segmentmodel.py 138 KB
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import pdb
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from pathlib import Path
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import numpy as np
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import random
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from .model.arbdmodel import PointParticle, ParticleType, Group, ArbdModel
from .coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
from .model.nonbonded import *
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from copy import copy, deepcopy
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from .model.nbPot import nbDnaScheme
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from scipy.special import erf
import scipy.optimize as opt
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from scipy import interpolate
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from .model.CanonicalNucleotideAtoms import canonicalNtFwd, canonicalNtRev, seqComplement
from .model.CanonicalNucleotideAtoms import enmTemplateHC, enmTemplateSQ, enmCorrectionsHC
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from .model.spring_from_lp import k_angle as angle_spring_from_lp

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import csv


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# import pdb
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"""
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TODO:
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 + fix handling of crossovers for atomic representation
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 + map to atomic representation
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    + add nicks
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    + transform ssDNA nucleotides 
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    - shrink ssDNA
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    + shrink dsDNA backbone
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    + make orientation continuous
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    + sequence
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    + handle circular dna
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 + ensure crossover bead potentials aren't applied twice 
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 + remove performance bottlenecks
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 - test for large systems
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 + assign sequence
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 + ENM
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 - rework Location class 
 - remove recursive calls
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 - document
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 - develop unit test suite
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 - 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
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"""
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class CircularDnaError(Exception):
    pass
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class ParticleNotConnectedError(Exception):
    pass

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class Location():
    """ Site for connection within an object """
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    def __init__(self, container, address, type_, on_fwd_strand = True):
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        ## TODO: remove cyclic references(?)
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        self.container = container
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        self.address = address  # represents position along contour length in segment
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        # assert( type_ in ("end3","end5") ) # TODO remove or make conditional
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        self.on_fwd_strand = on_fwd_strand
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        self.type_ = type_
        self.particle = None
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        self.connection = None
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        self.is_3prime_side_of_connection = None
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        self.prev_in_strand = None
        self.next_in_strand = None
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        self.combine = None     # some locations might be combined in bead model 
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    def get_connected_location(self):
        if self.connection is None:
            return None
        else:
            return self.connection.other(self)

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    def set_connection(self, connection, is_3prime_side_of_connection):
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        self.connection = connection # TODO weakref? 
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        self.is_3prime_side_of_connection = is_3prime_side_of_connection
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    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:
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                pos = self.container.num_nt-1
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            else:
                raise
        return pos

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    def __repr__(self):
        if self.on_fwd_strand:
            on_fwd = "on_fwd_strand"
        else:
            on_fwd = "on_rev_strand"
        return "<Location {}.{}[{:.2f},{:d}]>".format( self.container.name, self.type_, self.address, self.on_fwd_strand)
        
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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_
        
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    def other(self, location):
        if location is self.A:
            return self.B
        elif location is self.B:
            return self.A
        else:
            raise Exception("OutOfBoundsError")
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    def delete(self):
        self.A.container.connections.remove(self)
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        if self.B.container is not self.A.container:
            self.B.container.connections.remove(self)
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        self.A.connection = None
        self.B.connection = None

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    def __repr__(self):
        return "<Connection {}--{}--{}]>".format( self.A, self.type_, self.B )
        

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# class ConnectableElement(Transformable):
class ConnectableElement():
    """ Abstract base class """
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    def __init__(self, connection_locations=None, connections=None):
        if connection_locations is None: connection_locations = []
        if connections is None: connections = []

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        ## TODO decide on names
        self.locations = self.connection_locations = connection_locations
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        self.connections = connections

