keyval[1]))
- l.extend(keyval)
- return tuple(l)
-
- def __hash__(self):
- return hash(self.__hash_key())
-
- def _equal_check(a,b):
- if a.name == b.name:
- if a.__hash_key() != b.__hash_key():
- raise Exception("Two different ParticleTypes have same 'name' attribute")
-
- def __eq__(a,b):
- a._equal_check(b)
- return a.name == b.name
- def __lt__(a,b):
- a._equal_check(b)
- return a.name < b.name
- def __le__(a,b):
- a._equal_check(b)
- return a.name <= b.name
- def __gt__(a,b):
- a._equal_check(b)
- return a.name > b.name
- def __ge__(a,b):
- a._equal_check(b)
- return a.name >= b.name
-
-
-class PointParticle(Transformable, Child):
- def __init__(self, type_, position, name="A", **kwargs):
- parent = None
- if 'parent' in kwargs:
- parent = kwargs['parent']
- Child.__init__(self, parent=parent)
- Transformable.__init__(self,position)
-
- self.type_ = type_
- self.idx = None
- self.name = name
- self.counter = 0
- self.restraints = []
-
- for key,val in kwargs.items():
- self.__dict__[key] = val
-
- def add_restraint(self, restraint):
- ## TODO: how to handle duplicating and cloning bonds
- self.restraints.append( restraint )
-
- def get_restraints(self):
- return [(self,r) for r in self.restraints]
-
-
- def __getattr__(self, name):
- """
- First try to get attribute from the parent, then type_
-
- Note that this data structure seems to be fragile, can result in stack overflow
-
- """
- # return Child.__getattr__(self,name)
- try:
- return Child.__getattr__(self,name)
- except Exception as e:
- if 'type_' in self.__dict__:
- return getattr(self.type_, name)
- else:
- raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
-
- def _get_psfpdb_dictionary(self):
- p = self
- try:
- segname = p.segname
- except:
- segname = "A"
- try:
- resname = p.resname
- except:
- resname = p.name[:3]
- try:
- resid = p.resid
- except:
- resid = p.idx+1
-
- try:
- occ = p.occupancy
- except:
- occ = 0
- try:
- beta = p.beta
- except:
- beta = 0
-
- data = dict(segname = segname,
- resname = resname,
- name = str(p.name)[:4],
- chain = "A",
- resid = int(resid),
- idx = p.idx+1,
- type = p.type_.name[:4],
- charge = p.charge,
- mass = p.mass,
- occupancy = occ,
- beta = beta
- )
- return data
-
-
-class Group(Transformable, Parent, Child):
-
- def __init__(self, name=None, children = None, parent=None,
- position = np.array((0,0,0)),
- orientation = np.array(((1,0,0),(0,1,0),(0,0,1))),
- remove_duplicate_bonded_terms = False,
- **kwargs):
-
- Transformable.__init__(self, position, orientation)
- Child.__init__(self, parent) # Initialize Child first
- Parent.__init__(self, children, remove_duplicate_bonded_terms)
- self.name = name
- self.isClone = False
-
- for key,val in kwargs.items():
- self.__dict__[key] = val
-
-
- def clone(self):
- return Clone(self)
- g = copy(self)
- g.isClone = True # TODO: use?
- g.children = [copy(c) for c in g.children]
- for c in g.children:
- c.parent = g
- return g
- g = Group(position = self.position,
- orientation = self.orientation)
- g.children = self.children # lists point to the same object
-
- def duplicate(self):
- new = deepcopy(self)
- for c in new.children:
- c.parent = new
- return new
- # Group(position = self.position,
- # orientation = self.orientation)
- # g.children = deepcopy self.children.deepcopy() # lists are the same object
-
- ## TODO override deepcopy so parent can be excluded from copying?
-
- # def __getstate__(self):
- # return (self.children, self.parent, self.position, self.orientation)
-
- # def __setstate__(self, state):
- # self.children, self.parent, self.position, self.orientation = state
-
-
-class PdbModel(Transformable, Parent):
-
- def __init__(self, children=None, dimensions=None, remove_duplicate_bonded_terms=False):
- Transformable.__init__(self,(0,0,0))
- Parent.__init__(self, children, remove_duplicate_bonded_terms)
- self.dimensions = dimensions
- self.particles = [p for p in self]
- self.cacheInvalid = True
-
- def _updateParticleOrder(self):
- pass
-
- def writePdb(self, filename, beta_from_fixed=False):
- if self.cacheInvalid:
- self._updateParticleOrder()
- with open(filename,'w') as fh:
- ## Write header
- fh.write("CRYST1{:>9.3f}{:>9.3f}{:>9.3f} 90.00 90.00 90.00 P 1 1\n".format( *self.dimensions ))
-
- ## Write coordinates
- formatString = "ATOM {idx:>6.6s} {name:^4.4s} {resname:3.3s} {chain:1.1s}{resid:>5.5s} {x:8.8s}{y:8.8s}{z:8.8s}{occupancy:6.2f}{beta:6.2f} {charge:2d}{segname:>6s}\n"
- for p in self.particles:
- ## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
- data = p._get_psfpdb_dictionary()
- idx = data['idx']
-
- if np.log10(idx) >= 5:
- idx = " *****"
- else:
- idx = "{:>6d}".format(idx)
- data['idx'] = idx
-
- if beta_from_fixed:
- data['beta'] = 1 if 'fixed' in p.__dict__ else 0
-
- pos = p.collapsedPosition()
- dig = [max(int(np.log10(np.abs(x)+1e-6)//1),0)+1 for x in pos]
- for d in dig: assert( d <= 7 )
- # assert( np.all(dig <= 7) )
- fs = ["{: %d.%df}" % (8,7-d) for d in dig]
- x,y,z = [f.format(x) for f,x in zip(fs,pos)]
- data['x'] = x
- data['y'] = y
- data['z'] = z
- assert(data['resid'] < 1e5)
- data['charge'] = int(data['charge'])
- data['resid'] = "{:<4d}".format(data['resid'])
- fh.write( formatString.format(**data) )
-
- return
-
- def writePsf(self, filename):
- if self.cacheUpToDate == False:
- self._updateParticleOrder()
- with open(filename,'w') as fh:
- ## Write header
- fh.write("PSF NAMD\n\n") # create NAMD formatted psf
- fh.write("{:>8d} !NTITLE\n\n".format(0))
-
- ## ATOMS section
- fh.write("{:>8d} !NATOM\n".format(len(self.particles)))
-
- ## From vmd/plugins/molfile_plugin/src/psfplugin.c
- ## "%d %7s %10s %7s %7s %7s %f %f"
- formatString = "{idx:>8d} {segname:7.7s} {resid:<10.10s} {resname:7.7s}" + \
- " {name:7.7s} {type:7.7s} {charge:f} {mass:f}\n"
- for p in self.particles:
- data = p._get_psfpdb_dictionary()
- data['resid'] = "%d%c%c" % (data['resid']," "," ") # TODO: work with large indices
- fh.write( formatString.format(**data) )
- fh.write("\n")
-
- ## Write out bonds
- bonds = self.get_bonds()
- fh.write("{:>8d} !NBOND\n".format(len(bonds)))
- counter = 0
- for p1,p2,b,ex in bonds:
- fh.write( "{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1) )
- counter += 1
- if counter == 4:
- fh.write("\n")
- counter = 0
- else:
- fh.write(" ")
- fh.write("\n" if counter == 0 else "\n\n")
-
- ## Write out angles
- angles = self.get_angles()
- fh.write("{:>8d} !NTHETA\n".format(len(angles)))
- counter = 0
- for p1,p2,p3,a in angles:
- fh.write( "{:>8d}{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1,p3.idx+1) )
- counter += 1
- if counter == 3:
- fh.write("\n")
- counter = 0
- else:
- fh.write(" ")
- fh.write("\n" if counter == 0 else "\n\n")
-
- ## Write out dihedrals
- dihedrals = self.get_dihedrals()
- fh.write("{:>8d} !NPHI\n".format(len(dihedrals)))
- counter = 0
- for p1,p2,p3,p4,a in dihedrals:
- fh.write( "{:>8d}{:>8d}{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1,p3.idx+1,p4.idx+1) )
- counter += 1
- if counter == 2:
- fh.write("\n")
- counter = 0
- else:
- fh.write(" ")
- fh.write("\n" if counter == 0 else "\n\n")
-
- ## Write out impropers
- impropers = self.get_impropers()
- fh.write("{:>8d} !NIMPHI\n".format(len(impropers)))
- counter = 0
- for p1,p2,p3,p4,a in impropers:
- fh.write( "{:>8d}{:>8d}{:>8d}{:>8d}".format(p1.idx+1,p2.idx+1,p3.idx+1,p4.idx+1) )
- counter += 1
- if counter == 2:
- fh.write("\n")
- counter = 0
- else:
- fh.write(" ")
- fh.write("\n" if counter == 0 else "\n\n")
-
- fh.write("\n{:>8d} !NDON: donors\n\n\n".format(0))
- fh.write("\n{:>8d} !NACC: acceptors\n\n\n".format(0))
