beadModel.py 48.5 KB
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# -*- coding: utf-8 -*-
from datetime import datetime
from cadnano.cnenum import PointType
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from math import pi,sqrt,exp,floor
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import numpy as np
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from scipy.special import erf
import scipy.optimize as opt
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import os, sys, subprocess
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import nbPot
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from coords import minimizeRmsd, quaternionToMatrix3, rotationAboutAxis


class HarmonicPotential():
    def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, prefix="potentials/"):
        self.k = k
        self.r0 = r0
        self.maxForce = maxForce
        self.rRange = rRange
        self.prefix = prefix
        self.periodic = False
        self.type = "None"
        self._kscale = None
        self._init_hook()

    def filename(self):
        # raise NotImplementedError("Not implemented")
        return "%s%s-%.3f-$.3f.dat" % (self.prefix, self.type,
                                       self.k*self._kscale, self.r0)

    def write_file(self):
        r = np.arange( self.rRange[0], 
                       self.rRange[1]+self.resolution, 
                       self.resolution )
        dr = r-self.r0

        if self.periodic == True:
            rSpan = self.rRange[1]-self.rRange[0]
            assert(rSpan > 0)
            dr = np.mod( dr+0.5*rSpan, rSpan) - 0.5*rSpan 

        u = 0.5*self.k*dr**2

        if self.maxForce is not None:
            assert(self.maxForce > 0)
            f = np.diff(u)/np.diff(r)
            f[f>maxForce] = maxForce
            f[f<-maxForce] = -maxForce
            u[0] = 0
            u[1:] = np.cumsum(f*np.diff(r))
        np.savetxt( self.filename(), np.array([r, u]).T, fmt="%f" )

    def __hash__(self):
        assert(self.type != "None")
        return hash((self.type, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.prefix, self.periodic))

    def __eq__(self, other):
        for a in ("type", "k", "r0", "rRange", "resolution", "maxForce", "prefix", "periodic"):
            if self.__dict__[a] != other.__dict__[a]:
                return False
        return True

class NonBonded(HarmonicPotential):
    def _init_hook(self):
        self.type = "nonbonded"
        self._kscale = 1.0

class Bond(HarmonicPotential):
    def _init_hook(self):
        self.type = "bond"
        self._kscale = 1.0

class Angle(HarmonicPotential):
    def _init_hook(self):
        self.type = "angle"
        self._kscale = (180.0/pi)**2

class Dihedral(HarmonicPotential):
    def _init_hook(self):
        self.periodic = True
        self.type = "dihedral"
        self._kscale = (180.0/pi)**2
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class Node():
    def __init__(self, helix, pos, type="dsDNA"):
        self.helix    = helix
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        self.position = np.array(pos)
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        self.initialPosition = np.array(pos)
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        self.type     = type
        self.nodeAbove = None
        self.nodeBelow = None
        self.xovers = []
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        self.ssXovers = []
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        self.idx = helix.model.numParticles
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        helix.model.numParticles += 1
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    def addNodeAbove(self, node, separation):
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        assert(self.nodeAbove is None)
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        self.nodeAbove = node
        self.nodeAboveSep = separation # bp
    def addNodeBelow(self, node, separation):
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        assert(self.nodeBelow is None)
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        self.nodeBelow = node
        self.nodeBelowSep = separation # bp

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    def addXover(self, node, fwds, double=False):
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        ## TODO: what is meant by polarity?
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        self.xovers.append( (node,fwds,double) )
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    def addSsXover(self, node, fwds):
        self.ssXovers.append( (node,fwds) )
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    def getNodesAbove(self,numNodes,inclusive=False):
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        assert( type(numNodes) is int and numNodes > 0 )

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        nodeList,sepList = [[],[]]
        n = self
        if inclusive:
            nodeList.append(n)
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        for i in range(numNodes):
            if n.nodeAbove is None: break
            n = n.nodeAbove
            nodeList.append(n)
            sepList.append(n.nodeBelowSep)
            
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        return nodeList,sepList

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    def getNodesBelow(self,numNodes,inclusive=False):
        assert( type(numNodes) is int and numNodes > 0 )

        nodeList,sepList = [[],[]]
        n = self
        if inclusive:
            nodeList.append(n)

        for i in range(numNodes):
            if n.nodeBelow is None: break
            n = n.nodeBelow
            nodeList.append(n)
            sepList.append(n.nodeBelowSep)
            
