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Commit 287af0d9 authored by cmaffeo2's avatar cmaffeo2
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Added models with twist

parent c117923f
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arbdmodel.py
View file @ 287af0d9
......@@ -765,8 +765,6 @@ component "data" value 3
with open(self._dihedral_filename,'w') as fh:
for b in self.get_dihedrals():
if type(b) is not str:
b = b.filename()
item = tuple([p.idx for p in b[:-1]] + [str(b[-1])])
fh.write("DIHEDRAL %d %d %d %d %s\n" % item)
......
nonbonded.py
View file @ 287af0d9
......@@ -58,7 +58,7 @@ class TabulatedPotential(NonbondedScheme):
## Bonded potentials
class HarmonicPotential():
def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, prefix="potentials/"):
def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
self.k = k
self.r0 = r0
self.rRange = rRange
......@@ -67,6 +67,7 @@ class HarmonicPotential():
self.prefix = prefix
self.periodic = False
self.type_ = "None"
self.max_potential = max_potential
self.kscale_ = None # only used for
def filename(self):
......@@ -98,14 +99,28 @@ class HarmonicPotential():
f[f<-maxForce] = -maxForce
u[0] = 0
u[1:] = np.cumsum(f*np.diff(r))
if self.max_potential is not None:
f = np.diff(u)/np.diff(r)
ids = np.where( 0.5*(u[1:]+u[:-1]) > self.max_potential )[0]
w = np.sqrt(2*self.max_potential/self.k)
drAvg = 0.5*(np.abs(dr[ids]) + np.abs(dr[ids+1]))
f[ids] = f[ids] * np.exp(-(drAvg-w)/(w))
u[0] = 0
u[1:] = np.cumsum(f*np.diff(r))
u = u - np.min(u)
np.savetxt( self.filename(), np.array([r, u]).T, fmt="%f" )
def __hash__(self):
assert(self.type_ != "None")
return hash((self.type_, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.prefix, self.periodic))
return hash((self.type_, self.k, self.r0, self.rRange, self.resolution, self.maxForce, self.max_potential, self.prefix, self.periodic))
def __eq__(self, other):
for a in ("type_", "k", "r0", "rRange", "resolution", "maxForce", "prefix", "periodic"):
for a in ("type_", "k", "r0", "rRange", "resolution", "maxForce", "max_potential", "prefix", "periodic"):
if self.__dict__[a] != other.__dict__[a]:
return False
return True
......@@ -116,20 +131,20 @@ class HarmonicPotential():
# self.kscale_ = 1.0
class HarmonicBond(HarmonicPotential):
def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, prefix="potentials/"):
HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, prefix)
def __init__(self, k, r0, rRange=(0,50), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
self.type_ = "bond"
self.kscale_ = 1.0
class HarmonicAngle(HarmonicPotential):
def __init__(self, k, r0, rRange=(0,181), resolution=0.1, maxForce=None, prefix="potentials/"):
HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, prefix)
def __init__(self, k, r0, rRange=(0,181), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
self.type_ = "angle"
self.kscale_ = (180.0/np.pi)**2
class HarmonicDihedral(HarmonicPotential):
def __init__(self, k, r0, rRange=(-180,180), resolution=0.1, maxForce=None, prefix="potentials/"):
HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, prefix)
def __init__(self, k, r0, rRange=(-180,180), resolution=0.1, maxForce=None, max_potential=None, prefix="potentials/"):
HarmonicPotential.__init__(self, k, r0, rRange, resolution, maxForce, max_potential, prefix)
self.periodic = True
self.type_ = "dihedral"
self.kscale_ = (180.0/np.pi)**2
......
segmentmodel.py
View file @ 287af0d9
import numpy as np
from arbdmodel import PointParticle, ParticleType, Group, ArbdModel
from coords import rotationAboutAxis
from nonbonded import *
from copy import copy, deepcopy
from nbPot import nbDnaScheme
from scipy.special import erf
import scipy.optimize as opt
"""
# TODO:
TODO:
- document
-
"""
......@@ -52,6 +58,13 @@ class Segment(ConnectableElement, Group):
mass = 300,
radius = 3,
)
orientation_particle = ParticleType("O",
diffusivity = 100,
mass = 300,
radius = 1,
)
# orientation_bond = HarmonicBond(10,2)
orientation_bond = HarmonicBond(30,1.5)
ssDNA_particle = ParticleType("S",
diffusivity = 43.5,
......@@ -67,19 +80,24 @@ class Segment(ConnectableElement, Group):
Group.__init__(self, name, children=[])
ConnectableElement.__init__(self, connections=[])
self.start_orientation = None
self.twist_per_nt = 0
self.beads = [c for c in self.children] # self.beads will not contain orientation beads
self._bead_model_generation = 0 # TODO: remove?
self.segment_model = segment_model # TODO: remove?
