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scg4py.py
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#Module name:
# scg4py (Systematic Coarse-Graining for Python)
# (https://github.com/saeedMRT/scg4py)
#Author:
# Saeed Mortezazadeh
#For using this module you need python 3 and the following prerequisite modules:
#numpy, scipy, matplotlib, and mdtraj for parsing the ’dcd’ and ’xtc’ trajectory file formats.
#For ease of use, you can append the path of scg4py code to PYHTONPATH in the .bashrc file.
#
#export PYTHONPATH="/path/to/scg4py/:$PYTHONPATH"
import numpy as _np
from scipy import interpolate as _spint
from scipy import linalg as _linalg
from scipy.special import comb as _comb
from matplotlib import pyplot as _plt
import time as _time
import os as _os
import subprocess as _subP
import glob as _glob
#####################################################
#####################################################
def _isfloat(x):
try:
float(x)
return True
except ValueError:
return False
#####################################################
#####################################################
def _Rstrip(inStr, Char):
outStr = str(inStr)
if isinstance(Char, list):
pass
else:
Char = [Char]
for i in range(len(Char)):
if outStr.endswith(Char[i]):
outStr = outStr[0: -1*len(Char[i])]
return outStr
#####################################################
#####################################################
def _writeLMPtab(sysName, Btab, BONDtypeSet, Atab, ANGLEtypeSet, Dtab,
DIHEDRALtypeSet, NBtab, NonBONDEDtypeSet, refinePot=False):
NB_tabName = sysName + '.tab_NB'
B_tabName = sysName + '.tab_B'
A_tabName = sysName + '.tab_A'
D_tabName = sysName + '.tab_D'
nPairType = len(NonBONDEDtypeSet)
nBondType = len(BONDtypeSet)
nAngleType = len(ANGLEtypeSet)
nDihedralType = len(DIHEDRALtypeSet)
if refinePot:
space1 = ' '
space2 = ' '
else:
space1 = ''
space2 = ' '
print(space1 + 'writing the tabulated potentials for LAMMPS simulation:')
if nBondType > 0:
with open(B_tabName,'w') as tabFile:
print(space2 + B_tabName)
tabFile.write('\n#################################################################\n')
tabFile.write('######################## BOND POTENTIALS ########################\n')
tabFile.write('#################################################################\n')
for n in range(nBondType):
tabFile.write('\nBond_{0:d}\n'.format(BONDtypeSet[n] + 1))
x = Btab[n, 0][1:]
pot = Btab[n, 1][1:]
force = Btab[n, 2][1:]
tabFile.write('N {0:d}\n\n'.format(len(x)))
for i in _np.arange(len(x)):
tabFile.write('{0:5d} {1:12.6e} {2:.14e} {3:.14e}\n'.format(i + 1, x[i], pot[i], force[i]))
tabFile.write('\n#################################################################\n')
if nAngleType > 0:
with open(A_tabName,'w') as tabFile:
print(space2 + A_tabName)
tabFile.write('\n#################################################################\n')
tabFile.write('####################### ANGLE POTENTIALS ########################\n')
tabFile.write('#################################################################\n')
for n in range(nAngleType):
tabFile.write('\nAngle_{0:d}\n'.format(ANGLEtypeSet[n] + 1))
x = Atab[n, 0]
pot = Atab[n, 1]
force = Atab[n, 2]
tabFile.write('N {0:d}\n\n'.format(len(x)))
for i in _np.arange(len(x)):
tabFile.write('{0:5d} {1:12.6e} {2:.14e} {3:.14e}\n'.format(i + 1, x[i], pot[i], force[i]))
tabFile.write('\n#################################################################\n')
if nDihedralType > 0:
with open(D_tabName,'w') as tabFile:
print(space2 + D_tabName)
tabFile.write('\n#################################################################\n')
tabFile.write('###################### DIHEDRAL POTENTIALS ######################\n')
tabFile.write('#################################################################\n')
for n in range(nDihedralType):
tabFile.write('\nDihedral_{0:d}\n'.format(DIHEDRALtypeSet[n] + 1))
x = Dtab[n, 0][0:-1]
pot = Dtab[n, 1][0:-1]
force = Dtab[n, 2][0:-1]
tabFile.write('N %d\n\n' % (_np.size(x)))
for i in _np.arange(len(x)):
tabFile.write('{0:5d} {1:12.6e} {2:.14e} {3:.14e}\n'.format(i + 1, x[i], pot[i], force[i]))
tabFile.write('\n#################################################################\n')
with open(NB_tabName, 'w') as tabFile:
print(space2 + NB_tabName)
tabFile.write('\n#################################################################\n')
