Commit 5cb8536a authored by cmaffeo2's avatar cmaffeo2
Browse files

Updated import paths to use arbdmodel instead of (model.arbdmodel, coords, model.nonbonded).

parent 7bf73f95
import numpy as np
from scipy.optimize import newton
def minimizeRmsd(coordsB, coordsA, weights=None, maxIter=100):
## Going through many iterations wasn't really needed
tol = 1
count = 0
R = np.eye(3)
comB = np.zeros([3,])
cNext = coordsB
while tol > 1e-6:
q,cB,comA = _minimizeRmsd(cNext,coordsA, weights)
R = R.dot(quaternion_to_matrix(q))
assert( np.all(np.isreal( R )) )
comB += cB
cLast = cNext
cNext = (coordsB-comB).dot(R)
tol = np.sum(((cNext-cLast)**2)[:]) / np.max(np.shape(coordsB))
if count > maxIter:
Exception("Exceeded maxIter (%d)" % maxIter)
count += 1
print("%d iterations",count)
return R, comB, comA
def minimizeRmsd(coordsB, coordsA, weights=None):
q,comA,comB = _minimizeRmsd(coordsB, coordsA, weights)
assert( np.all(np.isreal( q )) )
return quaternion_to_matrix(q),comA,comB
## http://onlinelibrary.wiley.com/doi/10.1002/jcc.21439/full
def _minimizeRmsd(coordsB, coordsA, weights=None):
A = coordsA
B = coordsB
shapeA,shapeB = [np.shape(X) for X in (A,B)]
for s in (shapeA,shapeB): assert( len(s) == 2 )
A,B = [X.T if s[1] > s[0] else X for X,s in zip([A,B],(shapeA,shapeB))] # TODO: print warning
shapeA,shapeB = [np.shape(X) for X in (A,B)]
assert( shapeA == shapeB )
for X,s in zip((A,B),(shapeA,shapeB)):
assert( s[1] == 3 and s[0] >= s[1] )
# if weights is None: weights = np.ones(len(A))
if weights is None:
comA,comB = [np.mean( X, axis=0 ) for X in (A,B)]
else:
assert( len(weights[:]) == len(B) )
W = np.diag(weights)
comA,comB = [np.sum( W.dot(X), axis=0 ) / np.sum(W) for X in (A,B)]
A = np.array( A-comA )
B = np.array( B-comB )
if weights is None:
s = A.T.dot(B)
else:
s = A.T.dot(W.dot(B))
sxx,sxy,sxz = s[0,:]
syx,syy,syz = s[1,:]
szx,szy,szz = s[2,:]
K = [[ sxx+syy+szz, syz-szy, szx-sxz, sxy-syx],
[syz-szy, sxx-syy-szz, sxy+syx, sxz+szx],
[szx-sxz, sxy+syx, -sxx+syy-szz, syz+szy],
[sxy-syx, sxz+szx, syz+szy, -sxx-syy+szz]]
K = np.array(K)
# GA = np.trace( A.T.dot(W.dot(A)) )
# GB = np.trace( B.T.dot(W.dot(B)) )
## Finding GA/GB can be done more quickly
# I = np.eye(4)
# x0 = (GA+GB)*0.5
# vals = newtoon(lambda x: np.det(K-x*I), x0 = x0)
vals, vecs = np.linalg.eig(K)
i = np.argmax(vals)
q = vecs[:,i]
# RMSD = np.sqrt( (GA+GB-2*vals[i]) / len(A) )
# print("CHECK:", K.dot(q)-vals[i]*q )
return q, comB, comA
def quaternion_to_matrix(q):
assert(len(q) == 4)
## It looks like the wikipedia article I used employed a less common convention for q (see below
## http://en.wikipedia.org/wiki/Rotation_formalisms_in_three_dimensions#Rotation_matrix_.E2.86.94_quaternion
# q1,q2,q3,q4 = q
# R = [[1-2*(q2*q2 + q3*q3), 2*(q1*q2 - q3*q4), 2*(q1*q3 + q2*q4)],
# [ 2*(q1*q2 + q3*q4), 1-2*(q1*q1 + q3*q3), 2*(q2*q3 - q1*q4)],
# [ 2*(q1*q3 - q2*q4), 2*(q1*q4 + q2*q3), 1-2*(q2*q2 + q1*q1)]]
q = q / np.linalg.norm(q)