# self.end5 = Location( self, address=0, type_= "end5" )
# self.end3 = Location( self, address=-1, type_ = "end3" )
self.num_nts = num_nts
if end_position is None:
end_position = np.array((0,0,self.distance_per_nt*num_nts)) + start_position
self.start_position = start_position
self.end_position = end_position
def _generate_one_bead(self, pos, nts):
def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead ):
raise NotImplementedError
def _generate_one_bead(self, pos, nts, orientation=None):
raise NotImplementedError
def _assign_particles_to_locations(self):
......@@ -87,49 +105,52 @@ class Segment(ConnectableElement, Group):
def get_all_consecutive_beads(self, number):
assert(number >= 1)
## Assume that consecutive beads in self.children are bonded
## Assume that consecutive beads in self.beads are bonded
ret = []
for i in range(len(self.children)-number+1):
tmp = [self.children[i+j] for j in range(0,number)]
for i in range(len(self.beads)-number+1):
tmp = [self.beads[i+j] for j in range(0,number)]
ret.append( tmp )
return ret
def get_beads_before_bead(self, bead, number, inclusive=False):
## Assume that consecutive beads in self.children are bonded
i = self.children.index(bead)
l = len(self.children)
## Assume that consecutive beads in self.beads are bonded
i = self.beads.index(bead)
l = len(self.beads)
if i-number < 0:
raise Exception("Not enough beads after bead")
start = 1
if inclusive: start = 0
return [self.children[i-j] for j in range(start,number)]
return [self.beads[i-j] for j in range(start,number)]
def get_beads_after_bead(self, bead, number, inclusive=False):
## Assume that consecutive beads in self.children are bonded
i = self.children.index(bead)
l = len(self.children)
## Assume that consecutive beads in self.beads are bonded
i = self.beads.index(bead)
l = len(self.beads)
if i+number >= l:
raise Exception("Not enough beads after bead")
start = 1
if inclusive: start = 0
return [self.children[i+i] for j in range(start,number)]
return [self.beads[i+i] for j in range(start,number)]
# def get_bead_pairs_within(self, cutoff):
# for b1,b2 in self.get_all_consecutive_beads(self, number)
def _generate_beads(self, bead_model, max_nts_per_bead=4):
def _generate_beads(self, bead_model, max_basepairs_per_bead, max_nucleotides_per_bead):
""" Generate beads (positions, types, etcl) and bonds, angles, dihedrals, exclusions """
## TODO: decide whether to remove bead_model argument
# self._bead_model_generation += 1
# self._bead_model_max_nts_per_bead = max_nts_per_bead
direction = self.end_position - self.start_position
num_beads = (self.num_nts // max_nts_per_bead) + 1
num_beads = self._get_num_beads( max_basepairs_per_bead, max_nucleotides_per_bead )
nts_per_bead = float(self.num_nts)/num_beads
twist_per_bead = nts_per_bead * self.twist_per_nt
last = None
......@@ -140,9 +161,24 @@ class Segment(ConnectableElement, Group):
s = i*float(nts_per_bead)/(self.num_nts) # contour
pos = direction * s + self.start_position
if self.start_orientation is not None:
axis = self.start_orientation.dot( np.array((0,0,1)) )
orientation = rotationAboutAxis( axis, s*self.twist_per_nt*self.num_nts, normalizeAxis=False )
## TODO: ensure this is correct
# orientation = self.start_orientation.dot(orientation) # .dot( self.start_orientation )
orientation = orientation.dot( self.start_orientation )
else:
orientation = None
b = self._generate_one_bead(pos,nts)
b = self._generate_one_bead(pos,nts,orientation)