- fh.write("\n 0 !NNB\n\n")
- natoms = len(self.particles)
- for i in range(natoms//8):
- fh.write(" 0 0 0 0 0 0 0 0\n")
- for i in range(natoms-8*(natoms//8)):
- fh.write(" 0")
- fh.write("\n\n 1 0 !NGRP\n\n")
-
-
-class ArbdModel(PdbModel):
- def __init__(self, children, dimensions=(1000,1000,1000), origin=None, temperature=291, timestep=50e-6, cutoff=50, decompPeriod=10000, pairlistDistance=None, nonbondedResolution=0.1, remove_duplicate_bonded_terms=True, extra_bd_file_lines=""):
- PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms)
- self.temperature = temperature
-
- self.origin = origin
- self.timestep = timestep
- self.cutoff = cutoff
-
- if pairlistDistance == None:
- pairlistDistance = cutoff+2
-
- self.decompPeriod = decompPeriod
- self.pairlistDistance = pairlistDistance
-
- self.extra_bd_file_lines = extra_bd_file_lines
-
- self.numParticles = 0
- self.particles = []
- self.type_counts = None
-
- self.nbSchemes = []
- self._nbParamFiles = [] # This could be made more robust
- self.nbResolution = 0.1
-
- self._written_bond_files = dict()
-
- self.cacheUpToDate = False
-
- def clear_all(self, keep_children=False):
- Parent.clear_all(self, keep_children=keep_children)
- self.particles = []
- self.numParticles = 0
- self.type_counts = None
- self._nbParamFiles = []
- self._written_bond_files = dict()
-
- def _getNbScheme(self, typeA, typeB):
- scheme = None
- for s,A,B in self.nbSchemes:
- if A is None or B is None:
- if A is None and B is None:
- return s
- elif A is None and typeB == B:
- return s
- elif B is None and typeA == A:
- return s
- elif typeA == A and typeB == B:
- return s
- raise Exception("No nonbonded scheme found for %s and %s" % (typeA.name, typeB.name))
-
- def _countParticleTypes(self):
- ## TODO: check for modifications to particle that require
- ## automatic generation of new particle type
- type_counts = dict()
- for p in self:
- t = p.type_
- if t in type_counts:
- type_counts[t] += 1
- else:
- type_counts[t] = 1
- self.type_counts = type_counts
-
- def _updateParticleOrder(self):
- ## Create ordered list
- self.particles = [p for p in self]
- # self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))
-
- ## Update particle indices
- for p,i in zip(self.particles,range(len(self.particles))):
- p.idx = i
-
- # self.initialCoords = np.array([p.initialPosition for p in self.particles])
-
- def useNonbondedScheme(self, nbScheme, typeA=None, typeB=None):
- self.nbSchemes.append( (nbScheme, typeA, typeB) )
- if typeA != typeB:
- self.nbSchemes.append( (nbScheme, typeB, typeA) )
-
- def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', replicas=1, log_file=None):
- assert(type(gpu) is int)
- num_steps = int(num_steps)
-
- d_orig = os.getcwd()
- try:
- if not os.path.exists(directory):
- os.makedirs(directory)
- os.chdir(directory)
-
- if timestep is not None:
- self.timestep = timestep
-
- if self.cacheUpToDate == False: # TODO: remove cache?
- self._countParticleTypes()
- self._updateParticleOrder()
-
- if output_directory == '': output_directory='.'
-
- if arbd is None:
- for path in os.environ["PATH"].split(os.pathsep):
- path = path.strip('"')
- fname = os.path.join(path, "arbd")
- if os.path.isfile(fname) and os.access(fname, os.X_OK):
- arbd = fname
- break
-
- if arbd is None: raise Exception("ARBD was not found")
-
- if not os.path.exists(arbd):
- raise Exception("ARBD was not found")
- if not os.path.isfile(arbd):
- raise Exception("ARBD was not found")
- if not os.access(arbd, os.X_OK):
- raise Exception("ARBD is not executable")
-
- if not os.path.exists(output_directory):
- os.makedirs(output_directory)
- elif not os.path.isdir(output_directory):
- raise Exception("output_directory '%s' is not a directory!" % output_directory)
-
-
- self.writePdb( output_name + ".pdb" )
- self.writePsf( output_name + ".psf" )
- self.writeArbdFiles( output_name, numSteps=num_steps, outputPeriod=output_period )
- os.sync()
-
- ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
-
- cmd = [arbd, '-g', "%d" % gpu]
- if replicas > 1:
- cmd = cmd + ['-r',replicas]
- cmd = cmd + ["%s.bd" % output_name, "%s/%s" % (output_directory, output_name)]
- cmd = tuple(str(x) for x in cmd)
-
- print("Running ARBD with: %s" % " ".join(cmd))
- if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
- fd = sys.stdout if log_file is None else log_file
- process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
- for line in process.stdout:
- fd.write(line)
- fd.flush()
- else:
- with open(log_file,'w') as fd:
- process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
- process.communicate()
-
- except:
- raise
- finally:
- os.chdir(d_orig)
-
-
- # -------------------------- #
- # Methods for printing model #
- # -------------------------- #
-
- def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000):
- ## TODO: save and reference directories and prefixes using member data
- d = self.potential_directory = "potentials"
- if not os.path.exists(d):
- os.makedirs(d)
- self._restraint_filename = "%s/%s.restraint.txt" % (d, prefix)
- self._bond_filename = "%s/%s.bonds.txt" % (d, prefix)
- self._angle_filename = "%s/%s.angles.txt" % (d, prefix)
- self._dihedral_filename = "%s/%s.dihedrals.txt" % (d, prefix)
- self._exclusion_filename = "%s/%s.exculsions.txt" % (d, prefix)
-
- # self._writeArbdCoordFile( prefix + ".coord.txt" )
- self._writeArbdParticleFile( prefix + ".particles.txt" )
- self._writeArbdRestraintFile()
- self._writeArbdBondFile()
- self._writeArbdAngleFile()
- self._writeArbdDihedralFile()
- self._writeArbdExclusionFile()
- self._writeArbdPotentialFiles( prefix, directory = d )
- self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod )
-
- # def _writeArbdCoordFile(self, filename):
- # with open(filename,'w') as fh:
- # for p in self.particles:
- # fh.write("%f %f %f\n" % tuple(x for x in p.collapsedPosition()))
-
- def _writeArbdParticleFile(self, filename):
- with open(filename,'w') as fh:
- for p in self.particles:
- data = tuple([p.idx,p.type_.name] + [x for x in p.collapsedPosition()])
- fh.write("ATOM %d %s %f %f %f\n" % data)
-
-
- def _writeArbdConf(self, prefix, randomSeed=None, numSteps=100000000, outputPeriod=10000, restartCoordinateFile=None):
- ## TODO: raise exception if _writeArbdPotentialFiles has not been called
- filename = "%s.bd" % prefix
-
- ## Prepare a dictionary to fill in placeholders in the configuration file
- params = self.__dict__.copy() # get parameters from System object
-
- if randomSeed is None:
- params['randomSeed'] = ""
- else:
- params['randomSeed'] = "seed %s" % randomSeed
- params['numSteps'] = int(numSteps)
-
- # params['coordinateFile'] = "%s.coord.txt" % prefix
- params['particleFile'] = "%s.particles.txt" % prefix
- if restartCoordinateFile is None:
- params['restartCoordinates'] = ""
- else:
- params['restartCoordinates'] = "restartCoordinates %s" % restartCoordinateFile
- params['outputPeriod'] = outputPeriod
-
- for k,v in zip('XYZ', self.dimensions):
- params['dim'+k] = v
-
- if self.origin is None:
- for k,v in zip('XYZ', self.dimensions):
- params['origin'+k] = -v*0.5
- else:
- for k,v in zip('XYZ', self.origin):
- params['origin'+k] = v
-
-
- params['pairlistDistance'] -= params['cutoff']
-
- ## Actually write the file
- with open(filename,'w') as fh:
- fh.write("""{randomSeed}
-timestep {timestep}
-steps {numSteps}
-numberFluct 0 # deprecated
-
-interparticleForce 1 # other values deprecated
-fullLongRange 0 # deprecated
-temperature {temperature}
-
-outputPeriod {outputPeriod}
-## Energy doesn't actually get printed!