tabFile.write('##################### NON-BONDED POTENTIALS #####################\n')
tabFile.write('#################################################################\n')
for n in range(nPairType):
tabFile.write('\nNon-Bonded_{0:s}-{1:s}\n'.format(NonBONDEDtypeSet[n, 0], NonBONDEDtypeSet[n, 1]))
x = NBtab[n, 0][1:]
pot = NBtab[n, 1][1:]
force = NBtab[n, 2][1:]
tabFile.write('N {0:d} R {1:.6e} {2:.6e}\n\n'.format(len(x), x[0], x[-1]))
for i in _np.arange(len(x)):
tabFile.write('{0:5d} {1:12.6e} {2:.14e} {3:.14e}\n'.format(i + 1, x[i], pot[i], force[i]))
tabFile.write('\n################################################\n')
tabFile.write('\n#################################################################\n')
tabFile.write('################ REPULSIVE NON-BONDED POTENTIALS ################\n')
tabFile.write('#################################################################\n')
tabFile.write('\n{0:s}\n'.format('NB_repulsive'))
cutoff = x[-1]
binNB = _np.mean(_np.diff(x))
npoint = _np.int(_np.round(cutoff / binNB)) + 1
x = _np.linspace(0, cutoff, npoint)[1:]
maxNB = 1000
rRep = 3.5
a = float(maxNB) / (2 * rRep)
pot = a * (x - rRep) ** 2
force = -1 * 2 * a * (x - rRep)
pot[x > rRep] = 0.0
force[x > rRep] = 0.0
tabFile.write('N {0:d} R {1:.6e} {2:.6e}\n\n'.format(len(x), x[0], x[-1]))
for i in _np.arange(len(x)):
tabFile.write('{0:5d} {1:12.6e} {2:.14e} {3:.14e}\n'.format(i + 1, x[i], pot[i], force[i]))
tabFile.write('\n################################################\n')
#####################################################
#####################################################
class _scg4pyError(Exception):
pass
#####################################################
#####################################################
class _cMAP:
def __init__(self, inFile):
fid = open(inFile, 'r')
mapFile = fid.readlines()
fid.close()
self.AATRAJ = None
self.CGTRAJ = None
trj_types = ['.gro', '.pdb', '.lammpstrj', '.xtc', '.dcd']
for line in mapFile:
if 'AATRAJ' in line.split('#')[0]:
lsplit = line.split('#')[0].split('=')[1].strip()
if any([lsplit.endswith(i) for i in trj_types]):
self.AATRAJ = lsplit
else:
mes = '\nAtomistic trajectory should be one of :\n [".gro", ".pdb", ".lammpstrj", ".xtc", ".dcd"]'
raise _scg4pyError(mes)
elif 'CGTRAJ' in line.split('#')[0]:
lsplit = line.split('#')[0].split('=')[1].strip()
if any([lsplit.endswith(i) for i in trj_types]):
self.CGTRAJ = lsplit
else:
mes = '\nCoarse-Grained trajectory should be one of :\n [".gro", ".pdb", ".lammpstrj", ".xtc"]'
raise _scg4pyError(mes)
elif 'MOL' in line.split('#')[0].upper():
lsplit0 = line.split('#')[0].split('=')[0].strip()
lsplit1 = line.split('#')[0].split('=')[1].strip()
if lsplit0.upper() == 'MOL':
self.MOL = _np.array(lsplit1.split(), dtype='<U5')
elif lsplit0.upper() == 'NMOL':
self.nMOL = _np.array(lsplit1.split(), dtype=int)
if len(self.MOL) > len(_np.unique(self.MOL)):
mes = 'redundancy in the molecules name.'
raise _scg4pyError(mes)
if len(self.MOL) != len(self.nMOL):
raise ValueError('The length of "MOL" and "NMOL" entry should be equal.\n')
self.ATOMch = _np.zeros(len(self.MOL), dtype=object)
self.ATOMms = _np.zeros(len(self.MOL), dtype=object)
self.nATOM = _np.zeros(len(self.MOL), dtype=int)
self.BEADname = _np.zeros(len(self.MOL), dtype=object)
self.BEADtype = _np.zeros(len(self.MOL), dtype=object)
self.LMPtype = _np.zeros(len(self.MOL), dtype=object)
self.BEADmap = _np.zeros(len(self.MOL), dtype=object)
self.BEADch = _np.zeros(len(self.MOL), dtype=object)
self.BEADms = _np.zeros(len(self.MOL), dtype=object)
self.nBEAD = _np.zeros(len(self.MOL), dtype=int)
self.BONDterm = _np.zeros(len(self.MOL), dtype=bool)
self.BONDtype = _np.zeros(len(self.MOL), dtype=object)
self.nBONDtype = _np.zeros(len(self.MOL), dtype=int)
self.BONDtypeName = _np.zeros(len(self.MOL), dtype=object)
self.BONDtypeIdx = _np.zeros(len(self.MOL), dtype=object)
self.ANGLEterm = _np.zeros(len(self.MOL), dtype=bool)
self.ANGLEtype = _np.zeros(len(self.MOL), dtype=object)
self.nANGLEtype = _np.zeros(len(self.MOL), dtype=int)
self.ANGLEtypeName = _np.zeros(len(self.MOL), dtype=object)
self.ANGLEtypeIdx = _np.zeros(len(self.MOL), dtype=object)
self.DIHEDRALterm = _np.zeros(len(self.MOL), dtype=bool)
self.DIHEDRALtype = _np.zeros(len(self.MOL), dtype=object)
self.nDIHEDRALtype = _np.zeros(len(self.MOL), dtype=int)