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        return nodeList,sepList
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class helix():
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    def __init__(self, model, part, hid):
        self.model = model
        self.props = part.getModelProperties().copy() # TODO: maybe move this out of here
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        self.nodes = dict()
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        self.hid = hid
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        if self.props.get('point_type') == PointType.ARBITRARY:
            # TODO add code to encode Parts with ARBITRARY point configurations
            raise NotImplementedError("Not implemented")
        else:
            vh_props, origins = part.helixPropertiesAndOrigins()
            for x in vh_props:
                self.props[x] = vh_props[x][hid]

            self.origin = origins[hid]
            x,y = self.origin
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            self.zIdxToPos = lambda idx: (x*10,y*10,-3.4*idx)
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    def addNode(self, zIdx, strandOccupancies):
        ## Determine what kind of node we are making
        i = int(round(zIdx))
        if i in strandOccupancies[0] and i in strandOccupancies[1]:
            type = "dsDNA"
        elif i in strandOccupancies[0] or i in strandOccupancies[1]:
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            # type = "dsDNA"
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            type = "ssDNA"
        else:
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            raise Exception( "Attempt to add a node at %d where there is no DNA!\n Strand at indeces: %s" % (i,strandOccupancies) )
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        ## Add the node
        n = Node(self, self.zIdxToPos(zIdx), type)
        if zIdx in self.nodes:
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            raise Exception("Attempted to add a node in the same location (%d:%.1f) twice!" % (self.hid,zIdx))
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        self.nodes[zIdx] = n
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        ## Update ordered list of nodes 
        if self.model.particles is not None:
            model.buildOrderedParticlesList()

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        return n
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    def getOrigin(self):
        return self.origin

    def __iter__(self):
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        for x in sorted(self.nodes.items(), key=lambda x: x[0]):
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            yield x
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class beadModel():
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    def __init__(self, part, twistPersistenceLength=75.0, maxBpsPerDNode=4, maxNtsPerSNode=2):
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        self.numParticles = 0
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        self.helices = dict()
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        self.particles = None
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        self.particleTypeCounts = None
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        # self._nbParams = set()
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        self._bondParams = set()
        self._angleParams = set()
        self._dihedralParams = set()

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        self._nbParamFiles = []
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        self._bondParamFiles = set()
        self._angleParamFiles = set()
        self._dihedralParamFiles = set()
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        self.twistPersistenceLength = twistPersistenceLength

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        self._buildModel(part, maxBpsPerDNode, maxNtsPerSNode)
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        ## Post process the model
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        self.buildOrderedParticlesList()
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        self._setTypes()
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        self._countParticleTypes()
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        self.buildOrderedParticlesList()
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    def __iter__(self):
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        for x in sorted(self.helices.items(), key=lambda x: x[0]):
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            yield x
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    def buildOrderedParticlesList(self):
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        ## Create ordered list
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        particles = [(n,hid,zid) for hid,hlx in self for zid,n in hlx]        
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        self.particles = sorted(particles, key=lambda x: (x[0].type, x[0].idx))
        
        ## Update node indices
        for p,i in zip(self.particles,range(self.numParticles)):
            p[0].idx = i
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        self.initialCoords = np.array([p[0].initialPosition for p in self.particles])
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        self._nodeHids = np.array([p[1] for p in self.particles])
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    def _setTypes(self):
        for p,hid,zid in self.particles:
            bps = []
            if p.nodeAbove is not None: bps.append(p.nodeAboveSep)
            if p.nodeBelow is not None: bps.append(p.nodeBelowSep)
            if bps == []: bps = [3]
            p.bps = 10*np.mean(bps)

            if p.type == "ssDNA":
                p.bps *= 0.5

            p.bps = int(round(p.bps))
            p.type = "%s%d" % (p.type[0], p.bps)

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    def _countParticleTypes(self):
        particleTypeCounts = dict()
        for p in self.particles:
            t = p[0].type
            if t in particleTypeCounts:
                particleTypeCounts[t] += 1
            else:
                particleTypeCounts[t] = 1
        self.particleTypeCounts = particleTypeCounts
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    def addHelix(self, part, hid):
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        h = helix(self,part,hid)
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        self.helices[hid] = h
        return h
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    def _helixStrandsToEnds(self, helixStrands):

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        """Utility method to convert cadnano strand lists into list of
        indices of terminal points"""

        endLists = [[],[]]
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        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
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            if lastStrand is not None:
                endList.append(lastStrand[1])
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        return endLists
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    def simulate(self, outputPrefix, outputDirectory='output', numSteps=100000000, timestep=100e-6, gpu=0, arbd=None):
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        assert(type(gpu) is int)
        assert(type(numSteps) is int)
        if outputDirectory == '': outputDirectory='.'
            
