From 17a0c8c9b54f8816beb61294fbaa36ddb6076b14 Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Thu, 1 Aug 2024 11:50:22 -0500
Subject: [PATCH] add
---
.DS_Store | Bin 0 -> 6148 bytes
mrdna/.DS_Store | Bin 0 -> 8196 bytes
.../segmentmodel-checkpoint.py | 4240 +++++++++++++++++
mrdna/RELEASE-VERSION | 2 +-
.../.ipynb_checkpoints/__init__-checkpoint.py | 39 +
.../cadnano_segments-checkpoint.py | 727 +++
.../segmentmodel_from_lists-checkpoint.py | 495 ++
...egmentmodel_from_oxdna_pinyi-checkpoint.py | 162 +
mrdna/readers/cadnano_segments.py | 319 +-
mrdna/readers/segmentmodel_from_cadnano.py | 178 +-
.../readers/segmentmodel_from_oxdna_pinyi.py | 16 +-
11 files changed, 5837 insertions(+), 341 deletions(-)
create mode 100644 .DS_Store
create mode 100644 mrdna/.DS_Store
create mode 100644 mrdna/.ipynb_checkpoints/segmentmodel-checkpoint.py
create mode 100644 mrdna/readers/.ipynb_checkpoints/__init__-checkpoint.py
create mode 100644 mrdna/readers/.ipynb_checkpoints/cadnano_segments-checkpoint.py
create mode 100644 mrdna/readers/.ipynb_checkpoints/segmentmodel_from_lists-checkpoint.py
create mode 100644 mrdna/readers/.ipynb_checkpoints/segmentmodel_from_oxdna_pinyi-checkpoint.py
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diff --git a/mrdna/.ipynb_checkpoints/segmentmodel-checkpoint.py b/mrdna/.ipynb_checkpoints/segmentmodel-checkpoint.py
new file mode 100644
index 0000000..dddaf8c
--- /dev/null
+++ b/mrdna/.ipynb_checkpoints/segmentmodel-checkpoint.py
@@ -0,0 +1,4240 @@
+import logging
+import pdb
+import subprocess
+from pathlib import Path
+import numpy as np
+import random
+from .arbdmodel import PointParticle, ParticleType, Group, ArbdModel
+from .arbdmodel.coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
+from .arbdmodel.nonbonded import *
+from copy import copy, deepcopy
+from .model.nbPot import nbDnaScheme
+
+from . import get_resource_path
+from . import logger, devlogger
+
+import re
+
+from scipy.special import erf
+import scipy.optimize as opt
+from scipy import interpolate
+
+from .model.CanonicalNucleotideAtoms import canonicalNtFwd, canonicalNtRev, seqComplement
+from .model.CanonicalNucleotideAtoms import enmTemplateHC, enmTemplateSQ, enmCorrectionsHC
+
+from .model.spring_from_lp import k_angle as angle_spring_from_lp
+from .model.spring_from_lp import k_twist as twist_spring_from_lp
+
+import csv
+
+# import pdb
+"""
+TODO:
+ + fix handling of crossovers for atomic representation
+ + map to atomic representation
+ + add nicks
+ + transform ssDNA nucleotides
+ - shrink ssDNA
+ + shrink dsDNA backbone
+ + make orientation continuous
+ + sequence
+ + handle circular dna
+ + ensure crossover bead potentials aren't applied twice
+ + remove performance bottlenecks
+ - test for large systems
+ + assign sequence
+ + ENM
+ - rework Location class
+ - remove recursive calls
+ - document
+ - develop unit test suite
+ - refactor parts of Segment into an abstract_polymer class
+ - make each call generate_bead_model, generate_atomic_model, generate_oxdna_model return an object with only have a reference to original object
+"""
+
+_DEBUG_TRACE = False
+
+class CircularDnaError(Exception):
+ pass
+
+class ParticleNotConnectedError(Exception):
+ pass
+
+class Location():
+ """ Site for connection within an object """
+ def __init__(self, container, address, type_, on_fwd_strand = True):
+ ## TODO: remove cyclic references(?)
+ self.container = container
+ self.address = address # represents position along contour length in segment
+ # assert( type_ in ("end3","end5") ) # TODO remove or make conditional
+ self.on_fwd_strand = on_fwd_strand
+ self.type_ = type_
+ self.particle = None
+ self.connection = None
+ self.is_3prime_side_of_connection = None
+
+ self.combine = None # some locations might be combined in bead model
+
+ def get_connected_location(self):
+ if self.connection is None:
+ return None
+ else:
+ return self.connection.other(self)
+
+ def set_connection(self, connection, is_3prime_side_of_connection):
+ self.connection = connection # TODO weakref?
+ self.is_3prime_side_of_connection = is_3prime_side_of_connection
+
+ def get_nt_pos(self):
+ try:
+ pos = self.container.contour_to_nt_pos(self.address, round_nt=True)
+ except:
+ if self.address == 0:
+ pos = 0
+ elif self.address == 1:
+ pos = self.container.num_nt-1
+ else:
+ raise
+ return pos
+
+ def delete(self):
+ if self.particle is not None:
+ self.particle.locations.remove(self)
+ if self.connection is not None:
+ self.connection.delete()
+ self.connection = None
+ if self.container is not None:
+ self.container.locations.remove(self)
+
+ def __repr__(self):
+ if self.on_fwd_strand:
+ on_fwd = "on_fwd_strand"
+ else:
+ on_fwd = "on_rev_strand"
+
+ def __get_parent_name(obj):
+ try:
+ name = obj.name
+ except:
+ name = ''
+ if obj is None:
+ return '_'
+ else:
+ return __get_parent_name(obj) + [name]
+
+ try:
+ container_name = '.'.join(__get_parent_name(self.container))
+ except:
+ container_name = self.container.name
+
+ try:
+ return "<Location {}.{}[{:d},{}]>".format( container_name, self.type_, self.get_nt_pos(), on_fwd )
+ except:
+ return "<Location {}.{}[{:.2f},{:d}]>".format( container_name, self.type_, self.address, self.on_fwd_strand)
+
+class Connection():
+ """ Abstract base class for connection between two elements """
+ def __init__(self, A, B, type_ = None):
+ assert( isinstance(A,Location) )
+ assert( isinstance(B,Location) )
+ self.A = A
+ self.B = B
+ self.type_ = type_
+
+ def other(self, location):
+ if location is self.A:
+ return self.B
+ elif location is self.B:
+ return self.A
+ else:
+ raise Exception("OutOfBoundsError")
+
+ def delete(self):
+ self.A.container.connections.remove(self)
+ if self.B.container is not self.A.container:
+ self.B.container.connections.remove(self)
+ self.A.connection = None
+ self.B.connection = None
+ self.A.type_ = "3prime" # TODO move specialization to inherited class
+ self.B.type_ = "5prime"
+ self.A = self.B = None
+
+ def __repr__(self):
+ return "<Connection {}--{}--{}]>".format( self.A, self.type_, self.B )
+
+
+
+# class ConnectableElement(Transformable):
+class ConnectableElement():
+ """ Abstract base class """
+ def __init__(self, connection_locations=None, connections=None):
+ if connection_locations is None: connection_locations = []
+ if connections is None: connections = []
+
+ ## TODO decide on names
+ self.locations = self.connection_locations = connection_locations
+ self.connections = connections
+
+ def get_locations(self, type_=None, exclude=()):
+ locs = [l for l in self.connection_locations if (type_ is None or l.type_ == type_) and l.type_ not in exclude]
+ counter = dict()
+ for l in locs:
+ if l in counter:
+ counter[l] += 1
+ else:
+ counter[l] = 1
+ assert( np.all( [counter[l] == 1 for l in locs] ) )
+ return locs
+
+ def get_location_at(self, address, on_fwd_strand=True, new_type=None):
+ loc = None
+ if (self.num_nt == 1):
+ # import pdb
+ # pdb.set_trace()
+ ## Assumes that intrahelical connections have been made before crossovers
+ for l in self.locations:
+ if l.on_fwd_strand == on_fwd_strand and l.connection is None:
+ assert(loc is None)
+ loc = l
+ # assert( loc is not None )
+ else:
+ for l in self.locations:
+ if l.address == address and l.on_fwd_strand == on_fwd_strand:
+ assert(loc is None)
+ loc = l
+ if loc is None and new_type is not None:
+ loc = Location( self, address=address, type_=new_type, on_fwd_strand=on_fwd_strand )
+ return loc
+
+ def get_connections_and_locations(self, connection_type=None, exclude=()):
+ """ Returns a list with each entry of the form:
+ connection, location_in_self, location_in_other """
+ type_ = connection_type
+ ret = []
+ for c in self.connections:
+ if (type_ is None or c.type_ == type_) and c.type_ not in exclude:
+ if c.A.container is self:
+ ret.append( [c, c.A, c.B] )
+ elif c.B.container is self:
+ ret.append( [c, c.B, c.A] )
+ else:
+ import pdb
+ pdb.set_trace()
+ raise Exception("Object contains connection that fails to refer to object")
+ return ret
+
+ def _connect(self, other, connection, in_3prime_direction=None):
+ ## TODO fix circular references
+ A,B = [connection.A, connection.B]
+ if in_3prime_direction is not None:
+ A.is_3prime_side_of_connection = not in_3prime_direction
+ B.is_3prime_side_of_connection = in_3prime_direction
+
+ A.connection = B.connection = connection
+ self.connections.append(connection)
+ if other is not self:
+ other.connections.append(connection)
+
+ l = A.container.locations
+ if A not in l: l.append(A)
+ l = B.container.locations
+ if B not in l: l.append(B)
+
+
+ # def _find_connections(self, loc):
+ # return [c for c in self.connections if c.A == loc or c.B == loc]
+
+class SegmentParticle(PointParticle):
+ def __init__(self, type_, position, name="A", **kwargs):
+ self.name = name
+ self.contour_position = None
+ PointParticle.__init__(self, type_, position, name=name, **kwargs)
+ self.intrahelical_neighbors = []
+ self.other_neighbors = []
+ self.locations = []
+
+ def get_intrahelical_above(self, all_types=True):
+ """ Returns bead directly above self """
+ # assert( len(self.intrahelical_neighbors) <= 2 )
+ for b in self.intrahelical_neighbors:
+ if b.get_contour_position(self.parent, self.contour_position) > self.contour_position:
+ if all_types or isinstance(b,type(self)):
+ return b
+
+ def get_intrahelical_below(self, all_types=True):
+ """ Returns bead directly below self """
+ # assert( len(self.intrahelical_neighbors) <= 2 )
+ for b in self.intrahelical_neighbors:
+ if b.get_contour_position(self.parent, self.contour_position) < self.contour_position:
+ if all_types or isinstance(b,type(self)):
+ return b
+
+ def _neighbor_should_be_added(self,b):
+ if type(self.parent) != type(b.parent):
+ return True
+
+ c1 = self.contour_position
+ c2 = b.get_contour_position(self.parent,c1)
+ if c2 < c1:
+ b0 = self.get_intrahelical_below()
+ else:
+ b0 = self.get_intrahelical_above()
+
+ if b0 is not None:
+ c0 = b0.get_contour_position(self.parent,c1)
+ if np.abs(c2-c1) < np.abs(c0-c1):
+ ## remove b0
+ self.intrahelical_neighbors.remove(b0)
+ b0.intrahelical_neighbors.remove(self)
+ return True
+ else:
+ return False
+ return True
+
+ def make_intrahelical_neighbor(self,b):
+ add1 = self._neighbor_should_be_added(b)
+ add2 = b._neighbor_should_be_added(self)
+ if add1 and add2:
+ # assert(len(b.intrahelical_neighbors) <= 1)
+ # assert(len(self.intrahelical_neighbors) <= 1)
+ self.intrahelical_neighbors.append(b)
+ b.intrahelical_neighbors.append(self)
+
+ def conceptual_get_position(self, context):
+ """
+ context: object
+
+Q: does this function do too much?
+Danger of mixing return values
+
+Q: does context describe the system or present an argument?
+ """
+
+ ## Validate Inputs
+ ...
+
+ ## Algorithm
+ """
+context specifies:
+ - kind of output: real space, nt within segment, fraction of segment
+ - absolute or relative
+ - constraints: e.g. if passing through
+ """
+ """
+given context, provide the position
+ input
+"""
+
+ def get_nt_position(self, seg, near_address=None):
+ """ Returns the "address" of the nucleotide relative to seg in
+ nucleotides, taking the shortest (intrahelical) contour length route to seg
+ """
+ if seg == self.parent:
+ pos = self.contour_position
+ else:
+ pos = self.get_contour_position(seg,near_address)
+ return seg.contour_to_nt_pos(pos)
+
+ def get_contour_position(self,seg, address = None):
+ """ TODO: fix paradigm where a bead maps to exactly one location in a polymer
+ - One way: modify get_contour_position to take an optional argument that indicates where in the polymer you are looking from
+ """
+
+ if seg == self.parent:
+ return self.contour_position
+ else:
+ cutoff = 30*3
+ target_seg = seg
+
+ ## depth-first search
+ ## TODO cache distances to nearby locations?
+ def descend_search_tree(seg, contour_in_seg, distance=0, visited_segs=None):
+ nonlocal cutoff
+ if visited_segs is None: visited_segs = []
+
+ if seg == target_seg:
+ # pdb.set_trace()
+ ## Found a segment in our target
+ sign = 1 if contour_in_seg == 1 else -1
+ if sign == -1: assert( contour_in_seg == 0 )
+ if distance < cutoff: # TODO: check if this does anything
+ cutoff = distance
+ return [[distance, contour_in_seg+sign*seg.nt_pos_to_contour(distance)]], [(seg, contour_in_seg, distance)]
+ if distance > cutoff:
+ return None,None
+
+ ret_list = []
+ hist_list = []
+ ## Find intrahelical locations in seg that we might pass through
+ conn_locs = seg.get_connections_and_locations("intrahelical")
+ if isinstance(target_seg, SingleStrandedSegment):
+ tmp = seg.get_connections_and_locations("sscrossover")
+ conn_locs = conn_locs + list(filter(lambda x: x[2].container == target_seg, tmp))
+ for c,A,B in conn_locs:
+ if B.container in visited_segs: continue
+ dx = seg.contour_to_nt_pos( A.address, round_nt=False ) - seg.contour_to_nt_pos( contour_in_seg, round_nt=False)
+ dx = np.abs(dx)
+ results,history = descend_search_tree( B.container, B.address,
+ distance+dx, visited_segs + [seg] )
+ if results is not None:
+ ret_list.extend( results )
+ hist_list.extend( history )
+ return ret_list,hist_list
+
+ results,history = descend_search_tree(self.parent, self.contour_position)
+ if results is None or len(results) == 0:
+ raise Exception("Could not find location in segment") # TODO better error
+ if address is not None:
+ return sorted(results,key=lambda x:(x[0],(x[1]-address)**2))[0][1]
+ else:
+ return sorted(results,key=lambda x:x[0])[0][1]
+ # nt_pos = self.get_nt_position(seg)
+ # return seg.nt_pos_to_contour(nt_pos)
+
+ def combine(self, other):
+ assert(other in self.intrahelical_neighbors)
+ assert(self in other.intrahelical_neighbors)
+
+ self.intrahelical_neighbors.remove(other)
+ other.intrahelical_neighbors.remove(self)
+ for b in other.intrahelical_neighbors:
+ b.intrahelical_neighbors.remove(other)
+ b.intrahelical_neighbors.append(self)
+ self.intrahelical_neighbors.append(b)
+ for l in other.locations:
+ self.locations.append(l)
+ l.particle = self
+
+ ## Remove bead
+ other.parent.children.remove(other)
+ if other in other.parent.beads:
+ other.parent.beads.remove(other)
+ if 'orientation_bead' in other.__dict__:
+ other.parent.children.remove(other.orientation_bead)
+
+ for b in list(other.parent.bonds):
+ if other in b[:2]: other.parent.bonds.remove(b)
+
+ def update_position(self, contour_position):
+ self.contour_position = contour_position
+ self.position = self.parent.contour_to_position(contour_position)
+ if 'orientation_bead' in self.__dict__:
+ o = self.orientation_bead
+ o.contour_position = contour_position
+ orientation = self.parent.contour_to_orientation(contour_position)
+ if orientation is None:
+ print("WARNING: local_twist is True, but orientation is None; using identity")
+ orientation = np.eye(3)
+ o.position = self.position + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
+
+ def __repr__(self):
+ return "<SegmentParticle {} on {}[{:.2f}]>".format( self.name, self.parent, self.contour_position)
+
+
+## TODO break this class into smaller, better encapsulated pieces
+class Segment(ConnectableElement, Group):
+
+ """ Base class that describes a segment of DNA. When built from
+ cadnano models, should not span helices """
+
+ """Define basic particle types"""
+ dsDNA_particle = ParticleType("D",
+ diffusivity = 43.5,
+ mass = 300,
+ radius = 3,
+ )
+ orientation_particle = ParticleType("O",
+ diffusivity = 100,
+ mass = 300,
+ radius = 1,
+ )
+
+ # orientation_bond = HarmonicBond(10,2)
+ orientation_bond = HarmonicBond(30,1.5, rRange = (0,500) )
+
+ ssDNA_particle = ParticleType("S",
+ diffusivity = 43.5,
+ mass = 150,
+ radius = 3,
+ )
+
+ def __init__(self, name, num_nt,
+ start_position = None,
+ end_position = None,
+ segment_model = None,
+ resolution = None,
+ **kwargs):
+
+ if start_position is None: start_position = np.array((0,0,0))
+
+ Group.__init__(self, name, children=[], **kwargs)
+ ConnectableElement.__init__(self, connection_locations=[], connections=[])
+
+ if 'segname' not in kwargs:
+ self.segname = name
+ # self.resname = name
+ self.start_orientation = None
+ self.twist_per_nt = 0
+
+ self.beads = [c for c in self.children] # self.beads will not contain orientation beads
+
+ self._bead_model_generation = 0 # TODO: remove?
+ self.segment_model = segment_model # TODO: remove?
+ self.resolution = resolution
+
+ self.strand_pieces = dict()
+ for d in ('fwd','rev'):
+ self.strand_pieces[d] = []
+
+ self.num_nt = int(num_nt)
+ if end_position is None:
+ end_position = np.array((0,0,self.distance_per_nt*num_nt)) + start_position
+ self.start_position = start_position
+ self.end_position = end_position
+
+ ## Used to assign cadnano names to beads
+ self._generate_bead_callbacks = []
+ self._generate_nucleotide_callbacks = []
+
+ ## Set up interpolation for positions
+ self._set_splines_from_ends()
+
+ self.sequence = None
+
+ def __repr__(self):
+ return "<{} {}[{:d}]>".format( str(type(self)).split('.')[-1], self.name, self.num_nt )
+
+ def set_splines(self, contours, coords):
+ tck, u = interpolate.splprep( coords.T, u=contours, s=0, k=1)
+ self.position_spline_params = (tck,u)
+
+ def set_orientation_splines(self, contours, quaternions):
+ tck, u = interpolate.splprep( quaternions.T, u=contours, s=0, k=1)
+ self.quaternion_spline_params = (tck,u)
+
+ def get_center(self):
+ tck, u = self.position_spline_params
+ return np.mean(self.contour_to_position(u), axis=0)
+
+ def get_bounding_box( self, num_points=3 ):
+ positions = np.zeros( (num_points, 3) )
+ i = 0
+ for c in np.linspace(0,1,num_points):
+ positions[i] = self.contour_to_position(c)
+ i += 1
+ min_ = np.array([np.min(positions[:,i]) for i in range(3)])
+ max_ = np.array([np.max(positions[:,i]) for i in range(3)])
+ return min_,max_
+
+ def get_location_at_nt(self, nt, on_fwd_strand=True, new_type=None):
+ a = self.nt_pos_to_contour(nt)
+ return self.get_location_at(a, on_fwd_strand, new_type)
+
+ def _get_location_positions(self):
+ return [self.contour_to_nt_pos(l.address) for l in self.locations]
+
+ def insert_dna(self, at_nt: int, num_nt: int, seq=tuple()):
+ assert(np.isclose(np.around(num_nt),num_nt))
+ if at_nt < 0:
+ raise ValueError("Attempted to insert DNA into {} at a negative location".format(self))
+ if at_nt > self.num_nt-1:
+ raise ValueError("Attempted to insert DNA into {} at beyond the end of the Segment".format(self))
+ if num_nt < 0:
+ raise ValueError("Attempted to insert DNA a negative amount of DNA into {}".format(self))
+
+ num_nt = np.around(num_nt)
+ nt_positions = self._get_location_positions()
+ new_nt_positions = [p if p <= at_nt else p+num_nt for p in nt_positions]
+
+ ## TODO: handle sequence
+
+ self.num_nt = self.num_nt+num_nt
+
+ for l,p in zip(self.locations, new_nt_positions):
+ l.address = self.nt_pos_to_contour(p)
+
+ def remove_dna(self, first_nt:int, last_nt:int, remove_locations:bool = False):
+ """ Removes nucleotides between first_nt and last_nt, inclusive """
+ assert(np.isclose(np.around(first_nt),first_nt))
+ assert(np.isclose(np.around(last_nt),last_nt))
+ tmp = min((first_nt,last_nt))
+ last_nt = max((first_nt,last_nt))
+ fist_nt = tmp
+
+ ## Sanity check
+ for l in self.locations:
+ nt = self.contour_to_nt_pos(l.address)
+ if not (np.isclose(nt,int(np.round(nt))) or l.address in (0,1)):
+ raise Exception
+ l.old_address = (l.address, self.num_nt)
+
+ if first_nt < 0 or first_nt > self.num_nt-2:
+ raise ValueError("Attempted to remove DNA from {} starting at an invalid location {}".format(self, first_nt))
+ if last_nt < 1 or last_nt > self.num_nt-1:
+ raise ValueError("Attempted to remove DNA from {} ending at an invalid location {}".format(self, last_nt))
+ if first_nt == last_nt:
+ return
+
+ def _transform_contour_positions(contours, locations = None):
+ nt = self.contour_to_nt_pos(contours)
+ first = first_nt if first_nt > 0 else -np.inf
+ last = last_nt if last_nt < self.num_nt-1 else np.inf
+ bad_ids = (nt >= first-0.5) * (nt <= last+0.5)
+ nt[nt>last] = nt[nt>last]-removed_nt
+ nt[bad_ids] = np.nan
+ # if locations is not None:
+ # for i in np.where(nt == 0):
+ # l = locations[i]
+ # l.
+
+ return self.nt_pos_to_contour(nt)* self.num_nt/num_nt
+
+ first_nt = np.around(first_nt)
+ last_nt = np.around(last_nt)
+
+ removed_nt = last_nt-first_nt+1
+ num_nt = self.num_nt-removed_nt
+
+ c = np.array([l.address for l in self.locations])
+ new_c = _transform_contour_positions(c)
+
+ if np.any(np.isnan(new_c)) and not remove_locations:
+ raise Exception("Attempted to remove DNA containing locations from {} between {} and {}".format(self,first_nt,last_nt))
+
+ ## get locations at ends
+ end_locs = [self.get_location_at( nt, is_fwd )
+ for nt in (first_nt, last_nt) for is_fwd in (True,False)]
+
+ # print("Removing DNA:",first_nt,last_nt, self.num_nt, removed_nt)
+ # print(end_locs)
+ # print([l.connection for l in end_locs])
+ for l,v in zip(list(self.locations),new_c):
+ if np.isnan(v):
+ l.delete()
+ else:
+ if l.address not in (0,1):
+ # print(" Updating loc:", l.address, v, self.contour_to_nt_pos(l.address), v*num_nt-0.5 )
+ l.address = v
+ else:
+ idx = int((l.address == 1)*2 + l.on_fwd_strand)
+ if end_locs[idx] is not None and l is not end_locs[idx]:
+ l.delete()
+
+ assert( len(self.locations) == np.logical_not(np.isnan(new_c)).sum() )
+ tmp_nt = np.array([l.address*num_nt+0.5 for l in self.locations])
+ assert(np.all( (tmp_nt < 1) + (tmp_nt > num_nt-1) + np.isclose((np.round(tmp_nt) - tmp_nt), 0) ))
+
+ if self.sequence is not None and len(self.sequence) == self.num_nt:
+ self.sequence = [s for s,i in zip(self.sequence,range(self.num_nt))
+ if i < first_nt or i > last_nt]
+ assert( len(self.sequence) == num_nt )
+
+ ## Rescale splines
+ def _rescale_splines(u, get_coord_function, set_spline_function):
+ new_u = _transform_contour_positions(u)
+ ids = np.logical_not(np.isnan(new_u))
+ new_u = new_u[ids]
+ new_p = get_coord_function(u[ids])
+ set_spline_function( new_u, new_p )
+
+ # u = self.position_spline_params[1]
+ u = np.linspace(0,1,self.num_nt*2+2)
+ _rescale_splines(u,
+ self.contour_to_position,
+ self.set_splines)
+
+ if self.quaternion_spline_params is not None:
+ def _contour_to_quaternion(contours):
+ os = [self.contour_to_orientation(c) for c in contours]
+ qs = [quaternion_from_matrix( o ) for o in os]
+ return np.array(qs)
+ # u = self.quaternion_spline_params[1],
+ _rescale_splines(u,
+ _contour_to_quaternion,
+ self.set_orientation_splines)
+
+ if '_cadnano_bp_to_zidx' in self.__dict__:
+ assert( len(self._cadnano_bp_to_zidx) == self.num_nt )
+ self._cadnano_bp_to_zidx = self._cadnano_bp_to_zidx[:first_nt] + self._cadnano_bp_to_zidx[last_nt+1:]
+ assert( len(self._cadnano_bp_to_zidx) == num_nt )
+
+ self.num_nt = num_nt
+
+ ## Sanity check
+ for l in self.locations:
+ nt = self.contour_to_nt_pos(l.address)
+ if not (np.isclose(nt,int(np.round(nt))) or l.address in (0,1)):
+ raise Exception
+
+
+
+ def delete(self):
+ for c,loc,other in self.get_connections_and_locations():
+ c.delete()
+ self.parent.segments.remove(self)
+
+ def __filter_contours(contours, positions, position_filter, contour_filter):
+ u = contours
+ r = positions
+
+ ## Filter
+ ids = list(range(len(u)))
+ if contour_filter is not None:
+ ids = list(filter(lambda i: contour_filter(u[i]), ids))
+ if position_filter is not None:
+ ids = list(filter(lambda i: position_filter(r[i,:]), ids))
+ return ids
+
+ def translate(self, translation_vector, position_filter=None, contour_filter=None):
+ dr = np.array(translation_vector)
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = Segment.__filter_contours(u, r, position_filter, contour_filter)
+ if len(ids) == 0: return
+
+ ## Translate
+ r[ids,:] = r[ids,:] + dr[np.newaxis,:]
+ self.set_splines(u,r)
+
+ def rotate(self, rotation_matrix, about=None, position_filter=None, contour_filter=None):
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = Segment.__filter_contours(u, r, position_filter, contour_filter)
+ if len(ids) == 0: return
+
+ if about is None:
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in ids])
+ else:
+ dr = np.array(about)
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in ids])
+
+ self.set_splines(u,r)
+
+ if self.quaternion_spline_params is not None:
+ ## TODO: performance: don't shift between quaternion and matrix representations so much
+ tck, u = self.quaternion_spline_params
+ orientations = np.array([self.contour_to_orientation(v) for v in u])
+ for i in ids:
+ orientations[i,:] = rotation_matrix.dot(orientations[i])
+ quats = np.array([quaternion_from_matrix(o) for o in orientations])
+ self.set_orientation_splines(u, quats)
+
+ def _set_splines_from_ends(self, resolution=4):
+ self.quaternion_spline_params = None
+ r0 = np.array(self.start_position)[np.newaxis,:]
+ r1 = np.array(self.end_position)[np.newaxis,:]
+ u = np.linspace(0,1, max(3,self.num_nt//int(resolution)))
+ s = u[:,np.newaxis]
+ coords = (1-s)*r0 + s*r1
+ self.set_splines(u, coords)
+
+ def clear_all(self):
+ Group.clear_all(self) # TODO: use super?
+ self.beads = []
+ # for c,loc,other in self.get_connections_and_locations():
+ # loc.particle = None
+ # other.particle = None
+ for l in self.locations:
+ l.particle = None
+
+ def contour_to_nt_pos(self, contour_pos, round_nt=False):
+ nt = contour_pos*(self.num_nt) - 0.5
+ if round_nt:
+ # assert( np.isclose(np.around(nt),nt) and contour_pos not in (0,1) )
+ if contour_pos == 0:
+ nt = 0
+ elif contour_pos == 1:
+ nt = self.num_nt-1
+ else:
+ assert( np.isclose(np.around(nt),nt) )
+ nt = np.around(nt)
+ return nt
+
+ def nt_pos_to_contour(self,nt_pos):
+ return (nt_pos+0.5)/(self.num_nt)
+
+ def contour_to_position(self,s):
+ p = interpolate.splev( s, self.position_spline_params[0] )
+ if len(p) > 1: p = np.array(p).T
+ return p
+
+ def contour_to_tangent(self,s):
+ t = interpolate.splev( s, self.position_spline_params[0], der=1 )
+ t = (t / np.linalg.norm(t,axis=0))
+ return t.T
+
+
+ def contour_to_orientation(self,s):
+ assert( isinstance(s,float) or isinstance(s,int) or len(s) == 1 ) # TODO make vectorized version
+
+ if self.quaternion_spline_params is None:
+ axis = self.contour_to_tangent(s)
+ axis = axis / np.linalg.norm(axis)
+ rotAxis = np.cross(axis,np.array((0,0,1)))
+ rotAxisL = np.linalg.norm(rotAxis)
+ zAxis = np.array((0,0,1))
+
+ if rotAxisL > 0.001:
+ theta = np.arcsin(rotAxisL) * 180/np.pi
+ if axis.dot(zAxis) < 0: theta = 180-theta
+ orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta, normalizeAxis=False ).T
+ else:
+ orientation0 = np.eye(3) if axis.dot(zAxis) > 0 else \
+ rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
+ if self.start_orientation is not None:
+ orientation0 = orientation0.dot(self.start_orientation)
+
+ orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
+ orientation = orientation.dot(orientation0)
+ else:
+ q = interpolate.splev( s, self.quaternion_spline_params[0] )
+ if len(q) > 1: q = np.array(q).T # TODO: is this needed?