self.DIHEDRALtypeName = _np.zeros(len(self.MOL), dtype=object)
self.DIHEDRALtypeIdx = _np.zeros(len(self.MOL), dtype=object)
for mol in range(len(self.MOL)):
nbond_mol = 0
line = 0
while line < len(mapFile):
lsplit0 = mapFile[line].split('#')[0].split('=')[0].strip().split(':')
if len(lsplit0) == 3:
lsplit1 = mapFile[line].split('#')[0].split('=')[1].strip().upper()
lsplit0[0] = lsplit0[0].upper()
lsplit0[2] = lsplit0[2].upper()
if lsplit0[0] == 'MOL' and (lsplit0[2] == 'ATOM' or lsplit0[2] == 'MAPPING' or
lsplit0[2] == 'BOND' or lsplit0[2] == 'ANGLE' or lsplit0[
2] == 'DIHEDRAL'):
if lsplit0[1] in self.MOL:
pass
else:
mes = 'error in line {}.'.format(line + 1)
raise _scg4pyError(mes)
if lsplit0[0] == 'MOL' and lsplit0[1] == self.MOL[mol] and lsplit0[2] == 'ATOM':
natom = int(lsplit1)
n = 0
line += 1
atom_ch = _np.zeros(natom, dtype=float)
atom_ms = _np.zeros(natom, dtype=float)
while n < natom:
lco = mapFile[line].split('#')[0]
if 'MOL' in lco.upper():
raise TypeError('Error in "MOL:{}:ATOM" section'.format(self.MOL[mol]))
elif len(lco.split()) == 4:
try:
atom_ch[n] = lco.split()[2]
atom_ms[n] = lco.split()[3]
n += 1
except:
pass
line += 1
else:
line += 1
self.ATOMch[mol] = atom_ch
self.ATOMms[mol] = atom_ms
self.nATOM[mol] = natom
elif lsplit0[0] == 'MOL' and lsplit0[1] == self.MOL[mol] and lsplit0[2] == 'MAPPING':
nbead = int(lsplit1)
n = 0
line += 1
bead_name = _np.zeros(nbead, dtype='<U5')
bead_type = _np.zeros(nbead, dtype='<U5')
bead_map = _np.zeros(nbead, dtype=object)
while n < nbead:
lco = mapFile[line].split('#')[0]
if 'MOL' in lco:
raise TypeError('Error in "MOL:{}:MAPPING" section'.format(self.MOL[mol]))
elif len(lco.split(':')[0].split()) == 3:
try:
bead_name[n] = lco.split(':')[0].split()[1]
bead_type[n] = lco.split(':')[0].split()[2]
bead_map[n] = _np.array(lco.split(':')[1].split(), dtype=int)
n += 1
except:
pass
line += 1
else:
line += 1
self.BEADname[mol] = bead_name
self.BEADtype[mol] = bead_type
self.BEADmap[mol] = bead_map - 1
self.nBEAD[mol] = nbead
elif lsplit0[0] == 'MOL' and lsplit0[1] == self.MOL[mol] and lsplit0[2] == 'BOND':
nbond_type = int(lsplit1)
if nbond_type > 0:
self.BONDterm[mol] = True
elif nbond_type == 0:
self.BONDterm[mol] = False
else:
raise TypeError('Error in "MOL:{}:BOND" section'.format(self.MOL[mol]))
n = 0
line += 1
bond_type = _np.zeros(nbond_type, dtype=int)
bond_type_idx = _np.zeros(nbond_type, dtype=object)
while n < nbond_type:
lco = mapFile[line].split('#')[0]
if 'MOL' in lco:
raise TypeError('Error in "MOL:{}:BOND" section'.format(self.MOL[mol]))
elif len(lco.split(':')[0].split()) == 1:
try:
bond_type[n] = int(lco.split(':')[0])
temp = lco.split(':')[1].split(',')
temp = [i.split() for i in temp if bool(i.split())]
bond_type_idx[n] = _np.array(temp, dtype=int)
n += 1
except:
pass
line += 1
else:
line += 1
if nbond_type > 0:
self.BONDtype[mol] = bond_type - 1
self.BONDtypeIdx[mol] = bond_type_idx - 1
else:
self.BONDtype[mol] = _np.array([])
self.BONDtypeIdx[mol] = _np.array([])
self.nBONDtype[mol] = nbond_type
for i in range(nbond_type):
nbond_mol = nbond_mol + len(self.BONDtypeIdx[mol][i])
elif lsplit0[0] == 'MOL' and lsplit0[1] == self.MOL[mol] and lsplit0[2] == 'ANGLE':
if lsplit1 == 'YES':
if nbond_mol > 1:
self.ANGLEterm[mol] = True
else:
self.ANGLEterm[mol] = False
if not self.BONDterm[mol]:
self.ANGLEterm[mol] = False
elif lsplit1 == 'NO':
self.ANGLEterm[mol] = False
else:
raise TypeError('Error in "MOL:{}:ANGLE" section'.format(self.MOL[mol]))
elif lsplit0[0] == 'MOL' and lsplit0[1] == self.MOL[mol] and lsplit0[2] == 'DIHEDRAL':
if lsplit1 == 'YES':
if nbond_mol > 2:
self.DIHEDRALterm[mol] = True
else:
self.DIHEDRALterm[mol] = False
if not self.ANGLEterm[mol] or not self.BONDterm[mol]:
self.DIHEDRALterm[mol] = False
elif lsplit1 == 'NO':
self.DIHEDRALterm[mol] = False
else:
raise TypeError('Error in "MOL:{}:DIHEDRAL" section'.format(self.MOL[mol]))
line += 1
def do_classification(self):
TotAngles = _np.zeros(len(self.MOL), dtype=object)
TotAnglesType = _np.zeros(len(self.MOL), dtype=object)
TotAnglesTypeClass = _np.zeros([0, 2], dtype=int)
TotDihedral = _np.zeros(len(self.MOL), dtype=object)
TotDihedralType = _np.zeros(len(self.MOL), dtype=object)
TotDihedralTypeClass = _np.zeros([0, 3], dtype=int)
for mol in range(len(self.MOL)):
beadms = _np.zeros(self.nBEAD[mol])
beadch = _np.zeros(self.nBEAD[mol])