self.children.append(b)
self.beads.append(b) # don't add orientation bead
if "orientation_bead" in b.__dict__:
o = b.orientation_bead
self.children.append(o)
self.add_bond(b,o, Segment.orientation_bond)
# if last is not None:
# self.add_bond( i=last, j=b, bond="ssdna" )
# last = b
......@@ -163,15 +199,26 @@ class DoubleStrandedSegment(Segment):
def __init__(self, name, num_nts, start_position = np.array((0,0,0)),
end_position = None,
segment_model = None,
twist = None,
local_twist = False,
num_turns = None,
start_orientation = None):
self.distance_per_nt = 5
self.helical_rise = 10.44
self.distance_per_nt = 3.4
Segment.__init__(self, name, num_nts,
start_position,
end_position,
segment_model)
self.local_twist = local_twist
if num_turns is None:
num_turns = float(num_nts) / self.helical_rise
self.twist_per_nt = float(360 * num_turns) / num_nts
if start_orientation is None:
start_orientation = np.array(((1,0,0),(0,1,0),(0,0,1)))
self.start_orientation = start_orientation
self.nicks = []
self.start5 = Location( self, address=0, type_= "end5" )
......@@ -210,13 +257,28 @@ class DoubleStrandedSegment(Segment):
end1.container._connect( end2.container, Connection( end1, end2, type_="intrahelical" ) )
def _generate_one_bead(self, pos, nts):
return PointParticle( Segment.dsDNA_particle, pos, nts,
num_nts=nts, parent=self )
def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead):
return (self.num_nts // max_basepairs_per_bead) + 1
def _generate_one_bead(self, pos, nts, orientation=None):
if self.local_twist:
assert(orientation is not None)
# opos = pos + np.array((2,0,0)).dot(orientation)
opos = pos + orientation.dot( np.array((Segment.orientation_bond.r0,0,0)) )
o = PointParticle( Segment.orientation_particle, opos, nts,
num_nts=nts, parent=self )
bead = PointParticle( Segment.dsDNA_particle, pos, nts,
num_nts=nts, parent=self, orientation_bead=o )
else:
bead = PointParticle( Segment.dsDNA_particle, pos, nts,
num_nts=nts, parent=self )
return bead
def _assign_particles_to_locations(self):
self.start3.particle = self.start5.particle = self.children[0]
self.end3.particle = self.end5.particle = self.children[-1]
self.start3.particle = self.start5.particle = self.beads[0]
self.end3.particle = self.end5.particle = self.beads[-1]
def _generate_atomic(self, atomic_model):
...
......@@ -277,7 +339,10 @@ class SingleStrandedSegment(Segment):
self._connect( other.container, Connection( my_end, other, type_="intrahelical" ) )
def _generate_one_bead(self, pos, nts):
def _get_num_beads(self, max_basepairs_per_bead, max_nucleotides_per_bead):
return (self.num_nts // max_nucleotides_per_bead) + 1
def _generate_one_bead(self, pos, nts, orientation=None):
return PointParticle( Segment.ssDNA_particle, pos, nts,
num_nts=nts, parent=self )
......@@ -290,9 +355,9 @@ class SingleStrandedSegment(Segment):
class SegmentModel(ArbdModel):
def __init__(self, segments = [],
max_basepairs_per_bead = 7,
max_nucleotides_per_bead = 4,
def __init__(self, segments=[], local_twist=True,
max_basepairs_per_bead=7,
max_nucleotides_per_bead=4,
dimensions=(1000,1000,1000), temperature=291,
timestep=50e-6, cutoff=50,
decompPeriod=10000, pairlistDistance=None,
......@@ -304,13 +369,13 @@ class SegmentModel(ArbdModel):
decompPeriod, pairlistDistance=None,
nonbondedResolution=0)
self.max_basepairs_per_bead = max_basepairs_per_bead # dsDNA
self.max_nucleotides_per_bead = max_nucleotides_per_bead # ssDNA