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    def get_locations(self, type_=None, exclude=()):
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        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] ) )
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        return locs

    def get_location_at(self, address, on_fwd_strand=True, new_type="crossover"):
        loc = None
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        if (self.num_nt == 1):
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            # 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
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            # assert( loc is not None )
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        else:
            for l in self.locations:
                if l.address == address and l.on_fwd_strand == on_fwd_strand:
                    assert(loc is None)
                    loc = l
        if loc is None:
            loc = Location( self, address=address, type_=new_type, on_fwd_strand=on_fwd_strand )
        return loc
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    def get_connections_and_locations(self, connection_type=None, exclude=()):
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        """ Returns a list with each entry of the form:
            connection, location_in_self, location_in_other """
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        type_ = connection_type
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        ret = []
        for c in self.connections:
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            if (type_ is None or c.type_ == type_) and c.type_ not in exclude:
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                if   c.A.container is self:
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                    ret.append( [c, c.A, c.B] )
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                elif c.B.container is self:
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                    ret.append( [c, c.B, c.A] )
                else:
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                    import pdb
                    pdb.set_trace()
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                    raise Exception("Object contains connection that fails to refer to object")
        return ret

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    def _connect(self, other, connection, in_3prime_direction=None):
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        ## TODO fix circular references        
        A,B = [connection.A, connection.B]
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        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
            
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        A.connection = B.connection = connection
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        self.connections.append(connection)
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        if other is not self:
            other.connections.append(connection)
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        else:
            raise NotImplementedError("Segments cannot yet be connected to themselves; if you are attempting to make a circular object, try breaking the object into multiple segments")
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        l = A.container.locations
        if A not in l: l.append(A)
        l = B.container.locations
        if B not in l: l.append(B)
        

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    # def _find_connections(self, loc):
    #     return [c for c in self.connections if c.A == loc or c.B == loc]
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class SegmentParticle(PointParticle):
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    def __init__(self, type_, position, name="A", **kwargs):
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        self.name = name
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        self.contour_position = None
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        PointParticle.__init__(self, type_, position, name=name, **kwargs)
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        self.intrahelical_neighbors = []
        self.other_neighbors = []
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        self.locations = []
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    def get_intrahelical_above(self, all_types=True):
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        """ Returns bead directly above self """
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        # assert( len(self.intrahelical_neighbors) <= 2 )
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        for b in self.intrahelical_neighbors:
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            if b.get_contour_position(self.parent, self.contour_position) > self.contour_position:
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                if all_types or isinstance(b,type(self)):
                    return b
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    def get_intrahelical_below(self, all_types=True):
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        """ Returns bead directly below self """
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        # assert( len(self.intrahelical_neighbors) <= 2 )
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        for b in self.intrahelical_neighbors:
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            if b.get_contour_position(self.parent, self.contour_position) < self.contour_position:
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                if all_types or isinstance(b,type(self)):
                    return b
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    def _neighbor_should_be_added(self,b):
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        if type(self.parent) != type(b.parent):
            return True

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        c1 = self.contour_position
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        c2 = b.get_contour_position(self.parent,c1)
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        if c2 < c1:
            b0 = self.get_intrahelical_below()
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        else:
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            b0 = self.get_intrahelical_above()

        if b0 is not None:            
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            c0 = b0.get_contour_position(self.parent,c1)
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            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:
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            # assert(len(b.intrahelical_neighbors) <= 1)
            # assert(len(self.intrahelical_neighbors) <= 1)
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            self.intrahelical_neighbors.append(b)
            b.intrahelical_neighbors.append(self)
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    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):
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        """ Returns the "address" of the nucleotide relative to seg in
        nucleotides, taking the shortest (intrahelical) contour length route to seg
        """
        if seg == self.parent:
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            pos = self.contour_position
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        else:
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            pos = self.get_contour_position(seg,near_address)
        return seg.contour_to_nt_pos(pos)
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    def get_contour_position(self,seg, address = None):
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        """ 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
        """

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        if seg == self.parent:
            return self.contour_position
        else:
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            cutoff = 30*3
            target_seg = seg