for n in range(self.nBEAD[mol]):
ind = self.BEADmap[mol][n]
mass = _np.sum(self.ATOMms[mol][ind])
charge = _np.sum(self.ATOMch[mol][ind])
if _np.round(charge, 3) == 0.0:
charge = 0.0
beadms[n] = _np.round(mass, 4)
beadch[n] = _np.round(charge, 3)
self.BEADch[mol] = beadch
self.BEADms[mol] = beadms
############################################
############################################
bondtype_name = _np.zeros([self.nBONDtype[mol], 2], dtype='U5')
for i in range(self.nBONDtype[mol]):
ind = self.BONDtypeIdx[mol][i][0]
A = self.BEADtype[mol][ind[0]]
B = self.BEADtype[mol][ind[1]]
bondtype_name[i] = [A, B]
self.BONDtypeName[mol] = bondtype_name
nAllBond = 0
for i in range(self.nBONDtype[mol]):
nAllBond = nAllBond + len(self.BONDtypeIdx[mol][i])
allBOND = _np.zeros([nAllBond, 2], dtype=int)
n = 0
for i in range(self.nBONDtype[mol]):
m = len(self.BONDtypeIdx[mol][i])
allBOND[n:n + m] = self.BONDtypeIdx[mol][i]
n += m
BONDtree = _np.zeros(self.nBEAD[mol], dtype=object)
for bead in range(self.nBEAD[mol]):
maplist = _np.array([], dtype=int)
maplist = _np.append(maplist, allBOND[allBOND[:, 0] == bead][:, 1])
maplist = _np.append(maplist, allBOND[allBOND[:, 1] == bead][:, 0])
maplist = _np.unique(maplist)
BONDtree[bead] = maplist
############################################
############################################
if self.ANGLEterm[mol]:
m = int(_comb(nAllBond, 2))
allangle = _np.zeros([m, 3], dtype=int)
n = 0
for i in range(self.nBEAD[mol]):
for j in BONDtree[i]:
if j != i:
for k in BONDtree[j]:
if k != i and k != j:
cmp1 = _np.any(_np.all(allBOND == [i, k], axis=1))
cmp2 = _np.any(_np.all(allBOND == [k, i], axis=1))
if not (cmp1 or cmp2):
cmp1 = _np.any(_np.all(allangle[0:n] == [i, j, k], axis=1))
cmp2 = _np.any(_np.all(allangle[0:n] == [k, j, i], axis=1))
if not (cmp1 or cmp2):
allangle[n, :] = [i, j, k]
n += 1
TotAngles[mol] = _np.delete(allangle, range(n, m), axis=0)
allangleType = _np.zeros([len(TotAngles[mol]), 2], dtype=int)
for i in range(len(TotAngles[mol])):
angId_1 = TotAngles[mol][i, 0]
angId_2 = TotAngles[mol][i, 1]
angId_3 = TotAngles[mol][i, 2]
for bdT in range(len(self.BONDtypeIdx[mol])):
comp1 = [angId_1, angId_2] == self.BONDtypeIdx[mol][bdT]
comp2 = [angId_2, angId_1] == self.BONDtypeIdx[mol][bdT]
cmp1 = _np.any(_np.all(comp1, axis=1))
cmp2 = _np.any(_np.all(comp2, axis=1))
if cmp1 or cmp2:
allangleType[i, 0] = self.BONDtype[mol][bdT]
comp1 = [angId_2, angId_3] == self.BONDtypeIdx[mol][bdT]
comp2 = [angId_3, angId_2] == self.BONDtypeIdx[mol][bdT]
cmp1 = _np.any(_np.all(comp1, axis=1))
cmp2 = _np.any(_np.all(comp2, axis=1))
if cmp1 or cmp2:
allangleType[i, 1] = self.BONDtype[mol][bdT]
TotAnglesType[mol] = allangleType
m = len(TotAnglesType[mol])
allangleTypeClass = _np.zeros([m, 2], dtype=int)
n = 0
for i in range(m):
ind1 = TotAnglesType[mol][i, 0]
ind2 = TotAnglesType[mol][i, 1]
cmp1 = _np.any(_np.all(allangleTypeClass[0:n] == [ind1, ind2], axis=1))
cmp2 = _np.any(_np.all(allangleTypeClass[0:n] == [ind2, ind1], axis=1))
if not (cmp1 or cmp2):
allangleTypeClass[n] = [ind1, ind2]
n += 1
allangleTypeClass = _np.delete(allangleTypeClass, range(n, m), axis=0)
self.nANGLEtype[mol] = len(allangleTypeClass)
TotAnglesTypeClass = _np.append(TotAnglesTypeClass, allangleTypeClass, axis=0)
else:
self.nANGLEtype[mol] = 0
############################################
############################################
if self.DIHEDRALterm[mol]:
m = int(_comb(nAllBond, 3))
alldihedral = _np.zeros([m, 4], dtype=int)
n = 0
for i in range(self.nBEAD[mol]):
for j in BONDtree[i]:
if j != i:
for k in BONDtree[j]:
if k != j and k != i:
for l in BONDtree[k]:
if l != i and l != j and l != k:
cmp1 = _np.any(_np.all(allBOND == [i, l], axis=1))
cmp2 = _np.any(_np.all(allBOND == [l, i], axis=1))
if not (cmp1 or cmp2):
comp1 = alldihedral[0:n] == [i, j, k, l]
comp2 = alldihedral[0:n] == [l, k, j, i]
cmp1 = _np.any(_np.all(comp1, axis=1))
cmp2 = _np.any(_np.all(comp2, axis=1))
if not (cmp1 or cmp2):
alldihedral[n, :] = [i, j, k, l]
n += 1
TotDihedral[mol] = _np.delete(alldihedral, range(n, m), axis=0)
alldihedralType = _np.zeros([len(TotDihedral[mol]), 3], dtype=int)
for i in range(_np.size(TotDihedral[mol], axis=0)):
dihId_1 = TotDihedral[mol][i, 0]
dihId_2 = TotDihedral[mol][i, 1]
dihId_3 = TotDihedral[mol][i, 2]
dihId_4 = TotDihedral[mol][i, 3]