-outputEnergyPeriod {outputPeriod}
-outputFormat dcd
-
-## Infrequent domain decomposition because this kernel is still very slow
-decompPeriod {decompPeriod}
-cutoff {cutoff}
-pairlistDistance {pairlistDistance}
-
-origin {originX} {originY} {originZ}
-systemSize {dimX} {dimY} {dimZ}
-
-{extra_bd_file_lines}
-\n""".format(**params))
-
- ## Write entries for each type of particle
- for pt,num in self.getParticleTypesAndCounts():
- ## TODO create new particle types if existing has grid
- particleParams = pt.__dict__.copy()
- particleParams['num'] = num
- fh.write("""
-particle {name}
-num {num}
-diffusion {diffusivity}
-""".format(**particleParams))
- if 'grid' in particleParams:
- if not isinstance(pt.grid, list): pt.grid = [pt.grid]
- for g,s in pt.grid:
- ## TODO, use Path.relative_to?
- try:
- fh.write("gridFile {}\n".format(g.relative_to(os.getcwd())))
- except:
- fh.write("gridFile {}\n".format(g))
-
- fh.write("gridFileScale {}\n".format(s))
-
- else:
- fh.write("gridFile {}/null.dx\n".format(self.potential_directory))
-
- ## Write coordinates and interactions
- fh.write("""
-## Input coordinates
-inputParticles {particleFile}
-{restartCoordinates}
-
-## Interaction potentials
-tabulatedPotential 1
-## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file
-""".format(**params))
- for pair,f in zip(self._particleTypePairIter(), self._nbParamFiles):
- i,j,t1,t2 = pair
- fh.write("tabulatedFile %d@%d@%s\n" % (i,j,f))
-
- ## Bonded interactions
- restraints = self.get_restraints()
- bonds = self.get_bonds()
- angles = self.get_angles()
- dihedrals = self.get_dihedrals()
- exclusions = self.get_exclusions()
-
- if len(bonds) > 0:
- for b in list(set([b for i,j,b,ex in bonds])):
- fh.write("tabulatedBondFile %s\n" % b)
-
- if len(angles) > 0:
- for b in list(set([b for i,j,k,b in angles])):
- fh.write("tabulatedAngleFile %s\n" % b)
-
- if len(dihedrals) > 0:
- for b in list(set([b for i,j,k,l,b in dihedrals])):
- fh.write("tabulatedDihedralFile %s\n" % b)
-
- if len(restraints) > 0:
- fh.write("inputRestraints %s\n" % self._restraint_filename)
- if len(bonds) > 0:
- fh.write("inputBonds %s\n" % self._bond_filename)
- if len(angles) > 0:
- fh.write("inputAngles %s\n" % self._angle_filename)
- if len(dihedrals) > 0:
- fh.write("inputDihedrals %s\n" % self._dihedral_filename)
- if len(exclusions) > 0:
- fh.write("inputExcludes %s\n" % self._exclusion_filename)
-
- write_null_dx = False
- for pt,num in self.getParticleTypesAndCounts():
- if "grid" not in pt.__dict__:
- gridfile = "{}/null.dx".format(self.potential_directory)
- with open(gridfile, 'w') as fh:
- fh.write("""object 1 class gridpositions counts 2 2 2
-origin {originX} {originY} {originZ}
-delta {dimX} 0.000000 0.000000
-delta 0.000000 {dimY} 0.000000
-delta 0.000000 0.000000 {dimZ}
-object 2 class gridconnections counts 2 2 2
-object 3 class array type float rank 0 items 8 data follows
-0.0 0.0 0.0
-0.0 0.0 0.0
-0.0 0.0
-attribute "dep" string "positions"
-object "density" class field
-component "positions" value 1
-component "connections" value 2
-component "data" value 3
-""".format(**params))
- break
-
- def getParticleTypesAndCounts(self):
- ## TODO: remove(?)
- return sorted( self.type_counts.items(), key=lambda x: x[0] )
-
- def _particleTypePairIter(self):
- typesAndCounts = self.getParticleTypesAndCounts()
- for i in range(len(typesAndCounts)):
- t1 = typesAndCounts[i][0]
- for j in range(i,len(typesAndCounts)):
- t2 = typesAndCounts[j][0]
- yield( (i,j,t1,t2) )
-
- def _writeArbdPotentialFiles(self, prefix, directory = "potentials"):
- try:
- os.makedirs(directory)
- except OSError:
- if not os.path.isdir(directory):
- raise
-
- pathPrefix = "%s/%s" % (directory,prefix)
- self._writeNonbondedParameterFiles( pathPrefix + "-nb" )
- # self._writeBondParameterFiles( pathPrefix )
- # self._writeAngleParameterFiles( pathPrefix )
- # self._writeDihedralParameterFiles( pathPrefix )
-
- def _writeNonbondedParameterFiles(self, prefix):
- x = np.arange(0, self.cutoff, self.nbResolution)
- for i,j,t1,t2 in self._particleTypePairIter():
- f = "%s.%s-%s.dat" % (prefix, t1.name, t2.name)
- scheme = self._getNbScheme(t1,t2)
- scheme.write_file(f, t1, t2, rMax = self.cutoff)
- self._nbParamFiles.append(f)
-
- def _getNonbondedPotential(self,x,a,b):
- return a*(np.exp(-x/b))
-
- def _writeArbdRestraintFile( self ):
- with open(self._restraint_filename,'w') as fh:
- for i,restraint in self.get_restraints():
- item = [i.idx]
- if len(restraint) == 1:
- item.append(restraint[0])
- item.extend(i.get_collapsed_position())
- elif len(restraint) == 2:
- item.append(restraint[0])
- item.extend(restraint[1])
- elif len(restraint) == 5:
- item.extend(restraint)
- fh.write("RESTRAINT %d %f %f %f %f\n" % tuple(item))
-
- def _writeArbdBondFile( self ):
- for b in list( set( [b for i,j,b,ex in self.get_bonds()] ) ):
- if type(b) is not str:
- b.write_file()
-
- with open(self._bond_filename,'w') as fh:
- for i,j,b,ex in self.get_bonds():
- item = (i.idx, j.idx, str(b))
- if ex:
- fh.write("BOND REPLACE %d %d %s\n" % item)
- else:
- fh.write("BOND ADD %d %d %s\n" % item)
-
- def _writeArbdAngleFile( self ):
- for b in list( set( [b for i,j,k,b in self.get_angles()] ) ):
- if type(b) is not str:
- b.write_file()
-
- with open(self._angle_filename,'w') as fh:
- for b in self.get_angles():
- item = tuple([p.idx for p in b[:-1]] + [str(b[-1])])
- fh.write("ANGLE %d %d %d %s\n" % item)
-
- def _writeArbdDihedralFile( self ):
- for b in list( set( [b for i,j,k,l,b in self.get_dihedrals()] ) ):
- if type(b) is not str:
- b.write_file()
-
- with open(self._dihedral_filename,'w') as fh:
- for b in self.get_dihedrals():
- item = tuple([p.idx for p in b[:-1]] + [str(b[-1])])
- fh.write("DIHEDRAL %d %d %d %d %s\n" % item)
-
- def _writeArbdExclusionFile( self ):
- with open(self._exclusion_filename,'w') as fh:
- for ex in self.get_exclusions():
- item = tuple(int(p.idx) for p in ex)
- fh.write("EXCLUDE %d %d\n" % item)
-
- def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
- ## TODO: cache coordinates using numpy arrays for quick min/max
- raise(NotImplementedError)
-
- def write_namd_configuration( self, output_name, num_steps = 1e6,
- output_directory = 'output',
- update_dimensions=True, extrabonds=True ):
-
- format_data = self.__dict__.copy() # get parameters from System object
-
- format_data['extrabonds'] = """extraBonds on
-extraBondsFile $prefix.exb
-""" if extrabonds else ""
-
- if self.useTclForces:
- format_data['margin'] = ""
- format_data['tcl_forces'] = """tclForces on
-tclForcesScript $prefix.forces.tcl
-"""
- else:
- format_data['margin'] = """margin 30
-"""
- format_data['tcl_forces'] = ""
-
- if update_dimensions:
- format_data['dimensions'] = self.dimensions_from_structure()
-
- for k,v in zip('XYZ', format_data['dimensions']):
- format_data['origin'+k] = -v*0.5
- format_data['cell'+k] = v
-
- format_data['prefix'] = output_name
- format_data['num_steps'] = int(num_steps//12)*12