+ orientation = quaternion_to_matrix(q)
+
+ return orientation
+
+ def _ntpos_to_seg_and_ntpos(self, nt_pos, is_fwd=True, visited_segs=tuple()):
+ """ Cross intrahelical to obtain a tuple of the segment nucleotide position """
+ """ TODO: This function could perhaps replace parts of SegmentParticle.get_contour_position """
+
+ if nt_pos >= 0 and nt_pos < self.num_nt:
+ return (self,nt_pos,is_fwd)
+ else:
+ try:
+ c,A,B = self.get_contour_sorted_connections_and_locations(type_='intrahelical')[0 if nt_pos < 0 else -1]
+ except:
+ return None
+
+ ## Special logic for circular segments
+ assert(A.container == self)
+ if A.container == B.container:
+ if (nt_pos < 0 and A.address > B.address) or (nt_pos >= self.num_nt and A.address < B.address):
+ A,B = (B,A)
+
+ other_seg = B.container
+ if A.address == (0 if nt_pos < 0 else 1) and other_seg not in visited_segs:
+ ## Cross the crossover
+ other_pos = (nt_pos-self.num_nt) if nt_pos >= self.num_nt else -nt_pos-1
+ if B.address > 0.5:
+ other_pos = (other_seg.num_nt-1) - other_pos
+ other_fwd = not is_fwd if A.address == B.address else is_fwd
+ return other_seg._ntpos_to_seg_and_ntpos(other_pos, other_fwd,
+ list(visited_segs)+[self])
+
+ else:
+ ## Could not find a path to nt_pos
+ return None
+ assert(False)
+
+
+ def get_contour_sorted_connections_and_locations(self,type_):
+ sort_fn = lambda c: c[1].address
+ cl = self.get_connections_and_locations(type_)
+ return sorted(cl, key=sort_fn)
+
+ def randomize_unset_sequence(self):
+ bases = list(seqComplement.keys())
+ # bases = ['T'] ## FOR DEBUG
+ if self.sequence is None:
+ self.sequence = [random.choice(bases) for i in range(self.num_nt)]
+ else:
+ assert(len(self.sequence) == self.num_nt) # TODO move
+ for i in range(len(self.sequence)):
+ if self.sequence[i] is None:
+ self.sequence[i] = random.choice(bases)
+
+ def assign_unset_sequence(self, fill_sequence='T'):
+ if fill_sequence == 'random':
+ self.randomize_unset_sequence()
+ elif fill_sequence in 'A T C G'.split():
+ if self.sequence is None:
+ self.sequence = [fill_sequence]*self.num_nt
+ else:
+ assert(len(self.sequence) == self.num_nt) # TODO move
+ for i in range(len(self.sequence)):
+ if self.sequence[i] in (None,'?'):
+ self.sequence[i] = 'T'
+ else:
+ raise ValueError("'fill_sequence' parameter must be one of 'random' 'A' 'T' 'C' or 'G'.")
+
+
+ def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead ):
+ raise NotImplementedError
+
+ def _generate_one_bead(self, contour_position, nts):
+ raise NotImplementedError
+
+ def _generate_atomic_nucleotide(self, contour_position, is_fwd, seq, scale, strand_segment):
+ """ Seq should include modifications like 5T, T3 Tsinglet; direction matters too """
+
+ # print("Generating nucleotide at {}".format(contour_position))
+
+ pos = self.contour_to_position(contour_position)
+ orientation = self.contour_to_orientation(contour_position)
+
+ """ deleteme
+ ## TODO: move this code (?)
+ if orientation is None:
+ import pdb
+ pdb.set_trace()
+ axis = self.contour_to_tangent(contour_position)
+ angleVec = np.array([1,0,0])
+ if axis.dot(angleVec) > 0.9: angleVec = np.array([0,1,0])
+ angleVec = angleVec - angleVec.dot(axis)*axis
+ angleVec = angleVec/np.linalg.norm(angleVec)
+ y = np.cross(axis,angleVec)
+ orientation = np.array([angleVec,y,axis]).T
+ ## TODO: improve placement of ssDNA
+ # rot = rotationAboutAxis( axis, contour_position*self.twist_per_nt*self.num_nt, normalizeAxis=True )
+ # orientation = rot.dot(orientation)
+ else:
+ orientation = orientation
+ """
+ key = seq
+ nt_dict = canonicalNtFwd if is_fwd else canonicalNtRev
+
+ atoms = nt_dict[ key ].generate() # TODO: clone?
+ atoms.orientation = orientation.dot(atoms.orientation)
+ if isinstance(self, SingleStrandedSegment):
+ if scale is not None and scale != 1:
+ for a in atoms:
+ a.position = scale*a.position
+ atoms.position = pos - atoms.atoms_by_name["C1'"].collapsedPosition()
+ else:
+ if scale is not None and scale != 1:
+ if atoms.sequence in ("A","G"):
+ r0 = atoms.atoms_by_name["N9"].position
+ else:
+ r0 = atoms.atoms_by_name["N1"].position
+ for a in atoms:
+ if a.name[-1] in ("'","P","T"):
+ a.position = scale*(a.position-r0) + r0
+ else:
+ a.fixed = 1
+ atoms.position = pos
+
+ atoms.contour_position = contour_position
+ strand_segment.add(atoms)
+
+ for callback in self._generate_nucleotide_callbacks:
+ callback(atoms)
+
+ return atoms
+
+ def _generate_oxdna_nucleotide(self, contour_position, is_fwd, seq):
+ bp_center = self.contour_to_position(contour_position)
+ orientation = self.contour_to_orientation(contour_position)
+
+ DefaultOrientation = rotationAboutAxis([0,0,1], 90)
+ if is_fwd:
+ DefaultOrientation = rotationAboutAxis([1,0,0], 180).dot(DefaultOrientation)
+
+ o = orientation.dot(DefaultOrientation)
+
+ if isinstance(self, SingleStrandedSegment):
+ pos = bp_center
+ else:
+ pos = bp_center - 5*o.dot(np.array((1,0,0)))
+
+ nt = PointParticle("oxdna_nt", position= pos,
+ orientation = o)
+
+ nt.contour_position = contour_position
+ return nt
+
+
+ def add_location(self, nt, type_, on_fwd_strand=True):
+ ## Create location if needed, add to segment
+ c = self.nt_pos_to_contour(nt)
+ assert(c >= 0 and c <= 1)
+ # TODO? loc = self.Location( address=c, type_=type_, on_fwd_strand=is_fwd )
+ loc = Location( self, address=c, type_=type_, on_fwd_strand=on_fwd_strand )
+ self.locations.append(loc)
+
+ ## TODO? Replace with abstract strand-based model?
+
+ def add_nick(self, nt, on_fwd_strand=True):
+ if on_fwd_strand:
+ self.add_3prime(nt,on_fwd_strand)
+ self.add_5prime(nt+1,on_fwd_strand)
+ else:
+ self.add_5prime(nt,on_fwd_strand)
+ self.add_3prime(nt+1,on_fwd_strand)
+
+
+ def add_5prime(self, nt, on_fwd_strand=True):
+ if isinstance(self,SingleStrandedSegment):
+ on_fwd_strand = True
+ self.add_location(nt,"5prime",on_fwd_strand)
+
+ def add_3prime(self, nt, on_fwd_strand=True):
+ if isinstance(self,SingleStrandedSegment):
+ on_fwd_strand = True
+ self.add_location(nt,"3prime",on_fwd_strand)
+
+ ## Real work
+ def _connect_ends(self, end1, end2, type_, force_connection=False):
+ debug = False
+ ## TODO remove self?
+ ## validate the input
+ for end in (end1, end2):
+ assert( isinstance(end, Location) )
+ assert( end.type_ in ("end3","end5",'3prime','5prime') )
+ assert( end1.type_ != end2.type_ )
+
+ if ((isinstance(end1.container, SingleStrandedSegment) and
+ isinstance(end2.container, DoubleStrandedSegment)) or
+ (isinstance(end1.container, DoubleStrandedSegment) and
+ isinstance(end1.container, SingleStrandedSegment))):
+ type_ = 'sscrossover'
+
+ ## Remove other connections involving these points
+ if end1.connection is not None:
+ if debug: print("WARNING: reconnecting {}".format(end1))
+ end1.connection.delete()
+ if end2.connection is not None:
+ if debug: print("WARNING: reconnecting {}".format(end2))
+ end2.connection.delete()
+
+ ## Create and add connection
+ if end2.type_ == "end5":
+ end1.container._connect( end2.container, Connection( end1, end2, type_=type_ ), in_3prime_direction=True )
+ else:
+ end2.container._connect( end1.container, Connection( end2, end1, type_=type_ ), in_3prime_direction=True )
+
+ def get_3prime_locations(self):
+ return sorted(self.get_locations("3prime"),key=lambda x: x.address)
+
+ def get_5prime_locations(self):
+ ## TODO? ensure that data is consistent before _build_model calls
+ return sorted(self.get_locations("5prime"),key=lambda x: x.address)
+
+ def get_blunt_DNA_ends(self):
+ if isinstance(self, SingleStrandedSegment): return []
+ ret = []
+ cl = self.get_connections_and_locations("intrahelical")
+ if not any([c[1].address == 0 for c in cl]):
+ ret.append((self.start5,self.start3,-1))
+ if not any([c[1].address == 1 for c in cl]):
+ ret.append((self.end5,self.end3,1))
+ # return [c for c in cl if c[1].address == 0 or c[1].address == 1]
+ return ret
+
+ def iterate_connections_and_locations(self, reverse=False):
+ ## connections to other segments
+ cl = self.get_contour_sorted_connections_and_locations()
+ if reverse:
+ cl = cl[::-1]
+
+ for c in cl:
+ yield c
+
+ ## TODO rename
+ def _add_strand_piece(self, strand_piece):
+ """ Registers a strand segment within this object """
+
+ ## TODO use weakref
+ d = 'fwd' if strand_piece.is_fwd else 'rev'
+
+ ## Validate strand_piece (ensure no clashes)
+ for s in self.strand_pieces[d]:
+ l,h = sorted((s.start,s.end))
+ for value in (strand_piece.start,strand_piece.end):
+ if value >= l and value <= h:
+ raise Exception("Strand piece already exists! DNA may be circular.")
+
+ ## Add strand_piece in correct order
+ self.strand_pieces[d].append(strand_piece)
+ self.strand_pieces[d] = sorted(self.strand_pieces[d],
+ key = lambda x: x.start)
+
+ ## TODO rename
+ def get_strand_segment(self, nt_pos, is_fwd, move_at_least=0.5):
+ """ Walks through locations, checking for crossovers """
+ # if self.name in ("6-1","1-1"):
+ # import pdb
+ # pdb.set_trace()
+ move_at_least = 0
+
+ ## Iterate through locations
+ # locations = sorted(self.locations, key=lambda l:(l.address,not l.on_fwd_strand), reverse=(not is_fwd))
+ def loc_rank(l):
+ nt = l.get_nt_pos()
+ ## optionally add logic about type of connection
+ return (nt, not l.on_fwd_strand)
+ # locations = sorted(self.locations, key=lambda l:(l.address,not l.on_fwd_strand), reverse=(not is_fwd))
+ locations = sorted(self.locations, key=loc_rank, reverse=(not is_fwd))
+ # print(locations)
+
+ for l in locations:
+ # TODOTODO probably okay
+ if l.address == 0:
+ pos = 0.0
+ elif l.address == 1:
+ pos = self.num_nt-1
+ else:
+ pos = self.contour_to_nt_pos(l.address, round_nt=True)
+
+ ## DEBUG
+
+
+ ## Skip locations encountered before our strand
+ # tol = 0.1
+ # if is_fwd:
+ # if pos-nt_pos <= tol: continue
+ # elif nt_pos-pos <= tol: continue
+ if (pos-nt_pos)*(2*is_fwd-1) < move_at_least: continue
+ ## TODO: remove move_at_least
+ if np.isclose(pos,nt_pos):
+ if l.is_3prime_side_of_connection: continue
+
+ ## Stop if we found the 3prime end
+ if l.on_fwd_strand == is_fwd and l.type_ == "3prime" and l.connection is None:
+ if _DEBUG_TRACE:
+ print(" found end at",l)
+ return pos, None, None, None, None
+
+ ## Check location connections
+ c = l.connection
+ if c is None: continue
+ B = c.other(l)
+
+ ## Found a location on the same strand?
+ if l.on_fwd_strand == is_fwd:
+ if _DEBUG_TRACE:
+ print(" passing through",l)
+ print("from {}, connection {} to {}".format(nt_pos,l,B))
+ Bpos = B.get_nt_pos()
+ return pos, B.container, Bpos, B.on_fwd_strand, 0.5
+
+ ## Stop at other strand crossovers so basepairs line up
+ elif c.type_ == "crossover":
+ if nt_pos == pos: continue
+ if _DEBUG_TRACE:
+ print(" pausing at",l)
+ return pos, l.container, pos+(2*is_fwd-1), is_fwd, 0
+
+ raise Exception("Shouldn't be here")
+ # print("Shouldn't be here")
+ ## Made it to the end of the segment without finding a connection
+ return 1*is_fwd, None, None, None
+
+ def get_nearest_bead(self, contour_position):
+ if len(self.beads) < 1: return None
+ cs = np.array([b.contour_position for b in self.beads]) # TODO: cache
+ # TODO: include beads in connections?
+ i = np.argmin((cs - contour_position)**2)
+
+ return self.beads[i]
+
+ def _get_atomic_nucleotide(self, nucleotide_idx, is_fwd=True):
+ d = 'fwd' if is_fwd else 'rev'
+ for s in self.strand_pieces[d]:
+ try:
+ return s.get_nucleotide(nucleotide_idx)
+ except:
+ pass
+ raise Exception("Could not find nucleotide in {} at {}.{}".format( self, nucleotide_idx, d ))
+
+ def get_all_consecutive_beads(self, number):
+ assert(number >= 1)
+ ## Assume that consecutive beads in self.beads are bonded
+ ret = []
+ for i in range(len(self.beads)-number+1):
+ tmp = [self.beads[i+j] for j in range(0,number)]
+ ret.append( tmp )
+ return ret
+
+ def _add_bead(self,b):
+
+ # assert(b.parent is None)
+ if b.parent is not None:
+ b.parent.children.remove(b)
+ self.add(b)
+ self.beads.append(b) # don't add orientation bead
+ if "orientation_bead" in b.__dict__: # TODO: think of a cleaner approach
+ o = b.orientation_bead
+ o.contour_position = b.contour_position
+ if o.parent is not None:
+ o.parent.children.remove(o)
+ self.add(o)
+ self.add_bond(b,o, Segment.orientation_bond, exclude=True)
+
+ def _rebuild_children(self, new_children):
+ # print("_rebuild_children on %s" % self.name)
+ old_children = self.children
+ old_beads = self.beads
+ self.children = []
+ self.beads = []
+
+ if True:
+ ## TODO: remove this if duplicates are never found
+ # print("Searching for duplicate particles...")
+ ## Remove duplicates, preserving order
+ tmp = []
+ for c in new_children:
+ if c not in tmp:
+ tmp.append(c)
+ else:
+ print(" DUPLICATE PARTICLE FOUND!")
+ new_children = tmp
+
+ for b in new_children:
+ self.beads.append(b)
+ self.children.append(b)
+ if "orientation_bead" in b.__dict__: # TODO: think of a cleaner approach
+ self.children.append(b.orientation_bead)
+
+ # tmp = [c for c in self.children if c not in old_children]
+ # assert(len(tmp) == 0)
+ # tmp = [c for c in old_children if c not in self.children]
+ # assert(len(tmp) == 0)
+ assert(len(old_children) == len(self.children))
+ assert(len(old_beads) == len(self.beads))
+
+
+ def _generate_beads(self, bead_model, max_basepairs_per_bead, max_nucleotides_per_bead, one_bead_per_monomer=False):
+ """ Generate beads (positions, types, etc) and bonds, angles, dihedrals, exclusions """
+ ## TODO: decide whether to remove bead_model argument
+ ## (currently unused)
+
+ if self.resolution is not None:
+ max_basepairs_per_bead = max_nucleotides_per_bead = self.resolution
+
+ tmp_children = []
+
+ if one_bead_per_monomer:
+ last = None
+ for i in range(self.num_nt):
+ s = self.nt_pos_to_contour(i)
+ b = self._generate_one_bead(s,1)
+
+ if last is not None:
+ last.make_intrahelical_neighbor(b)
+ last = b
+ tmp_children.append(b)
+ else:
+ ## First find points between-which beads must be generated
+ # conn_locs = self.get_contour_sorted_connections_and_locations()
+ # locs = [A for c,A,B in conn_locs]
+ # existing_beads = [l.particle for l in locs if l.particle is not None]
+ # if self.name == "S001":
+ # pdb.set_trace()
+
+ # pdb.set_trace()
+ existing_beads0 = { (l.particle, l.particle.get_contour_position(self,l.address))
+ for l in self.locations if l.particle is not None }
+ existing_beads = sorted( list(existing_beads0), key=lambda bc: bc[1] )
+
+ # if self.num_nt == 1 and all([l.particle is not None for l in self.locations]):
+ # pdb.set_trace()
+ # return
+
+ for b,c in existing_beads:
+ assert(b.parent is not None)
+
+ ## Add ends if they don't exist yet
+ ## TODOTODO: test 1 nt segments?
+ if len(existing_beads) == 0 or (existing_beads[0][0].get_nt_position(self,0) >= 0.5 and 'is_circular_bead' not in existing_beads[0][0].__dict__):
+ # if len(existing_beads) > 0:
+ # assert(existing_beads[0].get_nt_position(self) >= 0.5)
+ c = self.nt_pos_to_contour(0)
+ if self.num_nt == 1: c -= 0.4
+ b = self._generate_one_bead(c, 0)
+ existing_beads = [(b,0)] + existing_beads
+
+ if (existing_beads[-1][0].get_nt_position(self,1)-(self.num_nt-1) < -0.5 and 'is_circular_bead' not in existing_beads[0][0].__dict__) or len(existing_beads)==1:
+ c = self.nt_pos_to_contour(self.num_nt-1)
+ if self.num_nt == 1: c += 0.4
+ b = self._generate_one_bead(c, 0)
+ existing_beads.append( (b,1) )
+ assert(len(existing_beads) > 1)
+
+ ## Walk through existing_beads, add beads between
+ last = None
+
+ for I in range(len(existing_beads)-1):
+ eb1,eb2 = [existing_beads[i][0] for i in (I,I+1)]
+ ec1,ec2 = [existing_beads[i][1] for i in (I,I+1)]
+ assert( (eb1,ec1) is not (eb2,ec2) )
+
+ # if np.isclose(eb1.position[2], eb2.position[2]):
+ # import pdb
+ # pdb.set_trace()
+
+ # print(" %s working on %d to %d" % (self.name, eb1.position[2], eb2.position[2]))
+ e_ds = ec2-ec1
+ num_beads = self._get_num_beads( e_ds, max_basepairs_per_bead, max_nucleotides_per_bead )
+
+ ## Ensure there is a ssDNA bead between dsDNA beads
+ if num_beads == 0 and isinstance(self,SingleStrandedSegment) and isinstance(eb1.parent,DoubleStrandedSegment) and isinstance(eb2.parent,DoubleStrandedSegment):
+ num_beads = 1
+ ## TODO similarly ensure there is a dsDNA bead between ssDNA beads
+
+ ds = e_ds / (num_beads+1)
+ nts = ds*self.num_nt
+ eb1.num_nt += 0.5*nts
+ eb2.num_nt += 0.5*nts
+
+ ## Add beads
+ if eb1.parent == self:
+ tmp_children.append(eb1)
+
+ s0 = ec1
+ if last is not None:
+ last.make_intrahelical_neighbor(eb1)
+ last = eb1
+ for j in range(num_beads):
+ s = ds*(j+1) + s0
+ # if self.name in ("51-2","51-3"):
+ # if self.name in ("31-2",):
+ # print(" adding bead at {}".format(s))
+ b = self._generate_one_bead(s,nts)
+
+ last.make_intrahelical_neighbor(b)
+ last = b
+ tmp_children.append(b)
+
+ last.make_intrahelical_neighbor(eb2)
+
+ if eb2.parent == self:
+ tmp_children.append(eb2)
+
+ # if self.name in ("31-2",):
+ # pdb.set_trace()
+ self._rebuild_children(tmp_children)
+
+ for callback in self._generate_bead_callbacks:
+ callback(self)
+
+ def _regenerate_beads(self, max_nts_per_bead=4, ):
+ ...
+
+
+class DoubleStrandedSegment(Segment):
+
+ """ Class that describes a segment of ssDNA. When built from
+ cadnano models, should not span helices """
+
+ def __init__(self, name, num_bp, start_position = np.array((0,0,0)),
+ end_position = None,
+ segment_model = None,
+ local_twist = False,
+ num_turns = None,
+ start_orientation = None,
+ twist_persistence_length = 90,
+ persistence_length = 50,
+ **kwargs):
+
+ self.helical_rise = 10.44
+ self.distance_per_nt = 3.4
+ Segment.__init__(self, name, num_bp,
+ start_position,
+ end_position,
+ segment_model,
+ **kwargs)
+ self.num_bp = self.num_nt
+
+ self.local_twist = local_twist
+ if num_turns is None:
+ num_turns = float(num_bp) / self.helical_rise
+ self.twist_per_nt = float(360 * num_turns) / num_bp
+
+ if start_orientation is None:
+ start_orientation = np.eye(3) # np.array(((1,0,0),(0,1,0),(0,0,1)))
+ self.start_orientation = start_orientation
+ self.twist_persistence_length = twist_persistence_length
+ self.persistence_length = persistence_length
+
+ self.nicks = []
+
+ self.start = self.start5 = Location( self, address=0, type_= "end5" )
+ self.start3 = Location( self, address=0, type_ = "end3", on_fwd_strand=False )
+
+ self.end = self.end3 = Location( self, address=1, type_ = "end3" )
+ self.end5 = Location( self, address=1, type_= "end5", on_fwd_strand=False )
+ # for l in (self.start5,self.start3,self.end3,self.end5):
+ # self.locations.append(l)
+
+ ## TODO: initialize sensible spline for orientation
+
+ ## Convenience methods
+ ## TODO: add errors if unrealistic connections are made
+ ## TODO: make connections automatically between unconnected strands
+ def connect_start5(self, end3, type_="intrahelical", force_connection=False):
+ if isinstance(end3, SingleStrandedSegment):
+ end3 = end3.end3
+ self._connect_ends( self.start5, end3, type_, force_connection = force_connection )
+ def connect_start3(self, end5, type_="intrahelical", force_connection=False):
+ if isinstance(end5, SingleStrandedSegment):
+ end5 = end5.start5
+ self._connect_ends( self.start3, end5, type_, force_connection = force_connection )
+ def connect_end3(self, end5, type_="intrahelical", force_connection=False):
+ if isinstance(end5, SingleStrandedSegment):
+ end5 = end5.start5
+ self._connect_ends( self.end3, end5, type_, force_connection = force_connection )
+ def connect_end5(self, end3, type_="intrahelical", force_connection=False):
+ if isinstance(end3, SingleStrandedSegment):
+ end3 = end3.end3
+ self._connect_ends( self.end5, end3, type_, force_connection = force_connection )
+
+ def add_crossover(self, nt, other, other_nt, strands_fwd=(True,False), nt_on_5prime=True, type_="crossover"):
+ """ Add a crossover between two helices """
+ ## Validate other, nt, other_nt
+ ## TODO
+
+ if isinstance(other,SingleStrandedSegment):
+ other.add_crossover(other_nt, self, nt, strands_fwd[::-1], not nt_on_5prime)
+ else:
+
+ ## Create locations, connections and add to segments
+ c = self.nt_pos_to_contour(nt)
+ assert(c >= 0 and c <= 1)
+
+
+ if nt == 0 and not strands_fwd[0]:
+ loc = self.start3
+ elif nt == self.num_nt-1 and strands_fwd[0]:
+ loc = self.end3
+ else:
+ loc = self.get_location_at(c, strands_fwd[0], new_type='crossover')
+
+ c = other.nt_pos_to_contour(other_nt)
+ # TODOTODO: may need to subtract or add a little depending on 3prime/5prime
+ assert(c >= 0 and c <= 1)
+
+ if other_nt == 0 and strands_fwd[1]:
+ other_loc = other.start5
+ elif other_nt == other.num_nt-1 and not strands_fwd[1]:
+ other_loc = other.end5
+ else:
+ other_loc = other.get_location_at(c, strands_fwd[1], new_type='crossover')
+
+ self._connect(other, Connection( loc, other_loc, type_=type_ ))
+ if nt_on_5prime:
+ loc.is_3prime_side_of_connection = False
+ other_loc.is_3prime_side_of_connection = True
+ else:
+ loc.is_3prime_side_of_connection = True
+ other_loc.is_3prime_side_of_connection = False
+
+ def _get_num_beads(self, contour, max_basepairs_per_bead, max_nucleotides_per_bead):
+ # return int(contour*self.num_nt // max_basepairs_per_bead)
+ return int(contour*(self.num_nt**2/(self.num_nt+1)) // max_basepairs_per_bead)
+
+ def _generate_one_bead(self, contour_position, nts):
+ pos = self.contour_to_position(contour_position)
+ if self.local_twist:
+ orientation = self.contour_to_orientation(contour_position)
+ if orientation is None:
+ print("WARNING: local_twist is True, but orientation is None; using identity")
+ orientation = np.eye(3)
+ opos = pos + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
+ # if np.linalg.norm(pos) > 1e3:
+ # pdb.set_trace()
+ assert(np.linalg.norm(opos-pos) < 10 )
+ o = SegmentParticle( Segment.orientation_particle, opos, name="O",
+ contour_position = contour_position,
+ num_nt=nts, parent=self )
+ bead = SegmentParticle( Segment.dsDNA_particle, pos, name="DNA",
+ num_nt=nts, parent=self,
+ orientation_bead=o,
+ contour_position=contour_position )
+
+ else:
+ bead = SegmentParticle( Segment.dsDNA_particle, pos, name="DNA",
+ num_nt=nts, parent=self,
+ contour_position=contour_position )
+ self._add_bead(bead)
+ return bead
+
+class SingleStrandedSegment(Segment):
+
+ """ Class that describes a segment of ssDNA. When built from
+ cadnano models, should not span helices """
+
+ def __init__(self, name, num_nt, start_position = None,
+ end_position = None,
+ segment_model = None,
+ **kwargs):
+
+ if start_position is None: start_position = np.array((0,0,0))
+ self.distance_per_nt = 5
+ Segment.__init__(self, name, num_nt,
+ start_position,
+ end_position,
+ segment_model,
+ **kwargs)
+
+ self.start = self.start5 = Location( self, address=0, type_= "end5" ) # TODO change type_?