            ## depth-first search
            ## TODO cache distances to nearby locations?
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            def descend_search_tree(seg, contour_in_seg, distance=0, visited_segs=None):
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                nonlocal cutoff
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                if visited_segs is None: visited_segs = []
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                if seg == target_seg:
                    # pdb.set_trace()
                    ## Found a segment in our target
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                    sign = 1 if contour_in_seg == 1 else -1
                    if sign == -1: assert( contour_in_seg == 0 )
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                    if distance < cutoff: # TODO: check if this does anything
                        cutoff = distance
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                    return [[distance, contour_in_seg+sign*seg.nt_pos_to_contour(distance)]], [(seg, contour_in_seg, distance)]
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                if distance > cutoff:
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                    return None,None
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                ret_list = []
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                hist_list = []
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                ## Find intrahelical locations in seg that we might pass through
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                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:
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                    if B.container in visited_segs: continue
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                    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,
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                                                   distance+dx, visited_segs + [seg] )
                    if results is not None:
                        ret_list.extend( results )
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                        hist_list.extend( history )
                return ret_list,hist_list
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            results,history = descend_search_tree(self.parent, self.contour_position)
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            if results is None or len(results) == 0:
                raise Exception("Could not find location in segment") # TODO better error
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            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]
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            # nt_pos = self.get_nt_position(seg)
            # return seg.nt_pos_to_contour(nt_pos)

    def update_position(self, contour_position):
        self.contour_position = contour_position
        self.position = self.parent.contour_to_position(contour_position)
        if 'orientation_bead' in self.__dict__:
            o = self.orientation_bead
            o.contour_position = contour_position
            orientation = self.parent.contour_to_orientation(contour_position)
            if orientation is None:
                print("WARNING: local_twist is True, but orientation is None; using identity")
                orientation = np.eye(3)
            o.position = self.position + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
            
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    def __repr__(self):
        return "<SegmentParticle {} on {}[{:.2f}]>".format( self.name, self.parent, self.contour_position)

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## TODO break this class into smaller, better encapsulated pieces
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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,                 
                              )
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    orientation_particle = ParticleType("O",
                                        diffusivity = 100,
                                        mass = 300,
                                        radius = 1,
                                    )
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    # orientation_bond = HarmonicBond(10,2)
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    orientation_bond = HarmonicBond(30,1.5, rRange = (0,500) )
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    ssDNA_particle = ParticleType("S",
                                  diffusivity = 43.5,
                                  mass = 150,
                                  radius = 3,                 
                              )

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    def __init__(self, name, num_nt, 
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                 start_position = None,
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                 end_position = None, 
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                 segment_model = None,
                 **kwargs):
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        if start_position is None: start_position = np.array((0,0,0))

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        Group.__init__(self, name, children=[], **kwargs)
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        ConnectableElement.__init__(self, connection_locations=[], connections=[])
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        if 'segname' not in kwargs:
            self.segname = name
        # self.resname = name
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        self.start_orientation = None
        self.twist_per_nt = 0

        self.beads = [c for c in self.children] # self.beads will not contain orientation beads

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        self._bead_model_generation = 0    # TODO: remove?
        self.segment_model = segment_model # TODO: remove?

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        self.strand_pieces = dict()
        for d in ('fwd','rev'):
            self.strand_pieces[d] = []

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        self.num_nt = int(num_nt)
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        if end_position is None:
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            end_position = np.array((0,0,self.distance_per_nt*num_nt)) + start_position
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        self.start_position = start_position
        self.end_position = end_position

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        ## Used to assign cadnano names to beads
        self._generate_bead_callbacks = []
        self._generate_nucleotide_callbacks = []

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        ## Set up interpolation for positions
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        self._set_splines_from_ends()

        self.sequence = None

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    def __repr__(self):
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        return "<{} {}[{:d}]>".format( str(type(self)).split('.')[-1], self.name, self.num_nt )
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    def set_splines(self, contours, coords):
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        tck, u = interpolate.splprep( coords.T, u=contours, s=0, k=1)
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        self.position_spline_params = (tck,u)
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    def set_orientation_splines(self, contours, quaternions):
        tck, u = interpolate.splprep( quaternions.T, u=contours, s=0, k=1)
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        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)