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        if arbd is None:
            for path in os.environ["PATH"].split(os.pathsep):
                path = path.strip('"')
                fname = os.path.join(path, "arbd")
                if os.path.isfile(fname) and os.access(fname, os.X_OK):
                    arbd = fname
                    break

        if not os.path.exists(arbd):
            raise Exception("ARBD was not found")
        if not os.path.isfile(arbd):
            raise Exception("ARBD was not found")
        if not os.access(arbd, os.X_OK):
            raise Exception("ARBD is not executable")

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        if not os.path.exists(outputDirectory):
            os.makedirs(outputDirectory)
        elif not os.path.isdir(outputDirectory):
            raise Exception("outputDirectory '%s' is not a directory!" % outputDirectory)
            

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        self.writePdb( outputPrefix + ".pdb" )
        self.writePsf( outputPrefix + ".psf" )
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        self.writeArbdFiles( outputPrefix, numSteps=numSteps, timestep=timestep )
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        env = os.environ.copy()
        env["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"

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        ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
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        # cmd = "%s -g %d %s.bd %s/%s" % (arbd, gpu, outputPrefix, outputDirectory, outputPrefix)
        # cmd = (arbd, (-g %d %s.bd %s/%s" % (gpu, outputPrefix, outputDirectory, outputPrefix))
        cmd = (arbd, '-g', "%d" % gpu, "%s.bd" % outputPrefix, "%s/%s" % (outputDirectory, outputPrefix))
        cmd = tuple(str(x) for x in cmd)

        print("Running ARBD with: %s" % " ".join(cmd))
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        process = subprocess.Popen(cmd, env=env, stdout=subprocess.PIPE, universal_newlines=True)
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        for line in process.stdout:
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        # for line in iter(process.stdout.readline, b''):
            sys.stdout.write(line)
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            sys.stdout.flush()
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            # sys.stdout.write(line.decode(sys.stdout.encoding))
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    # -------------------------- #
    # Methods for building model #
    # -------------------------- #
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    def _buildModel(self, part, maxBpsPerDNode, maxNtsPerSNode):
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        # maxVhelixId = part.getIdNumMax()
        
        props = part.getModelProperties().copy()
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        # print(props)
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        if props.get('point_type') == PointType.ARBITRARY:
            # TODO add code to encode Parts with ARBITRARY point configurations
            raise NotImplementedError("Not implemented")
        else:
            vh_props, origins = part.helixPropertiesAndOrigins()
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            # print(' VIRTUAL HELICES:', vh_props)
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            # # print(' ORIGINS:', origins)
            # group_props['virtual_helices'] = vh_props
            # group_props['origins'] = origins
            
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        ## TODO: compartmentalize following
        ## Loop over virtual helices and build lists of strands 
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        vh_list = []
        strand_list = []
        xover_list = []
        numHID = part.getIdNumMax() + 1
        for id_num in range(numHID):
            offset_and_size = part.getOffsetAndSize(id_num)
            if offset_and_size is None:
                # add a placeholder
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                vh_list.append((id_num, 0))
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                strand_list.append(None)
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                # prop_list.append(None)
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            else:
                offset, size = offset_and_size
                vh_list.append((id_num, size))
                fwd_ss, rev_ss = part.getStrandSets(id_num)
                # for s in fwd_ss:
                #     print(' VHELIX %d fwd_ss:' % id_num, s)
                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))

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                # if id_num < 2:
                #     print( fwd_idxs )
                #     for s in fwd_ss:
                #         print( s.insertionsOnStrand() )
                
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                ## prop_list.append((fwd_colors, rev_colors))
                # for s in strand_list:
                #     print( s )
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        ## Get dictionary of insertions 
        allInsertions = part.insertions()

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        ## Expand strand_lists for crossover filtering 
        expandedStrandList = []
        for fwdRevStrands in strand_list:
            tmp = []
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            if fwdRevStrands is not None:
                for strands in fwdRevStrands:
                    fwdOrRev = []
                    for a,b in strands: fwdOrRev.extend(range(a,b+1))
                    tmp.append(fwdOrRev)
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            expandedStrandList.append(tmp)
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        ## Find crossovers involving ssDNA and dsDNA
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        ssXoList, dsXoList, extraInterhelicalBondList = [[],[],[]]
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        for entry in xover_list:
            h1,f1,z1,h2,f2,z2 = entry
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            if strand_list[h1] is None or strand_list[h2] is None:
                print("WARNING: crossover to empty helix")
                continue