+ self.end = self.end3 = Location( self, address=1, type_ = "end3" )
+ # for l in (self.start5,self.end3):
+ # self.locations.append(l)
+
+ def connect_end3(self, end5, force_connection=False):
+ self._connect_end( end5, _5_to_3 = True, force_connection = force_connection )
+
+ def connect_start5(self, end3, force_connection=False):
+ self._connect_end( end3, _5_to_3 = False, force_connection = force_connection )
+
+ def _connect_end(self, other, _5_to_3, force_connection):
+ assert( isinstance(other, Location) )
+ if _5_to_3 == True:
+ seg1 = self
+ seg2 = other.container
+ end1 = self.end3
+ end2 = other
+ assert(other.type_ != "end3")
+ # if (other.type_ is not "end5"):
+ # print("WARNING: code does not prevent connecting 3prime to 3prime, etc")
+ else:
+ seg1 = other.container
+ seg2 = self
+ end1 = other
+ end2 = self.start
+ assert(other.type_ != "end5")
+ # if (other.type_ is not "end3"):
+ # print("WARNING: code does not prevent connecting 3prime to 3prime, etc")
+
+ ## Remove other connections involving these points
+ if end1.connection is not None:
+ print("WARNING: reconnecting {}".format(end1))
+ end1.connection.delete()
+ if end2.connection is not None:
+ print("WARNING: reconnecting {}".format(end2))
+ end2.connection.delete()
+
+ conn = Connection( end1, end2, type_="intrahelical" if isinstance(other,SingleStrandedSegment) else "sscrossover")
+ seg1._connect( seg2, conn, in_3prime_direction=True )
+
+
+ def add_crossover(self, nt, other, other_nt, strands_fwd=(True,False), nt_on_5prime=True, type_='sscrossover'):
+ """ Add a crossover between two helices """
+ ## TODO Validate other, nt, other_nt
+
+ assert(nt < self.num_nt)
+ assert(other_nt < other.num_nt)
+ if nt_on_5prime:
+ if nt == self.num_nt-1 and other_nt in (0,other.num_nt-1):
+ other_end = None
+ if strands_fwd[1] and other_nt == 0:
+ other_end = other.start5
+ elif (not strands_fwd[1]) and other_nt == other.num_nt-1:
+ other_end = other.end5
+ if other_end is not None:
+ self.connect_end3( other_end )
+ return
+ else:
+ if nt == 0 and other_nt in (0,other.num_nt-1):
+ other_end = None
+ if strands_fwd[1] and other_nt == other.num_nt-1:
+ other_end = other.end3
+ elif (not strands_fwd[1]) and other_nt == 0:
+ other_end = other.start3
+ if other_end is not None:
+ self.connect_start5( other_end )
+ return
+
+ # c1 = self.nt_pos_to_contour(nt)
+ # # TODOTODO
+ # ## Ensure connections occur at ends, otherwise the structure doesn't make sense
+ # # assert(np.isclose(c1,0) or np.isclose(c1,1))
+ # assert(np.isclose(nt,0) or np.isclose(nt,self.num_nt-1))
+ if nt == 0 and (self.num_nt > 1 or not nt_on_5prime):
+ c1 = 0
+ elif nt == self.num_nt-1:
+ c1 = 1
+ else:
+ raise Exception("Crossovers can only be at the ends of an ssDNA segment")
+ loc = self.get_location_at(c1, True, new_type='crossover')
+
+ if other_nt == 0:
+ c2 = 0
+ elif other_nt == other.num_nt-1:
+ c2 = 1
+ else:
+ c2 = other.nt_pos_to_contour(other_nt)
+
+ if isinstance(other,SingleStrandedSegment):
+ ## Ensure connections occur at opposing ends
+ assert(np.isclose(other_nt,0) or np.isclose(other_nt,self.num_nt-1))
+ other_loc = other.get_location_at( c2, True, new_type='crossover')
+ # if ("22-2" in (self.name, other.name)):
+ # pdb.set_trace()
+ if nt_on_5prime:
+ self.connect_end3( other_loc )
+ else:
+ other.connect_end3( self )
+
+ else:
+ assert(c2 >= 0 and c2 <= 1)
+ other_loc = other.get_location_at( c2, strands_fwd[1], new_type='crossover')
+ if nt_on_5prime:
+ self._connect(other, Connection( loc, other_loc, type_="sscrossover" ), in_3prime_direction=True )
+ else:
+ other._connect(self, Connection( other_loc, loc, type_="sscrossover" ), in_3prime_direction=True )
+
+ def _get_num_beads(self, contour, max_basepairs_per_bead, max_nucleotides_per_bead):
+ return int(contour*(self.num_nt**2/(self.num_nt+1)) // max_basepairs_per_bead)
+ # return int(contour*self.num_nt // max_nucleotides_per_bead)
+
+ def _generate_one_bead(self, contour_position, nts):
+ pos = self.contour_to_position(contour_position)
+ b = SegmentParticle( Segment.ssDNA_particle, pos,
+ name="NAS",
+ num_nt=nts, parent=self,
+ contour_position=contour_position )
+ self._add_bead(b)
+ return b
+
+class StrandInSegment(Group):
+ """ Represents a piece of an ssDNA strand within a segment """
+
+ def __init__(self, segment, start, end, is_fwd):
+ """ start/end should be provided expressed in nt coordinates, is_fwd tuples """
+ Group.__init__(self)
+ self.num_nt = 0
+ # self.sequence = []
+ self.segment = segment
+ self.start = start
+ self.end = end
+ self.is_fwd = is_fwd
+
+ if is_fwd:
+ assert(end>=start)
+ else:
+ assert(start>=end)
+
+ nts = np.abs(end-start)+1
+ self.num_nt = int(round(nts))
+ assert( np.isclose(self.num_nt,nts) )
+ segment._add_strand_piece(self)
+
+ def _nucleotide_ids(self):
+ nt0 = self.start # seg.contour_to_nt_pos(self.start)
+ assert( np.abs(nt0 - round(nt0)) < 1e-5 )
+ nt0 = int(round(nt0))
+ assert( (self.end-self.start) >= 0 or not self.is_fwd )
+
+ direction = (2*self.is_fwd-1)
+ return range(nt0,nt0 + direction*self.num_nt, direction)
+
+ def get_sequence(self):
+ """ return 5-to-3 """
+ # TODOTODO test
+ seg = self.segment
+ if self.is_fwd:
+ return [seg.sequence[nt] for nt in self._nucleotide_ids()]
+ else:
+ return [seqComplement[seg.sequence[nt]] for nt in self._nucleotide_ids()]
+
+ def get_contour_points(self):
+ c0,c1 = [self.segment.nt_pos_to_contour(p) for p in (self.start,self.end)]
+ return np.linspace(c0,c1,self.num_nt)
+
+ def get_nucleotide(self, idx):
+ """ idx expressed as nt coordinate within segment """
+
+ lo,hi = sorted((self.start,self.end))
+ if self.is_fwd:
+ idx_in_strand = idx - lo
+ else:
+ idx_in_strand = hi - idx
+ assert( np.isclose( idx_in_strand , int(round(idx_in_strand)) ) )
+ assert(idx_in_strand >= 0)
+ return self.children[int(round(idx_in_strand))]
+ def __repr__(self):
+ return "<StrandInSegment {}{}[{:.2f}-{:.2f},{:d}]>".format( self.parent.segname, self.segment.name, self.start, self.end, self.is_fwd)
+
+
+class Strand(Group):
+ """ Represents an entire ssDNA strand from 5' to 3' as it routes through segments """
+ def __init__(self, segname = None, is_circular = False):
+ Group.__init__(self)
+ self.num_nt = 0
+ self.children = self.strand_segments = []
+ self.oxdna_nt = []
+ self.segname = segname
+ self.is_circular = is_circular
+ self.debug = False
+
+ def __repr__(self):
+ return "<Strand {}({})>".format( self.segname, self.num_nt )
+
+ ## TODO disambiguate names of functions
+ def add_dna(self, segment, start, end, is_fwd):
+ """ start/end are given as nt """
+ if np.abs(start-end) <= 0.9:
+ if self.debug:
+ print( "WARNING: segment constructed with a very small number of nts ({})".format(np.abs(start-end)) )
+ # import pdb
+ # pdb.set_trace()
+ for s in self.strand_segments:
+ if s.segment == segment and s.is_fwd == is_fwd:
+ # assert( s.start not in (start,end) )
+ # assert( s.end not in (start,end) )
+ if s.start in (start,end) or s.end in (start,end):
+ raise CircularDnaError("Found circular DNA")
+
+ s = StrandInSegment( segment, start, end, is_fwd )
+ self.add( s )
+ self.num_nt += s.num_nt
+
+ def set_sequence(self,sequence): # , set_complement=True):
+ ## validate input
+ assert( len(sequence) >= self.num_nt )
+ assert( np.all( [i in ('A','T','C','G') for i in sequence] ) )
+
+ seq_idx = 0
+ ## set sequence on each segment
+ for s in self.children:
+ seg = s.segment
+ if seg.sequence is None:
+ seg.sequence = [None for i in range(seg.num_nt)]
+
+ if s.is_fwd:
+ for nt in s._nucleotide_ids():
+ seg.sequence[nt] = sequence[seq_idx]
+ seq_idx += 1
+ else:
+ for nt in s._nucleotide_ids():
+ seg.sequence[nt] = seqComplement[sequence[seq_idx]]
+ seq_idx += 1
+
+ # def get_sequence(self):
+ # sequence = []
+ # for ss in self.strand_segments:
+ # sequence.extend( ss.get_sequence() )
+
+ # assert( len(sequence) >= self.num_nt )
+ # ret = ["5"+sequence[0]] +\
+ # sequence[1:-1] +\
+ # [sequence[-1]+"3"]
+ # assert( len(ret) == self.num_nt )
+ # return ret
+
+ def link_nucleotides(self, nt5, nt3):
+ parent = nt5.parent if nt5.parent is nt3.parent else self
+ o3,c3,c4,c2,h3 = [nt5.atoms_by_name[n]
+ for n in ("O3'","C3'","C4'","C2'","H3'")]
+ p,o5,o1,o2,c5 = [nt3.atoms_by_name[n]
+ for n in ("P","O5'","O1P","O2P","C5'")]
+ parent.add_bond( o3, p, None )
+ parent.add_angle( c3, o3, p, None )
+ for x in (o5,o1,o2):
+ parent.add_angle( o3, p, x, None )
+ parent.add_dihedral(c3, o3, p, x, None )
+ for x in (c4,c2,h3):
+ parent.add_dihedral(x, c3, o3, p, None )
+ parent.add_dihedral(o3, p, o5, c5, None)
+
+ def generate_atomic_model(self, scale, first_atomic_index):
+ last = None
+ resid = 1
+ ## TODO relabel "strand_segment"
+ strand_segment_count = 0
+ for s in self.strand_segments:
+ strand_segment_count += 1
+ seg = s.segment
+ contour = s.get_contour_points()
+ # if s.end == s.start:
+ # pdb.set_trace()
+ # assert(s.end != s.start)
+ assert( s.num_nt == 1 or (np.linalg.norm( seg.contour_to_position(contour[-1]) - seg.contour_to_position(contour[0]) ) > 0.1) )
+ nucleotide_count = 0
+ for c,seq in zip(contour,s.get_sequence()):
+ nucleotide_count += 1
+ if last is None and not self.is_circular:
+ seq = "5"+seq
+ if strand_segment_count == len(s.strand_segments) and nucleotide_count == s.num_nt and not self.is_circular:
+ seq = seq+"3"
+
+ nt = seg._generate_atomic_nucleotide( c, s.is_fwd, seq, scale, s )
+
+ ## Join last basepairs
+ if last is not None:
+ self.link_nucleotides(last,nt)
+
+ nt.__dict__['resid'] = resid
+ resid += 1
+ last = nt
+ nt._first_atomic_index = first_atomic_index
+ first_atomic_index += len(nt.children)
+
+ if self.is_circular:
+ self.link_nucleotides(last,self.strand_segments[0].children[0])
+
+ return first_atomic_index
+
+ def generate_oxdna_model(self):
+ for s in self.strand_segments:
+ seg = s.segment
+ contour = s.get_contour_points()
+ assert( s.num_nt == 1 or (np.linalg.norm( seg.contour_to_position(contour[-1]) - seg.contour_to_position(contour[0]) ) > 0.1) )
+ for c,seq in zip(contour,s.get_sequence()):
+ nt = seg._generate_oxdna_nucleotide( c, s.is_fwd, seq )
+ self.oxdna_nt.append(nt)
+
+ def get_sequence(self):
+ return ''.join([''.join(s.get_sequence()) for s in self.strand_segments])
+
+ def get_nt_positions_orientations(self, bp_offset = (5,0,0)):
+ ## TODO: remove duplicate code
+ rs = []
+ os = []
+ for s in self.strand_segments:
+ seg = s.segment
+ contour = s.get_contour_points()
+ assert( s.num_nt == 1 or (np.linalg.norm( seg.contour_to_position(contour[-1]) - seg.contour_to_position(contour[0]) ) > 0.1) )
+
+ DefaultOrientation = rotationAboutAxis([0,0,1], 90)
+ if s.is_fwd:
+ DefaultOrientation = rotationAboutAxis([1,0,0], 180).dot(DefaultOrientation)
+
+ for c,seq in zip(contour,s.get_sequence()):
+ r = seg.contour_to_position(c)
+ o = seg.contour_to_orientation(c)
+ o = o.dot(DefaultOrientation)
+
+ if isinstance(seg, SingleStrandedSegment):
+ r = r
+ else:
+ r = r - o.dot(np.array(bp_offset))
+
+ rs.append(r)
+ os.append(quaternion_from_matrix(o))
+ return np.array(rs), np.array(os)
+
+
+class SegmentModel(ArbdModel):
+ def __init__(self, segments=[], local_twist=True, escapable_twist=True,
+ max_basepairs_per_bead=7,
+ max_nucleotides_per_bead=4,
+ origin = None,
+ dimensions=(5000,5000,5000), temperature=291,
+ timestep=50e-6, cutoff=50,
+ decompPeriod=10000, pairlistDistance=None,
+ nonbondedResolution=0, DEBUG=0,
+ integrator='Brown',
+ debye_length = None,
+ hj_equilibrium_angle = 0,
+ extra_bd_file_lines = "",
+ ):
+ self.DEBUG = DEBUG
+ if DEBUG > 0: print("Building ARBD Model")
+ ArbdModel.__init__(self,segments,
+ origin, dimensions,
+ temperature, timestep, integrator, cutoff,
+ decompPeriod, pairlist_distance=None,
+ nonbonded_resolution = 0,
+ extra_bd_file_lines = extra_bd_file_lines
+ )
+
+
+ # self.max_basepairs_per_bead = max_basepairs_per_bead # dsDNA
+ # self.max_nucleotides_per_bead = max_nucleotides_per_bead # ssDNA
+ if isinstance(segments,Segment):
+ segments = [segments]
+
+ self.children = self.segments = segments
+
+ if (hj_equilibrium_angle > 180) or (hj_equilibrium_angle < -180):
+ raise ValueError("Holliday junction equilibrium dihedral angle must be in the range from -180 to 180 degrees!")
+ self.hj_equilibrium_angle = hj_equilibrium_angle
+
+ self._generate_bead_callbacks = []
+
+ self._bonded_potential = dict() # cache for bonded potentials
+ self._generate_strands()
+ self.grid_potentials = []
+ self._generate_bead_model( max_basepairs_per_bead, max_nucleotides_per_bead, local_twist, escapable_twist)
+
+ if debye_length is not None:
+ nbDnaScheme.debye_length = debye_length
+ self.debye_length = debye_length
+
+ self.useNonbondedScheme( nbDnaScheme )
+ self.useTclForces = False
+
+ def set_debye_length(self, value):
+ if value <= 0:
+ raise ValueError("The Debye length must be positive")
+ for s,tA,tB in self.nbSchemes:
+ try:
+ s.debye_length = value
+ except:
+ ...
+ self.debye_length = value
+
+ def get_connections(self,type_=None,exclude=()):
+ """ Find all connections in model, without double-counting """
+ added=set()
+ ret=[]
+ for s in self.segments:
+ items = [e for e in s.get_connections_and_locations(type_,exclude=exclude) if e[0] not in added]
+ added.update([e[0] for e in items])
+ ret.extend( list(sorted(items,key=lambda x: x[1].address)) )
+ return ret
+
+ def _recursively_get_beads_within_bonds(self,b1,bonds,done=()):
+ ret = []
+ done = list(done)
+ done.append(b1)
+ if bonds == 0:
+ return [[]]
+
+ for b2 in b1.intrahelical_neighbors:
+ if b2 in done: continue
+ for tmp in self._recursively_get_beads_within_bonds(b2, bonds-1, done):
+ ret.append( [b2]+tmp )
+ return ret
+
+ def _get_intrahelical_beads(self,num=2):
+ ## TODO: add check that this is not called before adding intrahelical_neighbors in _generate_bead_model
+
+ assert(num >= 2)
+
+ ret = []
+ for s in self.segments:
+ for b1 in s.beads:
+ for bead_list in self._recursively_get_beads_within_bonds(b1, num-1):
+ assert(len(bead_list) == num-1)
+ if b1.idx < bead_list[-1].idx: # avoid double-counting
+ ret.append([b1]+bead_list)
+ return ret
+
+
+ def _get_intrahelical_angle_beads(self):
+ return self._get_intrahelical_beads(num=3)
+
+ def _get_potential(self, type_, kSpring, d, max_potential = None):
+ key = (type_, kSpring, d, max_potential)
+ if key not in self._bonded_potential:
+ assert( kSpring >= 0 )
+ if type_ == "bond":
+ self._bonded_potential[key] = HarmonicBond(kSpring,d, rRange=(0,1200), max_potential=max_potential)
+ elif type_ == "gbond":
+ self._bonded_potential[key] = HarmonicBond(kSpring,d, rRange=(0,1200), max_potential=max_potential, correct_geometry=True, temperature=self.temperature)
+ elif type_ == "angle":
+ self._bonded_potential[key] = HarmonicAngle(kSpring,d, max_potential=max_potential)
+ # , resolution = 1, maxForce=0.1)
+ elif type_ == "dihedral":
+ self._bonded_potential[key] = HarmonicDihedral(kSpring,d, max_potential=max_potential)
+ else:
+ raise Exception("Unhandled potential type '%s'" % type_)
+ return self._bonded_potential[key]
+ def get_bond_potential(self, kSpring, d, correct_geometry=False):
+ assert( d > 0.2 )
+ return self._get_potential("gbond" if correct_geometry else "bond",
+ kSpring, d)
+ def get_angle_potential(self, kSpring, d):
+ return self._get_potential("angle", kSpring, d)
+ def get_dihedral_potential(self, kSpring, d, max_potential=None):
+ while d > 180: d-=360
+ while d < -180: d+=360
+ return self._get_potential("dihedral", kSpring, d, max_potential)
+
+ def _get_wlc_sk_bond_potential(self, d):
+ ## https://aip.scitation.org/doi/full/10.1063/1.4968020
+ type_='wclsk-bond'
+ # lp = 2*5 # TODO place these parameters in a logical spot
+ lp = 15 # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
+ # https://www.pnas.org/content/pnas/109/3/799.full.pdf
+ lp = 12 # selected semi-empirically to make ssDNA force extension match
+ key = (type_, d, lp)
+ assert( d > 0.2 )
+ if key not in self._bonded_potential:
+ kT = self.temperature * 0.0019872065 # kcal/mol
+ self._bonded_potential[key] = WLCSKBond( d, lp, kT, rRange=(0,1200) )
+ return self._bonded_potential[key]
+
+ def _get_wlc_sk_angle_potential(self, d):
+ ## https://aip.scitation.org/doi/full/10.1063/1.4968020
+ type_='wclsk-angle'
+ ## TODO move
+ lp = 15 # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
+ # https://www.pnas.org/content/pnas/109/3/799.full.pdf
+ lp = 12 # selected semi-empirically to make ssDNA force extension match
+ key = (type_, d, lp)
+ assert( d > 0.2 )
+ if key not in self._bonded_potential:
+ kT = self.temperature * 0.0019872065 # kcal/mol
+ self._bonded_potential[key] = WLCSKAngle( d, lp, kT )
+ return self._bonded_potential[key]
+
+
+ def _getParent(self, *beads ):
+ if len(set([b.parent for b in beads])) == 1:
+ return beads[0].parent
+ else:
+ return self
+
+ def _get_twist_spring_constant(self, sep):
+ """ sep in nt """
+ twist_persistence_length = 90 # set semi-arbitrarily as there is a large spread in literature
+ ## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
+ Lp = twist_persistence_length/0.34
+
+ return twist_spring_from_lp(sep, Lp, self.temperature)
+
+ def extend(self, other, copy=False, include_strands=True):
+ if copy == True:
+ logger.warning("Forcing SegmentModel.extend(...,copy=False,...)")
+ copy = False
+ assert( isinstance(other, SegmentModel) )
+
+ try:
+ max_occupancy = max([s.occupancy for s in self.segments if 'occupancy' in s.__dict__])
+ occupancy0 = 10**np.ceil(np.log10(max_occupancy+1))
+ except:
+ pass
+
+ if copy:
+ for s in other.segments:
+ newseg = deepcopy(s)
+ try:
+ newseg.occupancy = occupancy0+s.occupancy
+ except:
+ pass
+ self.segments.append(newseg)
+ newseg.parent = self
+ if include_strands:
+ for s in other.strands:
+ newstrand = deepcopy(s)
+ self.strands.append(newstrand)
+ newstrand.parent = self
+ else:
+ for s in other.segments:
+ try:
+ s.occupancy = occupancy0+s.occupancy
+ except:
+ pass
+ self.segments.append(s)
+ s.parent = self
+ if include_strands:
+ for s in other.strands:
+ self.strands.append(s)
+ s.parent = self
+ self._clear_beads()
+
+ def update(self, segment , copy=False):
+ assert( isinstance(segment, Segment) )
+ if copy:
+ segment = deepcopy(segment)
+ segment.parent = self
+ self.segments.append(segment)
+ self._clear_beads()
+
+ """ Mapping between different resolution models """
+ def clear_atomic(self):
+ for strand in self.strands:
+ for s in strand.children:
+ s.clear_all()
+ s.oxdna_nt = []
+
+ for seg in self.segments:
+ for d in ('fwd','rev'):
+ seg.strand_pieces[d] = []
+ self._generate_strands()
+ ## Clear sequence if needed
+ for seg in self.segments:
+ if seg.sequence is not None and len(seg.sequence) != seg.num_nt:
+ seg.sequence = None
+
+ def clear_beads(self):
+ return self._clear_beads()
+
+ def _clear_beads(self):
+ ## TODO: deprecate
+ for s in self.segments:
+ try:
+ s.clear_all()
+ except:
+ ...
+ self.clear_all(keep_children=True)
+
+ try:
+ if len(self.strands[0].children[0].children) > 0:
+ self.clear_atomic()
+ except:
+ ...
+
+ ## Check that it worked
+ assert( len([b for b in self]) == 0 )
+ locParticles = []
+ for s in self.segments:
+ for c,A,B in s.get_connections_and_locations():
+ for l in (A,B):
+ if l.particle is not None:
+ locParticles.append(l.particle)
+ assert( len(locParticles) == 0 )
+ assert( len([b for s in self.segments for b in s.beads]) == 0 )
+
+ def _update_segment_positions(self, bead_coordinates):
+ print("WARNING: called deprecated command '_update_segment_positions; use 'update_splines' instead")
+ return self.update_splines(bead_coordinates)
+
+ ## Operations on spline coordinates
+ def translate(self, translation_vector, position_filter=None):
+ for s in self.segments:
+ s.translate(translation_vector, position_filter=position_filter)
+
+ def rotate(self, rotation_matrix, about=None, position_filter=None):
+ for s in self.segments:
+ s.rotate(rotation_matrix, about=about, position_filter=position_filter)
+
+ def get_center(self, include_ssdna=False):
+ if include_ssdna:
+ segments = self.segments
+ else:
+ segments = list(filter(lambda s: isinstance(s,DoubleStrandedSegment),
+ self.segments))
+ centers = [s.get_center() for s in segments]
+ weights = [s.num_nt*2 if isinstance(s,DoubleStrandedSegment) else s.num_nt for s in segments]
+ # centers,weights = [np.array(a) for a in (centers,weights)]
+ return np.average( centers, axis=0, weights=weights)
+
+ def update_splines(self, bead_coordinates):
+ """ Set new function for each segments functions
+ contour_to_position and contour_to_orientation """
+
+ for s in self.segments:
+ # if s.name == "61-1":
+ # pdb.set_trace()
+
+ cabs = s.get_connections_and_locations("intrahelical")
+ if isinstance(s,SingleStrandedSegment):
+ cabs = cabs + [[c,A,B] for c,A,B in s.get_connections_and_locations("sscrossover") if A.address == 0 or A.address == 1]
+ if np.any( [B.particle is None for c,A,B in cabs] ):
+ print( "WARNING: none type found in connection, skipping" )
+ cabs = [e for e in cabs if e[2].particle is not None]
+
+ def get_beads_and_contour_positions(s):
+ ret_list = []
+ def zip_bead_contour(beads,address=None):
+ if isinstance(address,list):
+ assert(False)
+ for b,a in zip(beads,address):
+ if b is None: continue
+ try:
+ ret_list.append((b, b.get_contour_position(s,a)))
+ except:
+ ...
+ else:
+ for b in beads:
+ if b is None: continue
+ try:
+ ret_list.append((b, b.get_contour_position(s,address)))
+ except:
+ ...
+ return ret_list
+
+ ## Add beads from segment s
+ beads_contours = zip_bead_contour(s.beads)
+ beads_contours.extend( zip_bead_contour([A.particle for c,A,B in cabs]) )
+ beads = set([b for b,c in beads_contours])
+
+ ## Add nearby beads
+ for c,A,B in cabs:
+ ## TODOTODO test?
+ filter_fn = lambda x: x is not None and x not in beads
+ bs = list( filter( filter_fn, B.particle.intrahelical_neighbors ) )
+ beads_contours.extend( zip_bead_contour( bs, A.address ) )
+ beads.update(bs)
+ for i in range(3):
+ bs = list( filter( filter_fn, [n for b in bs for n in b.intrahelical_neighbors] ) )
+ beads_contours.extend( zip_bead_contour( bs, A.address ) )
+ beads.update(bs)
+
+ beads_contours = list(set(beads_contours))
+ beads = list(beads)
+
+ ## Skip beads that are None (some locations were not assigned a particle to avoid double-counting)
+ # beads = [b for b in beads if b is not None]
+ assert( np.any([b is None for b,c in beads_contours]) == False )
+ # beads = list(filter(lambda x: x[0] is not None, beads))
+
+ if isinstance(s, DoubleStrandedSegment):
+ beads_contours = list(filter(lambda x: x[0].type_.name[0] == "D", beads_contours))
+ return beads_contours
+
+ beads_contours = get_beads_and_contour_positions(s)
+ contours = [c for b,c in beads_contours]
+ contour_idx = np.array( np.array(contours)*s.num_nt * 10, dtype=int )
+ contour_idx,ids1 = np.unique(contour_idx, return_index=True)
+ beads_contours = [beads_contours[i] for i in ids1]
+
+ ## TODO: keep closest beads beyond +-1.5 if there are fewer than 2 beads
+ tmp = []
+ dist = 1
+ while len(tmp) < 5 and dist < 3:
+ tmp = list(filter(lambda bc: np.abs(bc[1]-0.5) < dist, beads_contours))
+ dist += 0.1
+
+ if len(tmp) <= 1:
+ raise Exception("Failed to fit spline into segment {}".format(s))
+
+ beads = [b for b,c in tmp]
+ contours = [c for b,c in tmp]
+ ids = [b.idx for b in beads]
+
+ if len(beads) <= 1:
+ pdb.set_trace()
+
+
+ """ Get positions """
+ positions = bead_coordinates[ids,:].T
+
+ # print("BEADS NOT IN {}:".format(s))
+ # for b,c in filter(lambda z: z[0] not in s.beads, zip(beads,contours)):
+ # print(" {}[{:03f}]: {:0.3f}".format(b.parent.name, b.contour_position, c) )
+
+
+ tck, u = interpolate.splprep( positions, u=contours, s=0, k=1 )
+
+ # if len(beads) < 8:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+
+ # else:
+ # try:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=3, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+ # except:
+ # ret = interpolate.splprep( positions, u=contours, s=0, k=1, full_output=1 )
+ # tck = ret[0][0]
+ # if ret[2] > 0:
+ # pdb.set_trace()
+
+ s.position_spline_params = (tck,u)
+
+ """ Get orientation """
+ def get_orientation_vector(bead,tangent):
+ if 'orientation_bead' in bead.__dict__:
+ o = bead.orientation_bead
+ oVec = bead_coordinates[o.idx,:] - bead_coordinates[bead.idx,:]
+ oVec = oVec - oVec.dot(tangent)*tangent
+ oVec = oVec/np.linalg.norm(oVec)
+ else:
+ oVec = None
+ return oVec
+
+ def remove_tangential_projection(vector, tangent):
+ """ Assume tangent is normalized """
+ v = vector - vector.dot(tangent)*tangent
+ return v/np.linalg.norm(v)
+
+ def get_orientation_vector(bead,tangent):
+ if 'orientation_bead' in bead.__dict__:
+ o = bead.orientation_bead
+ oVec = bead_coordinates[o.idx,:] - bead_coordinates[bead.idx,:]
+ oVec = remove_tangential_projection(oVec,tangent)
+ else:
+ oVec = None
+ return oVec
+
+
+ def get_previous_idx_if_none(list_):
+ previous = None
+ result = []
+ i = 0
+ for e in list_:
+ if e is None:
+ result.append(previous)
+ else:
+ previous = i
+ i+=1
+ return result
+ def get_next_idx_if_none(list_):
+ tmp = get_previous_idx_if_none(list_[::-1])[::-1]
+ return [ len(list_)-1-idx if idx is not None else idx for idx in tmp ]
+
+ def fill_in_orientation_vectors(contours,orientation_vectors,tangents):
+ result = []
+ last_idx = get_previous_idx_if_none( orientation_vectors )
+ next_idx = get_next_idx_if_none( orientation_vectors )
+ none_idx = 0
+ for c,ov,t in zip(contours,orientation_vectors,tangents):
+ if ov is not None:
+ result.append(ov)
+ else:
+ p = last_idx[none_idx]
+ n = next_idx[none_idx]
+ none_idx += 1
+ if p is None:
+ if n is None:
+ ## Should be quite rare; give something random if it happens
+ print("WARNING: unable to interpolate orientation")
+ o = np.array((1,0,0))
+ result.append( remove_tangential_projection(o,t) )
+ else:
+ o = orientation_vectors[n]
+ result.append( remove_tangential_projection(o,t) )
+ else:
+ if n is None:
+ o = orientation_vectors[p]
+ result.append( remove_tangential_projection(o,t) )
+ else:
+ cp,cn = [contours[i] for i in (p,n)]
+ op,on = [orientation_vectors[i] for i in (p,n)]
+ if (cn-cp) > 1e-6:
+ o = ((cn-c)*op+(c-cp)*on)/(cn-cp)
+ else:
+ o = op+on
+ result.append( remove_tangential_projection(o,t) )
+ return result
+
+ tangents = s.contour_to_tangent(contours)
+ orientation_vectors = [get_orientation_vector(b,t) for b,t in zip(beads,tangents)]
+ if len(beads) > 3 and any([e is not None for e in orientation_vectors] ):
+ orientation_vectors = fill_in_orientation_vectors(contours, orientation_vectors, tangents)
+
+ quats = []
+ lastq = None
+ for b,t,oVec in zip(beads,tangents,orientation_vectors):
+ y = np.cross(t,oVec)
+ assert( np.abs(np.linalg.norm(y) - 1) < 1e-2 )
+ q = quaternion_from_matrix( np.array([oVec,y,t]).T)
+
+ if lastq is not None:
+ if q.dot(lastq) < 0:
+ q = -q
+ quats.append( q )
+ lastq = q
+
+ # pdb.set_trace()
+ quats = np.array(quats)
+ # tck, u = interpolate.splprep( quats.T, u=contours, s=3, k=3 ) ;# cubic spline not as good
+ tck, u = interpolate.splprep( quats.T, u=contours, s=0, k=1 )
+ s.quaternion_spline_params = (tck,u)
+
+ def get_segments_matching(self, pattern):
+ """ Returns a list of all segments that match the regular expression 'pattern' """
+
+ re_pattern = re.compile(pattern)
+ return [s for s in self.segments if re_pattern.match(s.name) is not None]
+
+ def get_crossovers_at_ends(self):
+ """
+ Return a list of all "regular" crossovers where both sides of
+ the crossover exist at the start or end of a segment
+ """
+
+ ret_list = []
+ for s in self.segments:
+ for c in filter(lambda c: c.type_ == "crossover", s.connections):
+ seg1 = c.A.container
+ seg2 = c.B.container
+ nt1 = c.A.get_nt_pos()
+ nt2 = c.B.get_nt_pos()
+ if (nt1 < 1 and nt2 > seg2.num_nt-2) or (nt2 < 1 and nt1 > seg1.num_nt-2):
+ if c not in ret_list:
+ ret_list.append(c)
+ return ret_list
+
+ def convert_crossover_to_intrahelical(self, crossover):
+ c = crossover
+ A = c.A if c.B.is_3prime_side_of_connection else c.B
+ B = c.B if c.B.is_3prime_side_of_connection else c.A
+ assert( not A.is_3prime_side_of_connection )
+ assert( B.is_3prime_side_of_connection )
+
+ seg1 = A.container
+ seg2 = B.container
+ nt1 = A.get_nt_pos()
+ nt2 = B.get_nt_pos()
+
+ # assert( c.A.on_fwd_strand == c.B.on_fwd_strand )
+ on_fwd_strand_A = A.on_fwd_strand
+ on_fwd_strand_B = B.on_fwd_strand
+
+ # print(nt1, nt2, on_fwd_strand_A, on_fwd_strand_B, c)
+
+ if on_fwd_strand_A:
+ assert( nt1 > seg1.num_nt-2 )
+ fn = seg1.connect_end3
+ if on_fwd_strand_B:
+ assert( nt2 < 1 )
+ arg = seg2.start5
+ else:
+ assert( nt2 > seg2.num_nt-2 )
+ arg = seg2.end5
+ else:
+ assert( nt1 < 1 )
+ fn = seg1.connect_start3
+ if on_fwd_strand_B:
+ assert( nt2 < 1 )
+ arg = seg2.start5
+ else:
+ assert( nt2 > seg2.num_nt-2 )
+ arg = seg2.end5
+ c.delete()
+ fn(arg)
+
+ def get_blunt_DNA_ends(self):
+ return sum([s.get_blunt_DNA_ends for s in self.segments],[])
+
+ def convert_crossovers_at_ends_beyond_cutoff_to_intrahelical(self,cutoff):
+ if cutoff < 0:
+ raise ValueError("Cutoff should be positive!")