for bdT in range(len(self.BONDtypeIdx[mol])):
comp1 = [dihId_1, dihId_2] == self.BONDtypeIdx[mol][bdT]
comp2 = [dihId_2, dihId_1] == self.BONDtypeIdx[mol][bdT]
cmp1 = _np.any(_np.all(comp1, axis=1))
cmp2 = _np.any(_np.all(comp2, axis=1))
if cmp1 or cmp2:
alldihedralType[i, 0] = self.BONDtype[mol][bdT]
comp1 = [dihId_2, dihId_3] == self.BONDtypeIdx[mol][bdT]
comp2 = [dihId_3, dihId_2] == self.BONDtypeIdx[mol][bdT]
cmp1 = _np.any(_np.all(comp1, axis=1))
cmp2 = _np.any(_np.all(comp2, axis=1))
if cmp1 or cmp2:
alldihedralType[i, 1] = self.BONDtype[mol][bdT]
comp1 = [dihId_3, dihId_4] == self.BONDtypeIdx[mol][bdT]
comp2 = [dihId_4, dihId_3] == self.BONDtypeIdx[mol][bdT]
cmp1 = _np.any(_np.all(comp1, axis=1))
cmp2 = _np.any(_np.all(comp2, axis=1))
if cmp1 or cmp2:
alldihedralType[i, 2] = self.BONDtype[mol][bdT]
TotDihedralType[mol] = alldihedralType
m = len(alldihedralType)
dihedralTypeClass = _np.zeros([m, 3], dtype=int)
n = 0
for i in range(m):
ind1 = TotDihedralType[mol][i, 0]
ind2 = TotDihedralType[mol][i, 1]
ind3 = TotDihedralType[mol][i, 2]
cmp1 = _np.any(_np.all(dihedralTypeClass[0:n] == [ind1, ind2, ind3], axis=1))
cmp2 = _np.any(_np.all(dihedralTypeClass[0:n] == [ind3, ind2, ind1], axis=1))
if not (cmp1 or cmp2):
dihedralTypeClass[n] = [ind1, ind2, ind3]
n += 1
dihedralTypeClass = _np.delete(dihedralTypeClass, range(n, m), axis=0)
self.nDIHEDRALtype[mol] = len(dihedralTypeClass)
TotDihedralTypeClass = _np.append(TotDihedralTypeClass, dihedralTypeClass, axis=0)
else:
self.nDIHEDRALtype[mol] = 0
#################################################################
#################################################################
massSeq = _np.concatenate(self.BEADms[:])
typeSeq = _np.concatenate(self.BEADtype[:])
lmpIdSeq = _np.zeros(len(typeSeq), dtype=int)
typeGroup = []
for i in range(len(typeSeq)):
if typeSeq[i] not in typeGroup:
typeGroup = _np.append(typeGroup, typeSeq[i])
tn = 1
for i in range(len(typeGroup)):
ind1 = typeSeq == typeGroup[i]
m_ind1_grp = []
for J in massSeq[ind1]:
if J not in m_ind1_grp:
m_ind1_grp = _np.append(m_ind1_grp, J)
for k in range(len(m_ind1_grp)):
ind2 = massSeq == m_ind1_grp[k]
ind = _np.logical_and(ind1, ind2)
lmpIdSeq[ind] = tn
tn += 1
ind = _np.append(0, _np.cumsum(self.nBEAD))
for mol in range(len(self.MOL)):
self.LMPtype[mol] = lmpIdSeq[ind[mol]:ind[mol + 1]]
#################################################################
#################################################################
m = len(TotAnglesTypeClass)
temp = _np.zeros([m, 2], dtype=int)
n = 0
for i in range(m):
ind1 = TotAnglesTypeClass[i, 0]
ind2 = TotAnglesTypeClass[i, 1]
cmp1 = _np.any(_np.all(temp[0:n] == [ind1, ind2], axis=1))
cmp2 = _np.any(_np.all(temp[0:n] == [ind2, ind1], axis=1))
if not (cmp1 or cmp2):
temp[n] = [ind1, ind2]
n += 1
TotAnglesTypeClass = _np.delete(temp, range(n, m), axis=0)
for mol in range(len(self.MOL)):
IDs_angletype = _np.zeros(self.nANGLEtype[mol], dtype=object)
angletype = _np.zeros(self.nANGLEtype[mol], dtype=int)
angletype_name = _np.zeros([self.nANGLEtype[mol], 3], dtype='U5')
if self.nANGLEtype[mol] > 0:
n = 0
for i in range(len(TotAnglesTypeClass)):
IDsTemp = _np.zeros([0, 3], dtype=int)
indT1 = TotAnglesTypeClass[i, 0]
indT2 = TotAnglesTypeClass[i, 1]
redundant = _np.all([indT1, indT2] == [indT2, indT1])
comp1 = TotAnglesType[mol] == [indT1, indT2]
comp2 = TotAnglesType[mol] == [indT2, indT1]
cmp1 = _np.all(comp1, axis=1)
cmp2 = _np.all(comp2, axis=1)
if _np.any(cmp1):
temp = TotAngles[mol][cmp1]
IDsTemp = _np.concatenate([IDsTemp, temp], axis=0)
ind1 = temp[0, 0]
ind2 = temp[0, 1]
ind3 = temp[0, 2]
A = self.BEADtype[mol][ind1]
B = self.BEADtype[mol][ind2]
C = self.BEADtype[mol][ind3]
angletype[n] = i
angletype_name[n] = [A, B, C]
IDs_angletype[n] = IDsTemp
n += 1
if _np.any(cmp2) and not redundant:
temp = TotAngles[mol][cmp2]
IDsTemp = _np.concatenate([IDsTemp, temp], axis=0)
ind1 = temp[0, 0]
ind2 = temp[0, 1]
ind3 = temp[0, 2]
A = self.BEADtype[mol][ind1]
B = self.BEADtype[mol][ind2]
C = self.BEADtype[mol][ind3]
angletype[n] = i
angletype_name[n] = [A, B, C]
IDs_angletype[n] = IDsTemp
n += 1
# IDsTemp = _np.delete(IDsTemp, 0, axis=0)
# IDs_angletype[n] = IDsTemp
# if _np.any(cmp1) or _np.any(cmp2):
# n += 1
self.ANGLEtypeIdx[mol] = IDs_angletype
self.ANGLEtype[mol] = angletype
self.ANGLEtypeName[mol] = angletype_name
else:
pass
# print('There is no angle interaction in the "' + self.MOL[mol] + '" molecule.')
########################################
########################################
m = len(TotDihedralTypeClass)
temp = _np.zeros([m, 3], dtype=int)
n = 0
for i in range(m):
ind = TotDihedralTypeClass[i]
cmp1 = _np.any(_np.all(temp[0:n] == ind, axis=1))
cmp2 = _np.any(_np.all(temp[0:n] == [ind[2], ind[1], ind[0]], axis=1))
if not (cmp1 or cmp2):
temp[n] = ind
n += 1
TotDihedralTypeClass = _np.delete(temp, range(n, m), axis=0)
for mol in range(len(self.MOL)):
IDs_dihedraltype = _np.zeros(self.nDIHEDRALtype[mol], dtype=object)
dihedraltype = _np.zeros(self.nDIHEDRALtype[mol], dtype=int)
dihedraltype_name = _np.zeros([self.nDIHEDRALtype[mol], 4], dtype='U5')
if self.nDIHEDRALtype[mol] > 0:
n = 0
for i in range(len(TotDihedralTypeClass)):
IDsTemp = _np.zeros([0, 4], dtype=int)
indT1 = TotDihedralTypeClass[i, 0]
indT2 = TotDihedralTypeClass[i, 1]
indT3 = TotDihedralTypeClass[i, 2]
redundant = _np.all([indT1, indT2, indT3] == [indT3, indT2, indT1])
comp1 = TotDihedralType[mol] == [indT1, indT2, indT3]
comp2 = TotDihedralType[mol] == [indT3, indT2, indT1]
cmp1 = _np.all(comp1, axis=1)
cmp2 = _np.all(comp2, axis=1)
if _np.any(cmp1):
temp = TotDihedral[mol][cmp1]
IDsTemp = _np.concatenate([IDsTemp, temp], axis=0)
ind1 = temp[0, 0]
ind2 = temp[0, 1]
ind3 = temp[0, 2]
ind4 = temp[0, 3]
A = self.BEADtype[mol][ind1]
B = self.BEADtype[mol][ind2]
C = self.BEADtype[mol][ind3]
D = self.BEADtype[mol][ind4]
dihedraltype[n] = i
dihedraltype_name[n] = [A, B, C, D]
IDs_dihedraltype[n] = IDsTemp
n += 1
if _np.any(cmp2) and not redundant:
temp = TotDihedral[mol][cmp2]
IDsTemp = _np.concatenate([IDsTemp, temp], axis=0)
ind1 = temp[0, 0]
ind2 = temp[0, 1]
ind3 = temp[0, 2]
ind4 = temp[0, 3]
A = self.BEADtype[mol][ind1]
B = self.BEADtype[mol][ind2]
C = self.BEADtype[mol][ind3]
D = self.BEADtype[mol][ind4]
dihedraltype[n] = i
dihedraltype_name[n] = [A, B, C, D]
IDs_dihedraltype[n] = IDsTemp
n += 1
# IDsTemp = _np.delete(IDsTemp, 0, axis=0)
# IDs_dihedraltype[n] = IDsTemp
# if _np.any(cmp1) or _np.any(cmp2):
# n += 1
self.DIHEDRALtypeIdx[mol] = IDs_dihedraltype
self.DIHEDRALtype[mol] = dihedraltype
self.DIHEDRALtypeName[mol] = dihedraltype_name
else:
pass
# print('There is no dihedral in the "' + self.MOL[mol] + '" molecule.')
#####################################################
#####################################################
class _cTRAJ:
def __init__(self, inFile, mode):
inFile = str(inFile)
self._mode = str(mode)
if inFile.endswith('.xtc'):
self.Type = 'XTC'
elif inFile.endswith('.gro'):
self.Type = 'GRO'
elif inFile.endswith('.pdb'):
self.Type = 'PDB'
elif inFile.endswith('.lammpstrj'):
self.Type = 'LMP'
elif inFile.endswith('.dcd'):
self.Type = 'DCD'
else:
raise _scg4pyError('trajectory should be one of: ".xtc", ".dcd", ".gro", ".pdb", ".lammpstrj"')
if self._mode == 'r':
if self.Type == 'XTC' or self.Type == 'DCD':
import mdtraj as _mdtraj
self._fid = _mdtraj.open(inFile, mode='r')
else:
self._fid = open(inFile, mode='r')
elif self._mode == 'w':
if self.Type == 'XTC' or self.Type == 'DCD':
import mdtraj as _mdtraj
self._fid = _mdtraj.open(inFile, mode='w')
else:
self._fid = open(inFile, mode='w')
else:
raise _scg4pyError('opening mode should be one of "r" or "w".')