- format_data['output_directory'] = output_directory
- filename = '{}.namd'.format(output_name)
-
- with open(filename,'w') as fh:
- fh.write("""
-set prefix {prefix}
-set nLast 0; # increment when continueing a simulation
-set n [expr $nLast+1]
-set out {output_directory}/$prefix-$n
-set temperature 300
-
-structure $prefix.psf
-coordinates $prefix.pdb
-
-outputName $out
-XSTfile $out.xst
-DCDfile $out.dcd
-
-#############################################################
-## SIMULATION PARAMETERS ##
-#############################################################
-
-# Input
-paraTypeCharmm on
-parameters charmm36.nbfix/par_all36_na.prm
-parameters charmm36.nbfix/par_water_ions_na.prm
-
-wrapAll off
-
-# Force-Field Parameters
-exclude scaled1-4
-1-4scaling 1.0
-switching on
-switchdist 8
-cutoff 10
-pairlistdist 12
-{margin}
-
-# Integrator Parameters
-timestep 2.0 ;# 2fs/step
-rigidBonds all ;# needed for 2fs steps
-nonbondedFreq 1
-fullElectFrequency 3
-stepspercycle 12
-
-# PME (for full-system periodic electrostatics)
-PME no
-PMEGridSpacing 1.2
-
-# Constant Temperature Control
-langevin on ;# do langevin dynamics
-# langevinDamping 1 ;# damping coefficient (gamma); used in original study
-langevinDamping 0.1 ;# less friction for faster relaxation
-langevinTemp $temperature
-langevinHydrogen off ;# don't couple langevin bath to hydrogens
-
-# output
-useGroupPressure yes
-xstFreq 4800
-outputEnergies 4800
-dcdfreq 4800
-restartfreq 48000
-
-#############################################################
-## EXTRA FORCES ##
-#############################################################
-
-# ENM and intrahelical extrabonds
-{extrabonds}
-{tcl_forces}
-
-#############################################################
-## RUN ##
-#############################################################
-
-# Continuing a job from the restart files
-cellBasisVector1 {cellX} 0 0
-cellBasisVector2 0 {cellY} 0
-cellBasisVector3 0 0 {cellZ}
-
-if {{$nLast == 0}} {{
- temperature 300
- fixedAtoms on
- fixedAtomsForces on
- fixedAtomsFile $prefix.fixed.pdb
- fixedAtomsCol B
- minimize 2400
- fixedAtoms off
- minimize 2400
-}} else {{
- bincoordinates {output_directory}/$prefix-$nLast.restart.coor
- binvelocities {output_directory}/$prefix-$nLast.restart.vel
-}}
-
-run {num_steps:d}
-""".format(**format_data))
-
- def atomic_simulate(self, output_name, output_directory='output', dry_run = False, namd2=None, log_file=None, num_procs=None, gpu=None):
- if self.cacheUpToDate == False: # TODO: remove cache?
- self._countParticleTypes()
- self._updateParticleOrder()
-
- if output_directory == '': output_directory='.'
- self.writePdb( output_name + ".pdb" )
- self.writePdb( output_name + ".fixed.pdb", beta_from_fixed=True )
- self.writePsf( output_name + ".psf" )
- self.write_namd_configuration( output_name, output_directory = output_directory )
- os.sync()
-
- if not dry_run:
- if namd2 is None:
- for path in os.environ["PATH"].split(os.pathsep):
- path = path.strip('"')
- fname = os.path.join(path, "namd2")
- if os.path.isfile(fname) and os.access(fname, os.X_OK):
- namd2 = fname
- break
-
- if namd2 is None: raise Exception("NAMD2 was not found")
-
- if not os.path.exists(namd2):
- raise Exception("NAMD2 was not found")
- if not os.path.isfile(namd2):
- raise Exception("NAMD2 was not found")
- if not os.access(namd2, os.X_OK):
- raise Exception("NAMD2 is not executable")
-
- if not os.path.exists(output_directory):
- os.makedirs(output_directory)
- elif not os.path.isdir(output_directory):
- raise Exception("output_directory '%s' is not a directory!" % output_directory)
-
- if num_procs is None:
- import multiprocessing
- num_procs = max(1,multiprocessing.cpu_count()-1)
-
- cmd = [namd2, '+p{}'.format(num_procs), "%s.namd" % output_name]
- cmd = tuple(str(x) for x in cmd)
-
- print("Running NAMD2 with: %s" % " ".join(cmd))
- if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
- fd = sys.stdout if log_file is None else log_file
- process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
- for line in process.stdout:
- fd.write(line)
- fd.flush()
- else:
- with open(log_file,'w') as fd:
- process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
- process.communicate()
-
-
- """ oxDNA """
- ## https://dna.physics.ox.ac.uk/index.php/Documentation#Input_file
-
-
- def _write_oxdna_configuration(self, filename):
-
- _angstroms_to_oxdna = 0.11739845 ## units "AA" "8.518e-10 m"
- with open(filename,'w') as fh:
- fh.write("""t = {temperature}
-b = {dimX} {dimY} {dimZ}
-E = 0 0 0
-""".format(temperature=self.temperature,
- dimX = self.dimensions[0]*_angstroms_to_oxdna,
- dimY = self.dimensions[1]*_angstroms_to_oxdna,
- dimZ = self.dimensions[2]*_angstroms_to_oxdna))
-
- base_vec = np.array((1,0,0)) # TODO
- norm_vec = np.array((0,0,1)) # TODO
-
- ## Traverse 3'-to-5'
- for nt in [nt for s in self.strands for nt in s.oxdna_nt[::-1]]:
- data = dict()
- # o = nt.collapsedOrientation()
- o = nt.orientation
- for k,v in zip('x y z'.split(),nt.collapsedPosition()):
- data[k] = v * _angstroms_to_oxdna
- for k,v in zip('x y z'.split(),o.dot(base_vec)):
- data['b'+k] = v
- for k,v in zip('x y z'.split(),o.dot(norm_vec)):
- data['n'+k] = v
- fh.write("{x} {y} {z} {bx} {by} {bz} {nx} {ny} {nz} 0 0 0 0 0 0\n".format(**data)
- )
-
- def _write_oxdna_topology(self,filename):
-
- strands = [s for s in self.strands if s.num_nt > 0]
- with open(filename,'w') as fh:
-
- fh.write("{num_nts} {num_strands}\n".format(
- num_nts = sum([s.num_nt for s in strands]),
- num_strands = len(self.strands)))
-
- idx = 0
- sidx = 1
- for strand in strands:
- prev = idx+len(strand.num_nt) if strand.is_circular else -1
- last = idx if strand.is_circular else -1
-
- ## Traverse 3'-to-5'
- sequence = [seq for s in strand.strand_segments
- for seq in s.get_sequence()][::-1]
- for seq in sequence[:-1]:
- ## strand seq 3' 5'
- fh.write("{} {} {} {}\n".format(sidx, seq, prev, idx+1))
- prev = idx
- idx += 1
- seq = sequence[-1]
- fh.write("{} {} {} {}\n".format(sidx, seq, prev, last))
- idx += 1
- sidx += 1
-
- def _write_oxdna_input(self, filename,
- topology,
- conf_file,
- trajectory_file,
- last_conf_file,
- log_file,
- num_steps = 1e6,
- interaction_type = 'DNA2',
- salt_concentration = None,
- print_conf_interval = None,
- print_energy_every = None,
- timestep = 0.003,
- sim_type = "MD",
- backend = None,
- backend_precision = None,
- seed = None,
- newtonian_steps = 103,
- diff_coeff = 2.50,
- thermostat = "john",
- list_type = "cells",
- ensemble = "nvt",
- delta_translation = 0.22,
- delta_rotation = 0.22,
- verlet_skin = 0.5,
- max_backbone_force = 5,
- ):
-
- if seed is None:
- import random
- seed = random.randint(1,99999)
-
- temperature = self.temperature
- num_steps = int(num_steps)
- newtonian_steps = int(newtonian_steps)
-
- if print_conf_interval is None:
- # print_conf_interval = min(num_steps//100)
- print_conf_interval = 10000