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            ds1 = z1 in expandedStrandList[h1][0] and z1 in expandedStrandList[h1][1]
            ds2 = z2 in expandedStrandList[h2][0] and z2 in expandedStrandList[h2][1]
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            occ1Above = z1+1 in expandedStrandList[h1][0] or z1+1 in expandedStrandList[h1][1]
            occ2Above = z2+1 in expandedStrandList[h2][0] or z2+1 in expandedStrandList[h2][1]

            occ1Below = z1-1 in expandedStrandList[h1][0] or z1-1 in expandedStrandList[h1][1]
            occ2Below = z2-1 in expandedStrandList[h2][0] or z2-1 in expandedStrandList[h2][1]

            if ((not occ1Above) and (not occ2Below)) or \
               ((not occ1Below) and (not occ2Above)):
                extraInterhelicalBondList.append(entry)
            else:
                if ds1 and ds2:
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                    dsXoList.append(entry)
                else:
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                    ssXoList.append(entry)
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        ## Build dictionary of dsDNA crossovers
        xoDicts = [dict() for i in range(numHID)]
        for hid1 in range(numHID):
            tmp = xoDicts[hid1]
            for hid2 in range(numHID):
                allXos       = {(z1,z2,f1,f2) for h1,f1,z1,h2,f2,z2 in dsXoList if h1 == hid1 and h2 == hid2}
                allXos.update( {(z2,z1,f2,f1) for h1,f1,z1,h2,f2,z2 in dsXoList if h2 == hid1 and h1 == hid2} )
                allXos = sorted(list(allXos), key = lambda x: (x[0],x[1]))

                ## Replace each double-crossover with a single one
                excludedXos, extraXos = [set(),set()]
                for i in range(len(allXos)):
                    xoi = allXos[i]
                    for j in range(i+1,len(allXos)):
                        xoj = allXos[j]
                        if xoj[0] - xoi[0] > 2: break
                        if xoi[0]+1 == xoj[0] and xoi[1]+1 == xoj[1] and \
                           xoi[2]   == xoj[2] and xoi[3]   == xoj[3]:
                            excludedXos.add(xoi)
                            excludedXos.add(xoj)
                            extraXos.add( (xoi[0]+0.5,xoi[1]+0.5,xoi[2],xoi[3]) )
                xos = {xo for xo in allXos if xo not in excludedXos}
                xos.update(extraXos)
            
                ## Set dictionary entry
                xos = list(xos)
                if len(xos) > 0:
                    tmp[hid2] = xos

        ## Build dictionary of dsDNA crossovers
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        xoDicts = [dict() for i in range(numHID)]
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        for hid1 in range(numHID):
            tmp = xoDicts[hid1]
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            for hid2 in range(numHID):
                allXos       = {(z1,z2,f1,f2) for h1,f1,z1,h2,f2,z2 in dsXoList if h1 == hid1 and h2 == hid2}
                allXos.update( {(z2,z1,f2,f1) for h1,f1,z1,h2,f2,z2 in dsXoList if h2 == hid1 and h1 == hid2} )
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                allXos = sorted(list(allXos), key = lambda x: (x[0],x[1]))

                ## Replace each double-crossover with a single one
                excludedXos, extraXos = [set(),set()]
                for i in range(len(allXos)):
                    xoi = allXos[i]
                    for j in range(i+1,len(allXos)):
                        xoj = allXos[j]
                        if xoj[0] - xoi[0] > 2: break
                        if xoi[0]+1 == xoj[0] and xoi[1]+1 == xoj[1] and \
                           xoi[2]   == xoj[2] and xoi[3]   == xoj[3]:
                            excludedXos.add(xoi)
                            excludedXos.add(xoj)
                            extraXos.add( (xoi[0]+0.5,xoi[1]+0.5,xoi[2],xoi[3]) )
                xos = {xo for xo in allXos if xo not in excludedXos}
                xos.update(extraXos)
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                ## Set dictionary entry
                xos = list(xos)
                if len(xos) > 0:
                    tmp[hid2] = xos

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        ## Build dictionary of ssDNA crossovers
        ssXoDicts = [dict() for i in range(numHID)]
        for hid1 in range(numHID):
            tmp = ssXoDicts[hid1]
            for hid2 in range(numHID):
                xos       = {(z1,z2,f1,f2) for h1,f1,z1,h2,f2,z2 in ssXoList if h1 == hid1 and h2 == hid2}
                xos.update( {(z2,z1,f2,f1) for h1,f1,z1,h2,f2,z2 in ssXoList if h2 == hid1 and h1 == hid2} )
                xos = sorted(list(xos), key = lambda x: (x[0],x[1]))
                ## Set dictionary entry
                if len(xos) > 0:
                    tmp[hid2] = xos

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        ## Build helices 
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        for hid in range(numHID):
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            # print("Working on helix",hid)
            
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            helixStrands = strand_list[hid]
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            if helixStrands is None: 
                continue
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            ## 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] )
            
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            ## Build list of strand ends and list of mandatory node locations
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            ends1,ends2 = self._helixStrandsToEnds(helixStrands)
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            # xoZids = [x for x in xoDicts2[hid].keys()]