self._setNone()
def _setNone(self):
self.time = None
self.timeStep = None
self.nAtom = None
self.atId = None
self.atName = None
self.atType = None
self.resId = None
self.resName = None
self.x = None
self.y = None
self.z = None
self.xs = None
self.ys = None
self.zs = None
self.xu = None
self.yu = None
self.zu = None
self.ix = None
self.iy = None
self.iz = None
self.fx = None
self.fy = None
self.fz = None
self.lmpBox = None
self.boxMat = None
self.boxCryst = None
self.eof = False
def close(self):
self._fid.close()
def read(self, nAtom=None):
self._setNone()
if self.Type == 'GRO':
self.readGROsnap(nAtom)
elif self.Type == 'PDB':
self.readPDBsnap(nAtom)
elif self.Type == 'XTC':
self.readXTCsnap(nAtom)
elif self.Type == 'LMP':
self.readLMPsnap(nAtom)
elif self.Type == 'DCD':
self.readDCDsnap(nAtom)
def write(self, modelN=None, sysName=None):
if self.Type == 'GRO':
self.writeGROsnap()
elif self.Type == 'PDB':
self.writePDBsnap(modelN, sysName)
elif self.Type == 'XTC':
self.writeXTCsnap()
elif self.Type == 'LMP':
self.writeLMPsnap()
elif self.Type == 'DCD':
self.writeDCDsnap()
def _box_mat2cryst(self):
if self.boxMat is not None:
lx, ly, lz, xy, xz, yz = self.boxMat[0], self.boxMat[1], self.boxMat[2], \
self.boxMat[3], self.boxMat[4], self.boxMat[5]
if lx == 0 or ly == 0 or lz == 0:
self.boxCryst = _np.zeros(6, dtype=_np.float32)
else:
a = lx
b = _np.sqrt(ly ** 2 + xy ** 2)
c = _np.sqrt(lz ** 2 + xz ** 2 + yz ** 2)
alpha = round(_np.rad2deg(_np.arccos((xy * xz + ly * yz) / (b * c))), 3)
beta = round(_np.rad2deg(_np.arccos(xz / c)), 3)
gamma = round(_np.rad2deg(_np.arccos(xy / b)), 3)
self.boxCryst = _np.array([a, b, c, alpha, beta, gamma], dtype=_np.float32)
else:
self.boxCryst = None
def _box_cryst2mat(self):
if len(self.boxCryst) is not None:
a, b, c, alpha, beta, gamma = self.boxCryst[0], self.boxCryst[1], self.boxCryst[2], \
self.boxCryst[3], self.boxCryst[4], self.boxCryst[5]
if a == 0 or b == 0 or c == 0:
self.boxMat = _np.zeros(6, dtype=_np.float32)
else:
lx = a
xy = b * _np.cos(_np.deg2rad(gamma))
xz = c * _np.cos(_np.deg2rad(beta))
ly = _np.sqrt(b ** 2 - xy ** 2)
yz = (b * c * _np.cos(_np.deg2rad(alpha)) - xy * xz) / ly
lz = _np.sqrt(c ** 2 - xz ** 2 - yz ** 2)
self.boxMat = _np.array([lx, ly, lz, xy, xz, yz], dtype=_np.float32)
else:
self.boxMat = None
def readGROsnap(self, nAtom=None):
try:
self.time = float(self._fid.readline().split('t=')[1].strip())
self.nAtom = int(self._fid.readline().strip())
if (nAtom is not None) and (self.nAtom != nAtom):
self.close()
raise _scg4pyError('Number of atoms in the structure and in the option file are not equal.')
self.resId = _np.zeros(self.nAtom, dtype=_np.int32)
self.resName = _np.zeros(self.nAtom, dtype='U5')
self.atName = _np.zeros(self.nAtom, dtype='U5')
self.atId = _np.zeros(self.nAtom, dtype=_np.int32)
self.x = _np.zeros(self.nAtom, dtype=_np.float32)
self.y = _np.zeros(self.nAtom, dtype=_np.float32)
self.z = _np.zeros(self.nAtom, dtype=_np.float32)
for i in _np.arange(self.nAtom):
line = self._fid.readline()
self.resName[i] = line[5:10].strip()
self.atName[i] = line[10:15].strip()
self.x[i] = float(line[20:28]) * 10
self.y[i] = float(line[28:36]) * 10
self.z[i] = float(line[36:44]) * 10
if i == 0:
self.resId[i] = 1
prevId = int(line[0:5])
else:
if int(line[0:5]) == prevId:
self.resId[i] = self.resId[i - 1]
else:
self.resId[i] = self.resId[i - 1] + 1
prevId = int(line[0:5])
self.atId = _np.arange(1, self.nAtom + 1)
VecComp = _np.array(self._fid.readline().split(), dtype=float)
VecComp = VecComp * 10
if _np.size(VecComp) == 3:
lx = VecComp[0]
ly = VecComp[1]
lz = VecComp[2]
xy = xz = yz = 0
else:
lx = VecComp[0]
ly = VecComp[1]
lz = VecComp[2]
xy = VecComp[5]
xz = VecComp[7]
yz = VecComp[8]
self.boxMat = _np.array([lx, ly, lz, xy, xz, yz], dtype=_np.float32)
self._box_mat2cryst()
except (IndexError, ValueError, TypeError, EOFError):
self.eof = True
def writeGROsnap(self):
cond = len(self.resId) == len(self.resName) == len(self.atName) == len(self.atId) == \
len(self.x) == len(self.y) == len(self.z) == self.nAtom
if not cond:
mess = '"gro" writing error: input variables are not compatible with each other.'
raise _scg4pyError(mess)
self._fid.write('Generated by SCG4PY program: t= {}\n'.format(self.time))
self._fid.write('{:6d}\n'.format(self.nAtom))
for i in _np.arange(len(self.atId)):
newResId = int(self.resId[i] % 1e5)
newAtId = int(self.atId[i] % 1e5)
self._fid.write('{0:5d}{1:<5s}{2:^5s}{3:5d}'.format(newResId, self.resName[i], self.atName[i], newAtId))
self._fid.write('{0:8.3f}{1:8.3f}{2:8.3f}\n'.format(self.x[i] / 10, self.y[i] / 10, self.z[i] / 10))
self.boxMat = self.boxMat / 10
lx, ly, lz, xy, xz, yz = self.boxMat[0], self.boxMat[1], self.boxMat[2], \
self.boxMat[3], self.boxMat[4], self.boxMat[5]
if xy == xz == yz == 0:
self._fid.write('{0:10.5f}{1:10.5f}{2:10.5f}\n'.format(lx, ly, lz))
else:
self._fid.write(
'{0:10.5f}{1:10.5f}{2:10.5f}{3:10.5f}{4:10.5f}{5:10.5f}{6:10.5f}{7:10.5f}{8:10.5f}\n'.format(
lx, ly, lz, 0, 0, xy, 0, xz, yz))
def readPDBsnap(self, nAtom=None):
try:
ftell = self._fid.tell()
self.boxCryst = _np.zeros(6, dtype=_np.float32)
self.time = 0.0
line = self._fid.readline()
while ('ATOM' not in line) and ('HETATM' not in line):
if ('TITLE' in line) and ('t=' in line):
x = line.split('t=')[1]
if _isfloat(x):
self.time = float(x)
else:
self.time = 0.0
elif 'CRYST1' in line:
a = float(line[6:15])
b = float(line[15:24])
c = float(line[24:33])
al = float(line[33:40])
bt = float(line[40:47])
gm = float(line[47:54])
self.boxCryst = _np.array([a, b, c, al, bt, gm], dtype=_np.float32)
line = self._fid.readline()
if self._fid.tell() != ftell:
ftell = self._fid.tell()
else:
raise EOFError
self._box_cryst2mat()
if any([i == 0 for i in self.boxMat]):
raise _scg4pyError('some snapshots do not have box information "CRYST1" section.')