- print_conf_interval = int(print_conf_interval)
-
- if print_energy_every is None:
- print_energy_every = print_conf_interval
- print_energy_every = int(print_energy_every)
-
- if max_backbone_force is not None:
- max_backbone_force = 'max_backbone_force = {}'.format(max_backbone_force)
-
-
- if interaction_type in ('DNA2',):
- if salt_concentration is None:
- try:
- ## units "80 epsilon0 295 k K / (2 (AA)**2 e**2/particle)" mM
- salt_concentration = 9331.3126/self.debye_length**2
- except:
- salt_concentration = 0.5
- salt_concentration = 'salt_concentration = {}'.format(salt_concentration)
- else:
- salt_concentration = ''
-
- if backend is None:
- backend = 'CUDA' if sim_type == 'MD' else 'CPU'
-
- if backend_precision is None:
- backend_precision = 'mixed' if backend == 'CUDA' else 'double'
-
- if sim_type == 'VMMC':
- ensemble = 'ensemble = {}'.format(ensemble)
- delta_translation = 'delta_translation = {}'.format(delta_translation)
- delta_rotation = 'delta_rotation = {}'.format(delta_rotation)
- else:
- ensemble = ''
- delta_translation = ''
- delta_rotation = ''
-
- with open(filename,'w') as fh:
- fh.write("""##############################
-#### PROGRAM PARAMETERS ####
-##############################
-interaction_type = {interaction_type}
-{salt_concentration}
-sim_type = {sim_type}
-backend = {backend}
-backend_precision = {backend_precision}
-#debug = 1
-seed = {seed}
-
-##############################
-#### SIM PARAMETERS ####
-##############################
-steps = {num_steps:d}
-newtonian_steps = {newtonian_steps:d}
-diff_coeff = {diff_coeff}
-thermostat = {thermostat}
-
-list_type = {list_type}
-{ensemble}
-{delta_translation}
-{delta_rotation}
-
-T = {temperature:f} K
-dt = {timestep}
-verlet_skin = {verlet_skin}
-{max_backbone_force}
-
-##############################
-#### INPUT / OUTPUT ####
-##############################
-topology = {topology}
-conf_file = {conf_file}
-lastconf_file = {last_conf_file}
-trajectory_file = {trajectory_file}
-refresh_vel = 1
-log_file = {log_file}
-no_stdout_energy = 1
-restart_step_counter = 1
-energy_file = {log_file}.energy.dat
-print_conf_interval = {print_conf_interval}
-print_energy_every = {print_energy_every}
-time_scale = linear
-external_forces = 0
-""".format( **locals() ))
-
- def simulate_oxdna(self, output_name, directory='.', output_directory='output', topology=None, configuration=None, oxDNA=None, **oxdna_args):
-
- if output_directory == '': output_directory='.'
- d_orig = os.getcwd()
- if not os.path.exists(directory):
- os.makedirs(directory)
-
- os.chdir(directory)
- try:
-
- if oxDNA is None:
- for path in os.environ["PATH"].split(os.pathsep):
- path = path.strip('"')
- fname = os.path.join(path, "oxDNA")
- if os.path.isfile(fname) and os.access(fname, os.X_OK):
- oxDNA = fname
- break
-
- if oxDNA is None: raise Exception("oxDNA was not found")
-
- if not os.path.exists(oxDNA):
- raise Exception("oxDNA was not found")
- if not os.path.isfile(oxDNA):
- raise Exception("oxDNA was not found")
- if not os.access(oxDNA, os.X_OK):
- raise Exception("oxDNA is not executable")
-
- if not os.path.exists(output_directory):
- os.makedirs(output_directory)
- elif not os.path.isdir(output_directory):
- raise Exception("output_directory '%s' is not a directory!" % output_directory)
-
-
- if configuration is None:
- configuration = "{}.conf".format(output_name)
- self._write_oxdna_configuration(configuration)
- # elif not Path(configuration).exists():
- # raise Exception("Unable to find oxDNA configuration file '{}'.".format(configuration))
-
- if topology is None:
- topology = "{}-topology.dat".format(output_name)
- self._write_oxdna_topology(topology)
- elif not Path(topology).exists():
- raise Exception("Unable to find oxDNA topology file '{}'.".format(topology))
-
- last_conf_file = "{}/{}.last.conf".format(output_directory,output_name)
- input_file = "{}-input".format(output_name)
-
- self._write_oxdna_input(input_file,
- topology = topology,
- conf_file = configuration,
- trajectory_file = "{}/{}.dat".format(output_directory,output_name),
- last_conf_file = last_conf_file,
- log_file="{}/{}.log".format(output_directory,output_name),
- **oxdna_args)
- os.sync()
- ## TODO: call oxdna
- cmd = [oxDNA, input_file]
-
- cmd = tuple(str(x) for x in cmd)
-
- print("Running oxDNA with: %s" % " ".join(cmd))
- process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
- for line in process.stdout:
- sys.stdout.write(line)
- sys.stdout.flush()
-
- return topology,last_conf_file
- finally:
- os.chdir(d_orig)
-
-
diff --git a/mrdna/model/nbPot.py b/mrdna/model/nbPot.py
index c26c3b07f116bc67121642c0a7dbf5c1d28df374..2329bc31d322c3a1135a7a8b368146dcda99e899 100644
--- a/mrdna/model/nbPot.py
+++ b/mrdna/model/nbPot.py
@@ -3,9 +3,9 @@ import scipy.optimize as opt
from scipy.interpolate import interp1d
from scipy.signal import savgol_filter as savgol
-from mrdna.model.nonbonded import NonbondedScheme
-from mrdna import get_resource_path
-from mrdna.config import CACHE_DIR
+from ..arbdmodel.nonbonded import NonbondedScheme
+from .. import get_resource_path
+from ..config import CACHE_DIR
from scipy.optimize import curve_fit
from pathlib import Path
diff --git a/mrdna/model/nonbonded.py b/mrdna/model/nonbonded.py
index 35ed22113877774093d143dc748c6a7dc20995b9..37d22a526aa8b58165e8ca091baefb07f65f1389 100644
--- a/mrdna/model/nonbonded.py
+++ b/mrdna/model/nonbonded.py
@@ -1,241 +1,4 @@
-from shutil import copyfile
-import os, sys
-import numpy as np
+from ..arbdmodel.nonbonded import *
-class NonbondedScheme():
- """ Abstract class for writing nonbonded interactions """
-
- def __init__(self, typesA=None, typesB=None, resolution=0.1, rMin=0):
- """If typesA is None, and typesB is None, then """
- self.resolution = resolution
- self.rMin = rMin
-
- def add_sim_system(self, simSystem):
- self.rMax = simSystem.cutoff
- self.r = np.arange(rMin,rMax,resolution)
-
- def potential(self, r, typeA, typeB):
- raise NotImplementedError
-
- def write_file(self, filename, typeA, typeB, rMax):
- r = np.arange(self.rMin, rMax+self.resolution, self.resolution)
- u = self.potential(r, typeA, typeB)
- np.savetxt(filename, np.array([r,u]).T)
-
-
-class LennardJones(NonbondedScheme):
- def potential(self, r, typeA, typeB):
- epsilon = sqrt( typeA.epsilon**2 + typeB.epsilon**2 )
- r0 = 0.5 * (typeA.radius + typeB.radius)
- r6 = (r0/r)**6
- r12 = r6**2
- u = epsilon * (r12-2*r6)
- u[0] = u[1] # Remove NaN
- return u
-LennardJones = LennardJones()
-
-class HalfHarmonic(NonbondedScheme):
- def potential(self, r, typeA, typeB):
- k = 10 # kcal/mol AA**2
- r0 = (typeA.radius + typeB.radius)
- u = 0.5 * k * (r-r0)**2
- u[r > r0] = np.zeros( np.shape(u[r > r0]) )
- return u
-HalfHarmonic = HalfHarmonic()
-
-class TabulatedPotential(NonbondedScheme):
- def __init__(self, tableFile, typesA=None, typesB=None, resolution=0.1, rMin=0):
- """If typesA is None, and typesB is None, then """
- self.tableFile = tableFile