            ## Find crossovers for this helix
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            xoZids = [x[1] for h0 in range(hid) if hid in xoDicts[h0] for x in xoDicts[h0][hid]]
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            xoZids.extend([x[0] for hid2,xos in xoDicts[hid].items() for x in xos])
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            xoZids.extend([x[1] for h0 in range(hid) if hid in ssXoDicts[h0] for x in ssXoDicts[h0][hid]])
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            xoZids.extend([x[0] for hid2,xos in ssXoDicts[hid].items() for x in xos])
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            reqNodeZids = sorted(list(set( ends1 + ends2 + xoZids ) ) )
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            ## 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) ]
            
           
            ## Build helix by adding nodes
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            beadHelix = self.addHelix(part,hid)
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            if hid in ():
                print("%d nodes:" %hid,reqNodeZids)
                print("orig xos:",[xo for xo in xover_list if xo[0] == hid or xo[3] == hid])
                print("xosZids:", sorted(xoZids) )
                print("strandOccupancy1:",strandOccupancies[0])
                print("strandOccupancy2:",strandOccupancies[1])
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            prevNode = None
            for i in range( len(reqNodeZids)-1 ):
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                zid1,zid2 = reqNodeZids[i:i+2]
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                ## Check that there are nts between zid1 and zid2 before adding nodes
                zMid = int(0.5*(zid1+zid2))
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                if zMid in strandOccupancies[0] and zMid in strandOccupancies[1]:
                    ## dsDNA
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                    maxBpsPerNode = maxBpsPerDNode
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                if zMid in strandOccupancies[0] or zMid in strandOccupancies[1]:
                    ## ssDNA
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                    maxBpsPerNode = maxNtsPerSNode
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                else:
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                    continue
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                numBps = zid2-zid1
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                # if numBps < 2:
                #     print(hid,zid1,zid2)
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                # assert(numBps >= 1)
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                for ins_idx,length in insertions:
                    ## TODO: ensure placement of insertions is correct
                    ##   (e.g. are insertions at the ends handled correctly?)
                    if ins_idx < zid1:
                        continue
                    if ins_idx >= zid2:
                        break
                    numBps += length
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                # if numBps = 0:
                #     print("WARNING: found stretch of DNA with 0 length; skipping")
                #     next

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                nodesBetween = round( float(numBps-1)/maxBpsPerNode )
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                if nodesBetween < 0: 
                    nodesBetween = 0
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                bpsPerNode = float(numBps)/(nodesBetween+1)
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                if bpsPerNode == 0: 
                    bpsPerNode = 0.1
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                zidPerNode = float(zid2-zid1)/(nodesBetween+1)
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                try:
                    if prevNode is None:
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                        prevNode = beadHelix.addNode( zid1, strandOccupancies )
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                    for i in range(nodesBetween):
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                        node = beadHelix.addNode( zid1+(i+1)*zidPerNode, strandOccupancies )
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                        self._connectNodes(prevNode, node, bpsPerNode)
                        prevNode = node
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                    node = beadHelix.addNode( zid2, strandOccupancies )
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                    self._connectNodes(prevNode, node, bpsPerNode)
                except:
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                    print(hid,zid1,zid2,nodesBetween,bpsPerNode)
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                    raise Exception("ERROR")
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                prevNode = None
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                if (int(floor(zid2+1)) in strandOccupancies[0]) or \
                   (int(floor(zid2+1)) in strandOccupancies[1]):
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                    prevNode = node
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        ## Add extra intrahelical bonds
        ## Add crossovers
        for entry in extraInterhelicalBondList:
            h1,f1,z1,h2,f2,z2 = entry
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            n1 = self.helices[h1].nodes[z1]
            n2 = self.helices[h2].nodes[z2]

            try:
                self._connectNodes(n1,n2,1)
            except:
                assert(True)
            try:
                self._connectNodes(n2,n1,1)
            except:
                assert(True)
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        ## Add crossovers
        for hid1 in range(numHID):
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            for hid2, xos in xoDicts[hid1].items():
                for xo in xos:
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                    self._addCrossover(hid1,hid2,xo)

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        ## Add ssDNA xovers    
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        for hid1 in range(numHID):
            for hid2, xos in ssXoDicts[hid1].items():
                for xo in xos:
                    self._addSsCrossover(hid1,hid2,xo)

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        return
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    def _connectNodes(self, below, above, sep):
        below.addNodeAbove(above, sep)
        above.addNodeBelow(below, sep)
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    def _addCrossover(self, hid1, hid2, xo):
        zid1, zid2, isFwd1, isFwd2 = xo
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        node1 = self.helices[hid1].nodes[zid1]
        node2 = self.helices[hid2].nodes[zid2]