+ return self.convert_crossovers_to_intrahelical(
+ position_filter = lambda r1,r2: np.linalg.norm(r2-r1) > cutoff,
+ terminal_only = True)
+
+
+ def convert_crossovers_to_intrahelical(self, position_filter=None, terminal_only=False):
+ conn = self.get_crossovers_at_ends() if terminal_only else [c for c,A,B in self.get_connections('crossover')]
+ for c in conn:
+ if position_filter is not None:
+ r1,r2 = [l.container.contour_to_position(l.address)
+ for l in (c.A,c.B)]
+ if position_filter(r1,r2):
+ self.convert_crossover_to_intrahelical(c)
+ else:
+ self.convert_crossover_to_intrahelical(c)
+
+ def convert_close_crossovers_to_intrahelical(self,cutoff):
+ if cutoff < 0:
+ raise ValueError("Cutoff should be positive!")
+
+ for c,A,B in self.get_connections('crossover'):
+ r1,r2 = [l.container.contour_to_position(l.address)
+ for l in (c.A,c.B)]
+ if np.linalg.norm(r2-r1) < cutoff:
+ self.convert_crossover_to_intrahelical(c)
+
+ def _generate_bead_model(self,
+ max_basepairs_per_bead = None,
+ max_nucleotides_per_bead = None,
+ local_twist=False,
+ escapable_twist=True):
+ ## TODO: deprecate
+ self.generate_bead_model( max_basepairs_per_bead = max_basepairs_per_bead,
+ max_nucleotides_per_bead = max_nucleotides_per_bead,
+ local_twist=local_twist,
+ escapable_twist=escapable_twist)
+
+ def generate_bead_model(self,
+ max_basepairs_per_bead = 7,
+ max_nucleotides_per_bead = 4,
+ local_twist=False,
+ escapable_twist=True,
+ sequence_dependent = False,
+ one_bead_per_monomer = False
+ ):
+ if sequence_dependent and not local_twist:
+ raise ValueError("Incompatible options: if sequence_dependent==True, then local_twist must be True")
+ if sequence_dependent and not one_bead_per_monomer:
+ raise ValueError("Incompatible options: if sequence_dependent==True, then one_bead_per_monomer must be True")
+
+ self.children = self.segments # is this okay?
+ self.clear_beads()
+
+ segments = self.segments
+ for s in segments:
+ s.local_twist = local_twist
+
+ """ Simplify connections """
+ # d_nt = dict() #
+ # for s in segments:
+ # d_nt[s] = 1.5/(s.num_nt-1)
+ # for s in segments:
+ # ## replace consecutive crossovers with
+ # cl = sorted( s.get_connections_and_locations("crossover"), key=lambda x: x[1].address )
+ # last = None
+ # for entry in cl:
+ # c,A,B = entry
+ # if last is not None and \
+ # (A.address - last[1].address) < d_nt[s]:
+ # same_type = c.type_ == last[0].type_
+ # same_dest_seg = B.container == last[2].container
+ # if same_type and same_dest_seg:
+ # if np.abs(B.address - last[2].address) < d_nt[B.container]:
+ # ## combine
+ # A.combine = last[1]
+ # B.combine = last[2]
+
+ # ...
+ # # if last is not None:
+ # # s.bead_locations.append(last)
+ # ...
+ # last = entry
+ # del d_nt
+
+ """ Generate beads at intrahelical junctions """
+ if self.DEBUG: print( "Adding intrahelical beads at junctions" )
+
+ if not one_bead_per_monomer:
+ ## Loop through all connections, generating beads at appropriate locations
+ for c,A,B in self.get_connections("intrahelical"):
+ s1,s2 = [l.container for l in (A,B)]
+
+ assert( A.particle is None )
+ assert( B.particle is None )
+
+ ## TODO: offload the work here to s1
+ # TODOTODO
+ a1,a2 = [l.address for l in (A,B)]
+ for a in (a1,a2):
+ assert( np.isclose(a,0) or np.isclose(a,1) )
+
+ ## TODO improve this for combinations of ssDNA and dsDNA (maybe a1/a2 should be calculated differently)
+
+ def _get_nearest(seg,address):
+ b = seg.get_nearest_bead(address)
+ if b is not None:
+ assert( b.parent is seg )
+ """ if above assertion is true, no problem here """
+ if np.abs(b.get_nt_position(seg) - seg.contour_to_nt_pos(address)) > 0.5:
+ b = None
+ return b
+
+ """ Search to see whether bead at location is already found """
+ b = None
+ if isinstance(s1,DoubleStrandedSegment):
+ b = _get_nearest(s1,a1)
+ if b is None and isinstance(s2,DoubleStrandedSegment):
+ b = _get_nearest(s2,a2)
+
+ if b is not None and b.parent not in (s1,s2):
+ b = None
+
+ if b is None:
+ ## need to generate a bead
+ if isinstance(s2,DoubleStrandedSegment):
+ b = s2._generate_one_bead(a2,0)
+ else:
+ b = s1._generate_one_bead(a1,0)
+ A.particle = B.particle = b
+ b.is_intrahelical = True
+ b.locations.extend([A,B])
+ if s1 is s2:
+ b.is_circular_bead = True
+
+ # pdb.set_trace()
+
+ """ Generate beads at other junctions """
+ for c,A,B in self.get_connections(exclude="intrahelical"):
+ s1,s2 = [l.container for l in (A,B)]
+ if A.particle is not None and B.particle is not None:
+ continue
+ # assert( A.particle is None )
+ # assert( B.particle is None )
+
+ ## TODO: offload the work here to s1/s2 (?)
+ a1,a2 = [l.address for l in (A,B)]
+
+ def maybe_add_bead(location, seg, address, ):
+ if location.particle is None:
+ b = seg.get_nearest_bead(address)
+ try:
+ distance = seg.contour_to_nt_pos(np.abs(b.contour_position-address))
+ if seg.resolution is not None:
+ max_distance = seg.resolution
+ else:
+ max_distance = min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
+ if "is_intrahelical" in b.__dict__:
+ max_distance = 0.5
+ if distance >= max_distance:
+ raise Exception("except")
+
+ ## combine beads
+ b.update_position( 0.5*(b.contour_position + address) ) # avg position
+ except:
+ b = seg._generate_one_bead(address,0)
+ location.particle = b
+ b.locations.append(location)
+
+ maybe_add_bead(A,s1,a1)
+ maybe_add_bead(B,s2,a2)
+
+ """ Some tests """
+ for c,A,B in self.get_connections("intrahelical"):
+ for l in (A,B):
+ if l.particle is None: continue
+ assert( l.particle.parent is not None )
+
+ """ Generate beads in between """
+ if self.DEBUG: print("Generating beads")
+ for s in segments:
+ s._generate_beads( self, max_basepairs_per_bead, max_nucleotides_per_bead )
+
+ else:
+ """ Generate beads in each segment """
+ if self.DEBUG: print("Generating beads")
+ for s in segments:
+ s._generate_beads( self, max_basepairs_per_bead, max_nucleotides_per_bead, one_bead_per_monomer )
+
+ """ Associate beads with junctions """
+ # for c,A,B in self.get_connections("intrahelical"):
+ for c,A,B in self.get_connections():
+ for l in (A,B):
+ seg = l.container
+ a = l.address
+ b = seg.get_nearest_bead(a)
+
+ l.particle = b
+ b.locations.append(l)
+ """
+ b.is_intrahelical = True
+ b.locations.extend([A,B])
+ if s1 is s2:
+ b.is_circular_bead = True
+ """
+
+ # """ Combine beads at junctions as needed """
+ # for c,A,B in self.get_connections():
+ # ...
+
+ # ## Debug
+ # all_beads = [b for s in segments for b in s.beads]
+ # positions = np.array([b.position for b in all_beads])
+ # dists = positions[:,np.newaxis,:] - positions[np.newaxis,:,:]
+ # ids = np.where( np.sum(dists**2,axis=-1) + 0.02**2*np.eye(len(dists)) < 0.02**2 )
+ # print( ids )
+ # pdb.set_trace()
+
+ """ Add intrahelical neighbors at connections """
+ special_seps = dict()
+ for c,A,B in self.get_connections("intrahelical"):
+ b1,b2 = [l.particle for l in (A,B)]
+ if b1 is b2:
+ ## already handled by Segment._generate_beads, unless A,B are on same segment
+ if A.container == B.container:
+ sorted_sites = sorted([(abs(L.address-b1.contour_position),L)
+ for L in (A,B)], key=lambda x: x[0])
+ close_site, far_site = [s[1] for s in sorted_sites]
+
+ b3 = far_site.container.get_nearest_bead(far_site.address)
+ b1.intrahelical_neighbors.append(b3)
+ b3.intrahelical_neighbors.append(b1)
+
+ if far_site.address > 0.5:
+ sep = b1.contour_position + (1-b3.contour_position)
+ else:
+ sep = b3.contour_position + (1-b1.contour_position)
+ sep = A.container.num_nt * sep
+ special_seps[(b1,b3)] = special_seps[(b3,b1)] = sep
+
+ else:
+ for b in (b1,b2): assert( b is not None )
+ b1.make_intrahelical_neighbor(b2)
+
+ def _combine_zero_sep_beads():
+ skip_keys = []
+ for b1,b2 in [k for k,v in special_seps.items() if v == 0]:
+ if (b1,b2) in skip_keys: continue
+ del special_seps[(b1,b2)]
+ del special_seps[(b2,b1)]
+ skip_keys.append((b2,b1))
+
+ for b in b2.intrahelical_neighbors:
+ if b is b1: continue
+ if b is not b1 and b.parent is b2.parent:
+ sep = np.abs(b2.contour_position - b.contour_position) * b.parent.num_nt
+ special_seps[(b,b1)] = sep
+ special_seps[(b1,b)] = sep
+ b1.combine(b2)
+
+ for k in list(special_seps.keys()):
+ if b2 in k:
+ if b2 == k[0]:
+ newkey = (b1,k[1])
+ else:
+ newkey = (k[0],b2)
+ special_seps[newkey] = special_seps[k]
+ del special_seps[k]
+ _combine_zero_sep_beads()
+
+ """ Reassign bead types """
+ if self.DEBUG: print("Assigning bead types")
+ beadtype_s = dict()
+ beadtype_count = dict(D=0,O=0,S=0)
+
+ def _assign_bead_type(bead, num_nt, decimals):
+ num_nt0 = bead.num_nt
+ bead.num_nt = np.around( np.float32(num_nt), decimals=decimals )
+ char = bead.type_.name[0].upper()
+ key = (char, bead.num_nt)
+ if key in beadtype_s:
+ bead.type_ = beadtype_s[key]
+ else:
+ t = deepcopy(bead.type_)
+ t.__dict__["nts"] = bead.num_nt*2 if char in ("D","O") else bead.num_nt
+ # t.name = t.name + "%03d" % (t.nts*10**decimals)
+ t.name = char + "%03d" % (beadtype_count[char])
+ t.mass = t.nts * 150
+ t.diffusivity = 120 if t.nts == 0 else min( 50 / np.sqrt(t.nts/5), 120)
+ beadtype_count[char] += 1
+ if self.DEBUG: print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
+ beadtype_s[key] = bead.type_ = t
+
+ # (cluster_size[c-1])
+
+
+ import scipy.cluster.hierarchy as hcluster
+ beads = [b for s in segments for b in s if b.type_.name[0].upper() in ("D","O")]
+ data = np.array([b.num_nt for b in beads])[:,np.newaxis]
+ order = int(2-np.log10(2*max_basepairs_per_bead)//1)
+ try:
+ clusters = hcluster.fclusterdata(data, float(max_basepairs_per_bead)/500, criterion="distance")
+ cluster_size = [np.mean(data[clusters == i]) for i in np.unique(clusters)]
+ except:
+ clusters = np.arange(len(data))+1
+ cluster_size = data.flatten()
+ for b,c in zip(beads,clusters):
+ _assign_bead_type(b, cluster_size[c-1], decimals=order)
+
+ beads = [b for s in segments for b in s if b.type_.name[0].upper() in ("S")]
+ data = np.array([b.num_nt for b in beads])[:,np.newaxis]
+ order = int(2-np.log10(max_nucleotides_per_bead)//1)
+ try:
+ clusters = hcluster.fclusterdata(data, float(max_nucleotides_per_bead)/500, criterion="distance")
+ cluster_size = [np.mean(data[clusters == i]) for i in np.unique(clusters)]
+ except:
+ clusters = np.arange(len(data))+1
+ cluster_size = data.flatten()
+ for b,c in zip(beads,clusters):
+ _assign_bead_type(b, cluster_size[c-1], decimals=order)
+
+ self._beadtype_s = beadtype_s
+ self._apply_grid_potentials_to_beads(beadtype_s)
+
+ # for bead in [b for s in segments for b in s]:
+ # num_nt0 = bead.num_nt
+ # # bead.num_nt = np.around( np.float32(num_nt), decimals=decimals )
+ # key = (bead.type_.name[0].upper(), bead.num_nt)
+ # if key in beadtype_s:
+ # bead.type_ = beadtype_s[key]
+ # else:
+ # t = deepcopy(bead.type_)
+ # t.__dict__["nts"] = bead.num_nt*2 if t.name[0].upper() in ("D","O") else bead.num_nt
+ # # t.name = t.name + "%03d" % (t.nts*10**decimals)
+ # t.name = t.name + "%.16f" % (t.nts)
+ # print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
+ # beadtype_s[key] = bead.type_ = t
+
+
+ """ Update bead indices """
+ self._countParticleTypes() # probably not needed here
+ self._updateParticleOrder()
+
+
+ def k_dsdna_bond(d):
+ conversion = 0.014393265 # units "pN/AA" kcal_mol/AA^2
+ elastic_modulus_times_area = 1000 # pN http://markolab.bmbcb.northwestern.edu/marko/Cocco.CRP.02.pdf
+ return conversion*elastic_modulus_times_area/d
+
+ def k_ssdna_bond(d):
+ # conversion = 0.014393265 # units "pN/AA" kcal_mol/AA^2
+ # ## TODO: get better numbers our ssDNA model
+ # elastic_modulus_times_area = 800 # pN http://markolab.bmbcb.northwestern.edu/marko/Cocco.CRP.02.pdf
+
+ return conversion*elastic_modulus_times_area/d
+
+ def k_dsdna_angle(sep, Lp=None):
+ Lp_eff = get_effective_dsDNA_Lp(sep, Lp)
+ Lp_eff = Lp_eff/0.34 # convert from nm to bp
+ return angle_spring_from_lp(sep,Lp_eff)
+
+ def k_xover_angle(sep, Lp=50):
+ Lp = Lp/0.34 # convert from nm to bp
+ return 0.25 * angle_spring_from_lp(sep,Lp)
+
+
+ """ Add intrahelical bond potentials """
+ if self.DEBUG: print("Adding intrahelical bond potentials")
+ dists = dict() # intrahelical distances built for later use
+ intra_beads = self._get_intrahelical_beads()
+ if self.DEBUG: print(" Adding %d bonds" % len(intra_beads))
+ for b1,b2 in intra_beads:
+ # assert( not np.isclose( np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()), 0 ) )
+ if np.linalg.norm(b1.collapsedPosition() - b2.collapsedPosition()) < 1:
+ # print("WARNING: some beads are very close")
+ ...
+
+ parent = self._getParent(b1,b2)
+
+ if (b1,b2) in special_seps:
+ sep = special_seps[(b1,b2)]
+ else:
+ seg = b2.parent
+ c0 = b2.contour_position
+ sep = np.abs(b1.get_nt_position(seg,c0)-b2.get_nt_position(seg))
+
+ is_dsdna = b1.type_.name[0] == "D" and b2.type_.name[0] == "D"
+ if is_dsdna:
+ d = 3.4*sep
+ else:
+ # d = 6.5*sep # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
+ d = 6.4*sep # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
+ if b1.type_.name[0] != b2.type_.name[0]:
+ """ Add a small extra distance to junction """
+ d += 3
+
+ if b1 not in dists:
+ dists[b1] = dict()
+ if b2 not in dists:
+ dists[b2] = dict()
+ # dists[b1].append([b2,sep])
+ # dists[b2].append([b1,sep])
+ dists[b1][b2] = sep
+ dists[b2][b1] = sep
+
+ if b1 is b2: continue
+
+ # dists[[b1,b2]] = dists[[b2,b1]] = sep
+ if is_dsdna:
+ k = k_dsdna_bond(d)
+ bond = self.get_bond_potential(k,d,correct_geometry=True)
+ else:
+ bond = self._get_wlc_sk_bond_potential(d)
+ parent.add_bond( b1, b2, bond, exclude=True )
+
+ # for s in self.segments:
+ # sepsum = 0
+ # beadsum = 0
+ # for b1 in s.beads:
+ # beadsum += b1.num_nt
+ # for bead_list in self._recursively_get_beads_within_bonds(b1, 1):
+ # assert(len(bead_list) == 1)
+ # if b1.idx < bead_list[-1].idx: # avoid double-counting
+ # for b2 in bead_list:
+ # if b2.parent == b1.parent:
+ # sepsum += dists[b1][b2]
+ # sepsum += sep
+ # print("Helix {}: bps {}, beads {}, separation {}".format(s.name, s.num_nt, beadsum, sepsum))
+
+ """ Add intrahelical angle potentials """
+ def get_effective_dsDNA_Lp(sep, Lp0=50):
+ """ The persistence length of our model was found to be a
+ little off (probably due to NB interactions). This
+ attempts to compensate """
+
+ ## For 1 bp, Lp=559, for 25 Lp = 524
+ beads_per_bp = sep/2
+ # return 0.93457944*Lp0 ;# factor1
+ return 0.97*Lp0 ;# factor2
+ # factor = bead_per_bp * (0.954-0.8944
+ # return Lp0 * bead_per_bp
+
+ if self.DEBUG: print("Adding intrahelical angle potentials")
+ for b1,b2,b3 in self._get_intrahelical_angle_beads():
+ parent = self._getParent(b1,b2,b3)
+ seg = b2.parent
+ c0 = b2.contour_position
+ sep = dists[b2][b1] + dists[b2][b3]
+
+
+ if b1.type_.name[0] == "D" and b2.type_.name[0] == "D" and b3.type_.name[0] == "D":
+ k = k_dsdna_angle(sep, seg.persistence_length)
+ if local_twist:
+ k_dihed = 0.25*k
+ k *= 0.75 # reduce because orientation beads impose similar springs
+ dihed = self.get_dihedral_potential(k_dihed,180)
+ parent.add_dihedral(b1,b2,b2.orientation_bead,b3, dihed)
+ angle = self.get_angle_potential(k,180)
+
+
+ elif b1.type_.name[0] == "S" and b2.type_.name[0] == "S" and b3.type_.name[0] == "S":
+ # angle = self._get_wlc_sk_angle_potential(sep*6.5) # TODO move 6.5 somewhere sensible
+ angle = self._get_wlc_sk_angle_potential(sep*6.4) # TODO move 6.4 somewhere sensible
+ else:
+ ## Considered as a sscrossover below
+ continue
+
+ parent.add_angle( b1, b2, b3, angle )
+
+ """ Add intrahelical exclusions """
+ if self.DEBUG: print("Adding intrahelical exclusions")
+ beads = dists.keys()
+ def _recursively_get_beads_within(b1,d,done=()):
+ ret = []
+ self
+ intra_beads
+ if b1 not in dists:
+ print("Skipping exclusions for",b1)
+ return ret
+ for b2,sep in dists[b1].items():
+ if b2 in done: continue
+ if sep < d:
+ ret.append( b2 )
+ done.append( b2 )
+ tmp = _recursively_get_beads_within(b2, d-sep, done)
+ if len(tmp) > 0: ret.extend(tmp)
+ return ret
+
+ exclusions = set()
+ for b1 in beads:
+ """ In addition to bond exclusiosn, only add exclusions
+ within like-type segments (i.e. dsDNA or ssDNA, not
+ junctions between the two) """
+
+ t = type(b1.parent)
+ if t is DoubleStrandedSegment:
+ cutoff = 20
+ elif t is SingleStrandedSegment:
+ cutoff = 5
+ else:
+ raise ValueError("Unexpected polymer segment type")
+
+ for b in _recursively_get_beads_within(b1, cutoff, done=[b1]):
+ if isinstance(b.parent,t):
+ exclusions.add((b1,b))
+ else:
+ break
+ # exclusions.update( tmp )
+
+ ## Add exclusions very near crossovers
+ for c,A,B in sum([self.get_connections(term) for term in ("crossover","terminal_crossover")],[]):
+ b1,b2 = [loc.particle for loc in (A,B)]
+ near_b1 = _recursively_get_beads_within(b1, 3, done=[])
+ near_b2 = _recursively_get_beads_within(b2, 3, done=[])
+ for bi in near_b1:
+ for bj in near_b2:
+ exclusions.add((bi,bj))
+
+ if self.DEBUG: print("Adding %d exclusions" % len(exclusions))
+ for b1,b2 in exclusions:
+ parent = self._getParent(b1,b2)
+ parent.add_exclusion( b1, b2 )
+
+ """ Twist potentials """
+ if local_twist:
+ if self.DEBUG: print("Adding twist potentials")
+
+ for b1 in beads:
+ if "orientation_bead" not in b1.__dict__: continue
+ for b2,sep in dists[b1].items():
+ if "orientation_bead" not in b2.__dict__: continue
+ if b2.idx < b1.idx: continue # Don't double-count
+
+ p1,p2 = [b.parent for b in (b1,b2)]
+ o1,o2 = [b.orientation_bead for b in (b1,b2)]
+
+ parent = self._getParent( b1, b2 )
+ _Lp = (p1.persistence_length + p2.persistence_length) * 0.5
+
+ """ Add heuristic 90 degree potential to keep orientation bead orthogonal """
+ k = 0.25*k_dsdna_angle(sep, _Lp)
+ pot = self.get_angle_potential(k,90)
+ parent.add_angle(o1,b1,b2, pot)
+ parent.add_angle(b1,b2,o2, pot)
+
+ ## TODO: improve this
+ twist_per_nt = 0.5 * (p1.twist_per_nt + p2.twist_per_nt)
+ angle = sep*twist_per_nt
+ if angle > 360 or angle < -360:
+ print("WARNING: twist angle out of normal range... proceeding anyway")
+ # raise Exception("The twist between beads is too large")
+
+ k = self._get_twist_spring_constant(sep)
+ if escapable_twist:
+ pot = self.get_dihedral_potential(k,angle,max_potential=1)
+ else:
+ pot = self.get_dihedral_potential(k,angle)
+ parent.add_dihedral(o1,b1,b2,o2, pot)
+
+
+ def count_crossovers(beads):
+ count = 0
+ for b in beads:
+ for l in b.locations:
+ if l.connection is not None:
+ if l.connection.type_ in ("crossover","terminal_crossover"):
+ count += 1
+ return count
+
+ def add_local_crossover_strand_orientation_potential(b1,b2, b1_on_fwd_strand):
+
+ """ Adds a dihedral angle potential so bead b2 at opposite
+ end of crossover stays on correct side of helix of b1 """
+
+ u1 = b1.get_intrahelical_above(all_types=False)
+ d1 = b1.get_intrahelical_below(all_types=False)
+
+ sign = 1 if b1_on_fwd_strand else -1
+
+ # if b1.parent.name == "8-1" or b2.parent.name == "8-1":
+ # print()
+ # print(b1.parent.name, b2.parent.name, b1_on_fwd_strand)
+ # import pdb
+ # pdb.set_trace()
+
+ a,b,c = b2,b1,d1
+ if c is None or c is a:
+ c = u1
+ sign *= -1
+ if c is None or c is a: return
+ try:
+ d = b1.orientation_bead
+ except:
+ return
+
+ k = k_xover_angle(sep=1) # TODO
+ pot = self.get_dihedral_potential(k, sign*120)
+ self.add_dihedral( a,b,c,d, pot )
+
+ def add_local_tee_orientation_potential(b1,b2, b1_on_fwd_strand, b2_on_fwd_strand):
+
+ """ b1 is the end of a helix, b2 is in the middle This
+ adds a dihedral angle potential so helix of b1 is oriented
+ properly relative to strand on b2 """
+
+ u1,u2 = [b.get_intrahelical_above(all_types=False) for b in (b1,b2)]
+ d1,d2 = [b.get_intrahelical_below(all_types=False) for b in (b1,b2)]
+
+ angle = 150
+ if not b2_on_fwd_strand: angle -= 180
+
+ a,b,c = u2,b2,b1
+ if a is None:
+ a = d2
+ angle -= 180
+ try:
+ d = b1.orientation_bead
+ except:
+ d = None
+ angle -= 120
+
+ while angle > 180:
+ angle -= 360
+ while angle < -180:
+ angle += 360
+
+ k = k_xover_angle(sep=1) # TODO
+ if a is not None and d is not None:
+ pot = self.get_dihedral_potential(k,angle)
+ self.add_dihedral( a,b,c,d, pot )
+
+ ## Add 180 degree angle potential
+ a,b,c = b2,b1,u1
+ if c is None: c = d1
+
+ if c is not None:
+ pot = self.get_angle_potential(0.5*k,180)
+ self.add_angle( a,b,c, pot )
+
+ def add_parallel_crossover_potential(b1,b2):
+
+ ## Get beads above and below
+ u1,u2 = [b.get_intrahelical_above(all_types=False) for b in (b1,b2)]
+ d1,d2 = [b.get_intrahelical_below(all_types=False) for b in (b1,b2)]
+ dotProduct = b1.parent.contour_to_tangent(b1.contour_position).dot(
+ b2.parent.contour_to_tangent(b2.contour_position) )
+ if dotProduct < 0:
+ tmp = d2
+ d2 = u2
+ u2 = tmp
+
+ a = None
+ if u1 is not None and u2 is not None:
+ t0 = self.hj_equilibrium_angle
+ a,b,c,d = (u1,b1,b2,u2)
+ elif d1 is not None and d2 is not None:
+ t0 = self.hj_equilibrium_angle
+ a,b,c,d = (d1,b1,b2,d2 )
+ elif d1 is not None and u2 is not None:
+ t0 = self.hj_equilibrium_angle-180
+ a,b,c,d = (d1,b1,b2,u2)
+ elif u1 is not None and d2 is not None:
+ t0 = self.hj_equilibrium_angle-180
+ a,b,c,d = (u1,b1,b2,d2)
+
+ if t0 > 180:
+ t0 = t0-360
+ elif t0 < -180:
+ t0 = t0+360
+
+ ## TODO?: Check length-dependence of this potential
+ if a is not None:
+ k_intrinsic = 0.00086
+ k = [1/k for k in (4*k_xover_angle( dists[b][a] ),
+ k_intrinsic,
+ 4*k_xover_angle( dists[c][d] ))]
+ k = sum(k)**-1
+ k = k * count_crossovers((b1,b2))/4
+
+ pot = self.get_dihedral_potential(k,t0)
+ self.add_dihedral( a,b,c,d, pot )
+ ...
+
+ """ Functions for adding crossover potentials """
+ def add_ss_crossover_potentials(connection,A,B, add_bond=True):
+ b1,b2 = [loc.particle for loc in (A,B)]
+
+ if (b1,b2,A.on_fwd_strand,B.on_fwd_strand) in processed_crossovers:
+ return
+ processed_crossovers.add((b1,b2,A.on_fwd_strand,B.on_fwd_strand))
+ processed_crossovers.add((b2,b1,B.on_fwd_strand,A.on_fwd_strand))
+
+ if b1 is b2:
+ """ Catch attempts to add "crossover potentials" at
+ intrahelical junctions between ds and ssDNA """
+ if A.container is not b1.parent:
+ b1 = A.container.get_nearest_bead(A.address)
+ if B.container is not b2.parent:
+ b2 = B.container.get_nearest_bead(B.address)
+ if b1 is b2:
+ return
+
+ if b1 is None or b2 is None:
+ return
+
+ ## TODO: improve parameters
+ if add_bond:
+ pot = self.get_bond_potential(4,12)
+ self.add_bond(b1,b2, pot)
+
+ ## Add potentials to provide a sensible orientation
+ ## TODO refine potentials against all-atom simulation data
+ if local_twist:
+ add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
+ add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
+
+ def add_crossover_potentials(connection,A,B):
+ ## TODO: use a better description here
+ b1,b2 = [loc.particle for loc in (A,B)]
+ if (b1,b2,A.on_fwd_strand,B.on_fwd_strand) in processed_crossovers:
+ return
+
+ processed_crossovers.add((b1,b2,A.on_fwd_strand,B.on_fwd_strand))
+ processed_crossovers.add((b2,b1,B.on_fwd_strand,A.on_fwd_strand))
+
+ if b1 is b2:
+ """ Catch attempts to add "crossover potentials" at
+ intrahelical junctions between ds and ssDNA """
+ return
+
+ """ Add parallel helices potential, possibly """
+ ## Add potential to provide a particular orinetation
+ nt1,nt2 = [l.get_nt_pos() for l in (A,B)]
+ is_end1, is_end2 = [nt in (0,l.container.num_nt-1) for nt,l in zip((nt1,nt2),(A,B))]
+ is_T_junction = (is_end1 and not is_end2) or (is_end2 and not is_end1)
+
+ if (not is_end1) and (not is_end2):
+ ## TODO?: Only apply this potential if not local_twist
+ add_parallel_crossover_potential(b1,b2)
+
+ # dotProduct = b1.parent.contour_to_tangent(b1.contour_position).dot(
+ # b2.parent.contour_to_tangent(b2.contour_position) )
+
+
+ if local_twist:
+ if is_T_junction:
+ """ Special case: one helix extends away from another in T-shaped junction """
+ """ Add bond potential """
+ k = 1.0 * count_crossovers((b1,b2))
+ pot = self.get_bond_potential(k,12.5)
+ self.add_bond(b1,b2, pot)
+
+ if is_end1:
+ b1_forward = A.on_fwd_strand if nt1 == 0 else not A.on_fwd_strand
+ add_local_tee_orientation_potential(b1,b2, b1_forward, B.on_fwd_strand)
+ else:
+ add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
+
+ if is_end2:
+ b2_forward = B.on_fwd_strand if nt2 == 0 else not B.on_fwd_strand
+ add_local_tee_orientation_potential(b2,b1, b2_forward, A.on_fwd_strand)
+ else:
+ add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
+
+ else:
+ """ Add bond potential """
+ k = 1.0 * count_crossovers((b1,b2))
+ pot = self.get_bond_potential(k,18.5)
+ self.add_bond(b1,b2, pot)
+
+ """ Normal case: add orientation potential """
+ add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
+ add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
+ else:
+ """ Add bond potential """
+ k = 1.0 * count_crossovers((b1,b2))
+ pot = self.get_bond_potential(k,18.5)
+ self.add_bond(b1,b2, pot)
+
+
+ """ Add connection potentials """
+ processed_crossovers = set()
+ # pdb.set_trace()
+ for c,A,B in self.get_connections("sscrossover"):
+ p1,p2 = [loc.container for loc in (A,B)]
+
+ assert(any([isinstance(p,SingleStrandedSegment) for p in (p1,p2)]))
+ add_ss_crossover_potentials(c,A,B)
+
+ for c,A,B in self.get_connections("intrahelical"):
+ ps = [loc.container for loc in (A,B)]
+
+ if any([isinstance(p,SingleStrandedSegment) for p in ps]) and \
+ any([isinstance(p,DoubleStrandedSegment) for p in ps]):
+ add_ss_crossover_potentials(c,A,B, add_bond=False)
+
+ for c,A,B in sum([self.get_connections(term) for term in ("crossover","terminal_crossover")],[]):
+ p1,p2 = [loc.container for loc in (A,B)]
+
+ if any([isinstance(p,SingleStrandedSegment) for p in (p1,p2)]):
+ add_ss_crossover_potentials(c,A,B)
+ else:
+ add_crossover_potentials(c,A,B)
+
+ ## todotodo check that this works
+ for crossovers in self.get_consecutive_crossovers():
+ if local_twist: break
+ ## filter crossovers
+ for i in range(len(crossovers)-2):
+ c1,A1,B1,dir1 = crossovers[i]
+ c2,A2,B2,dir2 = crossovers[i+1]
+ s1,s2 = [l.container for l in (A1,A2)]
+ sep = A1.particle.get_nt_position(s1,near_address=A1.address) - A2.particle.get_nt_position(s2,near_address=A2.address)
+ sep = np.abs(sep)
+
+ assert(sep >= 0)
+
+ n1,n2,n3,n4 = (B1.particle, A1.particle, A2.particle, B2.particle)
+
+ """
+ <cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
+ """
+
+ ## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
+ ## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
+ Lp = s1.twist_persistence_length/0.34 # set semi-arbitrarily as there is a large spread in literature
+
+ def get_spring(sep):
+ kT = self.temperature * 0.0019872065 # kcal/mol
+ fitFun = lambda x: np.real(erf( (4*np.pi*x + 1j)/(2*np.sqrt(x)) )) * np.exp(-1/(4*x)) / erf(2*np.sqrt(x)*np.pi) - np.exp(-sep/Lp)
+ k = opt.leastsq( fitFun, x0=np.exp(-sep/Lp) )
+ return k[0][0] * 2*kT*0.00030461742
+
+ k = get_spring( max(sep,1) )
+ k = (1/k + 2/k_xover_angle(sep=1))**-1
+
+ t0 = sep*s1.twist_per_nt # TODO weighted avg between s1 and s2
+
+ # pdb.set_trace()
+ if A1.on_fwd_strand: t0 -= 120
+ if dir1 != dir2:
+ A2_on_fwd = not A2.on_fwd_strand
+ else:
+ A2_on_fwd = A2.on_fwd_strand
+ if A2_on_fwd: t0 += 120
+
+ # t0 = (t0 % 360
+
+ # if n2.idx == 0:
+ # print( n1.idx,n2.idx,n3.idx,n4.idx,k,t0,sep )
+ if sep == 0:
+ # pot = self.get_angle_potential(k,t0)
+ # self.add_angle( n1,n2,n4, pot )
+ pass
+ elif len(set((n1,n2,n3,n4))) != 4:
+ print("WARNING: skipping crossover dihedral angle potential because beads are too close")
+ else:
+ pot = self.get_dihedral_potential(k,t0)
+ self.add_dihedral( n1,n2,n3,n4, pot )
+
+ for seg in self.segments:
+ for callback in seg._generate_bead_callbacks:
+ callback(seg)
+
+ for callback in self._generate_bead_callbacks:
+ callback(self)
+
+
+ # ## remove duplicate potentials; ## TODO ensure that they aren't added twice in the first place?
+ # self.remove_duplicate_terms()
+
+ def walk_through_helices(segment, direction=1, processed_segments=None):
+ """
+
+ First and last segment should be same for circular helices
+ """
+
+ assert( direction in (1,-1) )
+ if processed_segments == None:
+ processed_segments = set()
+
+ def segment_is_new_helix(s):
+ return isinstance(s,DoubleStrandedSegment) and s not in processed_segments
+
+ new_s = None
+ s = segment
+ ## iterate intrahelically connected dsDNA segments
+ while segment_is_new_helix(s):
+ conn_locs = s.get_contour_sorted_connections_and_locations("intrahelical")[::direction]
+ processed_segments.add(new_s)
+ new_s = None
+ new_dir = None
+ for i in range(len(conn_locs)):
+ c,A,B = conn_locs[i]
+ ## TODO: handle change of direction
+ # TODOTODO
+ address = 1*(direction==-1)
+ if A.address == address and segment_is_new_helix(B.container):
+ new_s = B.container
+ assert(B.address in (0,1))
+ new_dir = 2*(B.address == 0) - 1
+ break
+
+ yield s,direction
+ s = new_s # will break if None
+ direction = new_dir
+
+ # if new_s is None:
+ # break
+ # else:
+ # s = new_s
+ # yield s
+ ## return s
+
+
+ def get_consecutive_crossovers(self):
+ ## TODOTODO TEST
+ crossovers = []
+ processed_segments = set()
+ for s1 in self.segments:
+ if not isinstance(s1,DoubleStrandedSegment):
+ continue
+ if s1 in processed_segments: continue
+
+ s0,d0 = list(SegmentModel.walk_through_helices(s1,direction=-1))[-1]
+
+ # s,direction = get_start_of_helices()
+ tmp = []
+ for s,d in SegmentModel.walk_through_helices(s0,-d0):
+ if s == s0 and len(tmp) > 0:
+ ## end of circular helix, only add first crossover
+ cl_list = s.get_contour_sorted_connections_and_locations("crossover")
+ if len(cl_list) > 0:
+ tmp.append( cl_list[::d][0] + [d] )
+ else:
+ tmp.extend( [cl + [d] for cl in s.get_contour_sorted_connections_and_locations("crossover")[::d]] )
+ processed_segments.add(s)
+ crossovers.append(tmp)
+ return crossovers
+
+ def set_sequence(self, sequence, force=True, fill_sequence='random'):
+ if force:
+ self.strands[0].set_sequence(sequence)
+ else:
+ try:
+ self.strands[0].set_sequence(sequence)
+ except:
+ ...
+ for s in self.segments:
+ s.assign_unset_sequence(fill_sequence)
+
+
+ def _set_cadnano2_sequence(self, cadnano_sequence_csv_file, sequence_fill='T'):
+ try:
+ self.segments[0]._cadnano_helix
+ except:
+ raise Exception("Cannot set sequence of a non-cadnano model using a cadnano sequence file")
+
+ starts = dict()
+ for strand in self.strands[1:]:
+ if strand.is_circular: continue
+ s = strand.strand_segments[0]
+ hid = s.segment._cadnano_helix
+ idx = s.segment._cadnano_bp_to_zidx[int(s.start)]
+ starts["{:d}[{:d}]".format(hid,idx)] = strand
+
+ base_set = tuple('ATCG')
+ with open(cadnano_sequence_csv_file) as fh:
+ reader = csv.reader(fh)
+ for values in reader:
+ if values[0] == "Start": continue
+ start,end,seq = values[:3]
+ strand = starts[start]
+ if sequence_fill in base_set:
+ seq = [sequence_fill if s == '?' else s for s in seq]
+ else:
+ seq = [random.choice(base_set) if s == '?' else s for s in seq]
+ if len([s for s in seq if s not in base_set]) > 0:
+ print(seq)
+ strand.set_sequence(seq)
+
+ def _generate_strands(self):
+ ## clear strands
+ try:
+ for s in self.strands:
+ try:
+ self.children.remove(s)
+ except:
+ pass
+ except:
+ pass
+
+ try:
+ for seg in self.segments:
+ try:
+ for d in ('fwd','rev'):
+ seg.strand_pieces[d] = []
+ except:
+ pass
+ except:
+ pass
+ self.strands = strands = []
+
+ """ Ensure unconnected ends have 5prime Location objects """
+ for seg in self.segments:
+ ## TODO move into Segment calls
+ five_prime_locs = sum([seg.get_locations(s) for s in ("5prime","crossover","terminal_crossover")],[])
+ three_prime_locs = sum([seg.get_locations(s) for s in ("3prime","crossover","terminal_crossover")],[])
+
+ def is_start_5prime(l):
+ is_end = l.get_nt_pos() < 1 and l.on_fwd_strand
+ return is_end and (l.connection is None or l.is_3prime_side_of_connection is not False)
+ def is_end_5prime(l):
+ is_end = l.get_nt_pos() > seg.num_nt-2 and not l.on_fwd_strand
+ return is_end and (l.connection is None or l.is_3prime_side_of_connection is not False)
+ def is_start_3prime(l):
+ is_start = l.get_nt_pos() < 1 and not l.on_fwd_strand
+ return is_start and (l.connection is None or l.is_3prime_side_of_connection is not True)
+ def is_end_3prime(l):
+ is_start = l.get_nt_pos() > seg.num_nt-2 and l.on_fwd_strand
+ return is_start and (l.connection is None or l.is_3prime_side_of_connection is not True)
+
+ if seg.start5.connection is None:
+ if len(list(filter( is_start_5prime, five_prime_locs ))) == 0:
+ seg.add_5prime(0) # TODO ensure this is the same place
+
+ if 'end5' in seg.__dict__ and seg.end5.connection is None:
+ if len(list(filter( is_end_5prime, five_prime_locs ))) == 0:
+ seg.add_5prime(seg.num_nt-1,on_fwd_strand=False)
+
+ if 'start3' in seg.__dict__ and seg.start3.connection is None:
+ if len(list(filter( is_start_3prime, three_prime_locs ))) == 0:
+ seg.add_3prime(0,on_fwd_strand=False)
+
+ if seg.end3.connection is None:
+ if len(list(filter( is_end_3prime, three_prime_locs ))) == 0:
+ seg.add_3prime(seg.num_nt-1)
+
+ # print( [(l,l.get_connected_location()) for l in seg.locations] )
+ # addresses = np.array([l.address for l in seg.get_locations("5prime")])
+ # if not np.any( addresses == 0 ):
+ # ## check if end is connected
+ # for c,l,B in self.get_connections_and_locations():
+ # if c[0]
+
+ """ Build strands from connectivity of helices """
+ def _recursively_build_strand(strand, segment, pos, is_fwd, mycounter=0, move_at_least=0.5):
+ seg = segment
+ history = []
+ while True:
+ mycounter+=1
+ if mycounter > 10000:
+ raise Exception("Too many iterations")
+
+ #if seg.name == "22-1" and pos > 140:
+ # if seg.name == "22-2":
+ # import pdb
+ # pdb.set_trace()
+ # if _DEBUG_TRACE and seg.name == "69-0" and is_fwd == False:
+ # import pdb
+ # pdb.set_trace()
+
+ end_pos, next_seg, next_pos, next_dir, move_at_least = seg.get_strand_segment(pos, is_fwd, move_at_least)
+ history.append((seg,pos,end_pos,is_fwd))
+ try:
+ strand.add_dna(seg, pos, end_pos, is_fwd)
+ except CircularDnaError:
+ ## Circular DNA was found
+ break
+ except:
+ print("Unexpected error:", sys.exc_info()[0])
+ # import pdb
+ # pdb.set_trace()
+ # seg.get_strand_segment(pos, is_fwd, move_at_least)
+ # strand.add_dna(seg, pos, end_pos, is_fwd)
+ raise
+
+ if next_seg is None:
+ break
+ else:
+ seg,pos,is_fwd = (next_seg, next_pos, next_dir)
+ strand.history = list(history)
+ return history
+
+ strand_counter = 0
+ history = []
+ for seg in self.segments:
+ locs = filter(lambda l: l.connection is None, seg.get_5prime_locations())
+ if locs is None: continue
+ # for pos, is_fwd in locs:
+ for l in locs:
+ if _DEBUG_TRACE:
+ print("Tracing 5prime",l)
+ if l.connection is not None:
+ print(" Skipping connected 5prime",l)
+ continue
+ # TODOTODO
+ pos = seg.contour_to_nt_pos(l.address, round_nt=True)
+ is_fwd = l.on_fwd_strand
+ s = Strand(segname="S{:03d}".format(len(strands)))
+ strand_history = _recursively_build_strand(s, seg, pos, is_fwd)
+ history.append((l,strand_history))
+ # print("{} {}".format(seg.name,s.num_nt))
+ strands.append(s)
+
+ ## Trace circular DNA
+ def strands_cover_segment(segment, is_fwd=True):
+ direction = 'fwd' if is_fwd else 'rev'
+ nt = 0
+ for sp in segment.strand_pieces[direction]:
+ nt += sp.num_nt
+ return nt == segment.num_nt
+
+ def find_nt_not_in_strand(segment, is_fwd=True):
+ fwd_str = 'fwd' if is_fwd else 'rev'
+
+ def check(val):
+ assert(val >= 0 and val < segment.num_nt)
+ # print("find_nt_not_in_strand({},{}) returning {}".format(
+ # segment, is_fwd, val))
+ return val
+
+ if is_fwd:
+ last = -1
+ for sp in segment.strand_pieces[fwd_str]:
+ if sp.start-last > 1:
+ return check(last+1)
+ last = sp.end
+ return check(last+1)
+ else:
+ last = segment.num_nt
+ for sp in reversed(segment.strand_pieces[fwd_str]):
+ if last-sp.start > 1:
+ return check(last-1)
+ last = sp.end
+ return check(last-1)
+
+ def add_strand_if_needed(seg,is_fwd):
+ history = []
+ while not strands_cover_segment(seg, is_fwd):
+ pos = nt = find_nt_not_in_strand(seg, is_fwd)
+ if _DEBUG_TRACE:
+ print("Tracing circular strand", pos, is_fwd)
+ s = Strand(segname="S{:03d}".format(len(strands)),
+ is_circular = True)
+ history = _recursively_build_strand(s, seg, pos, is_fwd)
+ strands.append(s)
+ return history
+
+ for seg in self.segments:
+ add_strand_if_needed(seg,True)
+ if isinstance(seg, DoubleStrandedSegment):
+ add_strand_if_needed(seg,False)
+
+ self.strands = sorted(strands, key=lambda s:s.num_nt)[::-1]
+ def check_strands():
+ dsdna = filter(lambda s: isinstance(s,DoubleStrandedSegment), self.segments)
+ for s in dsdna:
+ nt_fwd = nt_rev = 0
+ for sp in s.strand_pieces['fwd']:
+ nt_fwd += sp.num_nt
+ for sp in s.strand_pieces['rev']:
+ nt_rev += sp.num_nt
+ assert( nt_fwd == s.num_nt and nt_rev == s.num_nt )
+ # print("{}: {},{} (fwd,rev)".format(s.name, nt_fwd/s.num_nt,nt_rev/s.num_nt))
+ check_strands()
+
+ ## relabel segname
+ counter = 0
+ for s in self.strands:
+ if s.segname is None:
+ s.segname = "D%03d" % counter
+ counter += 1
+
+ def _assign_basepairs(self):
+ ## Assign basepairs
+ for seg in self.segments:
+ if isinstance(seg, DoubleStrandedSegment):
+ strands1 = seg.strand_pieces['fwd'] # already sorted
+ strands2 = seg.strand_pieces['rev']
+
+ nts1 = [nt for s in strands1 for nt in s.children]
+ nts2 = [nt for s in strands2 for nt in s.children[::-1]]
+ assert(len(nts1) == len(nts2))
+ for nt1,nt2 in zip(nts1,nts2):
+ ## TODO weakref
+ nt1.basepair = nt2
+ nt2.basepair = nt1
+
+ def write_atomic_bp_restraints(self, output_name, spring_constant=1.0):
+ ## TODO: ensure atomic model was generated already
+ ## TODO: allow ENM to be created without first building atomic model
+
+ with open("%s.exb" % output_name,'w') as fh:
+ for seg in self.segments:
+ ## Continue unless dsDNA
+ if not isinstance(seg,DoubleStrandedSegment): continue
+ for strand_piece in seg.strand_pieces['fwd']:
+ assert( strand_piece.is_fwd )
+ for nt1 in strand_piece.children:
+ nt2 = nt1.basepair
+ if nt1.resname == 'ADE':
+ names = (('N1','N3'),('N6','O4'))
+ elif nt1.resname == 'GUA':
+ names = (('N2','O2'),('N1','N3'),('O6','N4'))
+ elif nt1.resname == 'CYT':
+ names = (('O2','N2'),('N3','N1'),('N4','O6'))
+ elif nt1.resname == 'THY':
+ names = (('N3','N1'),('O4','N6'))
+ else:
+ raise Exception("Unrecognized nucleotide!")
+ for n1, n2 in names:
+ i = nt1._get_atomic_index(name=n1)
+ j = nt2._get_atomic_index(name=n2)
+ fh.write("bond %d %d %f %.2f\n" % (i,j,spring_constant,2.8))
+
+ def write_atomic_ENM(self, output_name, lattice_type=None, interhelical_bonds=True):
+ ## TODO: ensure atomic model was generated already
+ if lattice_type is None:
+ try:
+ lattice_type = self.lattice_type
+ except:
+ lattice_type = "square"
+ else:
+ try:
+ if lattice_type != self.lattice_type:
+ print("WARNING: printing ENM with a lattice type ({}) that differs from model's lattice type ({})".format(lattice_type,self.lattice_type))
+ except:
+ pass
+
+ if lattice_type == "square":
+ enmTemplate = enmTemplateSQ
+ elif lattice_type == "honeycomb":
+ enmTemplate = enmTemplateHC
+ else:
+ raise Exception("Lattice type '%s' not supported" % self.latticeType)
+
+ ## TODO: allow ENM to be created without first building atomic model
+ noStackPrime = 0
+ noBasepair = 0
+
+ with open("%s.exb" % output_name,'w') as fh:
+ # natoms=0
+ pairtypes = ('pair','stack','cross','paircross')
+ bonds = {k:[] for k in pairtypes}
+
+ for seg in self.segments:
+ ## Continue unless dsDNA
+ if not isinstance(seg,DoubleStrandedSegment): continue
+ for strand_piece in seg.strand_pieces['fwd'] + seg.strand_pieces['rev']:
+ for nt1 in strand_piece.children:
+ other = []
+ nt2 = nt1.basepair
+ if strand_piece.is_fwd:
+ other.append((nt2,'pair'))
+
+ nt2 = nt2.get_intrahelical_above()
+ if nt2 is not None and strand_piece.is_fwd:
+ ## TODO: check if this already exists
+ other.append((nt2,'paircross'))
+
+ nt2 = nt1.get_intrahelical_above()
+ if nt2 is not None:
+ other.append((nt2,'stack'))
+ try:
+ nt2 = nt2.basepair
+ except:
+ assert( isinstance(nt2.parent.segment, SingleStrandedSegment) )
+ nt2 = None
+
+ if nt2 is not None and strand_piece.is_fwd:
+ other.append((nt2,'cross'))
+
+ for nt2,pairtype in other:
+ """
+ if np.linalg.norm(nt2.position-nt1.position) > 7:
+ import pdb
+ pdb.set_trace()
+ """
+ key = ','.join((pairtype,nt1.sequence[0],nt2.sequence[0]))
+ for n1, n2, d in enmTemplate[key]:
+ d = float(d)
+ k = 0.1
+ if lattice_type == 'honeycomb':
+ correctionKey = ','.join((key,n1,n2))
+ assert(correctionKey in enmCorrectionsHC)
+ dk,dr = enmCorrectionsHC[correctionKey]
+ k = float(dk)
+ d += float(dr)
+
+ i = nt1._get_atomic_index(name=n1)
+ j = nt2._get_atomic_index(name=n2)
+ bonds[pairtype].append((i,j,k,d))
+
+ # print("NO STACKS found for:", noStackPrime)
+ # print("NO BASEPAIRS found for:", noBasepair)
+
+ for k,bondlist in bonds.items():
+ if len(bondlist) != len(set(bondlist)):
+ devlogger.warning("Duplicate ENM bonds for pair type {}".format(k))
+ fh.write("# {}\n".format(k.upper()))
+ for b in set(bondlist):
+ fh.write("bond %d %d %f %.2f\n" % b)
+
+ ## Loop dsDNA regions
+ push_bonds = []
+ processed_segs = set()
+ ## TODO possibly merge some of this code with SegmentModel.get_consecutive_crossovers()
+ for segI in self.segments: # TODOTODO: generalize through some abstract intrahelical interface that effectively joins "segments", for now interhelical bonds that cross intrahelically-connected segments are ignored
+ if not isinstance(segI,DoubleStrandedSegment): continue
+
+ ## Loop over dsDNA regions connected by crossovers
+ conn_locs = segI.get_contour_sorted_connections_and_locations("crossover")
+ other_segs = list(set([B.container for c,A,B in conn_locs]))
+ for segJ in other_segs:
+ if (segI,segJ) in processed_segs:
+ continue
+ processed_segs.add((segI,segJ))
+ processed_segs.add((segJ,segI))
+
+ ## TODO perhaps handle ends that are not between crossovers
+
+ ## Loop over ordered pairs of crossovers between the two
+ cls = filter(lambda x: x[-1].container == segJ, conn_locs)
+ cls = sorted( cls, key=lambda x: x[1].get_nt_pos() )
+ for cl1,cl2 in zip(cls[:-1],cls[1:]):
+ c1,A1,B1 = cl1
+ c2,A2,B2 = cl2
+
+ ntsI1,ntsI2 = [segI.contour_to_nt_pos(A.address) for A in (A1,A2)]
+ ntsJ1,ntsJ2 = [segJ.contour_to_nt_pos(B.address) for B in (B1,B2)]
+ ntsI = ntsI2-ntsI1+1
+ ntsJ = ntsJ2-ntsJ1+1
+ # assert( np.isclose( ntsI, int(round(ntsI)) ) )
+ # assert( np.isclose( ntsJ, int(round(ntsJ)) ) )
+ ntsI,ntsJ = [int(round(i)) for i in (ntsI,ntsJ)]
+
+ ## Find if dsDNA "segments" are pointing in same direction
+ ## could move this block out of the loop
+ tangentA = segI.contour_to_tangent(A1.address)
+ tangentB = segJ.contour_to_tangent(B1.address)
+ dot1 = tangentA.dot(tangentB)
+ tangentA = segI.contour_to_tangent(A2.address)
+ tangentB = segJ.contour_to_tangent(B2.address)
+ dot2 = tangentA.dot(tangentB)
+
+ if dot1 > 0.5 and dot2 > 0.5:
+ ...
+ elif dot1 < -0.5 and dot2 < -0.5:
+ ## TODO, reverse
+ ...
+ # print("Warning: {} and {} are on antiparallel helices (not yet implemented)... skipping".format(A1,B1))
+ continue
+ else:
+ # print("Warning: {} and {} are on helices that do not point in similar direction... skipping".format(A1,B1))
+ continue
+
+ ## Go through each nucleotide between the two
+ for ijmin in range(min(ntsI,ntsJ)):
+ i=j=ijmin
+ if ntsI < ntsJ:
+ j = int(round(float(ntsJ*i)/ntsI))
+ elif ntsJ < ntsI:
+ i = int(round(float(ntsI*j)/ntsJ))
+ ntI_idx = int(round(ntsI1+i))
+ ntJ_idx = int(round(ntsJ1+j))
+
+ ## Skip nucleotides that are too close to crossovers
+ if i < 11 or j < 11: continue
+ if ntsI2-ntI_idx < 11 or ntsJ2-ntJ_idx < 11: continue
+
+ ## Find phosphates at ntI/ntJ
+ for direction in [True,False]:
+ try:
+ i = segI._get_atomic_nucleotide(ntI_idx, direction)._get_atomic_index(name="P")
+ j = segJ._get_atomic_nucleotide(ntJ_idx, direction)._get_atomic_index(name="P")
+ push_bonds.append((i,j))
+ except:
+ # print("WARNING: could not find 'P' atom in {}:{} or {}:{}".format( segI, ntI_idx, segJ, ntJ_idx ))
+ ...