q0,q1,q2,q3 = q
R = [[1-2*(q2*q2 + q3*q3), 2*(q1*q2 - q3*q0), 2*(q1*q3 + q2*q0)],
[ 2*(q1*q2 + q3*q0), 1-2*(q1*q1 + q3*q3), 2*(q2*q3 - q1*q0)],
[ 2*(q1*q3 - q2*q0), 2*(q1*q0 + q2*q3), 1-2*(q2*q2 + q1*q1)]]
return np.array(R)
def quaternion_from_matrix( R ):
e1 = R[0]
e2 = R[1]
e3 = R[2]
# d1 = 0.5 * np.sqrt( 1+R[0,0]+R[1,1]+R[2,2] )
# d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
# d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
# d2 = 0.5 * np.sqrt( 1+R[0,0]-R[1,1]-R[2,2] )
d1 = 1+R[0,0]+R[1,1]+R[2,2]
d2 = 1+R[0,0]-R[1,1]-R[2,2]
d3 = 1-R[0,0]+R[1,1]-R[2,2]
d4 = 1-R[0,0]-R[1,1]+R[2,2]
maxD = max((d1,d2,d3,d4))
d = 0.5 / np.sqrt(maxD)
if d1 == maxD:
return np.array(( 1.0/(4*d),
d * (R[2,1]-R[1,2]),
d * (R[0,2]-R[2,0]),
d * (R[1,0]-R[0,1]) ))
elif d2 == maxD:
return np.array(( d * (R[2,1]-R[1,2]),
1.0/(4*d),
d * (R[0,1]+R[1,0]),
d * (R[0,2]+R[2,0]) ))
elif d3 == maxD:
return np.array(( d * (R[0,2]-R[2,0]),
d * (R[0,1]+R[1,0]),
1.0/(4*d),
d * (R[1,2]+R[2,1]) ))
elif d4 == maxD:
return np.array(( d * (R[1,0]-R[0,1]),
d * (R[0,2]+R[2,0]),
d * (R[1,2]+R[2,1]),
1.0/(4*d) ))
def rotationAboutAxis(axis,angle, normalizeAxis=True):
if normalizeAxis: axis = axis / np.linalg.norm(axis)
angle = angle * 0.5 * np.pi/180
cos = np.cos( angle )
sin = np.sin( angle )
q = [cos] + [sin*x for x in axis]
return quaternion_to_matrix(q)
def readArbdCoords(fname):
coords = []
with open(fname) as fh:
for line in fh:
coords.append([float(x) for x in line.split()[1:]])
return np.array(coords)
def readAvgArbdCoords(psf,pdb,dcd,rmsdThreshold=3.5):
import MDAnalysis as mda
usel = mda.Universe(psf, dcd)
sel = usel.select_atoms("name D*")
# r0 = ref.xyz[0,ids,:]
ts = usel.trajectory[-1]
r0 = sel.positions
pos = []
for t in range(ts.frame-1,-1,-1):
usel.trajectory[t]
R,comA,comB = minimizeRmsd(sel.positions,r0)
r = np.array( [(r-comA).dot(R)+comB for r in sel.positions] )
rmsd = np.mean( (r-r0)**2 )
r = np.array( [(r-comA).dot(R)+comB for r in usel.atoms.positions] )
pos.append( r )
if rmsd > rmsdThreshold**2:
break
t0=t+1
print( "Averaging coordinates in %s after frame %d" % (dcd, t0) )
pos = np.mean(pos, axis=0)
return pos
def unit_quat_conversions():
for axis in [[0,0,1],[1,1,1],[1,0,0],[-1,-2,0]]:
for angle in np.linspace(-180,180,10):
R = rotationAboutAxis(axis, angle)
R2 = quaternion_to_matrix( quaternion_from_matrix( R ) )
if not np.all( np.abs(R-R2) < 0.01 ):
import pdb
pdb.set_trace()
quaternion_to_matrix( quaternion_from_matrix( R ) )
if __name__ == "__main__":
unit_quat_conversions()
import json
import numpy as np
import copy
from ..coords import rotationAboutAxis
from .arbdmodel import Group, PointParticle, ParticleType
from ..arbdmodel.coords import rotationAboutAxis
from ..arbdmodel import Group, PointParticle, ParticleType
from .. import get_resource_path
seqComplement = dict(A='T',G='C')
......
