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QresFEP.py
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QresFEP.py
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import argparse
import re
import os
import shutil
import sys
import glob
import functions as f
import settings as s
import IO
class Run(object):
"""
Setup residue FEPs using either a single or dual topology approach
"""
def __init__(self, cofactor, mutation, include, forcefield, windows,
sampling, system, cluster, temperature, replicates, dual,
preplocation, start, *args, **kwargs):
self.cofactor = [cofactor]
# Check whether all required files are there:
required = ['protein.pdb', 'water.pdb', 'protPREP.log']
if self.cofactor[0] != None:
extension = ['.pdb', '.lib', '.prm']
for filename in self.cofactor:
for line in extension:
required.append(filename + line)
for filename in required:
if os.path.exists(filename) == False:
required = ' '.join(required)
print("ERROR: {} are required files, exiting now.".format(required))
sys.exit()
if windows == None:
self.windows = s.WINDOWS
else:
self.windows = int(windows)
if sampling == None:
self.sampling = s.SAMPLING
else:
self.sampling = sampling
if temperature == None:
self.temperature = s.TEMPERATURE
else:
self.temperature = temperature
if replicates == None:
self.replicates = s.REPLICATES
else:
self.replicates = replicates
tmp = mutation.split(':')
if len(tmp) == 2:
self.chain = tmp[0]
self.mutation = re.split('(\d+)', tmp[1])
else:
self.chain = ' '
self.mutation = re.split('(\d+)', tmp[0])
self.include = include
self.forcefield = forcefield
self.preplocation = preplocation
self.lambdas = []
self.CYX = []
self.PDB = {}
self.PDB2Q = {}
self.systemsize = 0
self.system = system
self.cluster = cluster
self.FEPlist = []
self.dual = dual
self.start = start
self.dualMUT = {'0':[], '1':[]}
self.nonAA = False
self.replacements = {'ATOM_START_LIG1':'1',
'WATER_RESTRAINT':'',
'TEMP_VAR':self.temperature,
'RUN_VAR':self.replicates,
'RUNFILE':'run' + self.cluster + '.sh'
}
if self.start == '1':
self.replacements['EQ_LAMBDA'] = '1.000 0.000'
if self.start == '0.5':
self.replacements['EQ_LAMBDA'] = '0.500 0.500'
print(self.chain)
def checkFEP(self):
if len(self.mutation[0]) == 1:
AA_from = IO.AA(self.mutation[0])
else:
AA_from = self.mutation[0]
try:
if len(self.mutation[2]) == 1:
AA_to = IO.AA(self.mutation[2])
else:
AA_to = self.mutation[2]
except:
print("residue not found in library, assuming non-natural AA")
AA_to = 'X'
self.nonAA = True
mutation = '{}{}{}'.format(*self.mutation)
FEPdir = s.FF_DIR + '/.FEP/' + self.forcefield + '/' + AA_from + '_' + AA_to
if self.dual == True:
print('Generating dual topology inputfiles')
self.FEPlist = ['FEP1.fep']
self.FEPdir = None
elif not os.path.exists(FEPdir):
print('FATAL: no FEP files found for the {} mutation' \
'in {} exiting now.'.format(mutation,
FEPdir))
sys.exit()
else:
for line in sorted(glob.glob(FEPdir + '/FEP*.fep')):
line = line.split('/')
self.FEPlist.append(line[-1])
self.FEPdir = FEPdir
def create_environment(self):
self.directory = 'FEP_{}{}{}'.format(*self.mutation)
if not os.path.exists(self.directory):
os.makedirs(self.directory)
os.makedirs(self.directory + '/inputfiles')
files = {self.directory + '/inputfiles/' + self.forcefield + '.lib': \
s.FF_DIR + '/' + self.forcefield + '.lib',
}
if self.cofactor[0] != None:
for filename in self.cofactor:
files[self.directory + '/inputfiles/' + filename + '.lib'] = filename + '.lib'
for key in files:
shutil.copy(files[key], key)
def read_input(self):
block = 0
with open('protPREP.log') as infile:
for line in infile:
line = line.split()
if len(line) > 1:
if line[1] == 'center:':
self.sphere = line[2:]
if line[1] == 'radius:':
self.radius = line[2]
self.replacements['SPHERE'] = self.radius
if line[0] == 'Q_CYS1':
block = 1
if line[0] == 'pdbfile':
block = 2
if line[0][0] == '-':
block = 0
if block == 1:
if line[0].isdigit():
self.CYX.append([line[0], line[1]])
if block == 2 and len(line) > 2:
chain = line[2]
if chain not in self.PDB2Q:
self.PDB2Q[chain] = {}
self.PDB2Q[chain][line[1]] = line[0]
def readpdb(self):
atnr = 0
if len(self.mutation[2]) == 1:
if self.nonAA != True:
self.MUTresn = '{}2{}'.format(self.mutation[0],self.mutation[2])
else:
self.MUTresn = '{}2{}'.format(self.mutation[0],'X')
elif len(self.mutation[2]) == 3:
self.MUTresn = '{}2{}'.format(IO.AA(self.mutation[0]),IO.AA(self.mutation[2]))