self.nAtom = nAtom
self.resId = _np.zeros(self.nAtom, dtype=_np.int32)
self.resName = _np.zeros(self.nAtom, dtype='U5')
self.atName = _np.zeros(self.nAtom, dtype='U5')
self.atId = _np.zeros(self.nAtom, dtype=_np.int32)
self.x = _np.zeros(self.nAtom, dtype=_np.float32)
self.y = _np.zeros(self.nAtom, dtype=_np.float32)
self.z = _np.zeros(self.nAtom, dtype=_np.float32)
i = 0
while ('ENDMDL' not in line) and ('END' not in line):
if ('ATOM' in line) or ('HETATM' in line):
if (nAtom is not None) and (self.nAtom != nAtom):
self.close()
raise _scg4pyError('Number of atoms in the trajectory and in the option file are not equal.')
self.atId[i] = i + 1
self.atName[i] = line[12:16].strip()
self.resName[i] = line[17:21].strip()
if i == 0:
self.resId[i] = 1
prevId = int(line[22:26])
else:
if int(line[22:26]) == prevId:
self.resId[i] = self.resId[i - 1]
else:
self.resId[i] = self.resId[i - 1] + 1
prevId = int(line[22:26])
self.x[i] = line[30:38]
self.y[i] = line[38:46]
self.z[i] = line[46:54]
i += 1
line = self._fid.readline()
if self._fid.tell() != ftell:
ftell = self._fid.tell()
else:
raise EOFError
if (nAtom is not None) and (i != self.nAtom):
self.close()
raise _scg4pyError('Number of atoms in the trajectory and in the option file are not equal.')
except (IndexError, ValueError, TypeError, EOFError):
self.eof = True
def writePDBsnap(self, modelN=None, sysName=None):
cond = len(self.resId) == len(self.resName) == len(self.atName) == len(self.atId) == \
len(self.x) == len(self.y) == len(self.z) == self.nAtom
if not cond:
mess = '"pdb" writing error: input variables are not compatible with each other.'
raise _scg4pyError(mess)
if sysName is None:
sysName = ''
if modelN is None:
modelN = 1
if self.boxCryst is None:
self._box_mat2cryst()
self._fid.write('REMARK GENERATED BY SCG4PY\n')
self._fid.write('TITLE {0:} t={1:}\n'.format(sysName, self.time))
a, b, c, alpha, beta, gamma = self.boxCryst[0], self.boxCryst[1], self.boxCryst[2], \
self.boxCryst[3], self.boxCryst[4], self.boxCryst[5]
self._fid.write('{0:6s}{1:9.3f}{2:9.3f}{3:9.3f}{4:7.2f}{5:7.2f}{6:7.2f} {7:<11s}{8:4s}\n'.format(
'CRYST1', a, b, c, alpha, beta, gamma, 'P 1', '1'))
self._fid.write('{0:6} {1:4d}\n'.format('MODEL', int(modelN % 1e4)))
for i in _np.arange(self.nAtom):
self._fid.write('{0:6s}{1:5d} {2:^4s} {3:<4s} {4:4d} '.format(
'ATOM', int(self.atId[i] % 1e5), self.atName[i], self.resName[i], int(self.resId[i] % 1e4)))
self._fid.write(
'{0:8.3f}{1:8.3f}{2:8.3f} C\n'.format(self.x[i], self.y[i], self.z[i]))
self._fid.write('TER\nENDMDL\n')
def readXTCsnap(self, nAtom=None):
try:
snap = self._fid.read(1)
if len(snap[1]) != 0:
self.x = snap[0][0][:, 0] * 10
self.y = snap[0][0][:, 1] * 10
self.z = snap[0][0][:, 2] * 10
self.nAtom = len(self.x)
if (nAtom is not None) and (self.nAtom != nAtom):
self.close()
raise _scg4pyError('Number of atoms in the trajectory and in the option file are not equal.')
self.time = snap[1][0]
self.timeStep = snap[2][0]
lx = snap[3][0][0][0] * 10
ly = snap[3][0][1][1] * 10
lz = snap[3][0][2][2] * 10
xy = snap[3][0][1][0] * 10
xz = snap[3][0][2][0] * 10
yz = snap[3][0][2][1] * 10
self.boxMat = _np.array([lx, ly, lz, xy, xz, yz], dtype=_np.float32)
self._box_mat2cryst()
else:
self.eof = True
except:
self.eof = True
def writeXTCsnap(self):
if len(self.x) == len(self.y) == len(self.z):
pass
else:
mess = '"xtc" writing error: input variables are not compatible with each other.'
raise _scg4pyError(mess)
lx, ly, lz, xy, xz, yz = self.boxMat[0], self.boxMat[1], self.boxMat[2], \
self.boxMat[3], self.boxMat[4], self.boxMat[5]
time = _np.zeros(1, dtype=_np.float32)
step = _np.zeros(1, dtype=_np.int32)
box = _np.zeros([1, 3, 3], dtype=_np.float32)