# self.max_basepairs_per_bead = max_basepairs_per_bead # dsDNA
# self.max_nucleotides_per_bead = max_nucleotides_per_bead # ssDNA
self.children = self.segments = segments
self._bonded_potential = dict() # cache bonded potentials
self._generate_bead_model(segments, max_nucleotides_per_bead, max_nucleotides_per_bead)
self._generate_bead_model(segments, max_basepairs_per_bead, max_nucleotides_per_bead, local_twist)
def _get_intrahelical_beads(self):
ret = []
......@@ -393,15 +458,16 @@ class SegmentModel(ArbdModel):
# ret
def _get_potential(self, type_, kSpring, d):
def _get_potential(self, type_, kSpring, d, max_potential = None):
key = (type_,kSpring,d)
if key not in self._bonded_potential:
if type_ == "bond":
self._bonded_potential[key] = HarmonicBond(kSpring,d)
self._bonded_potential[key] = HarmonicBond(kSpring,d, max_potential=max_potential)
elif type_ == "angle":
self._bonded_potential[key] = HarmonicAngle(kSpring,d) # , resolution = 1, maxForce=0.1)
self._bonded_potential[key] = HarmonicAngle(kSpring,d, max_potential=max_potential)
# , resolution = 1, maxForce=0.1)
elif type_ == "dihedral":
self._bonded_potential[key] = HarmonicDihedral(kSpring,d)
self._bonded_potential[key] = HarmonicDihedral(kSpring,d, max_potential=max_potential)
else:
raise Exception("Unhandled potential type '%s'" % type_)
return self._bonded_potential[key]
......@@ -409,18 +475,51 @@ class SegmentModel(ArbdModel):
return self._get_potential("bond", kSpring, d)
def get_angle_potential(self, kSpring, d):
return self._get_potential("angle", kSpring, d)
def get_dihedral_potential(self, kSpring, d):
return self._get_potential("dihedral", kSpring, d)
def get_dihedral_potential(self, kSpring, d, max_potential=None):
while d > 180: d-=360
while d < -180: d+=360
return self._get_potential("dihedral", kSpring, d, max_potential)
def _getParent(self, *beads ):
## TODO: test
if np.all( [b1.parent == b2.parent
for b1,b2 in zip(beads[::2],beads[1::2])] ):
return beads[0].parent
else:
return self
def _get_twist_spring_constant(self, sep):
""" sep in nt """
kT = 0.58622522 # kcal/mol
twist_persistence_length = 90 # set semi-arbitrarily as there is a large spread in literature
## <cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
## Assume A is small
## int[B_] := Normal[Integrate[ Series[Cos[x] Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]/
## Integrate[Series[Exp[-B x^2], {B, 0, 1}], {x, 0, \[Pi]}]]
## Actually, without assumptions I get fitFun below
## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
Lp = twist_persistence_length/0.34
fitFun = lambda x: np.real(erf( (4*np.pi*x + 1j)/(2*np.sqrt(x)) )) * np.exp(-1/(4*x)) / erf(2*np.sqrt(x)*np.pi) - np.exp(-sep/Lp)
k = opt.leastsq( fitFun, x0=np.exp(-sep/Lp) )
return k[0][0] * 2*kT*0.00030461742
def _generate_bead_model(self, segments,
max_basepairs_per_bead = 7,
max_nucleotides_per_bead = 4):
max_nucleotides_per_bead = 4,
local_twist=False
):
""" Generate beads """
for s in segments:
s._generate_beads( max_nucleotides_per_bead )
if local_twist:
s.local_twist = True
s._generate_beads( self, max_basepairs_per_bead, max_nucleotides_per_bead )
""" Combine beads at junctions as needed """
for s in segments:
......@@ -441,9 +540,11 @@ class SegmentModel(ArbdModel):
t.__dict__["nts"] = b.num_nts*2
elif key[0] == "S":
t.__dict__["nts"] = b.num_nts
elif key[0] == "O":
t.__dict__["nts"] = b.num_nts
else:
raise Exception("TODO")
print(t.nts)
# print(t.nts)
t.name = t.name + "%03d" % (100*t.nts)
beadtype_s[key] = b.type_ = t