+
+ if len(push_bonds) != len(set(push_bonds)):
+ devlogger.warning("Duplicate enrgmd push bonds")
+ push_bonds = list(set( push_bonds ))
+
+ # print("PUSH BONDS:", len(push_bonds))
+ if interhelical_bonds:
+ if not self.useTclForces:
+ with open("%s.exb" % output_name, 'a') as fh:
+ fh.write("# PUSHBONDS\n")
+ for i,j in push_bonds:
+ fh.write("bond %d %d %f %.2f\n" % (i,j,1.0,31))
+ else:
+ flat_push_bonds = list(sum(push_bonds))
+ atomList = list(set( flat_push_bonds ))
+ with open("%s.forces.tcl" % output_name,'w') as fh:
+ fh.write("set atomList {%s}\n\n" %
+ " ".join([str(x-1) for x in atomList]) )
+ fh.write("set bonds {%s}\n" %
+ " ".join([str(x-1) for x in flat_push_bonds]) )
+ fh.write("""
+foreach atom $atomList {
+ addatom $atom
+}
+
+proc calcforces {} {
+ global atomList bonds
+ loadcoords rv
+
+ foreach i $atomList {
+ set force($i) {0 0 0}
+ }
+
+ foreach {i j} $bonds {
+ set rvec [vecsub $rv($j) $rv($i)]
+ # lassign $rvec x y z
+ # set r [expr {sqrt($x*$x+$y*$y+$z*$z)}]
+ set r [getbond $rv($j) $rv($i)]
+ set f [expr {2*($r-31.0)/$r}]
+ vecadd $force($i) [vecscale $f $rvec]
+ vecadd $force($j) [vecscale [expr {-1.0*$f}] $rvec]
+ }
+
+ foreach i $atomList {
+ addforce $i $force($i)
+ }
+
+}
+""")
+
+ def get_bounding_box( self, num_points=3 ):
+ positions = np.zeros( (len(self.segments)*num_points, 3) )
+ i = 0
+ for s in self.segments:
+ for c in np.linspace(0,1,num_points):
+ positions[i] = (s.contour_to_position(c))
+ i += 1
+ min_ = np.array([np.min(positions[:,i]) for i in range(3)])
+ max_ = np.array([np.max(positions[:,i]) for i in range(3)])
+ return min_,max_
+
+ def get_bounding_box_center( self, num_points=3 ):
+ min_,max_ = self.get_bounding_box(num_points)
+ return 0.5*(max_+min_)
+
+ def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
+ min_,max_ = self.get_bounding_box()
+ dx,dy,dz = (max_-min_+30)*padding_factor
+ if isotropic:
+ dx = dy = dz = max((dx,dy,dz))
+ return np.array([dx,dy,dz])
+
+ def add_grid_potential(self, grid_file, scale=1, per_nucleotide=True, filter_fn=None):
+ grid_file = Path(grid_file)
+ if not grid_file.is_file():
+ raise ValueError("Grid file {} does not exist".format(grid_file))
+ if not grid_file.is_absolute():
+ grid_file = Path.cwd() / grid_file
+ self.grid_potentials.append((grid_file,scale,per_nucleotide, filter_fn))
+ try:
+ self._apply_grid_potentials_to_beads(self._beadtype_s)
+ except:
+ pass
+
+ def _apply_grid_potentials_to_beads(self, bead_type_dict ):
+ for grid_file, scale, per_nucleotide, filter_fn in self.grid_potentials:
+ def add_grid_to_type(particle_type):
+ if particle_type.name[0] == "O": return
+ s = scale*particle_type.nts if per_nucleotide else scale
+ try:
+ particle_type.grid = list(particle_type.grid) + [(grid_file, s)]
+ except:
+ particle_type.grid = [(grid_file, s)]
+ particle_type.grid = tuple(particle_type.grid)
+
+ if filter_fn is None:
+ for key,particle_type in bead_type_dict.items():
+ add_grid_to_type(particle_type)
+ else:
+ grid_types = dict()
+ for b in filter(filter_fn, sum([seg.beads for seg in self.segments],[])):
+ t = b.type_
+ if t.name[0] == "O": continue
+ if t not in grid_types:
+ new_type = ParticleType(name=t.name+'G',charge=t.charge, parent=t)
+ add_grid_to_type(new_type)
+ grid_types[t] = new_type
+ b.type_ = grid_types[t]
+
+
+ def _generate_atomic_model(self, scale=1):
+ ## TODO: deprecate
+ self.generate_atomic_model(scale=scale)
+
+ def generate_atomic_model(self, scale=1):
+ self.clear_beads()
+ self.children = self.strands # TODO: is this going to be okay? probably
+ first_atomic_index = 0
+ for s in self.strands:
+ first_atomic_index = s.generate_atomic_model(scale,first_atomic_index)
+ self._assign_basepairs()
+
+ """ OxDNA """
+ ## https://dna.physics.ox.ac.uk/index.php/Documentation#Input_file
+ def generate_oxdna_model(self, scale=1):
+ self.clear_beads()
+ self.children = self.strands
+ for s in self.strands:
+ s.generate_oxdna_model()
+
+ def _write_oxdna_configuration(self, filename, gpu=0):
+
+ _angstroms_to_oxdna = 0.11739845 ## units "AA" "8.518e-10 m"
+ with open(filename,'w') as fh:
+ fh.write("""t = {temperature}
+b = {dimX} {dimY} {dimZ}
+E = 0 0 0
+""".format(temperature=self.temperature,
+ dimX = self.dimensions[0]*_angstroms_to_oxdna,
+ dimY = self.dimensions[1]*_angstroms_to_oxdna,
+ dimZ = self.dimensions[2]*_angstroms_to_oxdna))
+
+ base_vec = np.array((1,0,0)) # TODO
+ norm_vec = np.array((0,0,1)) # TODO
+
+ ## Traverse 3'-to-5'
+ for nt in [nt for s in self.strands for nt in s.oxdna_nt[::-1]]:
+ data = dict()
+ # o = nt.collapsedOrientation()
+ o = nt.orientation
+ for k,v in zip('x y z'.split(),nt.collapsedPosition()):
+ data[k] = v * _angstroms_to_oxdna
+ for k,v in zip('x y z'.split(),o.dot(base_vec)):
+ data['b'+k] = v
+ for k,v in zip('x y z'.split(),o.dot(norm_vec)):
+ data['n'+k] = v
+ fh.write("{x} {y} {z} {bx} {by} {bz} {nx} {ny} {nz} 0 0 0 0 0 0\n".format(**data)
+ )
+
+ def _write_oxdna_topology(self,filename):
+
+ strands = [s for s in self.strands if s.num_nt > 0]
+ with open(filename,'w') as fh:
+
+ fh.write("{num_nts} {num_strands}\n".format(
+ num_nts = sum([s.num_nt for s in strands]),
+ num_strands = len(self.strands)))
+
+ idx = 0
+ sidx = 1
+ for strand in strands:
+ prev = idx+strand.num_nt-1 if strand.is_circular else -1
+ last = idx if strand.is_circular else -1
+
+ ## Traverse 3'-to-5'
+ sequence = [seq for s in strand.strand_segments
+ for seq in s.get_sequence()][::-1]
+ for seq in sequence[:-1]:
+ ## strand seq 3' 5'
+ fh.write("{} {} {} {}\n".format(sidx, seq, prev, idx+1))
+ prev = idx
+ idx += 1
+ seq = sequence[-1]
+ fh.write("{} {} {} {}\n".format(sidx, seq, prev, last))
+ idx += 1
+ sidx += 1
+
+ def _write_oxdna_input(self, filename,
+ topology,
+ conf_file,
+ trajectory_file,
+ last_conf_file,
+ log_file,
+ num_steps = 1e6,
+ interaction_type = 'DNA2',
+ salt_concentration = None,
+ print_conf_interval = None,
+ print_energy_every = None,
+ timestep = 0.003,
+ sim_type = "MD",
+ backend = None,
+ backend_precision = None,
+ seed = None,
+ newtonian_steps = 103,
+ diff_coeff = 2.50,
+ thermostat = "john",
+ list_type = "cells",
+ ensemble = "nvt",
+ delta_translation = 0.22,
+ delta_rotation = 0.22,
+ verlet_skin = 0.5,
+ max_backbone_force = 100,
+ external_forces_file = None,
+ seq_dep_file = None,
+ gpu = 0
+ ):
+
+ if seed is None:
+ import random
+ seed = random.randint(1,99999)
+
+ temperature = self.temperature
+ num_steps = int(num_steps)
+ newtonian_steps = int(newtonian_steps)
+
+ if print_conf_interval is None:
+ # print_conf_interval = min(num_steps//100)
+ print_conf_interval = 10000
+ print_conf_interval = int(print_conf_interval)
+
+ if print_energy_every is None:
+ print_energy_every = print_conf_interval
+ print_energy_every = int(print_energy_every)
+
+ if max_backbone_force is not None:
+ max_backbone_force = 'max_backbone_force = {}'.format(max_backbone_force)
+
+
+ if interaction_type in ('DNA2',):
+ if salt_concentration is None:
+ try:
+ ## units "80 epsilon0 295 k K / (2 (AA)**2 e**2/particle)" mM
+ salt_concentration = 9331.3126/self.debye_length**2
+ except:
+ salt_concentration = 0.5
+ salt_concentration = 'salt_concentration = {}'.format(salt_concentration)
+ else:
+ salt_concentration = ''
+
+ if backend is None:
+ backend = 'CUDA' if sim_type == 'MD' else 'CPU'
+
+ if backend_precision is None:
+ backend_precision = 'mixed' if backend == 'CUDA' else 'double'
+
+ if sim_type == 'VMMC':
+ ensemble = 'ensemble = {}'.format(ensemble)
+ delta_translation = 'delta_translation = {}'.format(delta_translation)
+ delta_rotation = 'delta_rotation = {}'.format(delta_rotation)
+ else:
+ ensemble = ''
+ delta_translation = ''
+ delta_rotation = ''
+
+ if external_forces_file is None:
+ external_forces = "external_forces = 0"
+ else:
+ external_forces = "external_forces = 1\nexternal_forces_file = {}".format(external_forces_file)
+
+ if seq_dep_file is None:
+ sequence_dependence = ""
+ else:
+
+ if seq_dep_file == "oxDNA2":
+ seq_dep_file = get_resource_path("oxDNA2_sequence_dependent_parameters.txt")
+ elif seq_dep_file == "oxDNA1":
+ seq_dep_file = get_resource_path("oxDNA1_sequence_dependent_parameters.txt")
+ sequence_dependence = "use_average_seq = 1\nseq_dep_file = {}".format(seq_dep_file)
+
+ with open(filename,'w') as fh:
+ fh.write("""##############################
+#### PROGRAM PARAMETERS ####
+##############################
+interaction_type = {interaction_type}
+{salt_concentration}
+sim_type = {sim_type}
+backend = {backend}
+CUDA_device = {gpu}
+backend_precision = {backend_precision}
+#debug = 1
+seed = {seed}
+
+##############################
+#### SIM PARAMETERS ####
+##############################
+steps = {num_steps:d}
+newtonian_steps = {newtonian_steps:d}
+diff_coeff = {diff_coeff}
+thermostat = {thermostat}
+
+list_type = {list_type}
+{ensemble}
+{delta_translation}
+{delta_rotation}
+
+T = {temperature:f} K
+dt = {timestep}
+verlet_skin = {verlet_skin}
+{max_backbone_force}
+
+{external_forces}
+{sequence_dependence}
+
+##############################
+#### INPUT / OUTPUT ####
+##############################
+box_type = orthogonal
+topology = {topology}
+conf_file = {conf_file}
+lastconf_file = {last_conf_file}
+trajectory_file = {trajectory_file}
+refresh_vel = 1
+log_file = {log_file}
+no_stdout_energy = 1
+restart_step_counter = 1
+energy_file = {log_file}.energy.dat
+print_conf_interval = {print_conf_interval}
+print_energy_every = {print_energy_every}
+time_scale = linear
+""".format( **locals() ))
+
+ def simulate_oxdna(self, output_name, directory='.', output_directory='output', topology=None, configuration=None, oxDNA=None, gpu=0, **oxdna_args):
+
+ if output_directory == '': output_directory='.'
+ d_orig = os.getcwd()
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+
+ os.chdir(directory)
+ try:
+
+ if oxDNA is None:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ fname = os.path.join(path, "oxDNA")
+ if os.path.isfile(fname) and os.access(fname, os.X_OK):
+ oxDNA = fname
+ break
+
+ if oxDNA is None: raise Exception("oxDNA was not found")
+
+ if not os.path.exists(oxDNA):
+ raise Exception("oxDNA was not found")
+ if not os.path.isfile(oxDNA):
+ raise Exception("oxDNA was not found")
+ if not os.access(oxDNA, os.X_OK):
+ raise Exception("oxDNA is not executable")
+
+ if not os.path.exists(output_directory):
+ os.makedirs(output_directory)
+ elif not os.path.isdir(output_directory):
+ raise Exception("output_directory '%s' is not a directory!" % output_directory)
+
+
+ if configuration is None:
+ configuration = "{}.conf".format(output_name)
+ self._write_oxdna_configuration(configuration)
+ # elif not Path(configuration).exists():
+ # raise Exception("Unable to find oxDNA configuration file '{}'.".format(configuration))
+
+ if topology is None:
+ topology = "{}-topology.dat".format(output_name)
+ self._write_oxdna_topology(topology)
+ elif not Path(topology).exists():
+ raise Exception("Unable to find oxDNA topology file '{}'.".format(topology))
+
+ last_conf_file = "{}/{}.last.conf".format(output_directory,output_name)
+ input_file = "{}-input".format(output_name)
+
+ self._write_oxdna_input(input_file,
+ topology = topology,
+ conf_file = configuration,
+ trajectory_file = "{}/{}.dat".format(output_directory,output_name),
+ last_conf_file = last_conf_file,
+ log_file="{}/{}.log".format(output_directory,output_name),
+ gpu = gpu,
+ **oxdna_args)
+ # os.sync()
+ ## TODO: call oxdna
+ cmd = [oxDNA, input_file]
+
+ cmd = tuple(str(x) for x in cmd)
+
+ print("Running oxDNA with: %s" % " ".join(cmd))
+ process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for line in process.stdout:
+ sys.stdout.write(line)
+ sys.stdout.flush()
+
+ return topology,last_conf_file
+ finally:
+ os.chdir(d_orig)
+
+ """ Visualization """
+ def vmd_tube_tcl(self, file_name="drawTubes.tcl"):
+ with open(file_name, 'w') as tclFile:
+ tclFile.write("## beginning TCL script \n")
+
+ def draw_tube(segment,radius_value=10, color="cyan", resolution=5):
+ tclFile.write("## Tube being drawn... \n")
+
+ contours = np.linspace(0,1, max(2,1+segment.num_nt//resolution) )
+ rs = [segment.contour_to_position(c) for c in contours]
+
+ radius_value = str(radius_value)
+ tclFile.write("graphics top color {} \n".format(str(color)))
+ for i in range(len(rs)-2):
+ r0 = rs[i]
+ r1 = rs[i+1]
+ filled = "yes" if i in (0,len(rs)-2) else "no"
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled {} \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value), filled))
+ tclFile.write("graphics top sphere {{ {} {} {} }} radius {} resolution 30\n".format(r1[0], r1[1], r1[2], str(radius_value)))
+ r0 = rs[-2]
+ r0 = rs[-1]
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value)))
+
+ ## material
+ tclFile.write("graphics top materials on \n")
+ tclFile.write("graphics top material AOEdgy \n")
+
+ ## iterate through the model segments
+ for s in self.segments:
+ if isinstance(s,DoubleStrandedSegment):
+ tclFile.write("## dsDNA! \n")
+ draw_tube(s,10,"cyan")
+ elif isinstance(s,SingleStrandedSegment):
+ tclFile.write("## ssDNA! \n")
+ draw_tube(s,3,"orange",resolution=1.5)
+ else:
+ raise Exception ("your model includes beads that are neither ssDNA nor dsDNA")
+ ## tclFile complete
+ tclFile.close()
+
+ def vmd_cylinder_tcl(self, file_name="drawCylinders.tcl"):
+ #raise NotImplementedError
+ with open(file_name, 'w') as tclFile:
+ tclFile.write("## beginning TCL script \n")
+ def draw_cylinder(segment,radius_value=10,color="cyan"):
+ tclFile.write("## cylinder being drawn... \n")
+ r0 = segment.contour_to_position(0)
+ r1 = segment.contour_to_position(1)
+
+ radius_value = str(radius_value)
+ color = str(color)
+
+ tclFile.write("graphics top color {} \n".format(color))
+ tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], radius_value))
+
+ ## material
+ tclFile.write("graphics top materials on \n")
+ tclFile.write("graphics top material AOEdgy \n")
+
+ ## iterate through the model segments
+ for s in self.segments:
+ if isinstance(s,DoubleStrandedSegment):
+ tclFile.write("## dsDNA! \n")
+ draw_cylinder(s,10,"cyan")
+ elif isinstance(s,SingleStrandedSegment):
+ tclFile.write("## ssDNA! \n")
+ draw_cylinder(s,3,"orange")
+ else:
+ raise Exception ("your model includes beads that are neither ssDNA nor dsDNA")
+ ## tclFile complete
+ tclFile.close()
diff --git a/mrdna/RELEASE-VERSION b/mrdna/RELEASE-VERSION
index c6f5b60..d474fc0 100644
--- a/mrdna/RELEASE-VERSION
+++ b/mrdna/RELEASE-VERSION
@@ -1 +1 @@
-1.0a.dev71
+1.0a.dev74
diff --git a/mrdna/readers/.ipynb_checkpoints/__init__-checkpoint.py b/mrdna/readers/.ipynb_checkpoints/__init__-checkpoint.py
new file mode 100644
index 0000000..7e0e4db
--- /dev/null
+++ b/mrdna/readers/.ipynb_checkpoints/__init__-checkpoint.py
@@ -0,0 +1,39 @@
+## TODO: make module this package conform to a single style for input/output
+
+def read_cadnano(json_file, sequence=None, fill_sequence='T', **model_parameters):
+ from .cadnano_segments import read_json_file
+ from .cadnano_segments import read_model as model_from_cadnano_json
+
+ data = read_json_file(json_file)
+ return model_from_cadnano_json(data, sequence, fill_sequence, **model_parameters)
+
+def read_vhelix(maya_file, **model_parameters):
+ from .polygon_mesh import parse_maya_file, convert_maya_bases_to_segment_model
+
+ maya_bases = parse_maya_file(maya_file)
+ model = convert_maya_bases_to_segment_model( maya_bases, **model_parameters )
+ return model
+
+def read_list(infile,**model_parameters):
+ import numpy as np
+ try:
+ data = np.loadtxt(infile)
+ except:
+ data = np.loadtxt(infile,skiprows=1) # strip header
+ coords = data[:,:3]*10
+ bp = data[:,3]
+ stack = data[:,4]
+ three_prime = data[:,5]
+
+ from .segmentmodel_from_lists import model_from_basepair_stack_3prime
+ return model_from_basepair_stack_3prime(coords, bp, stack, three_prime)
+
+
+def read_atomic_pdb(pdb_file, **model_parameters):
+ from .segmentmodel_from_pdb import SegmentModelFromPdb
+ return SegmentModelFromPdb(pdb_file)
+
+def read_oxdna(coordinate_file, topology_file, idealized_coordinate_file=None, **model_parameters):
+ """ Idealized coordinate file: coordinates for detecting stacks and base pairs, defaults to coordinate_file """
+ from .segmentmodel_from_oxdna import mrdna_model_from_oxdna
+ return mrdna_model_from_oxdna(coordinate_file, topology_file, idealized_coordinate_file, **model_parameters)
diff --git a/mrdna/readers/.ipynb_checkpoints/cadnano_segments-checkpoint.py b/mrdna/readers/.ipynb_checkpoints/cadnano_segments-checkpoint.py
new file mode 100644
index 0000000..b39bd2e
--- /dev/null
+++ b/mrdna/readers/.ipynb_checkpoints/cadnano_segments-checkpoint.py
@@ -0,0 +1,727 @@
+# -*- coding: utf-8 -*-
+import pdb
+import numpy as np
+import os,sys
+from glob import glob
+import re
+
+from ..arbdmodel.coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
+from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from ..model.dna_sequence import m13 as m13seq
+
+
+## TODO: separate SegmentModel from ArbdModel so multiple parts can be combined
+## TODO: catch circular strands in "get_5prime" cadnano calls
+## TODO: handle special motifs
+## - doubly-nicked helices
+## - helices that should be stacked across an empty region (crossovers from and end in the helix to another end in the helix)
+## - circular constructs
+
+def combineRegionLists(loHi1,loHi2,intersect=False):
+
+ """Combines two lists of (lo,hi) pairs specifying integer
+ regions a single list of regions. """
+
+ ## Validate input
+ for l in (loHi1,loHi2):
+ ## Assert each region in lists is sorted
+ for pair in l:
+ assert(len(pair) == 2)
+ assert(pair[0] <= pair[1])
+
+ if len(loHi1) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi2
+ if len(loHi2) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi1
+
+ ## Break input into lists of compact regions
+ compactRegions1,compactRegions2 = [[],[]]
+ for compactRegions,loHi in zip(
+ [compactRegions1,compactRegions2],
+ [loHi1,loHi2]):
+ tmp = []
+ lastHi = loHi[0][0]-1
+ for lo,hi in loHi:
+ if lo-1 != lastHi:
+ compactRegions.append(tmp)
+ tmp = []
+ tmp.append((lo,hi))
+ lastHi = hi
+ if len(tmp) > 0:
+ compactRegions.append(tmp)
+
+ ## Build result
+ result = []
+ region = []
+ i,j = [0,0]
+ compactRegions1.append([[1e10]])
+ compactRegions2.append([[1e10]])
+ while i < len(compactRegions1)-1 or j < len(compactRegions2)-1:
+ cr1 = compactRegions1[i]
+ cr2 = compactRegions2[j]
+
+ ## initialize region
+ if len(region) == 0:
+ if cr1[0][0] <= cr2[0][0]:
+ region = cr1
+ i += 1
+ continue
+ else:
+ region = cr2
+ j += 1
+ continue
+
+ if region[-1][-1] >= cr1[0][0]:
+ region = combineCompactRegionLists(region, cr1, intersect=False)
+ i+=1
+ elif region[-1][-1] >= cr2[0][0]:
+ region = combineCompactRegionLists(region, cr2, intersect=False)
+ j+=1
+ else:
+ result.extend(region)
+ region = []
+
+ assert( len(region) > 0 )
+ result.extend(region)
+ result = sorted(result)
+
+ # print("loHi1:",loHi1)
+ # print("loHi2:",loHi2)
+ # print(result,"\n")
+
+ if intersect:
+ lo = max( [loHi1[0][0], loHi2[0][0]] )
+ hi = min( [loHi1[-1][1], loHi2[-1][1]] )
+ result = [r for r in result if r[0] >= lo and r[1] <= hi]
+
+ return result
+
+def combineCompactRegionLists(loHi1,loHi2,intersect=False):
+
+ """Combines two lists of (lo,hi) pairs specifying regions within a
+ compact integer set into a single list of regions.
+
+ examples:
+ loHi1 = [[0,4],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 4), (5, 7), (8, 9)]
+
+ loHi1 = [[0,3],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
+ """
+
+ ## Validate input
+ for l in (loHi1,loHi2):
+ ## Assert each region in lists is sorted
+ for pair in l:
+ assert(len(pair) == 2)
+ assert(pair[0] <= pair[1])
+ ## Assert lists are compact
+ for pair1,pair2 in zip(l[::2],l[1::2]):
+ assert(pair1[1]+1 == pair2[0])
+
+ if len(loHi1) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi2
+ if len(loHi2) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi1
+
+ ## Find the ends of the region
+ lo = min( [loHi1[0][0], loHi2[0][0]] )
+ hi = max( [loHi1[-1][1], loHi2[-1][1]] )
+
+ ## Make a list of indices where each region will be split
+ splitAfter = []
+ for l,h in loHi2:
+ if l != lo:
+ splitAfter.append(l-1)
+ if h != hi:
+ splitAfter.append(h)
+
+ for l,h in loHi1:
+ if l != lo:
+ splitAfter.append(l-1)
+ if h != hi:
+ splitAfter.append(h)
+ splitAfter = sorted(list(set(splitAfter)))
+
+ # print("splitAfter:",splitAfter)
+
+ split=[]
+ last = -2
+ for s in splitAfter:
+ split.append(s)
+ last = s
+
+ # print("split:",split)
+ returnList = [(i+1,j) if i != j else (i,j) for i,j in zip([lo-1]+split,split+[hi])]
+
+ if intersect:
+ lo = max( [loHi1[0][0], loHi2[0][0]] )
+ hi = min( [loHi1[-1][1], loHi2[-1][1]] )
+ returnList = [r for r in returnList if r[0] >= lo and r[1] <= hi]
+
+ # print("loHi1:",loHi1)
+ # print("loHi2:",loHi2)
+ # print(returnList,"\n")
+ return returnList
+
+class cadnano_part(SegmentModel):
+ def __init__(self, part,
+ **kwargs
+ ):
+ self.part = part
+ self.lattice_type = _get_lattice(part)
+
+ self._cadnano_part_to_segments(part)
+ # SegmentModel.__init__(self,...)
+ # self.segments = [seg for hid,segs in self.helices.items() for seg in segs]
+ self.segments = [seg for hid,segs in sorted(self.helices.items()) for seg in segs]
+ self._add_intrahelical_connections()
+ self._add_crossovers()
+ self._add_prime_ends()
+ SegmentModel.__init__(self, self.segments,
+ **kwargs)
+
+ def _get_helix_angle(self, helix_id, indices):
+ """ Get "start_orientation" for helix """
+ # import ipdb
+ # ipdb.set_trace()
+
+ """ FROM CADNANO2.5
+ + angle is CCW
+ - angle is CW
+ Right handed DNA rotates clockwise from 5' to 3'
+ we use the convention the 5' end starts at 0 degrees
+ and it's pair is minor_groove_angle degrees away
+ direction, hence the minus signs. eulerZ
+ """
+
+ hp, bpr, tpr, eulerZ, mgroove = self.part.vh_properties.loc[helix_id,
+ ['helical_pitch',
+ 'bases_per_repeat',
+ 'turns_per_repeat',
+ 'eulerZ',
+ 'minor_groove_angle']]
+ twist_per_base = tpr*360./bpr
+ # angle = eulerZ - twist_per_base*indices + 0.5*mgroove + 180
+ angle = eulerZ + twist_per_base*indices - 0.5*mgroove
+ return angle
+
+ def _cadnano_part_to_segments(self,part):
+ try:
+ from cadnano.cnenum import PointType
+ except:
+ try:
+ from cadnano.proxies.cnenum import PointType
+ except:
+ from cadnano.proxies.cnenum import PointEnum as PointType
+
+ segments = dict()
+ self.helices = helices = dict()
+ self.helix_ranges = helix_ranges = dict()
+
+ props = part.getModelProperties().copy()
+
+ if props.get('point_type') == PointType.ARBITRARY:
+ # TODO add code to encode Parts with ARBITRARY point configurations
+ raise NotImplementedError("Not implemented")
+ else:
+ try:
+ vh_props, origins = part.helixPropertiesAndOrigins()
+ except:
+ origins = {hid:part.getVirtualHelixOrigin(hid)[:2] for hid in part.getidNums()}
+
+ self.origins = origins
+
+ vh_list = []
+ strand_list = []
+ xover_list = []
+ self.xovers_from = dict()
+ self.xovers_to = dict()
+
+ try:
+ numHID = part.getMaxIdNum() + 1
+ except:
+ numHID = part.getIdNumMax() + 1
+
+ for id_num in range(numHID):
+ try:
+ offset_and_size = part.getOffsetAndSize(id_num)
+ except:
+ offset_and_size = None
+ if offset_and_size is None:
+ ## Add a placeholder for empty helix
+ vh_list.append((id_num, 0))
+ strand_list.append(None)
+ else:
+ offset, size = offset_and_size
+ vh_list.append((id_num, size))
+ fwd_ss, rev_ss = part.getStrandSets(id_num)
+ fwd_idxs, fwd_colors = fwd_ss.dump(xover_list)
+ rev_idxs, rev_colors = rev_ss.dump(xover_list)
+ strand_list.append((fwd_idxs, rev_idxs))
+
+ self.xovers_from[id_num] = []
+ self.xovers_to[id_num] = []
+
+ for xo in xover_list:
+ h1,f1,z1,h2,f2,z2 = xo
+ self.xovers_from[h1].append(xo)
+ self.xovers_to[h2].append(xo)
+
+ ## Get lists of 5/3prime ends
+ strands5 = [o.strand5p() for o in part.oligos()]
+ strands3 = [o.strand3p() for o in part.oligos()]
+
+ self._5prime_list = [(s.idNum(),s.isForward(),s.idx5Prime()) for s in strands5]
+ self._3prime_list = [(s.idNum(),s.isForward(),s.idx3Prime()) for s in strands3]
+
+ ## Get dictionary of insertions
+ self.insertions = allInsertions = part.insertions()
+ self.strand_occupancies = dict()
+
+ ## Build helices
+ for hid in range(numHID):
+ # print("Working on helix",hid)
+ helices[hid] = []
+ helix_ranges[hid] = []
+ self.strand_occupancies[hid] = []
+
+ helixStrands = strand_list[hid]
+ if helixStrands is None: continue
+
+ ## Build list of tuples containing (idx,length) of insertions/skips
+ insertions = sorted( [(i[0],i[1].length()) for i in allInsertions[hid].items()],
+ key=lambda x: x[0] )
+
+ ## TODO: make the following code (until "regions = ...") more readable
+ ## Build list of strand ends and list of mandatory node locations
+ ends1,ends2 = self._helixStrandsToEnds(helixStrands)
+
+ ## Find crossovers for this helix
+ reqNodeZids = sorted(list(set( ends1 + ends2 ) ) )
+
+ ## Build lists of which nt sites are occupied in the helix
+ strandOccupancies = [ [x for i in range(0,len(e),2)
+ for x in range(e[i],e[i+1]+1)]
+ for e in (ends1,ends2) ]
+ self.strand_occupancies[hid] = strandOccupancies
+
+ ends1,ends2 = [ [(e[i],e[i+1]) for i in range(0,len(e),2)] for e in (ends1,ends2) ]
+
+ regions = combineRegionLists(ends1,ends2)
+
+ ## Split regions in event of ssDNA crossover
+ split_regions = []
+ for zid1,zid2 in regions:
+ zMid = int(0.5*(zid1+zid2))
+ if zMid in strandOccupancies[0] and zMid in strandOccupancies[1]:
+ split_regions.append( (zid1,zid2) )
+ else:
+ is_fwd = zMid in strandOccupancies[0]
+ ends = [z for h,f,z in self._get_crossover_locations( hid, range(zid1+1,zid2), is_fwd )]
+ z1 = zid1
+ for z in sorted(ends):
+ z2 = z
+ if z2 > z1:
+ split_regions.append( (z1,z2) )
+ z1 = z2+1
+ z2 = zid2
+ split_regions.append( (z1,z2) )
+
+ # if hid == 43:
+ # import pdb
+ for zid1,zid2 in split_regions:
+ zMid = int(0.5*(zid1+zid2))
+ assert( zMid in strandOccupancies[0] or zMid in strandOccupancies[1] )
+
+ bp_to_zidx = []
+ insertion_dict = {idx:length for idx,length in insertions}
+ for i in range(zid1,zid2+1):
+ if i in insertion_dict:
+ l = insertion_dict[i]
+ else:
+ l = 0
+ for j in range(i,i+1+l):
+ bp_to_zidx.append(i)
+ numBps = len(bp_to_zidx)
+
+ # print("Adding helix with length",numBps,zid1,zid2)
+
+ name = "%d-%d" % (hid,len(helices[hid]))
+ # "H%03d" % hid
+ kwargs = dict(name=name, segname=name, occupancy=hid)
+
+ posargs1 = dict( start_position = self._get_cadnano_position(hid,zid1-0.25),
+ end_position = self._get_cadnano_position(hid,zid2+0.25) )
+ posargs2 = dict( start_position = posargs1['end_position'],
+ end_position = posargs1['start_position'])
+
+ ## TODO get sequence from cadnano api
+ if zMid in strandOccupancies[0] and zMid in strandOccupancies[1]:
+ kwargs['num_bp'] = numBps
+ _angle = self._get_helix_angle(hid, zid1)
+ start_orientation = rotationAboutAxis(np.array((0,0,1)), _angle)
+ seg = DoubleStrandedSegment(**kwargs,**posargs1, start_orientation = start_orientation)
+ elif zMid in strandOccupancies[0]:
+ kwargs['num_nt'] = numBps
+ seg = SingleStrandedSegment(**kwargs,**posargs1)
+ elif zMid in strandOccupancies[1]:
+ kwargs['num_nt'] = numBps
+ seg = SingleStrandedSegment(**kwargs,**posargs2)
+ else:
+ raise Exception("Segment could not be found")
+
+ seg._cadnano_helix = hid
+ seg._cadnano_start = zid1
+ seg._cadnano_end = zid2
+ seg._cadnano_bp_to_zidx = bp_to_zidx
+
+ def callback(segment):
+ for b in segment.beads:
+ bp = int(round(b.get_nt_position(segment)))
+ if bp < 0: bp = 0
+ if bp >= segment.num_nt: bp = segment.num_nt-1
+ try:
+ b.beta = segment._cadnano_bp_to_zidx[bp]
+ if 'orientation_bead' in b.__dict__:
+ b.orientation_bead.beta = segment._cadnano_bp_to_zidx[bp]
+ except:
+ pass
+ seg._generate_bead_callbacks.append(callback)
+
+ def atomic_callback(nucleotide, bp_to_zidx=bp_to_zidx):
+ nt = nucleotide
+ segment = nucleotide.parent.segment
+ bp = int(round(segment.contour_to_nt_pos( nt.contour_position )))
+ if bp < 0: bp = 0
+ if bp >= segment.num_nt: bp = segment.num_nt-1
+ try:
+ nt.beta = bp_to_zidx[bp]
+ nt.parent.occupancy = segment.occupancy
+ except:
+ pass
+ seg._generate_nucleotide_callbacks.append(atomic_callback)
+
+
+ helices[hid].append( seg )
+ helix_ranges[hid].append( (zid1,zid2) )
+
+ def _get_cadnano_position(self, hid, zid):
+ return [10*a for a in self.origins[hid]] + [-3.4*zid]
+
+ def _helixStrandsToEnds(self, helixStrands):
+ """Utility method to convert cadnano strand lists into list of
+ indices of terminal points"""
+
+ endLists = [[],[]]
+ for endList, strandList in zip(endLists,helixStrands):
+ lastStrand = None
+ for s in strandList:
+ if lastStrand is None:
+ ## first strand
+ endList.append(s[0])
+ elif lastStrand[1] != s[0]-1:
+ assert( s[0] > lastStrand[1] )
+ endList.extend( [lastStrand[1], s[0]] )
+ lastStrand = s
+ if lastStrand is not None:
+ endList.append(lastStrand[1])
+ return endLists
+
+ def _helix_strands_to_segment_ranges(self, helix_strands):
+ """Utility method to convert cadnano strand lists into list of
+ indices of terminal points"""
+ def _join(strands):
+ ends = []
+ lastEnd = None
+ for start,end in strands:
+ if lastEnd is None:
+ ends.append([start])
+ elif lastEnd != start-1:
+ ends[-1].append(lastEnd)
+ ends.append([start])
+ lastEnd = end
+ if lastEnd is not None:
+ ends[-1].append(lastEnd)
+ return ends
+
+ s1,s2 = [_join(s) for s in helix_strands]
+ i = j = 0
+
+ ## iterate through strands
+ while i < len(s1) and j < len(s2):
+ min(s1[i][0],s2[j][0])
+
+ def _get_segment(self, hid, zid):
+ ## TODO: rename these variables to segments
+ segs = self.helices[hid]
+ ranges = self.helix_ranges[hid]
+ for i in range(len(ranges)):
+ zmin,zmax = ranges[i]
+ if zmin <= zid and zid <= zmax:
+ return segs[i]
+ raise Exception("Could not find segment in helix %d at position %d" % (hid,zid))
+
+ def _get_nucleotide(self, hid, zid):
+ raise Exception("Deprecated")
+ seg = self._get_segment(hid,zid)
+ sid = self.helices[hid].index(seg)
+ zmin,zmax = self.helix_ranges[hid][sid]
+
+ nt = zid-zmin
+
+ ## Find insertions
+ # TODO: for i in range(zmin,zid+1): ?