        ## TODO add polarity
        polarity = 0
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        node1.addXover(node2, (isFwd1, isFwd2))
        node2.addXover(node1, (isFwd2, isFwd1))
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    def _addSsCrossover(self, hid1, hid2, xo):
        zid1, zid2, isFwd1, isFwd2 = xo
        node1 = self.helices[hid1].nodes[zid1]
        node2 = self.helices[hid2].nodes[zid2]

        ## TODO add polarity
        polarity = 0
        node1.addSsXover(node2, isFwd1)
        node2.addSsXover(node1, isFwd2)

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    def addModel(self, model):
        assert( isinstance(model, type(self)) )

        hidOffset = max( self.helices.keys() ) + 1
        # nidOffset = self.numParticles
        for hid,h in model:
            self.helices[hid+hidOffset] = h

        self.numParticles += model.numParticles

        self.buildOrderedParticlesList()
        self._setTypes()
        self._countParticleTypes()


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    def backmap(self, simplerModel, simplerModelCoords, 
                dsDnaHelixNeighborDist=50, dsDnaAllNeighborDist=30,
                ssDnaHelixNeighborDist=20, ssDnaAllNeighborDist=15):

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        ## Assign each bead to a bead in simplerModel
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        mapToSimplerModel = dict()
        cgWeight = dict()
        for hDict,cgHDict in zip(self,simplerModel):
            assert(hDict[0] == cgHDict[0])
            h,cgH = [x[1] for x in (hDict,cgHDict)] # get helix

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            zIdxs = np.array( sorted([i for i,b in cgH]) )
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            for i,b in h:
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                cgi = np.searchsorted(zIdxs,i,side='left',sorter=None)
                cgi, = [zIdxs[x] if x < len(zIdxs) else zIdxs[-1] for x in (cgi,)]
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                mapToSimplerModel[b.idx] = [cgH.nodes[x] for x in (cgi,)]
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        ## Find new axis and position of each bead using neighborhood
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        beads = [b for h in self for i,b in h[1].nodes.items()]
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        ## Find transformation for each bead of simplerModel
        trans = dict()
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        for b in list(set([b for i,bs in mapToSimplerModel.items() for b in bs])):
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            helixCutoff = dsDnaHelixNeighborDist if b.type[0] == 'd' else ssDnaHelixNeighborDist
            allCutoff = dsDnaAllNeighborDist if b.type[0] == 'd' else ssDnaAllNeighborDist

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            ids = []
            attempts = 0
            while len(ids) <= 3:
                if attempts > 15: raise Exception("Too many attempts to find a neighborhood for backmaping bead %d" % b.idx)
                ids = simplerModel._getNeighborhoodIds(b, simplerModelCoords, helixCutoff, allCutoff)
                allCutoff *= 1.2
                attempts+=1
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            posOld = np.array( [simplerModel.particles[i][0].initialPosition for i in ids] )
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            posNew = np.array( [simplerModelCoords[i] for i in ids] )
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            try:
                trans[b.idx] = minimizeRmsd( posOld, posNew )
            except:
                raise Error("Crapola")
                # print("ugly")
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        ## Optionally smooth orientations
            
        ## Apply transformation to each bead of self
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        for b in beads:
            cgb, = mapToSimplerModel[b.idx]
            cgi = cgb.idx
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            r0 = simplerModel.particles[cgi][0].initialPosition
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            R,c0,c1 = trans[cgi]
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            b.position = (b.initialPosition - r0).dot(R) + simplerModelCoords[cgi]
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            assert( np.all(np.isreal( b.position )) )
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    def _getNeighborhoodIds(self, bead, coords, helixCutoff=50, allCutoff=np.sqrt(35)):
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        i = bead.idx

        coords0 = self.initialCoords
        # print(coords0[i,:])
        coordsI = np.outer(coords0[i,:],np.ones([len(coords0),1])).T
        dr2Initial = np.sum((coords0 - coordsI)**2, axis=-1)
        dr2Final = np.sum((coords - coords[i,:])**2, axis=-1)
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        ## Include all in same helix within 5 nm of bead after simulation        
        ret = list( np.where( (dr2Final < helixCutoff**2) * (self._nodeHids == bead.helix.hid) )[0] )
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        ret = list( np.where( (dr2Final < helixCutoff**2) * (self._nodeHids == bead.helix.hid) * (dr2Initial < 100**2) )[0] )
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        ## Include all within 3.5 nm both before AND after simulation
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        ret.extend( list( np.where( (dr2Final < allCutoff**2) * (dr2Initial < allCutoff**2) )[0] ) )
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        return sorted(list(set(ret)))