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    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_

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    def _get_location_positions(self):
        return [self.contour_to_nt_pos(l.address) for l in self.locations]

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    def insert_dna(self, at_nt: int, num_nt: int, seq=tuple()):
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        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]

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        ## TODO: handle sequence

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        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):
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        """ Removes nucleotides between first_nt and last_nt, inclusive """
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        assert(np.isclose(np.around(first_nt),first_nt))
        assert(np.isclose(np.around(last_nt),last_nt))
        tmp = min((first_nt,last_nt))
        last_nt = max((first_nt,last_nt))
        fist_nt = tmp

        if first_nt < 0 or first_nt > self.num_nt-2:
            raise ValueError("Attempted to remove DNA from {} starting at an invalid location {}".format(self, first_nt))
        if last_nt < 1 or last_nt > self.num_nt-1:
            raise ValueError("Attempted to remove DNA from {} ending at an invalid location {}".format(self, last_nt))
        if first_nt == last_nt:
            return

        first_nt = np.around(first_nt)
        last_nt = np.around(last_nt)

        nt_positions = self._get_location_positions()

        bad_locations = list(filter(lambda p: p >= first_nt and p <= last_nt, nt_positions))
        if len(bad_locations) > 0:
            raise Exception("Attempted to remove DNA containing locations {} from {} between {} and {}".format(bad_locations,self,first_nt,last_nt))

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        removed_nt = last_nt-first_nt+1
        new_nt_positions = [p if p <= last_nt else p-removed_nt for p in nt_positions]
        num_nt = self.num_nt-removed_nt

        if self.sequence is not None and len(self.sequence) == self.num_nt:
            self.sequence = [s for s,i in zip(self.sequence,range(self.num_nt)) 
                                if i < first_nt or i > last_nt]
            assert( len(self.sequence) == num_nt )
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        self.num_nt = num_nt
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        for l,p in zip(self.locations, new_nt_positions):
            l.address = self.nt_pos_to_contour(p)

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    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

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    def translate(self, translation_vector, position_filter=None, contour_filter=None):
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        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)
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        if len(ids) == 0: return
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        ## Translate
        r[ids,:] = r[ids,:] + dr[np.newaxis,:]
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        self.set_splines(u,r)
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    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)
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        if len(ids) == 0: return
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        if about is None:
            ## TODO: do this more efficiently
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            r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in ids])
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        else:
            dr = np.array(about)
            ## TODO: do this more efficiently
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            r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in ids])
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        self.set_splines(u,r)
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        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
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            orientations = [self.contour_to_orientation(v) for v in u]
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            for i in ids:
                orientations[i,:] = rotation_matrix.dot(orientations[i])
            quats = [quaternion_from_matrix(o) for o in orientations]
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            self.set_orientation_splines(u, quats)
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    def _set_splines_from_ends(self, resolution=4):
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        self.quaternion_spline_params = None
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        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)
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    def clear_all(self):
        Group.clear_all(self)  # TODO: use super?
        self.beads = []
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        # for c,loc,other in self.get_connections_and_locations():
        #     loc.particle = None
        #     other.particle = None
        for l in self.locations:
            l.particle = None
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    def contour_to_nt_pos(self, contour_pos, round_nt=False):
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        nt = contour_pos*(self.num_nt) - 0.5
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        if round_nt:
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            assert( np.isclose(np.around(nt),nt) )
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            nt = np.around(nt)
        return nt