+ for i in range(zmin,zid):
+ if i in self.insertions[hid]:
+ nt += self.insertions[hid][i].length()
+ return nt
+
+ def _get_segment_nucleotide(self, hid, zid, get_forward_location=False):
+ """ returns segments and zero-based nucleotide index """
+ seg = self._get_segment(hid,zid)
+ sid = self.helices[hid].index(seg)
+ zmin,zmax = self.helix_ranges[hid][sid]
+
+ zMid = int(0.5*(zmin+zmax))
+ occ = self.strand_occupancies[hid]
+ ins = self.insertions[hid]
+
+ ## TODO combine if/else when nested TODO is resolved
+ # if zid in self.insertions[hid]:
+ # import pdb
+ # pdb.set_trace()
+
+ if (zMid not in occ[0]) and (zMid in occ[1]):
+ ## reversed ssDNA strand
+ nt = zmax-zid
+ # TODO: for i in range(zmin,zid+1): ?
+ for i in range(zid,zmax+1):
+ if i in self.insertions[hid]:
+ nt += self.insertions[hid][i].length()
+ else:
+ ## normal condition
+ if get_forward_location:
+ while zid in ins and ins[zid].length() < 0 and zid <= zmax:
+ zid+=1
+ # else:
+ # while zid in ins and ins[zid].length() > 0 and zid >= zmax:
+ # zid-=1
+ nt = zid-zmin
+ for i in range(zmin,zid):
+ if i in ins:
+ nt += ins[i].length()
+
+ if not get_forward_location and zid in ins:
+ nt += ins[zid].length()
+
+ ## Find insertions
+ return seg, nt
+
+
+
+ """ Routines to add connnections between helices """
+ def _add_intrahelical_connections(self):
+ for hid,segs in self.helices.items():
+ occ = self.strand_occupancies[hid]
+ for i in range(len(segs)-1):
+ seg1,seg2 = [segs[j] for j in (i,i+1)]
+ if isinstance(seg1,SingleStrandedSegment) and isinstance(seg2,SingleStrandedSegment):
+ continue
+ r1,r2 = [self.helix_ranges[hid][j] for j in (i,i+1)]
+ if r1[1]+1 == r2[0]:
+ ## TODO: handle nicks that are at intrahelical connections(?)
+ zmid1 = int(0.5*(r1[0]+r1[1]))
+ zmid2 = int(0.5*(r2[0]+r2[1]))
+
+ ## TODO: validate
+ if zmid1 in occ[0] and zmid2 in occ[0]:
+ seg1.connect_end3(seg2.start5)
+
+ if zmid1 in occ[1] and zmid2 in occ[1]:
+ if zmid1 in occ[0]:
+ end = seg1.end5
+ else:
+ end = seg1.start5
+ if zmid2 in occ[0]:
+ seg2.connect_start3(end)
+ else:
+ seg2.connect_end3(end)
+
+
+ def _get_crossover_locations(self, helix_idx, nt_idx_range, fwd_strand=None):
+ xos = []
+ def append_if_in_range(h,f,z):
+ if fwd_strand in (None,f) and z in nt_idx_range:
+ xos.append((h,f,z))
+
+ for xo in self.xovers_from[helix_idx]:
+ ## h1,f1,z1,h2,f2,z2 = xo[3:]
+
+ append_if_in_range(*xo[:3])
+ for xo in self.xovers_to[helix_idx]:
+ append_if_in_range(*xo[3:])
+ return xos
+
+ def _add_crossovers(self):
+ for hid,xos in self.xovers_from.items():
+ for h1,f1,z1,h2,f2,z2 in xos:
+ seg1, nt1 = self._get_segment_nucleotide(h1,z1,not f1)
+ seg2, nt2 = self._get_segment_nucleotide(h2,z2,f2)
+ ## TODO: use different types of crossovers
+ ## fwd?
+ ## 5'-to-3' direction
+ if isinstance(seg1, SingleStrandedSegment): f1 = True
+ if isinstance(seg2, SingleStrandedSegment): f2 = True
+ seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
+
+ def _add_prime_ends(self):
+ for h,fwd,z in self._5prime_list:
+ seg, nt = self._get_segment_nucleotide(h,z, fwd)
+ if isinstance(seg, SingleStrandedSegment): fwd = True
+ # print("adding 5prime",seg.name,nt,fwd)
+ seg.add_5prime(nt,fwd)
+
+ for h,fwd,z in self._3prime_list:
+ seg, nt = self._get_segment_nucleotide(h,z, not fwd)
+ if isinstance(seg, SingleStrandedSegment): fwd = True
+ # print("adding 3prime",seg.name,nt,fwd)
+ seg.add_3prime(nt,fwd)
+
+ def get_bead(self, hid, zid):
+ # get segment, get nucleotide,
+ seg, nt = self._get_segment_nucleotide(h,z)
+ # return seg.get_nearest_bead(seg,nt / seg.num_nt)
+ return seg.get_nearest_bead(seg,nt / (seg.num_nt-1))
+
+def read_json_file(filename):
+ import json
+ import re
+
+ try:
+ with open(filename) as ch:
+ data = json.load(ch)
+ except:
+ with open(filename) as ch:
+ content = ""
+ for l in ch:
+ l = re.sub(r"'", r'"', l)
+ # https://stackoverflow.com/questions/4033633/handling-lazy-json-in-python-expecting-property-name
+ # l = re.sub(r"{\s*(\w)", r'{"\1', l)
+ # l = re.sub(r",\s*(\w)", r',"\1', l)
+ # l = re.sub(r"(\w):", r'\1":', l)
+ content += l+"\n"
+ data = json.loads(content)
+ return data
+
+def decode_cadnano_part(json_data):
+ import cadnano
+ from cadnano.document import Document
+
+ try:
+ doc = Document()
+ cadnano.fileio.v3decode.decode(doc, json_data)
+ decoder = 3
+ except:
+ doc = Document()
+ cadnano.fileio.v2decode.decode(doc, json_data)
+ decoder = 2
+
+ parts = [p for p in doc.getParts()]
+ if len(parts) != 1:
+ raise Exception("Only documents containing a single cadnano part are implemented at this time.")
+ part = parts[0]
+
+ if decoder == 2:
+ """ It seems cadnano2.5 (as of ce6ff019) does not set the EulerZ for square lattice structures correctly, doing so here """
+ l = _get_lattice(part)
+ if l == 'square':
+ for id_num in part.getIdNums():
+ if part.vh_properties.loc[id_num,'eulerZ'] == 0:
+ part.vh_properties.loc[id_num,'eulerZ'] = 360*(6/10.5)
+
+ return part
+
+def _get_lattice(part):
+ lattice_type = None
+ _gt = part.getGridType()
+ try:
+ lattice_type = _gt.name.lower()
+ except:
+ if _gt == 1:
+ lattice_type = 'square'
+ elif _gt == 2:
+ lattice_type = 'honeycomb'
+ else:
+ print("WARNING: unable to determine cadnano part lattice type")
+ return lattice_type
+
+def package_archive( name, directory ):
+ ...
+
+def read_model(json_data, sequence=None, fill_sequence='T', **kwargs):
+ """ Read in data """
+ part = decode_cadnano_part(json_data)
+ model = cadnano_part(part,
+ **kwargs)
+
+ # TODO
+ # try:
+ # model.set_cadnano_sequence()
+ # finally:
+ # ...
+ # if sequence is not None and len() :
+ # model.strands[0].set_sequence(seq)
+
+ if sequence is None or len(sequence) == 0:
+ ## default m13mp18
+ model.set_sequence(m13seq,force=False, fill_sequence=fill_sequence)
+ else:
+ model.set_sequence(sequence, fill_sequence=fill_sequence)
+
+ return model
+
+# pynvml.nvmlInit()
+# gpus = range(pynvml.nvmlDeviceGetCount())
+# pynvml.nvmlShutdown()
+# gpus = [0,1,2]
+# print(gpus)
+
+if __name__ == '__main__':
+ loHi1 = [[0,4],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 4), (5, 7), (8, 9)]
+ print(loHi1)
+ print(loHi2)
+ print(combineRegionLists(loHi1,loHi2))
+ print(combineCompactRegionLists(loHi1,loHi2))
+
+ loHi1 = [[0,3],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
+ print(loHi1)
+ print(loHi2)
+ print(combineRegionLists(loHi1,loHi2))
+ print(combineCompactRegionLists(loHi1,loHi2))
+
+ combineRegionLists
+
+ # for f in glob('json/*'):
+ # print("Working on {}".format(f))
+ # out = re.match('json/(.*).json',f).group(1)
+ # data = read_json_file(f)
+ # run_simulation_protocol( out, "job-id", data, gpu=0 )
diff --git a/mrdna/readers/.ipynb_checkpoints/segmentmodel_from_lists-checkpoint.py b/mrdna/readers/.ipynb_checkpoints/segmentmodel_from_lists-checkpoint.py
new file mode 100644
index 0000000..84eb17e
--- /dev/null
+++ b/mrdna/readers/.ipynb_checkpoints/segmentmodel_from_lists-checkpoint.py
@@ -0,0 +1,495 @@
+# -*- coding: utf-8 -*-
+
+import pdb
+import numpy as np
+import os,sys
+import scipy
+
+from mrdna import logger, devlogger
+from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from ..arbdmodel.coords import quaternion_from_matrix, rotationAboutAxis, quaternion_slerp
+from .. import get_resource_path
+
+ref_stack_position = np.array((-2.41851735, -0.259761333, 3.39999978))
+
+def _three_prime_list_to_five_prime(three_prime):
+ five_prime = -np.ones(three_prime.shape, dtype=int)
+ has_three_prime = np.where(three_prime >= 0)[0]
+ five_prime[three_prime[has_three_prime]] = has_three_prime
+ return five_prime
+
+def _primes_list_to_strands(three_prime, five_prime):
+ five_prime_ends = np.where(five_prime < 0)[0]
+ strands = []
+ strand_is_circular = []
+
+ idx_to_strand = -np.ones(three_prime.shape, dtype=int)
+
+ def build_strand(nt_idx, conditional):
+ strand = [nt_idx]
+ idx_to_strand[nt_idx] = len(strands)
+ while conditional(nt_idx):
+ nt_idx = three_prime[nt_idx]
+ strand.append(nt_idx)
+ idx_to_strand[nt_idx] = len(strands)
+ strands.append( np.array(strand, dtype=int) )
+
+ for nt_idx in five_prime_ends:
+ build_strand(nt_idx,
+ lambda nt: three_prime[nt] >= 0)
+ strand_is_circular.append(False)
+
+ while True:
+ ## print("WARNING: working on circular strand {}".format(len(strands)))
+ ids = np.where(idx_to_strand < 0)[0]
+ if len(ids) == 0: break
+ build_strand(ids[0],
+ lambda nt: three_prime[nt] >= 0 and \
+ idx_to_strand[three_prime[nt]] < 0)
+ strand_is_circular.append(True)
+
+ return strands, strand_is_circular
+
+def find_stacks(centers, transforms):
+
+ ## Find orientation and center of each nucleotide
+ expected_stack_positions = []
+ for R,c in zip(transforms,centers):
+ expected_stack_positions.append( c + ref_stack_position.dot(R) )
+
+ expected_stack_positions = np.array(expected_stack_positions, dtype=np.float32)
+
+ dists = scipy.spatial.distance_matrix(expected_stack_positions, centers)
+ dists = dists + 5*np.eye(len(dists))
+ idx1, idx2 = np.where(dists < 3.5)
+
+ ## Convert distances to stacks
+ stacks_above = -np.ones(len(centers), dtype=int)
+ _z = np.array((0,0,1))
+ for i in np.unique(idx1):
+ js = idx2[ idx1 == i ]
+ with np.errstate(divide='ignore',invalid='ignore'):
+ angles = [np.arccos( transforms[j].T.dot( transforms[i].dot(_z) ).dot( _z ) ) for j in js]
+ angles = np.array( angles )
+ tmp = np.argmin(dists[i][js] + 1.0*angles)
+ j = js[tmp]
+ stacks_above[i] = j
+
+ return stacks_above
+
+def basepairs_and_stacks_to_helixmap(basepairs,stacks_above):
+
+ helixmap = -np.ones(basepairs.shape, dtype=int)
+ helixrank = -np.ones(basepairs.shape)
+ is_fwd = np.ones(basepairs.shape, dtype=int)
+
+ ## Remove stacks with nts lacking a basepairs
+ nobp = np.where(basepairs < 0)[0]
+ stacks_above[nobp] = -1
+ stacks_with_nobp = np.in1d(stacks_above, nobp)
+ stacks_above[stacks_with_nobp] = -1
+
+ end_ids = np.where( (stacks_above < 0)*(basepairs >= 0) )[0]
+
+ hid = 0
+ for end in end_ids:
+ if helixmap[end] >= 0:
+ continue
+ rank = 0
+ nt = basepairs[end]
+ bp = basepairs[nt]
+ assert( bp == end )
+ if helixmap[nt] >= 0 or helixmap[bp] >= 0:
+ logger.warning(f'Ill-formed helix: problematic basepair or stacking data near nucleotide {nt} or {bp}... skipping')
+ continue
+ # assert(helixmap[nt] == -1)
+ # assert(helixmap[bp] == -1)
+ helixmap[nt] = helixmap[bp] = hid
+ helixrank[nt] = helixrank[bp] = rank
+ is_fwd[bp] = 0
+ rank +=1
+
+ _tmp = [(nt,bp)]
+
+ while stacks_above[nt] >= 0:
+ nt = stacks_above[nt]
+ if basepairs[nt] < 0: break
+ bp = basepairs[nt]
+ if helixmap[nt] >= 0 or helixmap[bp] >= 0:
+ logger.warning(f'Ill-formed helix: problematic basepair or stacking data near nucleotide {nt} or {bp}... skipping')
+ break
+ helixmap[nt] = helixmap[bp] = hid
+ helixrank[nt] = helixrank[bp] = rank
+ is_fwd[bp] = 0
+ _tmp.append((nt,bp))
+ rank +=1
+
+ hid += 1
+
+ ## Create "helix" for each circular segment
+ intrahelical = []
+ processed = set()
+ unclaimed_bases = np.where( (basepairs >= 0)*(helixmap == -1) )[0]
+ for nt0 in unclaimed_bases:
+ if nt0 in processed: continue
+
+ nt = nt0
+ all_nts = [nt]
+
+ rank = 0
+ nt = nt0
+ bp = basepairs[nt]
+ if helixmap[nt] >= 0 or helixmap[bp] >= 0:
+ logger.warning(f'Ill-formed cylic helix: problematic basepair or stacking data near nucleotide {nt} or {bp}... skipping')
+ continue
+ helixmap[nt] = helixmap[bp] = hid
+ helixrank[nt] = helixrank[bp] = rank
+ is_fwd[bp] = 0
+ rank +=1
+ processed.add(nt)
+ processed.add(bp)
+
+ counter = 0
+ while stacks_above[nt] >= 0:
+ lastnt = nt
+ nt = stacks_above[nt]
+ bp = basepairs[nt]
+ if nt == nt0 or nt == basepairs[nt0]:
+ intrahelical.append((lastnt,nt0))
+ break
+
+ assert( bp >= 0 )
+ if helixmap[nt] >= 0 or helixmap[bp] >= 0:
+ logger.warning(f'Ill-formed cyclic helix: problematic basepair or stacking data near nucleotide {nt} or {bp}... skipping')
+ break
+
+ helixmap[nt] = helixmap[bp] = hid
+ helixrank[nt] = helixrank[bp] = rank
+ is_fwd[bp] = 0
+ processed.add(nt)
+ processed.add(bp)
+ rank +=1
+ hid += 1
+
+ return helixmap, helixrank, is_fwd, intrahelical
+
+
+def set_splines(seg, coordinate, hid, hmap, hrank, fwd, basepair, orientation=None):
+ maxrank = np.max( hrank[hmap==hid] )
+ if maxrank == 0:
+ ids = np.where((hmap == hid))[0]
+ pos = np.mean( [coordinate[r,:] for r in ids ], axis=0 )
+ coords = [pos,pos]
+ contours = [0,1]
+ if orientation is not None:
+ ids = np.where((hmap == hid) * fwd)[0]
+ assert( len(ids) == 1 )
+ q = quaternion_from_matrix( orientation[ids[0]] )
+ quats = [q, q]
+ coords[-1] = pos + orientation[ids[0]].dot(np.array((0,0,1)))
+
+ else:
+ coords,contours,quats = [[],[],[]]
+ last_q = None
+ for rank in range(int(maxrank)+1):
+ ids = np.where((hmap == hid) * (hrank == rank))[0]
+
+ coords.append(np.mean( [coordinate[r,:] for r in ids ], axis=0 ))
+ contours.append( float(rank+0.5)/(maxrank+1) )
+ if orientation is not None:
+ ids = np.where((hmap == hid) * (hrank == rank) * fwd)[0]
+ assert(len(ids) == 1)
+ q = quaternion_from_matrix( orientation[ids[0]] )
+
+ if last_q is not None and last_q.dot(q) < 0:
+ q = -q
+
+ ## Average quaterion with reverse direction
+ bp = basepair[ids[0]]
+ if bp >= 0:
+ bp_o = orientation[bp].dot(rotationAboutAxis(np.array((1,0,0)),180))
+ q2 = quaternion_from_matrix( bp_o )
+ if q.dot(q2) < 0:
+ q2 = -q2
+
+ ## probably good enough, but slerp is better: q = (q + q2)*0.5
+ q = quaternion_slerp(q,q2,0.5)
+
+ quats.append(q)
+ last_q = q
+
+ coords = np.array(coords)
+ seg.set_splines(contours,coords)
+ if orientation is not None:
+ quats = np.array(quats)
+ seg.set_orientation_splines(contours,quats)
+
+ seg.start_position = coords[0,:]
+ seg.end_position = coords[-1,:]
+
+
+def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
+ sequence=None, orientation=None,
+ max_basepairs_per_bead = 5,
+ max_nucleotides_per_bead = 5,
+ local_twist = False,
+ dimensions=(5000,5000,5000),
+ **model_parameters):
+ """
+ Creates a SegmentModel object from lists of each nucleotide's
+ basepair, its stack (on 3' side) and its 3'-connected nucleotide
+
+ The first argument should be an N-by-3 numpy array containing the
+ coordinate of each nucleotide, where N is the number of
+ nucleotides. The following three arguments should be integer lists
+ where the i-th element corresponds to the i-th nucleotide; the
+ list element should the integer index of the corresponding
+ basepaired / stacked / phosphodiester-bonded nucleotide. If there
+ is no such nucleotide, the value should be -1.