- # self.resolution = resolution
- # self.rMin = rMin
-
- ## TODO: check that tableFile exists and is regular file
-
- def write_file(self, filename, typeA, typeB, rMax):
- if filename != self.tableFile:
- copyfile(self.tableFile, filename)
-
-## Bonded potentials
-class BasePotential():
- def __init__(self, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
- self.r0 = r0
- self.rRange = rRange
- self.resolution = resolution
- self.maxForce = maxForce
- self.prefix = prefix
- self.periodic = False
- self.type_ = "None"
- self.max_potential = max_potential
- self.kscale_ = None # only used for
-
- def filename(self):
- raise NotImplementedError("Not implemented")
-
- def potential(self,dr):
- raise NotImplementedError("Not implemented")
-
- def __str__(self):
- return self.filename()
-
- def write_file(self):
- r = np.arange( self.rRange[0],
- self.rRange[1]+self.resolution,
- self.resolution )
- dr = r-self.r0
-
- if self.periodic == True:
- rSpan = self.rRange[1]-self.rRange[0]
- assert(rSpan > 0)
- dr = np.mod( dr+0.5*rSpan, rSpan) - 0.5*rSpan
-
- u = self.potential(dr)
-
- maxForce = self.maxForce
- if maxForce is not None:
- assert(maxForce > 0)
- f = np.diff(u)/np.diff(r)
- f[f>maxForce] = maxForce
- f[f<-maxForce] = -maxForce
- u[0] = 0
- u[1:] = np.cumsum(f*np.diff(r))
-
- if self.max_potential is not None:
- f = np.diff(u)/np.diff(r)
- ids = np.where( 0.5*(u[1:]+u[:-1]) > self.max_potential )[0]
-
- w = np.sqrt(2*self.max_potential/self.k)
- drAvg = 0.5*(np.abs(dr[ids]) + np.abs(dr[ids+1]))
-
- f[ids] = f[ids] * np.exp(-(drAvg-w)/(w))
- u[0] = 0
- u[1:] = np.cumsum(f*np.diff(r))
-
- u = u - np.min(u)
-
- np.savetxt( self.filename(), np.array([r, u]).T, fmt="%f" )
-
-class HarmonicPotential(BasePotential):
- def __init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix, correct_geometry=False):
- self.k = k
- self.kscale_ = None
- BasePotential.__init__(self, r0, rRange, resolution, maxForce, max_potential, prefix)
-
- def filename(self):
- return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
- self.k*self.kscale_, self.r0)
- def potential(self,dr):
- return 0.5*self.k*dr**2
-
- def __hash__(self):
- assert(self.type_ != "None")
- return hash((self.type_, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
-
- def __eq__(self, other):
- for a in ("type_", "k", "r0", "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
- if self.__dict__[a] != other.__dict__[a]:
- return False
- return True
-
-# class NonBonded(HarmonicPotential):
-# def _init_hook(self):
-# self.type = "nonbonded"
-# self.kscale_ = 1.0
-
-class HarmonicBond(HarmonicPotential):
- def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/", correct_geometry=False, temperature=295):
- HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
- self.type_ = "gbond" if correct_geometry else "bond"
- self.kscale_ = 1.0
- self.correct_geometry = correct_geometry
- self.temperature = temperature
-
- def potential(self,dr):
- u = HarmonicPotential.potential(self,dr)
- if self.correct_geometry:
- with np.errstate(divide='ignore',invalid='ignore'):
- du = 2*0.58622592*np.log(dr+self.r0) * self.temperature/295
- du[np.logical_not(np.isfinite(du))] = 0
- u = u-du
- return u
-
-
-class HarmonicAngle(HarmonicPotential):
- def __init__(self, k, r0, rRange=(0,181), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
- HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
- self.type_ = "angle"
- self.kscale_ = (180.0/np.pi)**2
-
-class HarmonicDihedral(HarmonicPotential):
- def __init__(self, k, r0, rRange=(-180,180), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
- HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
- self.periodic = True
- self.type_ = "dihedral"
- self.kscale_ = (180.0/np.pi)**2
-
-class WLCSKBond(BasePotential):
- """ ## https://aip.scitation.org/doi/full/10.1063/1.4968020 """
- def __init__(self, d, lp, kT, rRange=(0,50), resolution=0.02, maxForce=100, max_potential=None, prefix="potentials/"):
- BasePotential.__init__(self, 0, rRange, resolution, maxForce, max_potential, prefix)
- self.type_ = "wlcbond"
- self.d = d # separation
- self.lp = lp # persistence length
- self.kT = kT
-
- def filename(self):
- return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
- self.d, self.lp)
- def potential(self, dr):
- nk = self.d / (2*self.lp)
- q2 = (dr / self.d)**2
- a1,a2 = 1, -7.0/(2*nk)
- a3 = 3.0/32 - 3.0/(8*nk) - 6.0/(4*nk**2)
- p0,p1,p2,p3,p4 = 13.0/32, 3.4719,2.5064,-1.2906,0.6482
- a4 = (p0 + p1/(2*nk) + p2*(2*nk)**-2) / (1+p3/(2*nk)+p4*(2*nk)**-2)
- with np.errstate(divide='ignore',invalid='ignore'):
- u = self.kT * nk * ( a1/(1-q2) - a2*np.log(1-q2) + a3*q2 - 0.5*a4*q2*(q2-2) )
- max_force = np.diff(u[q2<1][-2:]) / np.diff(dr).mean()
- max_u = u[q2<1][-1]
- max_dr = dr[q2<1][-2]
- assert( max_force >= 0 )
- u[q2>=1] = (dr[q2>=1]-max_dr)*max_force + max_u
- return u
-
- def __hash__(self):
- assert(self.type_ != "None")
- return hash((self.type_, self.d, self.lp, self.kT, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
-
- def __eq__(self, other):
- for a in ("type_", "d", "lp", "kT" "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
- if self.__dict__[a] != other.__dict__[a]:
- return False
- return True
-
-class WLCSKAngle(BasePotential):
- ## https://aip.scitation.org/doi/full/10.1063/1.4968020
- def __init__(self, d, lp, kT, rRange=(0,181), resolution=0.5, maxForce=None, max_potential=None, prefix="potentials/"):
- BasePotential.__init__(self, 180, rRange, resolution, maxForce, max_potential, prefix)
- self.type_ = "wlcangle"
- self.d = d # separation
- self.lp = lp # persistence length
- self.kT = kT
-
- def filename(self):
- return "%s%s-%.3f-%.3f.dat" % (self.prefix, self.type_,
- self.d, self.lp)
- def potential(self,dr):
- nk = self.d / (2*self.lp)
- p1,p2,p3,p4 = -1.237, 0.8105, -1.0243, 0.4595
- C = (1 + p1*(2*nk) + p2*(2*nk)**2) / (2*nk+p3*(2*nk)**2+p4*(2*nk)**3)
- u = self.kT * C * (1-np.cos(dr * np.pi / 180))
- return u
-
- def __hash__(self):
- assert(self.type_ != "None")
- return hash((self.type_, self.d, self.lp, self.kT, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
-
- def __eq__(self, other):
- for a in ("type_", "d", "lp", "kT" "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
- if self.__dict__[a] != other.__dict__[a]:
- return False
- return True
+from sys import stderr
+stderr.write("WARNING: the module 'mrdna.model.nonbonded' has been deprecated. Please change your scripts to use 'mrdna.arbdmodel.nonbonded'\n")
diff --git a/mrdna/readers/cadnano_segments.py b/mrdna/readers/cadnano_segments.py
index 304171843f0f975cdec8e492c8ac67b3652696a8..f5986074e8c633860c1dd6f041c26c41747c9246 100644
--- a/mrdna/readers/cadnano_segments.py
+++ b/mrdna/readers/cadnano_segments.py
@@ -5,7 +5,7 @@ import os,sys
from glob import glob
import re
-from ..coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
+from ..arbdmodel.coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
from ..model.dna_sequence import m13 as m13seq
diff --git a/mrdna/readers/polygon_mesh.py b/mrdna/readers/polygon_mesh.py
index ec41a6774f6f5ef80373235acc999002bd4bd103..15ba8a26aa81b3430e85090de24425416a963b5e 100644
--- a/mrdna/readers/polygon_mesh.py
+++ b/mrdna/readers/polygon_mesh.py
@@ -1,7 +1,7 @@
import numpy as np
import sys
import re
-from ..coords import rotationAboutAxis, minimizeRmsd
+from ..arbdmodel.coords import rotationAboutAxis, minimizeRmsd
from ..version import maintainer
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
@@ -310,8 +310,8 @@ def write_pdb_psf(bases, prefix):
""" Function for debugging .ma parser """
- from ..model.arbdmodel import ArbdModel,ParticleType, PointParticle, Group
- from ..model.nonbonded import HarmonicBond
+ from ..arbdmodel import ArbdModel,ParticleType, PointParticle, Group
+ from ..arbdmodel.nonbonded import HarmonicBond
types = {c:ParticleType(c.upper(), mass=1,radius=1) for c in "bfuxyzs"}
bond=HarmonicBond(k=0,r0=1)
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index 277573d351e2eb327f79fd1f3413e1e5a8ed6a3c..475988982f5368eca84b9b03e63ca34e5ef8a2c3 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -6,7 +6,7 @@ import os,sys
import scipy
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
-from ..coords import quaternion_from_matrix
+from ..arbdmodel.coords import quaternion_from_matrix
from .. import get_resource_path
ref_stack_position = np.array((-2.41851735, -0.259761333, 3.39999978))
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 1512a7b033f814dc790aed39fcd4eba1af3fe0b9..7915b9fd18dbe21ba1be502a5aa2afbe79f3a47b 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -2,9 +2,9 @@ import pdb
from pathlib import Path
import numpy as np
import random
-from .model.arbdmodel import PointParticle, ParticleType, Group, ArbdModel
-from .coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
-from .model.nonbonded import *
+from .arbdmodel import PointParticle, ParticleType, Group, ArbdModel
+from .arbdmodel.coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
+from .arbdmodel.nonbonded import *
from copy import copy, deepcopy
from .model.nbPot import nbDnaScheme
@@ -453,6 +453,16 @@ class Segment(ConnectableElement, Group):
tck, u = self.position_spline_params
return np.mean(self.contour_to_position(u), axis=0)
+ def get_bounding_box( self, num_points=3 ):
+ positions = np.zeros( num_points, 3)
+ i = 0
+ for c in linspace(0,1,num_points):
+ positions[i] = self.contour_to_position(c)
+ i += 1
+ min_ = np.array([np.min(positions[:,i]) for i in range(3)])
+ max_ = np.array([np.max(positions[:,i]) for i in range(3)])
+ return min_,max_
+
def _get_location_positions(self):
return [self.contour_to_nt_pos(l.address) for l in self.locations]
@@ -558,7 +568,7 @@ class Segment(ConnectableElement, Group):
if self.quaternion_spline_params is not None:
## TODO: performance: don't shift between quaternion and matrix representations so much
tck, u = self.quaternion_spline_params
- orientations = [self.contour_to_orientation(v) for v in u]
+ orientations = np.array([self.contour_to_orientation(v) for v in u])
for i in ids:
orientations[i,:] = rotation_matrix.dot(orientations[i])
quats = [quaternion_from_matrix(o) for o in orientations]
@@ -1551,6 +1561,7 @@ class SegmentModel(ArbdModel):
timestep=50e-6, cutoff=50,
decompPeriod=10000, pairlistDistance=None,
nonbondedResolution=0, DEBUG=0,
+ integrator='Brown',
debye_length = None,
extra_bd_file_lines = "",
):
@@ -1558,9 +1569,9 @@ class SegmentModel(ArbdModel):
if DEBUG > 0: print("Building ARBD Model")
ArbdModel.__init__(self,segments,
origin, dimensions,
- temperature, timestep, cutoff,
- decompPeriod, pairlistDistance=None,
- nonbondedResolution = 0,
+ temperature, timestep, integrator,
+ cutoff, decompPeriod, pairlist_distance=None,
+ nonbonded_resolution = 0,
extra_bd_file_lines = extra_bd_file_lines
)
@@ -2428,7 +2439,7 @@ class SegmentModel(ArbdModel):
parent = self._getParent( b1, b2 )
""" Add heuristic 90 degree potential to keep orientation bead orthogonal """
- k = 0.5*k_dsdna_angle(sep)
+ k = 0.25*k_dsdna_angle(sep)
pot = self.get_angle_potential(k,90)
parent.add_angle(o1,b1,b2, pot)
parent.add_angle(b1,b2,o2, pot)
@@ -2835,10 +2846,20 @@ class SegmentModel(ArbdModel):
## clear strands
try:
for s in self.strands:
- self.children.remove(s)
+ try:
+ self.children.remove(s)
+ except:
+ pass
+ except:
+ pass
+
+ try:
for seg in self.segments:
- for d in ('fwd','rev'):
- seg.strand_pieces[d] = []
+ try:
+ for d in ('fwd','rev'):
+ seg.strand_pieces[d] = []
+ except:
+ pass
except:
pass
self.strands = strands = []
@@ -3210,17 +3231,27 @@ proc calcforces {} {
}
""")
- def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
- positions = []
+ def get_bounding_box( self, num_points=3 ):
+ positions = np.zeros( (len(self.segments)*num_points, 3) )
+ i = 0
for s in self.segments:
- positions.append(s.contour_to_position(0))
- positions.append(s.contour_to_position(0.5))
- positions.append(s.contour_to_position(1))
- positions = np.array(positions)
- dx,dy,dz = [(np.max(positions[:,i])-np.min(positions[:,i])+30)*padding_factor for i in range(3)]
+ for c in linspace(0,1,num_points):
+ positions[i] = (s.contour_to_position(c))
+ i += 1
+ min_ = np.array([np.min(positions[:,i]) for i in range(3)])
+ max_ = np.array([np.max(positions[:,i]) for i in range(3)])
+ return min_,max_
+
+ def get_bounding_box_center( self, num_points=3 ):
+ min_,max_ = self.get_bounding_box(num_points)
+ return 0.5*(max_+min_)
+
+ def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
+ min_,max_ = self.get_bounding_box()
+ dx,dy,dz = (max_-min_+30)*padding_factor
if isotropic:
dx = dy = dz = max((dx,dy,dz))
- return [dx,dy,dz]
+ return np.array([dx,dy,dz])
def add_grid_potential(self, grid_file, scale=1, per_nucleotide=True):
grid_file = Path(grid_file)
@@ -3255,12 +3286,265 @@ proc calcforces {} {
first_atomic_index = s.generate_atomic_model(scale,first_atomic_index)
self._assign_basepairs()
+ """ OxDNA """
+ ## https://dna.physics.ox.ac.uk/index.php/Documentation#Input_file
def generate_oxdna_model(self, scale=1):
self.clear_beads()
self.children = self.strands
for s in self.strands:
s.generate_oxdna_model()
+ def _write_oxdna_configuration(self, filename):
+
+ _angstroms_to_oxdna = 0.11739845 ## units "AA" "8.518e-10 m"
+ with open(filename,'w') as fh:
+ fh.write("""t = {temperature}
+b = {dimX} {dimY} {dimZ}
+E = 0 0 0
+""".format(temperature=self.temperature,
+ dimX = self.dimensions[0]*_angstroms_to_oxdna,
+ dimY = self.dimensions[1]*_angstroms_to_oxdna,
+ dimZ = self.dimensions[2]*_angstroms_to_oxdna))
+
+ base_vec = np.array((1,0,0)) # TODO
+ norm_vec = np.array((0,0,1)) # TODO
+
+ ## Traverse 3'-to-5'
+ for nt in [nt for s in self.strands for nt in s.oxdna_nt[::-1]]:
+ data = dict()
+ # o = nt.collapsedOrientation()
+ o = nt.orientation
+ for k,v in zip('x y z'.split(),nt.collapsedPosition()):