......@@ -451,13 +552,12 @@ class SegmentModel(ArbdModel):
""" Add intrahelical bond potentials """
dists = dict() # built for later use
for b1,b2 in self._get_intrahelical_beads():
parent = self._getParent(b1,b2)
if b1.parent == b2.parent:
sep = 0.5*(b1.num_nts+b2.num_nts)
parent = b1.parent
else:
sep = 1
parent = self
conversion = 0.014393265 # units "pN/AA" kcal_mol/AA^2
if b1.type_.name[0] == "D" and b1.type_.name[0] == "D":
elastic_modulus = 1000 # pN http://markolab.bmbcb.northwestern.edu/marko/Cocco.CRP.02.pdf
......@@ -493,10 +593,7 @@ class SegmentModel(ArbdModel):
else:
sep += 1
if b1.parent == b2.parent and b2.parent == b3.parent:
parent = b1.parent
else:
parent = self
parent = self._getParent(b1,b2,b3)
kT = 0.58622522 # kcal/mol
if b1.type_.name[0] == "D" and b2.type_.name[0] == "D" and b3.type_.name[0] == "D":
......@@ -504,6 +601,8 @@ class SegmentModel(ArbdModel):
## <cos(q)> ~ 1 - 3/4A
## where A = k_spring / (2 kT)
k = 1.5 * kT * (1.0 / (1-np.exp(-float(sep)/147))) * 0.00030461742; # kcal_mol/degree^2
if local_twist:
k *= 0.5 # halve because orientation beads have similar springs
else:
## TODO: get correct number from ssDNA model
k = 1.5 * kT * (1.0 / (1-np.exp(-float(sep)/3))) * 0.00030461742; # kcal_mol/degree^2
......@@ -528,11 +627,48 @@ class SegmentModel(ArbdModel):
for b1 in beads:
exclusions.update( [(b1,b) for b in _recursively_get_beads_within(b1, 20, done=[b1])] )
for b1,b2 in exclusions:
if b1.parent == b2.parent:
parent = b1.parent
else:
parent = self
parent = self._getParent(b1,b2)
parent.add_exclusion( b1, b2 )
""" Twist potentials """
if local_twist:
## TODO: decide whether to add bond here
# """Add bonds between orientation bead and parent"""
# for s in self.segments:
# for b,o in zip(s.children[::2],s.children[1::2]):
# s.add_bond(
for b1 in beads:
if "orientation_bead" not in b1.__dict__: continue
for b2,sep in dists[b1]:
if "orientation_bead" not in b2.__dict__: continue
p1,p2 = [b.parent for b in (b1,b2)]
o1,o2 = [b.orientation_bead for b in (b1,b2)]
parent = self._getParent( b1, b2 )
""" Add heuristic 90 degree potential to keep orientation bead orthogonal """
k = (1.0/2) * 1.5 * kT * (1.0 / (1-np.exp(-float(sep)/147))) * 0.00030461742; # kcal_mol/degree^2
pot = self.get_angle_potential(k,90)
parent.add_angle(o1,b1,b2, pot)
parent.add_angle(b1,b2,o2, pot)
## TODO: improve this
twist_per_nt = 0.5 * (p1.twist_per_nt + p2.twist_per_nt)
angle = sep*twist_per_nt
if angle > 360 or angle < -360:
raise Exception("The twist between beads is too large")
k = self._get_twist_spring_constant(sep)
pot = self.get_dihedral_potential(k,angle,max_potential=1)
parent.add_dihedral(o1,b1,b2,o2, pot)
""" Add connection potentials """
## TODO
......
segmentmodel_example.py
View file @ 287af0d9
......@@ -14,7 +14,7 @@ PATH=/home/cmaffeo2/anaconda3/bin:$PATH; source activate cadnano
if __name__ == "__main__":
seg1 = DoubleStrandedSegment("strand", num_nts = 46)
seg1 = DoubleStrandedSegment("strand", num_nts = 46, local_twist=True)
seg2 = SingleStrandedSegment("strand",
start_position = seg1.end_position + np.array((5,0,5)),
......@@ -34,7 +34,10 @@ if __name__ == "__main__":
seg1.connect_end5(seg3)
seg1.connect_start3(seg3)
model = SegmentModel( [seg1, seg2, seg3],
model = SegmentModel( [seg1, seg2, seg3],
local_twist = True,
max_basepairs_per_bead = 5,
max_nucleotides_per_bead = 5,
dimensions=(5000,5000,5000),
)
......
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