......@@ -3,9 +3,9 @@ import scipy.optimize as opt
from scipy.interpolate import interp1d
from scipy.signal import savgol_filter as savgol
from mrdna.model.nonbonded import NonbondedScheme
from mrdna import get_resource_path
from mrdna.config import CACHE_DIR
from ..arbdmodel.nonbonded import NonbondedScheme
from .. import get_resource_path
from ..config import CACHE_DIR
from scipy.optimize import curve_fit
from pathlib import Path
......
......@@ -5,7 +5,7 @@ import os,sys
from glob import glob
import re
from ..coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
from ..arbdmodel.coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
from ..model.dna_sequence import m13 as m13seq
......
import numpy as np
import sys
import re
from ..coords import rotationAboutAxis, minimizeRmsd
from ..arbdmodel.coords import rotationAboutAxis, minimizeRmsd
from ..version import maintainer
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
......@@ -310,8 +310,8 @@ def write_pdb_psf(bases, prefix):
""" Function for debugging .ma parser """
from ..model.arbdmodel import ArbdModel,ParticleType, PointParticle, Group
from ..model.nonbonded import HarmonicBond
from ..arbdmodel import ArbdModel,ParticleType, PointParticle, Group
from ..arbdmodel.nonbonded import HarmonicBond
types = {c:ParticleType(c.upper(), mass=1,radius=1) for c in "bfuxyzs"}
bond=HarmonicBond(k=0,r0=1)
......
......@@ -6,7 +6,7 @@ import os,sys
import scipy
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
from ..coords import quaternion_from_matrix
from ..arbdmodel.coords import quaternion_from_matrix
from .. import get_resource_path
ref_stack_position = np.array((-2.41851735, -0.259761333, 3.39999978))
......
......@@ -2,9 +2,9 @@ import pdb
from pathlib import Path
import numpy as np
import random
from .model.arbdmodel import PointParticle, ParticleType, Group, ArbdModel
from .coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
from .model.nonbonded import *
from .arbdmodel import PointParticle, ParticleType, Group, ArbdModel
from .arbdmodel.coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
from .arbdmodel.nonbonded import *
from copy import copy, deepcopy
from .model.nbPot import nbDnaScheme
......@@ -1545,14 +1545,16 @@ class SegmentModel(ArbdModel):
timestep=50e-6, cutoff=50,
decompPeriod=10000, pairlistDistance=None,
nonbondedResolution=0, DEBUG=0,
integrator='Brown',
debye_length = None,
extra_bd_file_lines = "",
):
self.DEBUG = DEBUG
if DEBUG > 0: print("Building ARBD Model")
ArbdModel.__init__(self,segments,
dimensions, temperature, timestep, cutoff,
decompPeriod, pairlistDistance=None,
dimensions, temperature,
timestep, integrator,
cutoff, decompPeriod, pairlistDistance=None,
nonbondedResolution = 0,
extra_bd_file_lines = extra_bd_file_lines
)
......
import os
import tempfile
from .coords import readArbdCoords, readAvgArbdCoords
from .arbdmodel.coords import readArbdCoords, readAvgArbdCoords
import shutil
from . import get_resource_path
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment