diff --git a/mrdna/arbdmodel/__init__.py b/mrdna/arbdmodel/__init__.py
index 7e66eabc4d02c7f965bce891c703686a907f01c0..cb9a342a9141db68dab9821fc1d1c984f16f687f 100644
--- a/mrdna/arbdmodel/__init__.py
+++ b/mrdna/arbdmodel/__init__.py
@@ -9,6 +9,9 @@ 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():
@@ -69,8 +72,9 @@ class Parent():
self.impropers = []
self.exclusions = []
- ## TODO: self.cacheInvalid = True # What will be in the cache?
+ 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
@@ -82,6 +86,19 @@ class Parent():
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:
@@ -96,7 +113,8 @@ class Parent():
def remove(self,x):
if x in self.children:
self.children.remove(x)
- x.parent = None
+ if x.parent is self:
+ x.parent = None
def add_bond(self, i,j, bond, exclude=False):
## TODO: how to handle duplicating and cloning bonds
@@ -235,11 +253,17 @@ class Child():
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)
@@ -307,25 +331,35 @@ class ParticleType():
excludedAttributes = ("idx","type_",
"position",
"children",
- "parent", "excludedAttributes",
+ "parent", "excludedAttributes","rigid"
)
- def __init__(self, name, charge=0, **kargs):
- # parent = None
- # if "parent" in kargs: parent = kargs["parent"]
- # Child.__init__(self, parent)
+ 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)
@@ -352,7 +386,10 @@ class ParticleType():
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):
@@ -378,6 +415,9 @@ class PointParticle(Transformable, Child):
def get_restraints(self):
return [(self,r) for r in self.restraints]
+ def duplicate(self):
+ new = deepcopy(self)
+ return new
def __getattr__(self, name):
"""
@@ -401,6 +441,10 @@ class PointParticle(Transformable, Child):
segname = p.segname
except:
segname = "A"
+ try:
+ chain = p.chain
+ except:
+ chain = "A"
try:
resname = p.resname
except:
@@ -409,6 +453,10 @@ class PointParticle(Transformable, Child):
resid = p.resid
except:
resid = p.idx+1
+ try:
+ mass = p.mass
+ except:
+ mass = 1
try:
occ = p.occupancy
@@ -422,12 +470,12 @@ class PointParticle(Transformable, Child):
data = dict(segname = segname,
resname = resname,
name = str(p.name)[:4],
- chain = "A",
+ chain = chain[0],
resid = int(resid),
idx = p.idx+1,
- type = p.type_.name[:4],
+ type = p.type_.name[:7],
charge = p.charge,
- mass = p.mass,
+ mass = mass,
occupancy = occ,
beta = beta
)
@@ -622,15 +670,21 @@ class PdbModel(Transformable, Parent):
class ArbdModel(PdbModel):
- def __init__(self, children, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6, cutoff=50, decompPeriod=10000, pairlistDistance=None, nonbondedResolution=0.1, remove_duplicate_bonded_terms=True):
+ def __init__(self, children, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6,
+ particle_integrator = 'Brown',
+ cutoff=50, decompPeriod=1000, pairlistDistance=None, nonbondedResolution=0.1,
+ remove_duplicate_bonded_terms=True):
+
PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms)
self.temperature = temperature
self.timestep = timestep
self.cutoff = cutoff
+ self.particle_integrator = particle_integrator
+
if pairlistDistance == None:
- pairlistDistance = cutoff+2
+ pairlistDistance = cutoff+30
self.decompPeriod = decompPeriod
self.pairlistDistance = pairlistDistance
@@ -661,11 +715,11 @@ class ArbdModel(PdbModel):
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:
+ elif A is None and typeB.is_same_type(B):
return s
- elif B is None and typeA == A:
+ elif B is None and typeA.is_same_type(A):
return s
- elif typeA == A and typeB == B:
+ 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))
@@ -697,7 +751,7 @@ class ArbdModel(PdbModel):
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):
+ 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, dry_run = False):
assert(type(gpu) is int)
num_steps = int(num_steps)
@@ -716,22 +770,26 @@ class ArbdModel(PdbModel):
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 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 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(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)
@@ -741,7 +799,7 @@ class ArbdModel(PdbModel):
self.writePdb( output_name + ".pdb" )
self.writePsf( output_name + ".psf" )
- self.writeArbdFiles( output_name, numSteps=num_steps, outputPeriod=output_period )
+ 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
@@ -752,11 +810,14 @@ class ArbdModel(PdbModel):
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))
- process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
- for line in process.stdout:
- sys.stdout.write(line)
- sys.stdout.flush()
+ if dry_run:
+ print("Run with: %s" % " ".join(cmd))
+ else:
+ print("Running ARBD 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()
except:
raise
@@ -768,7 +829,7 @@ class ArbdModel(PdbModel):
# Methods for printing model #
# -------------------------- #
- def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000):
+ 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):
@@ -787,7 +848,7 @@ class ArbdModel(PdbModel):
self._writeArbdDihedralFile()
self._writeArbdExclusionFile()
self._writeArbdPotentialFiles( prefix, directory = d )
- self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod )
+ self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod, restart_file=restart_file )
# def _writeArbdCoordFile(self, filename):
# with open(filename,'w') as fh:
@@ -796,12 +857,49 @@ class ArbdModel(PdbModel):
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):
+ 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
@@ -816,10 +914,10 @@ class ArbdModel(PdbModel):
# params['coordinateFile'] = "%s.coord.txt" % prefix
params['particleFile'] = "%s.particles.txt" % prefix
- if restartCoordinateFile is None:
+ if restart_file is None:
params['restartCoordinates'] = ""
else:
- params['restartCoordinates'] = "restartCoordinates %s" % restartCoordinateFile
+ params['restartCoordinates'] = "restartCoordinates %s" % restart_file
params['outputPeriod'] = outputPeriod
for k,v in zip('XYZ', self.dimensions):
@@ -828,6 +926,26 @@ class ArbdModel(PdbModel):
params['pairlistDistance'] -= 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}
@@ -838,6 +956,7 @@ numberFluct 0 # deprecated
interparticleForce 1 # other values deprecated
fullLongRange 0 # deprecated
temperature {temperature}
+ParticleDynamicType {particle_integrator}
outputPeriod {outputPeriod}
## Energy doesn't actually get printed!
@@ -858,10 +977,28 @@ systemSize {dimX} {dimY} {dimZ}
## 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}
-diffusion {diffusivity}
+{dynamics}
""".format(**particleParams))
if 'grid' in particleParams:
if not isinstance(pt.grid, list): pt.grid = [pt.grid]
@@ -996,7 +1133,7 @@ component "data" value 3
def _writeArbdBondFile( self ):
for b in list( set( [b for i,j,b,ex in self.get_bonds()] ) ):
- if type(b) is not str:
+ if type(b) is not str and not isinstance(b, Path):
b.write_file()
with open(self._bond_filename,'w') as fh:
@@ -1009,7 +1146,7 @@ component "data" value 3
def _writeArbdAngleFile( self ):
for b in list( set( [b for i,j,k,b in self.get_angles()] ) ):
- if type(b) is not str:
+ if type(b) is not str and not isinstance(b, Path):
b.write_file()
with open(self._angle_filename,'w') as fh:
@@ -1019,7 +1156,7 @@ component "data" value 3
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:
+ if type(b) is not str and not isinstance(b, Path):
b.write_file()
with open(self._dihedral_filename,'w') as fh:
@@ -1075,7 +1212,7 @@ 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
+set temperature {temperature}
structure $prefix.psf
coordinates $prefix.pdb
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..8b7ae920cd2ce3972d2ec3107fb316a29e99bf0a
--- /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 = 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/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
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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
index 0000000000000000000000000000000000000000..f7705c141d9d9008f7e36a0394171d1b0b659069
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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
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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
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new file mode 100644
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+0 0.002154
+2 0.001387
+4 0.000269
+6 0.000000
+8 0.000080
+10 0.010572
+12 0.010622
+14 0.013736
+16 0.017045
+18 0.033739
+20 0.048157
+22 0.060371
+24 0.073661
+26 0.102425
+28 0.121034
+30 0.146200
+32 0.157730
+34 0.183955
+36 0.193021
+38 0.205705
+40 0.208412
+42 0.230895
+44 0.243342
+46 0.260527
+48 0.261798
+50 0.268291
+52 0.281542
+54 0.289614
+56 0.301048
+58 0.304241
+60 0.308697
+62 0.321239
+64 0.331523
+66 0.360957
+68 0.378023
+70 0.403674
+72 0.418397
+74 0.436186
+76 0.458524
+78 0.472007
+80 0.485402
+82 0.488541
+84 0.496830
+86 0.511168
+88 0.519624
+90 0.534245
+92 0.537758
+94 0.540560
+96 0.545529
+98 0.552555
+100 0.562928
+102 0.561080
+104 0.563666
+106 0.573167
+108 0.578486
+110 0.578920
+112 0.565700
+114 0.576042
+116 0.575288
+118 0.583509
+120 0.577520
+122 0.576253
+124 0.574493
+126 0.565240
+128 0.571560
+130 0.565958
+132 0.560775
+134 0.543710
+136 0.548994
+138 0.549055
+140 0.551426
+142 0.535725
+144 0.540487
+146 0.535907
+148 0.544173
+150 0.535025
+152 0.536973
+154 0.527365
+156 0.525082
+158 0.524349
+160 0.530925
+162 0.529991
+164 0.528378
+166 0.525491
+168 0.535666
+170 0.541837
+172 0.538046
+174 0.538587
+176 0.538206
+178.000000 0.538206
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
index 0000000000000000000000000000000000000000..bd893784794cf6012e3f27e0b773a7c01fa40af9
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-pri.bea
@@ -0,0 +1,14 @@
+ATOM 1 O 0.670 -0.235 -37.199
+ATOM 2 O 1.321 0.042 -37.278
+ATOM 3 O 1.422 0.542 -36.822
+ATOM 4 O 1.295 1.186 -37.112
+ATOM 5 O 0.690 1.467 -37.071
+ATOM 6 O 1.800 1.509 -37.397
+ATOM 7 O 2.350 1.291 -37.430
+ATOM 8 O 1.654 2.115 -37.618
+ATOM 9 O 1.092 2.451 -37.506
+ATOM 10 O 1.086 3.040 -37.581
+ATOM 11 O 0.564 2.069 -37.268
+ATOM 12 O -0.081 2.373 -37.150
+ATOM 13 O 1.005 0.362 -36.249
+ATOM 14 O 0.859 0.785 -35.953
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
new file mode 100644
index 0000000000000000000000000000000000000000..f9c9ba05346311deef19065f198bb48eaf7153eb
--- /dev/null
+++ b/mrdna/arbdmodel/resources/two_bead_model/diffusion/b-bead.hydropro-pri.vrml
@@ -0,0 +1,127 @@
+#VRML V2.0 utf8
+Transform {
+ translation -0.12224E+01 -0.25392E+00 -0.58241E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.10178E+01 0.25926E+00 -0.37039E+00
+ children [
+ Shape {
+ geometry Sphere { radius 0.11637E+01 }
+ appearance Appearance { material Material{ diffuseColor 1.0 1.0 0.0 } }
+ }
+ ]
+}
+Transform {
+ translation -0.73304E+00 0.17242E+00 0.11453E+00
+ children [
+ Shape {
+ 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
+-122 0.405452
+-120 0.396897
+-118 0.396377
+-116 0.391831
+-114 0.381875
+-112 0.378410
+-110 0.371038
+-108 0.374191
+-106 0.362868
+-104 0.352374
+-102 0.343466
+-100 0.349973
+-98 0.337400
+-96 0.330375
+-94 0.313766
+-92 0.324400
+-90 0.316124
+-88 0.304002
+-86 0.287405
+-84 0.272551
+-82 0.270613
+-80 0.255013
+-78 0.254488
+-76 0.242488
+-74 0.228795
+-72 0.218269
+-70 0.205314
+-68 0.208409
+-66 0.182237
+-64 0.173722
+-62 0.160758
+-60 0.163178
+-58 0.153167
+-56 0.138261
+-54 0.137087
+-52 0.132396
+-50 0.133878
+-48 0.128352
+-46 0.128606
+-44 0.124664
+-42 0.118276
+-40 0.116375
+-38 0.116042
+-36 0.108532
+-34 0.101769
+-32 0.098384
+-30 0.104061
+-28 0.093049
+-26 0.086992
+-24 0.077681
+-22 0.086766
+-20 0.067358
+-18 0.056292
+-16 0.038906
+-14 0.053421
+-12 0.045711
+-10 0.034005
+-8 0.019798
+-6 0.012138
+-4 0.015972
+-2 0.000000
+0 0.006525
+2 0.002471
+4 0.011939
+6 0.016578
+8 0.013909
+10 0.017481
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new file mode 100644
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new file mode 100644
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new file mode 100644
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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
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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
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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 )