Newer
Older
# -*- coding: utf-8 -*-
from datetime import datetime
from cadnano.cnenum import PointType
from math import pi,sqrt,exp,floor
import numpy as np
from scipy.special import erf
import scipy.optimize as opt
import os, sys, subprocess
import nbPot
from coords import minimizeRmsd, quaternionToMatrix3, rotationAboutAxis
class HarmonicPotential:
def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, maxPotential=None):
self.maxPotential = maxPotential
self.periodic = False
self.type = "None"
self._kscale = None
def filename(self, prefix='potentials/'):
return "%s%s-%.3f-%.3f.dat" % (prefix, self.type,
def write_file(self, prefix='potentials/'):
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 > self.maxForce] = self.maxForce
f[f < -self.maxForce] = -self.maxForce
u = u - np.min(u)
if self.maxPotential is not None:
cmaffeo2
committed
f = np.diff(u)/np.diff(r)
ids = np.where( 0.5*(u[1:]+u[:-1]) > self.maxPotential )[0]
w = np.sqrt(2*self.maxPotential/self.k)
drAvg = 0.5*(np.abs(dr[ids]) + np.abs(dr[ids+1]))
f[ids] = f[ids] * np.exp(-(drAvg-w)/(w))
u[0] = 0
u[1:] = np.cumsum(f*np.diff(r))
u = u - np.min(u)
np.savetxt( self.filename(prefix), np.array([r, u]).T, fmt="%f" )
return hash((self.type, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.maxPotential, self.periodic))
for a in ("type", "k", "r0", "rRange", "resolution", "maxForce", "maxPotential", "periodic"):
if self.__dict__[a] != other.__dict__[a]:
return False
return True
class NonBonded(HarmonicPotential):
def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, maxPotential=None):
super().__init__(k,r0,rRange,resolution,maxForce,maxPotential)
self.type = "nonbonded"
self._kscale = 1.0
class Bond(HarmonicPotential):
def __init__(self, k, r0, rRange=(0,800), resolution=0.1, maxForce=5, maxPotential=None):
super().__init__(k,r0,rRange,resolution,maxForce,maxPotential)
self.type = "bond"
self._kscale = 1.0
class Angle(HarmonicPotential):
def __init__(self, k, r0, rRange=(0,180), resolution=0.5, maxForce=None, maxPotential=None):
super().__init__(k,r0,rRange,resolution,maxForce,maxPotential)
self.type = "angle"
self._kscale = (180.0/pi)**2
class Dihedral(HarmonicPotential):
def __init__(self, k, r0, rRange=(-180,180), resolution=1, maxForce=None, maxPotential=None):
super().__init__(k,r0,rRange,resolution,maxForce,maxPotential)
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
self.periodic = True
self.type = "dihedral"
self._kscale = (180.0/pi)**2
class Node():
def __init__(self, helix, pos, type="dsDNA"):
self.helix = helix
self.position = np.array(pos)
self.initialPosition = np.array(pos)
self.type = type
self.nodeAbove = None
self.nodeBelow = None
self.xovers = []
self.ssXovers = []
self.orientationNode = None
self.parentNode = None
self.idx = helix.model.numParticles
helix.model.numParticles += 1
def addNodeAbove(self, node, separation):
assert(self.nodeAbove is None)
self.nodeAbove = node
self.nodeAboveSep = separation # bp
def addNodeBelow(self, node, separation):
assert(self.nodeBelow is None)
self.nodeBelow = node
self.nodeBelowSep = separation # bp
def addXover(self, node, fwds, double=False):
## TODO: what is meant by polarity?
self.xovers.append( (node,fwds,double) )
def addSsXover(self, node, fwds):
self.ssXovers.append( (node,fwds) )
def getNodesAbove(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.nodeAbove is None: break
n = n.nodeAbove
nodeList.append(n)
sepList.append(n.nodeBelowSep)
return nodeList,sepList
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)
return nodeList,sepList
def addOrientationNode(self, node):
assert(self.nodeBelow is None)
self.orientationNode = node
node.parentNode = self
class helix():
def __init__(self, model, part, hid):
self.model = model
self.props = part.getModelProperties().copy() # TODO: maybe move this out of here
self.nodes = dict()
self.orientationNodes = dict()
self.hid = hid
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
self.zIdxToPos = lambda idx: (x*10,y*10,-3.4*idx)
## get twizt
keys = ['bases_per_repeat',
'turns_per_repeat',
'eulerZ','z']
bpr,tpr,eulerZ,z = [vh_props[k][hid] for k in keys]
twist_per_base = tpr*360./bpr
Loading
Loading full blame...