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    # -------------------------- #
    # Methods for querying model #
    # -------------------------- #
    def _getIntrahelicalNodeSeries(self,seriesLen):
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        nodeSeries = set() 
        for hid,hlx in self:
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            for zid,n in hlx:
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                nodeList,sepList = n.getNodesAbove(seriesLen-1, inclusive = True)
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                if len(nodeList) == seriesLen:
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                    nodeList = tuple(nodeList)
                    sepList = tuple(sepList)
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                    nodeSeries.add( tuple((nodeList,sepList)) )
        return nodeSeries

    def _getIntrahelicalBonds(self):
        return self._getIntrahelicalNodeSeries(2)

    def _getIntrahelicalAngles(self):
        return self._getIntrahelicalNodeSeries(3)

    def _getCrossoverBonds(self):
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        return { ((n, xo[0]), xo[1])
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                 for hid,hlx in self
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                 for zid,n in hlx for xo in n.xovers if n.idx < xo[0].idx }

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    def _getSsCrossoverBonds(self):
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        return { ((n, xo[0]), xo[1]) 
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                 for hid,hlx in self
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                 for zid,n in hlx for xo in n.ssXovers if n.idx < xo[0].idx }


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    def _getCrossoverAnglesAndDihedrals(self):
        angles,dihedrals = [set(),set()]
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        contiguousCrossovers = []
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        for hid,hlx in self.helices.items():
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            crossovers = []
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            bpsBetween = 0
            for zid,n in hlx:
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                ## Search for contiguous crossovers
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                if n.nodeBelow is None or n.type[0] != "d":
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                    ## Found ssDNA or a gap; reset search
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                    if len(crossovers) > 0:
                        contiguousCrossovers.append(crossovers)
                    crossovers = []
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                    bpsBetween = 0

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                if n.nodeBelow is not None:
                    bpsBetween += n.nodeBelowSep
                if len(n.xovers) > 0:
                    crossovers.append( (n,bpsBetween) )
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            if len(crossovers) > 0:
                contiguousCrossovers.append(crossovers)

        ## Process contiguousCrossovers
        for crossovers in contiguousCrossovers:
            for i in range(len(crossovers)-1):
                ni,bpi = crossovers[i]
                # for j in range(i+1,len(crossovers)):
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                for j in range(i+1,i+2): # Just look at adjacent crossovers
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                    assert(j == i+1)
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                    nj,bpj = crossovers[j]
                    bpsBetween = bpj-bpi
                    if bpsBetween < 60:
                        for xo1 in ni.xovers:
                            for xo2 in nj.xovers:
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                                assert( bpsBetween != 0 )
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                                angles.add( ((xo1[0], ni, nj), bpsBetween) )
                                angles.add( ((ni, nj, xo2[0]), bpsBetween) )
                                dihedrals.add( ((xo1[0], ni, nj, xo2[0]), bpsBetween, xo1[1], xo2[1]) )
                    else:
                        break
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        return angles, dihedrals
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    def _removeIntrahelicalConnectionsBeyond(self, cutoff):
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        bonds = self._getIntrahelicalBonds()
        for b in bonds:
            n1,n2 = b[0]
            r2 = np.sum( (n1.position - n2.position)**2 )
            if r2 > cutoff**2:
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                if n1.nodeAbove == n2:
                    assert(n2.nodeBelow == n1)
                    n1.nodeAbove = None
                    n2.nodeBelow = None
                elif n2.nodeAbove == n1:
                    assert(n1.nodeBelow == n2)
                    n1.nodeBelow = None
                    n2.nodeAbove = None
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                else:
                    raise

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    def _removeCrossoversBeyond(self, cutoff):
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        for hid,hlx in self:
            for zid,n1 in hlx:
                newXovers = []
                for xo in n1.xovers:
                    n2 = xo[0]
                    r2 = np.sum( (n1.position - n2.position)**2 )
                    if r2 < cutoff**2:
                        newXovers.append(xo)
                n1.xovers = newXovers
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        for hid,hlx in self:
            for zid,n1 in hlx:
                newXovers = []
                for xo in n1.ssXovers:
                    n2 = xo[0]
                    r2 = np.sum( (n1.position - n2.position)**2 )
                    if r2 < cutoff**2:
                        newXovers.append(xo)
                n1.ssXovers = newXovers

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    def _getBonds(self):
        bonds = self._getIntrahelicalBonds()
        bonds.update( self._getCrossoverBonds() )
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        bonds.update( self._getSsCrossoverBonds() )
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        return bonds


    # -------------------------- #
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    # Methods for prinitng model #
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    # -------------------------- #
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    def writePdb(self, filename):
        with open(filename,'w') as fh:
            ## Write header
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            fh.write("CRYST1    1000.    1000.    1000.  90.00  90.00  90.00 P 1           1\n")
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            ## Write coordinates
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            formatString = "ATOM  {:>5d} {:^4s}{:1s}{:3s} {:1s}{:>5s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2s}{:2f}\n"
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            for n,hid,zid in self.particles:
                ## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
                idx = n.idx
                name = n.type
                resname = name[:3]
                chain = "A"
                charge = 0
                occ = hid
                beta = zid
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                x,y,z = [x for x in n.position]
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                assert(idx < 1e5)
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                resid = "{:<4d}".format(idx)
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                fh.write( formatString.format(
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                    idx, name[:1], "", resname, chain, resid, x, y, z, occ, beta, "", charge ))
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        return
        