+
+ Args:
+ basepair: List of each nucleotide's basepair's index
+ stack: List containing index of the nucleotide stacked on the 3' of each nucleotide
+ three_prime: List of each nucleotide's the 3' end of each nucleotide
+
+ Returns:
+ SegmentModel
+ """
+
+ """ Validate Input """
+ inputs = (basepair,three_prime)
+ try:
+ basepair,three_prime = [np.array(a,dtype=int) for a in inputs]
+ except:
+ raise TypeError("One or more of the input lists could not be converted into a numpy array")
+ inputs = (basepair,three_prime)
+ coordinate = np.array(coordinate)
+
+ if np.any( [len(a.shape) > 1 for a in inputs] ):
+ raise ValueError("One or more of the input lists has the wrong dimensionality")
+
+ if len(coordinate.shape) != 2:
+ raise ValueError("Coordinate array has the wrong dimensionality")
+
+ inputs = (coordinate,basepair,three_prime)
+ if not np.all(np.diff([len(a) for a in inputs]) == 0):
+ raise ValueError("Inputs are not the same length")
+
+ num_nt = len(basepair)
+ if sequence is not None and len(sequence) != num_nt:
+ raise ValueError("The 'sequence' parameter is the wrong length {} != {}".format(len(sequence),num_nt))
+
+ if orientation is not None:
+ orientation = np.array(orientation)
+ if len(orientation.shape) != 3:
+ raise ValueError("The 'orientation' array has the wrong dimensionality (should be Nx3x3)")
+ if orientation.shape != (num_nt,3,3):
+ raise ValueError("The 'orientation' array is not properly formatted")
+
+ if stack is None:
+ if orientation is not None:
+ stack = find_stacks(coordinate, orientation)
+ else:
+ ## Guess stacking based on 3' connectivity
+ stack = np.array(three_prime,dtype=int) # Assume nts on 3' ends are stacked
+ _stack_below = _three_prime_list_to_five_prime(stack)
+ _has_bp = (basepair >= 0)
+ _nostack = np.where( (stack == -1)*_has_bp )[0]
+ _has_stack_below = _stack_below[basepair[_nostack]] >= 0
+ _nostack2 = _nostack[_has_stack_below]
+ stack[_nostack2] = basepair[_stack_below[basepair[_nostack2]]]
+
+ else:
+ try:
+ stack = np.array(stack,dtype=int)
+ except:
+ raise TypeError("The 'stack' array could not be converted into a numpy integer array")
+
+ if len(stack.shape) != 1:
+ raise ValueError("The 'stack' array has the wrong dimensionality")
+
+ if len(stack) != num_nt:
+ raise ValueError("The length of the 'stack' array does not match other inputs")
+
+ bps = basepair # alias
+
+ """ Fix stacks: require that the stack of a bp of a base's stack is its bp """
+ _has_bp = (bps >= 0)
+ _has_stack = (stack >= 0)
+ _stack_has_basepair = (bps[stack] >= 0) * _has_stack
+ stack = np.where( (stack[bps[stack]] == bps) * _has_bp * _has_stack * _has_bp,
+ stack, -np.ones(len(stack),dtype=int) )
+
+ five_prime = _three_prime_list_to_five_prime(three_prime)
+
+ """ Build map of dsDNA helices and strands """
+ hmap,hrank,fwd,intrahelical = basepairs_and_stacks_to_helixmap(bps,stack)
+ double_stranded_helices = np.unique(hmap[hmap >= 0])
+ strands, strand_is_circular = _primes_list_to_strands(three_prime, five_prime)
+
+ """ Add ssDNA to hmap """
+ if len(double_stranded_helices) > 0:
+ hid = double_stranded_helices[-1]+1
+ else:
+ hid = 0
+ ss_residues = hmap < 0
+ #
+ if np.any(bps[ss_residues] != -1):
+ logger.warning(f'{np.sum(bps[ss_residues] != -1)} ssDNA nucleotides appear to have basepairs... ignoring')
+
+ for s,c in zip(strands, strand_is_circular):
+ strand_segment_ends = [i for i in np.where( np.diff(hmap[s]) != 0 )[0]] + [len(s)-1]
+ seg_start = 0
+ for i in strand_segment_ends:
+ if hmap[s[i]] < 0:
+ ## Found single-stranded segment
+ ids = s[seg_start:i+1]
+ assert( np.all(hmap[ids] == -1) )
+ hmap[ids] = hid
+ hrank[ids] = np.arange(i+1-seg_start)
+ hid+=1
+ seg_start = i+1
+
+ if len(double_stranded_helices) > 0:
+ single_stranded_helices = np.arange(double_stranded_helices[-1]+1,hid)
+ else:
+ single_stranded_helices = np.arange(hid)
+
+ ## Create double-stranded segments
+ doubleSegments = []
+ for hid in double_stranded_helices:
+ seg = DoubleStrandedSegment(name=str(hid),
+ num_bp = np.sum(hmap==hid)//2)
+ set_splines(seg, coordinate, hid, hmap, hrank, fwd, basepair, orientation)
+
+ assert(hid == len(doubleSegments))
+ doubleSegments.append(seg)
+
+ ## Create single-stranded segments
+ singleSegments = []
+ for hid in single_stranded_helices:
+ seg = SingleStrandedSegment(name=str(hid),
+ num_nt = np.sum(hmap==hid))
+ set_splines(seg, coordinate, hid, hmap, hrank, fwd, basepair, orientation)
+
+ assert(hid == len(doubleSegments) + len(singleSegments))
+ singleSegments.append(seg)
+
+ ## Find crossovers and 5prime/3prime ends
+ crossovers,prime5,prime3 = [[],[],[]]
+ for s,c in zip(strands,strand_is_circular):
+ tmp = np.where(np.diff(hmap[s]) != 0)[0]
+ for i in tmp:
+ crossovers.append( (s[i],s[i+1]) )
+ if c:
+ if hmap[s[-1]] != hmap[s[0]]:
+ crossovers.append( (s[-1],s[0]) )
+ else:
+ prime5.append(s[0])
+ prime3.append(s[-1])
+
+ ## Add connections
+ allSegments = doubleSegments+singleSegments
+
+ for r1,r2 in crossovers:
+ seg1,seg2 = [allSegments[hmap[i]] for i in (r1,r2)]
+ nt1,nt2 = [hrank[i] for i in (r1,r2)]
+ f1,f2 = [fwd[i] for i in (r1,r2)]
+
+ ## Handle connections at the ends
+ is_terminal1 = (nt1,f1) in ((0,0),(seg1.num_nt-1,1))
+ is_terminal2 = (nt2,f2) in ((0,1),(seg2.num_nt-1,0))
+
+ print(seg1,seg2, r1, r2, is_terminal1, is_terminal2)
+ if is_terminal1 or is_terminal2:
+ """ Ensure that we don't have three-way dsDNA junctions """
+ if is_terminal1 and (bps[r1] >= 0) and (five_prime[bps[r1]] >= 0) and (three_prime[r1] >= 0):
+ if (bps[five_prime[bps[r1]]] >= 0) and (bps[three_prime[r1]] >= 0):
+ # is_terminal1 = (three_prime[r1] == bps[five_prime[bps[r1]]])
+ is_terminal1 = hmap[five_prime[bps[r1]]] == hmap[three_prime[r1]]
+ if is_terminal2 and (bps[r2] >= 0) and (three_prime[bps[r2]] >= 0) and (five_prime[r2] >= 0):
+ if (bps[three_prime[bps[r2]]] >= 0) and (bps[five_prime[r2]] >= 0):
+ # is_terminal2 = (five_prime[r2] == bps[three_prime[bps[r2]]])
+ is_terminal2 = hmap[three_prime[bps[r2]]] == hmap[five_prime[r2]]
+
+ """ Place connection """
+ if is_terminal1 and is_terminal2:
+ end1 = seg1.end3 if f1 else seg1.start3
+ end2 = seg2.start5 if f2 else seg2.end5
+ seg1._connect_ends( end1, end2, type_='intrahelical')
+ else:
+ seg1.add_crossover(nt1,seg2,nt2,[f1,f2],type_="terminal_crossover")
+ else:
+ seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
+
+ ## Add 5prime/3prime ends
+ for r in prime5:
+ seg = allSegments[hmap[r]]
+ seg.add_5prime(hrank[r],fwd[r])
+ for r in prime3:
+ seg = allSegments[hmap[r]]
+ seg.add_3prime(hrank[r],fwd[r])
+
+ ## Add intrahelical connections to circular helical sections
+ for nt0,nt1 in intrahelical:
+ seg = allSegments[hmap[nt0]]
+ assert( seg is allSegments[hmap[nt1]] )
+ if three_prime[nt0] >= 0:
+ if hmap[nt0] == hmap[three_prime[nt0]]:
+ seg.connect_end3(seg.start5)
+
+ bp0,bp1 = [bps[nt] for nt in (nt0,nt1)]
+ if three_prime[bp1] >= 0:
+ if hmap[bp1] == hmap[three_prime[bp1]]:
+ seg.connect_start3(seg.end5)
+
+ ## Assign sequence
+ if sequence is not None:
+ for hid in range(len(allSegments)):
+ resids = np.where( (hmap==hid)*(fwd==1) )[0]
+ s = allSegments[hid]
+ s.sequence = [sequence[r] for r in sorted(resids,key=lambda x: hrank[x])]
+
+
+ ## Build model
+ model = SegmentModel( allSegments,
+ max_basepairs_per_bead = max_basepairs_per_bead,
+ max_nucleotides_per_bead = max_nucleotides_per_bead,
+ local_twist = local_twist,
+ dimensions = dimensions,
+ **model_parameters )
+
+
+ model._reader_list_coordinates = coordinate
+ model._reader_list_basepair = basepair
+ model._reader_list_stack = stack
+ model._reader_list_three_prime = three_prime
+ model._reader_list_five_prime = five_prime
+ model._reader_list_sequence = sequence
+ model._reader_list_orientation = orientation
+ model._reader_list_hmap = hmap
+ model._reader_list_fwd = fwd
+ model._reader_list_hrank = hrank
+
+ if sequence is None:
+ for s in model.segments:
+ s.randomize_unset_sequence()
+
+ return model
+
+def UNIT_circular():
+ """ Make a circular DNA strand, with dsDNA in the middle """
+ coordinate = [(0,0,3.4*i) for i in range(7)]
+ stack = -1*np.ones(len(coordinate))
+ three_prime = [ 1, 2, 4,-1, 6, 3, 0]
+ basepair = [-1,-1, 3, 2, 5, 4,-1]
+ stack = [-1,-1, 4,-1,-1, 3,-1]
+ for i in [3,5]:
+ coordinate[i] = (1,0,3.4*i)
+
+ model = model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
+ max_basepairs_per_bead=1,
+ max_nucleotides_per_bead=1,
+ local_twist=True)
+
+ model.simulate(output_name='circular', directory='unittest')
diff --git a/mrdna/readers/.ipynb_checkpoints/segmentmodel_from_oxdna_pinyi-checkpoint.py b/mrdna/readers/.ipynb_checkpoints/segmentmodel_from_oxdna_pinyi-checkpoint.py
new file mode 100644
index 0000000..b107283
--- /dev/null
+++ b/mrdna/readers/.ipynb_checkpoints/segmentmodel_from_oxdna_pinyi-checkpoint.py
@@ -0,0 +1,162 @@
+from mrdna import logger, devlogger
+from .segmentmodel_from_lists import model_from_basepair_stack_3prime
+from ..arbdmodel.coords import rotationAboutAxis
+
+from oxlibs import *
+import numpy as np
+from scipy.spatial import distance_matrix
+
+_seq_to_int_dict = dict(A=0,T=1,C=2,G=3)
+_seq_to_int_dict = {k:str(v) for k,v in _seq_to_int_dict.items()}
+
+_yrot = rotationAboutAxis(axis=(0,1,0), angle=180).dot(rotationAboutAxis(axis=(0,0,1),angle=-40))
+
+def mrdna_model_from_oxdna(coordinate_file, topology_file, virt2nuc=None, **model_parameters):
+ """ Construct an mrdna model from oxDNA coordinate and topology files """
+ top_data = np.loadtxt(topology_file, skiprows=1,
+ unpack=True,
+ dtype=np.dtype('i4,U1,i4,i4')
+ )
+ conf_data = np.loadtxt(idealized_coordinate_file, skiprows=3)
+
+ if idealized_coordinate_file is not None:
+ import pickle
+ df = pickle.load(virt2nuc)
+ vh_vb2nuc_rev, vhelix_pattern=df
+
+
+
+ ## Reverse direction so indices run 5'-to-3'
+ top_data = [a[::-1] for a in top_data]
+ conf_data = conf_data[::-1,:]
+
+ r = conf_data[:,:3] * 8.518
+ base_dir = conf_data[:,3:6]
+ # basepair_pos = r + base_dir*6.0
+ basepair_pos = r + base_dir*10.0
+ normal_dir = -conf_data[:,6:9]
+ perp_dir = np.cross(base_dir, normal_dir)
+ orientation = np.array([np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)])
+
+ def _get_bp(sequence=None):
+ dists = distance_matrix(r,basepair_pos) + np.eye(len(r))*1000
+ dists = 0.5*(dists + dists.T)
+
+ bp = np.array([np.argmin(da) for da in dists])
+
+ for i,j in enumerate(bp):
+ if j == -1: continue
+ # devlogger.info(f'bp {i} {j} {dists[i,j]}')
+ if dists[i,j] > 2:
+ bp[i] = -1
+ elif bp[j] != i:
+ bpj = bp[j]
+ logger.warning( " ".join([str(_x) for _x in ["Bad pair", i, j, bp[i], bp[j], dists[i,j], dists[j,i], dists[bpj,j], dists[j,bpj]]]) )
+
+ for i,j in enumerate(bp):
+ if j == -1: continue
+ if bp[j] != i:
+ bpj = bp[j]
+ logger.warning( " ".join([str(_x) for _x in ["Bad pair2", i, j, bp[i], bp[j], dists[i,j], dists[j,i], dists[bpj,j], dists[j,bpj]]]) )
+ raise Exception
+
+ if sequence is not None:
+ seq = sequence
+ bp_seq = sequence[bp]
+ bp_seq[bp==-1] = 'X'
+ bad_bps = np.where( (bp >= 0) &
+ (((seq == 'C') & (bp_seq != 'G')) |
+ ((seq == 'G') & (bp_seq != 'C')) |
+ ((seq == 'T') & (bp_seq != 'A')) |
+ ((seq == 'U') & (bp_seq != 'A')) |
+ ((seq == 'A') & ((bp_seq != 'T') | (bp_seq != 'U')))
+ ) )[0]
+ bp[bp[bad_bps]] = -1
+ bp[bad_bps] = -1
+
+ return bp
+
+ def _get_stack():
+ dists = distance_matrix( r + 3.5*normal_dir + 2.1*perp_dir -1*base_dir, r ) + np.eye(len(r))*1000
+ stack = np.array([np.argmin(da) for da in dists])
+ for i,j in enumerate(stack):
+ if dists[i,j] > 8:
+ stack[i] = -1
+ elif i < 10:
+ ## development info
+ # devlogger.info([i,j,dists[i,j]])
+ # dr = r[j] - (r[i] - normal_dir[i]*3.4 + perp_dir[i]*1 + base_dir[i]*1)
+ dr = r[j] - r[i]
+ # devlogger.info([normal_dir[i].dot(dr), perp_dir[i].dot(dr), base_dir[i].dot(dr)])
+ return np.array(stack)
+
+ seq = top_data[1]
+ bp = _get_bp(seq)
+ stack = _get_stack()
+
+ three_prime = len(r) - top_data[2] -1
+ five_prime = len(r) - top_data[3] -1
+ three_prime[three_prime >= len(r)] = -1
+ five_prime[five_prime >= len(r)] = -1
+
+ def _debug_write_bonds():
+ from ..arbdmodel import ParticleType, PointParticle, ArbdModel, Group
+ bond = tuple()
+ b_t = ParticleType('BASE')
+ p_t = ParticleType('PHOS')
+
+ parts = []
+ for i,(r0,r_bp,three_prime0,bp0,stack0,seq0) in enumerate(zip(r,basepair_pos, three_prime, bp, stack, seq)):
+ p = PointParticle(p_t, name='PHOS', position = r0, resid=i)
+ b = PointParticle(b_t, name=seq0, position = 0.5*(r0+r_bp), resid=i)
+ parts.extend((p,b))
+
+ model = ArbdModel(parts)
+ model.writePdb('test.pdb')
+
+ for i,(r0,r_bp,three_prime0,bp0,stack0) in enumerate(zip(r,basepair_pos, three_prime, bp, stack)):
+ model.add_bond(parts[2*i],parts[2*i+1],bond)
+ j = three_prime0
+ if j >= 0:
+ model.add_bond(parts[2*i],parts[2*j],bond)
+ j = bp0
+ if j >= 0:
+ model.add_bond(parts[2*i+1],parts[2*j+1],bond)
+ model.writePsf('test.psf')
+
+ model.bonds = []
+ for i,(r0,r_bp,three_prime0,bp0,stack0) in enumerate(zip(r,basepair_pos, three_prime, bp, stack)):
+ j = stack0
+ if j >= 0:
+ model.add_bond(parts[2*i],parts[2*j],bond)
+ model.writePsf('test.stack.psf')
+ ## _debug_write_bonds()
+
+ logger.info(f'mrdna_model_from_oxdna: num_bp, num_ss_nt, num_stacked: {np.sum(bp>=0)//2} {np.sum(bp<0)} {np.sum(stack >= 0)}')
+
+ if coordinate_file != idealized_coordinate_file:
+ conf_data = conf_data[::-1,:]
+
+ r = conf_data[:,:3] * 8.518
+ base_dir = conf_data[:,3:6]
+ basepair_pos = r + base_dir*10.0
+ normal_dir = -conf_data[:,6:9]
+ perp_dir = np.cross(base_dir, normal_dir)
+ orientation = np.array([np.array(o).T.dot(_yrot) for o in zip(perp_dir,-base_dir,-normal_dir)])
+
+ model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
+
+ """
+ model.DEBUG = True
+ model.generate_bead_model(1,1,False,True,one_bead_per_monomer=True)
+ for seg in model.segments:
+ for bead in seg.beads:
+ bead.position = bead.position + np.random.standard_normal(3)
+
+ simulate( model, output_name='test', directory='test4' )
+ """
+ return model
+
+if __name__ == "__main__":
+ mrdna_model_from_oxdna("0-from-collab/nanopore.oxdna","0-from-collab/nanopore.top")
+ # mrdna_model_from_oxdna("2-oxdna.manual/output/from_mrdna-oxdna-min.last.conf","0-from-collab/nanopore.top")
diff --git a/mrdna/readers/cadnano_segments.py b/mrdna/readers/cadnano_segments.py
index b39bd2e..47cf148 100644
--- a/mrdna/readers/cadnano_segments.py
+++ b/mrdna/readers/cadnano_segments.py
@@ -17,166 +17,7 @@ from ..model.dna_sequence import m13 as m13seq
## - helices that should be stacked across an empty region (crossovers from and end in the helix to another end in the helix)
## - circular constructs
-def combineRegionLists(loHi1,loHi2,intersect=False):
-
- """Combines two lists of (lo,hi) pairs specifying integer
- regions a single list of regions. """
-
- ## Validate input
- for l in (loHi1,loHi2):
- ## Assert each region in lists is sorted
- for pair in l:
- assert(len(pair) == 2)
- assert(pair[0] <= pair[1])
-
- if len(loHi1) == 0:
- if intersect:
- return []
- else:
- return loHi2
- if len(loHi2) == 0:
- if intersect:
- return []
- else:
- return loHi1
-
- ## Break input into lists of compact regions
- compactRegions1,compactRegions2 = [[],[]]
- for compactRegions,loHi in zip(
- [compactRegions1,compactRegions2],
- [loHi1,loHi2]):
- tmp = []
- lastHi = loHi[0][0]-1
- for lo,hi in loHi:
- if lo-1 != lastHi:
- compactRegions.append(tmp)
- tmp = []
- tmp.append((lo,hi))
- lastHi = hi
- if len(tmp) > 0:
- compactRegions.append(tmp)
-
- ## Build result
- result = []
- region = []
- i,j = [0,0]
- compactRegions1.append([[1e10]])
- compactRegions2.append([[1e10]])
- while i < len(compactRegions1)-1 or j < len(compactRegions2)-1:
- cr1 = compactRegions1[i]
- cr2 = compactRegions2[j]
-
- ## initialize region
- if len(region) == 0:
- if cr1[0][0] <= cr2[0][0]:
- region = cr1
- i += 1
- continue
- else:
- region = cr2
- j += 1
- continue
-
- if region[-1][-1] >= cr1[0][0]:
- region = combineCompactRegionLists(region, cr1, intersect=False)
- i+=1
- elif region[-1][-1] >= cr2[0][0]:
- region = combineCompactRegionLists(region, cr2, intersect=False)
- j+=1
- else:
- result.extend(region)
- region = []
-
- assert( len(region) > 0 )
- result.extend(region)
- result = sorted(result)
-
- # print("loHi1:",loHi1)
- # print("loHi2:",loHi2)
- # print(result,"\n")
-
- if intersect:
- lo = max( [loHi1[0][0], loHi2[0][0]] )
- hi = min( [loHi1[-1][1], loHi2[-1][1]] )
- result = [r for r in result if r[0] >= lo and r[1] <= hi]
-
- return result
-
-def combineCompactRegionLists(loHi1,loHi2,intersect=False):
-
- """Combines two lists of (lo,hi) pairs specifying regions within a
- compact integer set into a single list of regions.
-
- examples:
- loHi1 = [[0,4],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 4), (5, 7), (8, 9)]
-
- loHi1 = [[0,3],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
- """
-
- ## Validate input
- for l in (loHi1,loHi2):
- ## Assert each region in lists is sorted
- for pair in l:
- assert(len(pair) == 2)
- assert(pair[0] <= pair[1])
- ## Assert lists are compact
- for pair1,pair2 in zip(l[::2],l[1::2]):
- assert(pair1[1]+1 == pair2[0])
-
- if len(loHi1) == 0:
- if intersect:
- return []
- else:
- return loHi2
- if len(loHi2) == 0:
- if intersect:
- return []
- else:
- return loHi1
- ## Find the ends of the region
- lo = min( [loHi1[0][0], loHi2[0][0]] )
- hi = max( [loHi1[-1][1], loHi2[-1][1]] )
-
- ## Make a list of indices where each region will be split
- splitAfter = []
- for l,h in loHi2:
- if l != lo:
- splitAfter.append(l-1)
- if h != hi:
- splitAfter.append(h)
-
- for l,h in loHi1:
- if l != lo:
- splitAfter.append(l-1)
- if h != hi:
- splitAfter.append(h)
- splitAfter = sorted(list(set(splitAfter)))
-
- # print("splitAfter:",splitAfter)
-
- split=[]
- last = -2
- for s in splitAfter:
- split.append(s)
- last = s
-
- # print("split:",split)
- returnList = [(i+1,j) if i != j else (i,j) for i,j in zip([lo-1]+split,split+[hi])]
-
- if intersect:
- lo = max( [loHi1[0][0], loHi2[0][0]] )
- hi = min( [loHi1[-1][1], loHi2[-1][1]] )
- returnList = [r for r in returnList if r[0] >= lo and r[1] <= hi]
-
- # print("loHi1:",loHi1)
- # print("loHi2:",loHi2)
- # print(returnList,"\n")
- return returnList
class cadnano_part(SegmentModel):
def __init__(self, part,
@@ -700,6 +541,166 @@ def read_model(json_data, sequence=None, fill_sequence='T', **kwargs):
# pynvml.nvmlShutdown()
# gpus = [0,1,2]
# print(gpus)
+def combineRegionLists(loHi1,loHi2,intersect=False):
+
+ """Combines two lists of (lo,hi) pairs specifying integer
+ regions a single list of regions. """
+
+ ## Validate input
+ for l in (loHi1,loHi2):
+ ## Assert each region in lists is sorted
+ for pair in l:
+ assert(len(pair) == 2)
+ assert(pair[0] <= pair[1])
+
+ if len(loHi1) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi2
+ if len(loHi2) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi1
+
+ ## Break input into lists of compact regions
+ compactRegions1,compactRegions2 = [[],[]]
+ for compactRegions,loHi in zip(
+ [compactRegions1,compactRegions2],
+ [loHi1,loHi2]):
+ tmp = []
+ lastHi = loHi[0][0]-1
+ for lo,hi in loHi:
+ if lo-1 != lastHi:
+ compactRegions.append(tmp)
+ tmp = []
+ tmp.append((lo,hi))
+ lastHi = hi
+ if len(tmp) > 0:
+ compactRegions.append(tmp)
+
+ ## Build result
+ result = []
+ region = []
+ i,j = [0,0]
+ compactRegions1.append([[1e10]])
+ compactRegions2.append([[1e10]])
+ while i < len(compactRegions1)-1 or j < len(compactRegions2)-1:
+ cr1 = compactRegions1[i]
+ cr2 = compactRegions2[j]
+
+ ## initialize region
+ if len(region) == 0:
+ if cr1[0][0] <= cr2[0][0]:
+ region = cr1
+ i += 1
+ continue
+ else:
+ region = cr2
+ j += 1
+ continue
+
+ if region[-1][-1] >= cr1[0][0]:
+ region = combineCompactRegionLists(region, cr1, intersect=False)
+ i+=1
+ elif region[-1][-1] >= cr2[0][0]:
+ region = combineCompactRegionLists(region, cr2, intersect=False)
+ j+=1
+ else:
+ result.extend(region)
+ region = []
+
+ assert( len(region) > 0 )
+ result.extend(region)
+ result = sorted(result)
+
+ # print("loHi1:",loHi1)
+ # print("loHi2:",loHi2)
+ # print(result,"\n")
+
+ if intersect:
+ lo = max( [loHi1[0][0], loHi2[0][0]] )
+ hi = min( [loHi1[-1][1], loHi2[-1][1]] )
+ result = [r for r in result if r[0] >= lo and r[1] <= hi]
+
+ return result
+
+def combineCompactRegionLists(loHi1,loHi2,intersect=False):
+
+ """Combines two lists of (lo,hi) pairs specifying regions within a
+ compact integer set into a single list of regions.
+
+ examples:
+ loHi1 = [[0,4],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 4), (5, 7), (8, 9)]
+
+ loHi1 = [[0,3],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
+ """
+
+ ## Validate input
+ for l in (loHi1,loHi2):
+ ## Assert each region in lists is sorted
+ for pair in l:
+ assert(len(pair) == 2)
+ assert(pair[0] <= pair[1])
+ ## Assert lists are compact
+ for pair1,pair2 in zip(l[::2],l[1::2]):
+ assert(pair1[1]+1 == pair2[0])
+
+ if len(loHi1) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi2
+ if len(loHi2) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi1
+
+ ## Find the ends of the region
+ lo = min( [loHi1[0][0], loHi2[0][0]] )
+ hi = max( [loHi1[-1][1], loHi2[-1][1]] )
+
+ ## Make a list of indices where each region will be split
+ splitAfter = []
+ for l,h in loHi2:
+ if l != lo:
+ splitAfter.append(l-1)
+ if h != hi:
+ splitAfter.append(h)
+
+ for l,h in loHi1:
+ if l != lo:
+ splitAfter.append(l-1)
+ if h != hi:
+ splitAfter.append(h)
+ splitAfter = sorted(list(set(splitAfter)))
+
+ # print("splitAfter:",splitAfter)
+
+ split=[]
+ last = -2
+ for s in splitAfter:
+ split.append(s)
+ last = s
+
+ # print("split:",split)
+ returnList = [(i+1,j) if i != j else (i,j) for i,j in zip([lo-1]+split,split+[hi])]
+
+ if intersect:
+ lo = max( [loHi1[0][0], loHi2[0][0]] )
+ hi = min( [loHi1[-1][1], loHi2[-1][1]] )
+ returnList = [r for r in returnList if r[0] >= lo and r[1] <= hi]
+
+ # print("loHi1:",loHi1)
+ # print("loHi2:",loHi2)
+ # print(returnList,"\n")
+ return returnList
if __name__ == '__main__':
loHi1 = [[0,4],[5,7]]
diff --git a/mrdna/readers/segmentmodel_from_cadnano.py b/mrdna/readers/segmentmodel_from_cadnano.py
index b39bd2e..32d4471 100644
--- a/mrdna/readers/segmentmodel_from_cadnano.py
+++ b/mrdna/readers/segmentmodel_from_cadnano.py
@@ -17,166 +17,6 @@ from ..model.dna_sequence import m13 as m13seq
## - helices that should be stacked across an empty region (crossovers from and end in the helix to another end in the helix)
## - circular constructs
-def combineRegionLists(loHi1,loHi2,intersect=False):
-
- """Combines two lists of (lo,hi) pairs specifying integer
- regions a single list of regions. """
-
- ## Validate input
- for l in (loHi1,loHi2):
- ## Assert each region in lists is sorted
- for pair in l:
- assert(len(pair) == 2)
- assert(pair[0] <= pair[1])
-
- if len(loHi1) == 0:
- if intersect:
- return []
- else:
- return loHi2
- if len(loHi2) == 0:
- if intersect:
- return []
- else:
- return loHi1
-
- ## Break input into lists of compact regions
- compactRegions1,compactRegions2 = [[],[]]
- for compactRegions,loHi in zip(
- [compactRegions1,compactRegions2],
- [loHi1,loHi2]):
- tmp = []
- lastHi = loHi[0][0]-1
- for lo,hi in loHi:
- if lo-1 != lastHi:
- compactRegions.append(tmp)
- tmp = []
- tmp.append((lo,hi))
- lastHi = hi
- if len(tmp) > 0:
- compactRegions.append(tmp)
-
- ## Build result
- result = []
- region = []
- i,j = [0,0]
- compactRegions1.append([[1e10]])
- compactRegions2.append([[1e10]])
- while i < len(compactRegions1)-1 or j < len(compactRegions2)-1:
- cr1 = compactRegions1[i]
- cr2 = compactRegions2[j]
-
- ## initialize region
- if len(region) == 0:
- if cr1[0][0] <= cr2[0][0]:
- region = cr1
- i += 1
- continue
- else:
- region = cr2
- j += 1
- continue
-
- if region[-1][-1] >= cr1[0][0]:
- region = combineCompactRegionLists(region, cr1, intersect=False)
- i+=1
- elif region[-1][-1] >= cr2[0][0]:
- region = combineCompactRegionLists(region, cr2, intersect=False)
- j+=1
- else:
- result.extend(region)
- region = []
-
- assert( len(region) > 0 )
- result.extend(region)
- result = sorted(result)
-
- # print("loHi1:",loHi1)
- # print("loHi2:",loHi2)
- # print(result,"\n")
-
- if intersect:
- lo = max( [loHi1[0][0], loHi2[0][0]] )
- hi = min( [loHi1[-1][1], loHi2[-1][1]] )
- result = [r for r in result if r[0] >= lo and r[1] <= hi]
-
- return result
-
-def combineCompactRegionLists(loHi1,loHi2,intersect=False):
-
- """Combines two lists of (lo,hi) pairs specifying regions within a
- compact integer set into a single list of regions.
-
- examples:
- loHi1 = [[0,4],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 4), (5, 7), (8, 9)]
-
- loHi1 = [[0,3],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
- """
-
- ## Validate input
- for l in (loHi1,loHi2):
- ## Assert each region in lists is sorted
- for pair in l:
- assert(len(pair) == 2)
- assert(pair[0] <= pair[1])
- ## Assert lists are compact
- for pair1,pair2 in zip(l[::2],l[1::2]):
- assert(pair1[1]+1 == pair2[0])
-
- if len(loHi1) == 0:
- if intersect:
- return []
- else:
- return loHi2
- if len(loHi2) == 0:
- if intersect:
- return []
- else:
- return loHi1
-
- ## Find the ends of the region
- lo = min( [loHi1[0][0], loHi2[0][0]] )
- hi = max( [loHi1[-1][1], loHi2[-1][1]] )
-
- ## Make a list of indices where each region will be split
- splitAfter = []
- for l,h in loHi2:
- if l != lo:
- splitAfter.append(l-1)
- if h != hi:
- splitAfter.append(h)
-
- for l,h in loHi1:
- if l != lo:
- splitAfter.append(l-1)
- if h != hi:
- splitAfter.append(h)
- splitAfter = sorted(list(set(splitAfter)))
-
- # print("splitAfter:",splitAfter)
-
- split=[]
- last = -2
- for s in splitAfter:
- split.append(s)
- last = s
-
- # print("split:",split)
- returnList = [(i+1,j) if i != j else (i,j) for i,j in zip([lo-1]+split,split+[hi])]
-
- if intersect:
- lo = max( [loHi1[0][0], loHi2[0][0]] )
- hi = min( [loHi1[-1][1], loHi2[-1][1]] )
- returnList = [r for r in returnList if r[0] >= lo and r[1] <= hi]
-
- # print("loHi1:",loHi1)
- # print("loHi2:",loHi2)
- # print(returnList,"\n")
- return returnList
class cadnano_part(SegmentModel):
def __init__(self, part,
@@ -702,23 +542,7 @@ def read_model(json_data, sequence=None, fill_sequence='T', **kwargs):
# print(gpus)
if __name__ == '__main__':
- loHi1 = [[0,4],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 4), (5, 7), (8, 9)]
- print(loHi1)
- print(loHi2)
- print(combineRegionLists(loHi1,loHi2))
- print(combineCompactRegionLists(loHi1,loHi2))
-
- loHi1 = [[0,3],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
- print(loHi1)
- print(loHi2)
- print(combineRegionLists(loHi1,loHi2))
- print(combineCompactRegionLists(loHi1,loHi2))
-
- combineRegionLists
+
# for f in glob('json/*'):
# print("Working on {}".format(f))
diff --git a/mrdna/readers/segmentmodel_from_oxdna_pinyi.py b/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
index d7ed041..d2fd60e 100644
--- a/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
+++ b/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
@@ -2,6 +2,7 @@ from mrdna import logger, devlogger
from .segmentmodel_from_lists import model_from_basepair_stack_3prime
from ..arbdmodel.coords import rotationAboutAxis
+from oxlibs import *
import numpy as np
from scipy.spatial import distance_matrix
@@ -10,11 +11,8 @@ _seq_to_int_dict = {k:str(v) for k,v in _seq_to_int_dict.items()}
_yrot = rotationAboutAxis(axis=(0,1,0), angle=180).dot(rotationAboutAxis(axis=(0,0,1),angle=-40))
-def mrdna_model_from_oxdna(coordinate_file, topology_file, idealized_coordinate_file=None, **model_parameters):
+def mrdna_model_from_oxdna(coordinate_file, topology_file, ,idealized_coordinate_file=None,virt2nuc=None, **model_parameters):
""" Construct an mrdna model from oxDNA coordinate and topology files """
- if idealized_coordinate_file is None:
- idealized_coordinate_file = coordinate_file
-
top_data = np.loadtxt(topology_file, skiprows=1,
unpack=True,
dtype=np.dtype('i4,U1,i4,i4')
@@ -141,6 +139,16 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file, idealized_coordinate_
model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
+ def find_cadnano_strands(virt2nuc):
+ import pickle
+ if virt2nuc is not None:
+ df = pickle.load(virt2nuc)
+ vh_vb2nuc_rev, vhelix_pattern=df #vhelix_pattern is the position on yzplane
+
+
+ else:
+ print("virt2nuc not found")
+
"""
model.DEBUG = True
model.generate_bead_model(1,1,False,True,one_bead_per_monomer=True)
--
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