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    def nt_pos_to_contour(self,nt_pos):
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        return (nt_pos+0.5)/(self.num_nt)
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    def contour_to_position(self,s):
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        p = interpolate.splev( s, self.position_spline_params[0] )
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        if len(p) > 1: p = np.array(p).T
        return p

    def contour_to_tangent(self,s):
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        t = interpolate.splev( s, self.position_spline_params[0], der=1 )
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        t = (t / np.linalg.norm(t,axis=0))
        return t.T
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    def contour_to_orientation(self,s):
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        assert( isinstance(s,float) or isinstance(s,int) or len(s) == 1 )   # TODO make vectorized version
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        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)
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            zAxis = np.array((0,0,1))
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            if rotAxisL > 0.001:
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                theta = np.arcsin(rotAxisL) * 180/np.pi
                if axis.dot(zAxis) < 0: theta = 180-theta
                orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta, normalizeAxis=False ).T
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            else:
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                orientation0 = np.eye(3) if axis.dot(zAxis) > 0 else \
                               rotationAboutAxis( np.array((1,0,0)), 180, normalizeAxis=False )
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            if self.start_orientation is not None:
                orientation0 = orientation0.dot(self.start_orientation)

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            orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
            orientation = orientation.dot(orientation0)
        else:
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            q = interpolate.splev( s, self.quaternion_spline_params[0] )
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            if len(q) > 1: q = np.array(q).T # TODO: is this needed?
            orientation = quaternion_to_matrix(q)
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        return orientation
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    def get_contour_sorted_connections_and_locations(self,type_):
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        sort_fn = lambda c: c[1].address
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        cl = self.get_connections_and_locations(type_)
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        return sorted(cl, key=sort_fn)
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    def randomize_unset_sequence(self):
        bases = list(seqComplement.keys())
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        # bases = ['T']        ## FOR DEBUG
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        if self.sequence is None:
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            self.sequence = [random.choice(bases) for i in range(self.num_nt)]
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        else:
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            assert(len(self.sequence) == self.num_nt) # TODO move
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            for i in range(len(self.sequence)):
                if self.sequence[i] is None:
                    self.sequence[i] = random.choice(bases)
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    def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead ):
        raise NotImplementedError

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    def _generate_one_bead(self, contour_position, nts):
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        raise NotImplementedError

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    def _generate_atomic_nucleotide(self, contour_position, is_fwd, seq, scale, strand_segment):
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        """ 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)
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        orientation = self.contour_to_orientation(contour_position)
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        """ 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                            
        """
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        key = seq
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        nt_dict = canonicalNtFwd if is_fwd else canonicalNtRev

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        atoms = nt_dict[ key ].generate() # TODO: clone?
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        atoms.orientation = orientation.dot(atoms.orientation)
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        if isinstance(self, SingleStrandedSegment):
            if scale is not None and scale != 1:
                for a in atoms:
                    a.position = scale*a.position
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            atoms.position = pos - atoms.atoms_by_name["C1'"].collapsedPosition()
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        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
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                    else:
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                        a.fixed = 1
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            atoms.position = pos
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        atoms.contour_position = contour_position
        strand_segment.add(atoms)

        for callback in self._generate_nucleotide_callbacks:
            callback(atoms)
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        return atoms
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    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


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    def add_location(self, nt, type_, on_fwd_strand=True):
        ## Create location if needed, add to segment
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        c = self.nt_pos_to_contour(nt)
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        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?
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    def add_nick(self, nt, on_fwd_strand=True):
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        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)

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    def add_5prime(self, nt, on_fwd_strand=True):
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        if isinstance(self,SingleStrandedSegment):
            on_fwd_strand = True
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        self.add_location(nt,"5prime",on_fwd_strand)
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    def add_3prime(self, nt, on_fwd_strand=True):
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        if isinstance(self,SingleStrandedSegment):
            on_fwd_strand = True
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        self.add_location(nt,"3prime",on_fwd_strand)
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    ## 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") )
        assert( end1.type_ != end2.type_ )

        ## Remove other connections involving these points
        if end1.connection is not None:
            if debug: print("WARNING: reconnecting {}".format(end1))
            end1.connection.delete()
        if end2.connection is not None:
            if debug: print("WARNING: reconnecting {}".format(end2))
            end2.connection.delete()

        ## Create and add connection
        if end2.type_ == "end5":
            end1.container._connect( end2.container, Connection( end1, end2, type_=type_ ), in_3prime_direction=True )
        else:
            end2.container._connect( end1.container, Connection( end2, end1, type_=type_ ), in_3prime_direction=True )