+ data[k] = v * _angstroms_to_oxdna
+ for k,v in zip('x y z'.split(),o.dot(base_vec)):
+ data['b'+k] = v
+ for k,v in zip('x y z'.split(),o.dot(norm_vec)):
+ data['n'+k] = v
+ fh.write("{x} {y} {z} {bx} {by} {bz} {nx} {ny} {nz} 0 0 0 0 0 0\n".format(**data)
+ )
+
+ def _write_oxdna_topology(self,filename):
+
+ strands = [s for s in self.strands if s.num_nt > 0]
+ with open(filename,'w') as fh:
+
+ fh.write("{num_nts} {num_strands}\n".format(
+ num_nts = sum([s.num_nt for s in strands]),
+ num_strands = len(self.strands)))
+
+ idx = 0
+ sidx = 1
+ for strand in strands:
+ prev = idx+len(strand.num_nt) if strand.is_circular else -1
+ last = idx if strand.is_circular else -1
+
+ ## Traverse 3'-to-5'
+ sequence = [seq for s in strand.strand_segments
+ for seq in s.get_sequence()][::-1]
+ for seq in sequence[:-1]:
+ ## strand seq 3' 5'
+ fh.write("{} {} {} {}\n".format(sidx, seq, prev, idx+1))
+ prev = idx
+ idx += 1
+ seq = sequence[-1]
+ fh.write("{} {} {} {}\n".format(sidx, seq, prev, last))
+ idx += 1
+ sidx += 1
+
+ def _write_oxdna_input(self, filename,
+ topology,
+ conf_file,
+ trajectory_file,
+ last_conf_file,
+ log_file,
+ num_steps = 1e6,
+ interaction_type = 'DNA2',
+ salt_concentration = None,
+ print_conf_interval = None,
+ print_energy_every = None,
+ timestep = 0.003,
+ sim_type = "MD",
+ backend = None,
+ backend_precision = None,
+ seed = None,
+ newtonian_steps = 103,
+ diff_coeff = 2.50,
+ thermostat = "john",
+ list_type = "cells",
+ ensemble = "nvt",
+ delta_translation = 0.22,
+ delta_rotation = 0.22,
+ verlet_skin = 0.5,
+ max_backbone_force = 5,
+ ):
+
+ if seed is None:
+ import random
+ seed = random.randint(1,99999)
+
+ temperature = self.temperature
+ num_steps = int(num_steps)
+ newtonian_steps = int(newtonian_steps)
+
+ if print_conf_interval is None:
+ # print_conf_interval = min(num_steps//100)
+ print_conf_interval = 10000
+ print_conf_interval = int(print_conf_interval)
+
+ if print_energy_every is None:
+ print_energy_every = print_conf_interval
+ print_energy_every = int(print_energy_every)
+
+ if max_backbone_force is not None:
+ max_backbone_force = 'max_backbone_force = {}'.format(max_backbone_force)
+
+
+ if interaction_type in ('DNA2',):
+ if salt_concentration is None:
+ try:
+ ## units "80 epsilon0 295 k K / (2 (AA)**2 e**2/particle)" mM
+ salt_concentration = 9331.3126/self.debye_length**2
+ except:
+ salt_concentration = 0.5
+ salt_concentration = 'salt_concentration = {}'.format(salt_concentration)
+ else:
+ salt_concentration = ''
+
+ if backend is None:
+ backend = 'CUDA' if sim_type == 'MD' else 'CPU'
+
+ if backend_precision is None:
+ backend_precision = 'mixed' if backend == 'CUDA' else 'double'
+
+ if sim_type == 'VMMC':
+ ensemble = 'ensemble = {}'.format(ensemble)
+ delta_translation = 'delta_translation = {}'.format(delta_translation)
+ delta_rotation = 'delta_rotation = {}'.format(delta_rotation)
+ else:
+ ensemble = ''
+ delta_translation = ''
+ delta_rotation = ''
+
+ with open(filename,'w') as fh:
+ fh.write("""##############################
+#### PROGRAM PARAMETERS ####
+##############################
+interaction_type = {interaction_type}
+{salt_concentration}
+sim_type = {sim_type}
+backend = {backend}
+backend_precision = {backend_precision}
+#debug = 1
+seed = {seed}
+
+##############################
+#### SIM PARAMETERS ####
+##############################
+steps = {num_steps:d}
+newtonian_steps = {newtonian_steps:d}
+diff_coeff = {diff_coeff}
+thermostat = {thermostat}
+
+list_type = {list_type}
+{ensemble}
+{delta_translation}
+{delta_rotation}
+
+T = {temperature:f} K
+dt = {timestep}
+verlet_skin = {verlet_skin}
+{max_backbone_force}
+
+##############################
+#### INPUT / OUTPUT ####
+##############################
+topology = {topology}
+conf_file = {conf_file}
+lastconf_file = {last_conf_file}
+trajectory_file = {trajectory_file}
+refresh_vel = 1
+log_file = {log_file}
+no_stdout_energy = 1
+restart_step_counter = 1
+energy_file = {log_file}.energy.dat
+print_conf_interval = {print_conf_interval}
+print_energy_every = {print_energy_every}
+time_scale = linear
+external_forces = 0
+""".format( **locals() ))
+
+ def simulate_oxdna(self, output_name, directory='.', output_directory='output', topology=None, configuration=None, oxDNA=None, **oxdna_args):
+
+ if output_directory == '': output_directory='.'
+ d_orig = os.getcwd()
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+
+ os.chdir(directory)
+ try:
+
+ if oxDNA is None:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ fname = os.path.join(path, "oxDNA")
+ if os.path.isfile(fname) and os.access(fname, os.X_OK):
+ oxDNA = fname
+ break
+
+ if oxDNA is None: raise Exception("oxDNA was not found")
+
+ if not os.path.exists(oxDNA):
+ raise Exception("oxDNA was not found")
+ if not os.path.isfile(oxDNA):
+ raise Exception("oxDNA was not found")
+ if not os.access(oxDNA, os.X_OK):
+ raise Exception("oxDNA is not executable")
+
+ if not os.path.exists(output_directory):
+ os.makedirs(output_directory)
+ elif not os.path.isdir(output_directory):
+ raise Exception("output_directory '%s' is not a directory!" % output_directory)
+
+
+ if configuration is None:
+ configuration = "{}.conf".format(output_name)
+ self._write_oxdna_configuration(configuration)
+ # elif not Path(configuration).exists():
+ # raise Exception("Unable to find oxDNA configuration file '{}'.".format(configuration))
+
+ if topology is None:
+ topology = "{}-topology.dat".format(output_name)
+ self._write_oxdna_topology(topology)
+ elif not Path(topology).exists():
+ raise Exception("Unable to find oxDNA topology file '{}'.".format(topology))
+
+ last_conf_file = "{}/{}.last.conf".format(output_directory,output_name)
+ input_file = "{}-input".format(output_name)
+
+ self._write_oxdna_input(input_file,
+ topology = topology,
+ conf_file = configuration,
+ trajectory_file = "{}/{}.dat".format(output_directory,output_name),
+ last_conf_file = last_conf_file,
+ log_file="{}/{}.log".format(output_directory,output_name),
+ **oxdna_args)
+ os.sync()
+ ## TODO: call oxdna
+ cmd = [oxDNA, input_file]
+
+ cmd = tuple(str(x) for x in cmd)
+
+ print("Running oxDNA with: %s" % " ".join(cmd))
+ process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for line in process.stdout:
+ sys.stdout.write(line)
+ sys.stdout.flush()
+
+ return topology,last_conf_file
+ finally:
+ os.chdir(d_orig)
+
+ """ Visualization """
def vmd_tube_tcl(self, file_name="drawTubes.tcl"):
with open(file_name, 'w') as tclFile:
tclFile.write("## beginning TCL script \n")
diff --git a/mrdna/simulate.py b/mrdna/simulate.py
index e8aa7eaebc8469d24f941996820b32eced975f69..c388a4ab10e8a9c4ef23e19dec1043c82724c76f 100644
--- a/mrdna/simulate.py
+++ b/mrdna/simulate.py
@@ -1,6 +1,6 @@
import os
import tempfile
-from .coords import readArbdCoords, readAvgArbdCoords
+from .arbdmodel.coords import readArbdCoords, readAvgArbdCoords
import shutil
from . import get_resource_path