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    def writePsf(self, filename):
        with open(filename,'w') as fh:
            ## Write header
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            fh.write("PSF NAMD\n\n") # create NAMD formatted psf
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            ## ATOMS section
            idx=1
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            for hid,hlx in self:
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                for x in hlx:
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                    idx += 1
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            fh.write("{:>8d} !NATOM\n".format(idx-1))

            ## From vmd/plugins/molfile_plugin/src/psfplugin.c
            ## "%d %7s %10s %7s %7s %7s %f %f"
            formatString = "{idx:>8d} {segname:7s} {resid:<10s} {resname:7s}" + \
                           " {name:7s} {type:7s} {charge:f} {mass:f}\n"
            for n,hid,zid in self.particles:
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                idx = n.idx + 1
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                data = dict(
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                    idx     = idx,
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                    segname = "A",
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                    resid   = "%d%c%c" % (idx," "," "), # TODO: work with large indeces
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                    name    = n.type[:1],
                    resname = n.type[:3],
                    type    = n.type[:1],
                    charge  = 0,
                    mass    = 100,
                )
                fh.write(formatString.format( **data ))
            fh.write("\n")

            ## Write out bonds
            bonds = self._getBonds()
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            fh.write("{:>8d} !NBOND\n".format(len(bonds)))
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            counter = 0
            for n,seps in bonds:
                fh.write( "{:d} {:d} ".format(n[0].idx+1,n[1].idx+1) )
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                counter += 1
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                if counter == 3:
                    fh.write("\n")
                    counter = 0
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            fh.write("\n")
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        return
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    def writeArbdFiles(self, prefix, numSteps=100000000, timestep=100e-6):
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        ## TODO: save and reference directories and prefixes using member data
        d = "potentials"
        self._writeArbdCoordFile( prefix + ".coord.txt" )
        self._writeArbdBondFile(  prefix, directory = d )
        self._writeArbdAngleFile( prefix, directory = d )
        self._writeArbdDihedralFile( prefix, directory = d )
        self._writeArbdExclFile(  prefix + ".excludes.txt" )
        self._writeArbdPotentialFiles( prefix, directory = d )
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        self._writeArbdConf( prefix, numSteps, timestep )
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    def _writeArbdCoordFile(self, filename):
        with open(filename,'w') as fh:
            for n,hid,zid in self.particles:
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                fh.write("%f %f %f\n" % tuple(x for x in n.position))
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    def _writeArbdConf(self, prefix, numSteps=100000000, timestep=100e-6 ):
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        ## TODO: raise exception if _writeArbdPotentialFiles has not been called
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        filename = "%s.bd" % prefix
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        with open(filename,'w') as fh:
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            fh.write("""# seed 1234
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timestep %f
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steps %d
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numberFluct 0
interparticleForce 1
fullLongRange 0
temperature 291
electricField 0.0

outputPeriod 10000
outputEnergyPeriod 10000
outputFormat dcd

decompPeriod 100000
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cutoff 40.0
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pairlistDistance 100
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""" % (timestep, numSteps))
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            for x in self.getParticleTypesAndCounts():
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                fh.write("\nparticle %s\nnum %d\n" % x)
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                ## TODO: look up better values in dictionary for particle types
                fh.write("gridFile null.dx\ndiffusion 100\n")

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            fh.write("\ninputCoordinates %s.coord.txt\n"  % prefix )
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            if os.path.exists("test.0.restart"):
                fh.write("restartCoordinates test.0.restart\n" )
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            fh.write("""\n## Interaction potentials
tabulatedPotential  1
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## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file
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""")
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            for pair,f in zip(self._particleTypePairIter(), self._nbParamFiles):
                i,j,t1,t2 = pair
                fh.write("tabulatedFile %d@%d@%s\n" % (i,j,f))

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            fh.write("\n")
            for f in self._bondParamFiles:
                fh.write("tabulatedBondFile %s\n" % f)

            fh.write("\n")
            for f in self._angleParamFiles:
                fh.write("tabulatedAngleFile %s\n" % f)

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            fh.write("\n")
            for f in self._dihedralParamFiles:
                fh.write("tabulatedDihedralFile %s\n" % f)

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            fh.write("""\n## Files that specify connectivity of particles
inputBonds {prefix}.bonds.txt
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