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    def get_3prime_locations(self):
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        return sorted(self.get_locations("3prime"),key=lambda x: x.address)
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    def get_5prime_locations(self):
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        ## TODO? ensure that data is consistent before _build_model calls
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        return sorted(self.get_locations("5prime"),key=lambda x: x.address)
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    def iterate_connections_and_locations(self, reverse=False):
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        ## connections to other segments
        cl = self.get_contour_sorted_connections_and_locations()
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        if reverse:
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            cl = cl[::-1]
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        for c in cl:
            yield c
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    ## 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):
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                if value >= l and value <= h:
                    raise Exception("Strand piece already exists! DNA may be circular.")
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        ## 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)

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    ## TODO rename
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    def get_strand_segment(self, nt_pos, is_fwd, move_at_least=0.5):
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        """ Walks through locations, checking for crossovers """
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        # if self.name in ("6-1","1-1"):
        #     import pdb
        #     pdb.set_trace()
        move_at_least = 0
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        ## Iterate through locations
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        # locations = sorted(self.locations, key=lambda l:(l.address,not l.on_fwd_strand), reverse=(not is_fwd))
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        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))
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        # print(locations)

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        for l in locations:
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            # TODOTODO probably okay
            if l.address == 0:
                pos = 0.0
            elif l.address == 1:
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                pos = self.num_nt-1
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            else:
                pos = self.contour_to_nt_pos(l.address, round_nt=True)
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            ## DEBUG

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            ## Skip locations encountered before our strand
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            # 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
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            ## Stop if we found the 3prime end
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            if l.on_fwd_strand == is_fwd and l.type_ == "3prime" and l.connection is None:
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                # print("  found end at",l)
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                return pos, None, None, None, None
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            ## 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:
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                # print("  passing through",l)
                # print("from {}, connection {} to {}".format(nt_pos,l,B))
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                Bpos = B.get_nt_pos()
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                return pos, B.container, Bpos, B.on_fwd_strand, 0.5
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            ## Stop at other strand crossovers so basepairs line up
            elif c.type_ == "crossover":
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                if nt_pos == pos: continue
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                # print("  pausing at",l)
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                return pos, l.container, pos+(2*is_fwd-1), is_fwd, 0
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        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

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    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
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        # TODO: include beads in connections?
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        i = np.argmin((cs - contour_position)**2)

        return self.beads[i]
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    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 ))

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    def get_all_consecutive_beads(self, number):
        assert(number >= 1)
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        ## Assume that consecutive beads in self.beads are bonded
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        ret = []
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        for i in range(len(self.beads)-number+1):
            tmp = [self.beads[i+j] for j in range(0,number)]
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            ret.append( tmp )
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        return ret   
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    def _add_bead(self,b):
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        # assert(b.parent is None)
        if b.parent is not None:
            b.parent.children.remove(b)
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        self.add(b)
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        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)
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            self.add(o)
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            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 = []
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        if True:
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            ## TODO: remove this if duplicates are never found 
            # print("Searching for duplicate particles...")
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            ## Remove duplicates, preserving order
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            tmp = []
            for c in new_children:
                if c not in tmp:
                    tmp.append(c)
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                else:
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                    print("  DUPLICATE PARTICLE FOUND!")
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            new_children = tmp

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        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)
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        # 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)
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        assert(len(old_children) == len(self.children))
        assert(len(old_beads) == len(self.beads))
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    def _generate_beads(self, bead_model, max_basepairs_per_bead, max_nucleotides_per_bead):
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        """ Generate beads (positions, types, etc) and bonds, angles, dihedrals, exclusions """
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        ## TODO: decide whether to remove bead_model argument
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        ##       (currently unused)
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        ## First find points between-which beads must be generated
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        # 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]
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        # if self.name == "S001":
        #     pdb.set_trace()
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        # 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] )