#self.backbone = []
self.backbone = ['C', 'O', 'CA', 'N', 'H', 'HA']
# Read in the mutant residue
if self.dual == True:
MUT = []
with open(self.mutation[2] + '.pdb') as infile:
for line in infile:
line = IO.pdb_parse_in(line)
# The residue name should match the mutant residue number
# relative to Q numbering from protPREP.log
line[6] = int(self.PDB2Q[self.mutation[1]])
if line[2] in self.backbone:
continue
else:
MUT.append(line)
pdb_files = ['protein.pdb']
if self.cofactor[0] != None:
for line in self.cofactor:
pdb_files.append(line + '.pdb')
for pdb_file in pdb_files:
with open(pdb_file) as infile:
for line in infile:
if line.startswith(self.include):
atnr += 1
line = IO.pdb_parse_in(line)
if pdb_file != 'protein.pdb':
line[6] = resoffset + 1
line[1] = self.systemsize
line[1] = atnr
# Change to hybrid residue name
if self.dual == True:
if str(line[6]) == self.PDB2Q[self.mutation[1]]:
line[4] = self.MUTresn
# Generate the dual topology residue in the PDB dictionary
# Construct the PDB dictionary
try:
self.PDB[line[6]].append(line)
except:
self.PDB[line[6]] = [line]
if self.dual == True:
if str(line[6]) == self.PDB2Q[self.mutation[1]]:
if line[2] == 'O':
for MUTat in MUT:
atnr += 1
if MUTat[2] not in self.backbone:
# Atom name cannot be longer than 4 characters
#if len(MUTat[2]) <= 3:
# MUTat[2] = MUTat[2] + 'x'
#elif len(MUTat[2]) == 4:
# MUTat[2] = MUTat[2][0:1] + 'x'
MUTat[2] = MUTat[2].lower()
MUTat[1] = atnr
MUTat[4] = self.MUTresn
try:
self.PDB[MUTat[6]].append(MUTat)
except:
self.PDB[MUTat[6]] = [MUTat]
self.dualMUT['0'].append(MUTat)
self.dualMUT['1'].append(line)
self.systemsize += 1
resoffset = len(self.PDB)
def create_dual_lib(self):
FFlib = {}
self.merged_lib = {}
replacements = {}
if self.dual == False:
return None
headers =['[atoms]',
'[bonds]',
'[connections]',
'[impropers]',
'[info]'
]
if self.forcefield[0:4] == 'OPLS':
headers.append('[charge_groups]')
libfiles = [s.FF_DIR + '/' + self.forcefield + '.lib']
if self.nonAA == True:
libfiles.append(self.mutation[2] + '.lib')
for libfile in libfiles:
with open(libfile) as infile:
for line in infile:
if line[0] == '*':
continue
if line[0] == '{':
RESname = line.split('}')[0][1:]
continue
try:
FFlib[RESname].append(line)
except:
FFlib[RESname] = [line]
# Read the WT residue
if len(self.mutation[0]) == 1:
AA = AA(self.mutation[0])
else:
AA = self.mutation[0]
for line in FFlib[AA]:
if line.strip() in headers:
header = line.strip()
self.merged_lib[header] = []
else:
self.merged_lib[header].append(line)
# Add CA CBx bond
self.merged_lib['[bonds]'].append(' CA cb\n')
## Read the mutant residue
# Construct atom name replacements
if len(self.mutation[2]) == 1:
AA = IO.AA(self.mutation[2])
else:
AA = self.mutation[2]
for line in FFlib[AA]:
line = line.strip()
line = line.split()
if line != headers[0]:
if len(line) > 2:
atom = line[1]
if atom != 'H':
replacements[atom] = atom.lower()
if line == header[1]:
break
for line in FFlib[AA]:
if line.strip() in headers:
header = line.strip()
if line[0] == '!':
continue
if len(line.split()) < 2:
continue
else:
# connection flag only needs to be there once
if header == headers[2]:
continue
# Remove overlapping backbone definitions
if line.split()[0] == 'O' \
or line.split()[0] == 'C' \
or line.split()[0] == 'CA' \
or line.split()[0] == 'N' \
or line.split()[0] == 'H' \
or line.split()[0] == 'HA':
continue
if line.split()[1] == 'O' \
or line.split()[1] == 'C' \
or line.split()[1] == 'CA' \
or line.split()[1] == 'N' \
or line.split()[1] == 'H' \
or line.split()[1] == 'HA':
continue
# Merge the library on the reference
line = IO.replace(line, replacements)
self.merged_lib[header].append(line)
# Write out the merged library file
out = self.directory + '/inputfiles/' + self.MUTresn + '.lib'
with open(out, 'w') as outfile:
self.merged_lib['[charge_groups]'] = []
cnt = 0
outfile.write('{' + self.MUTresn + '}\n\n')
for header in headers:
outfile.write('\n ' + header + '\n')
if not header in self.merged_lib:
continue
for line in self.merged_lib[header]:
if header == '[atoms]':
cnt += 1
line = line.split()
outfile.write(' {:2d} {:<10}{:<10}{:<10}\n'.format(cnt,
line[1],
line[2],
line[3]))
else:
outfile.write(line)
def get_zeroforcebonded(self):
if self.dual == False:
return None
self.zerofk = {'[angles]':[],
'[bonds]':[],
'[impropers]':[],
'[torsions]':[]
}
prmfile = [s.FF_DIR + '/' + self.forcefield + '.prm']
libfile = self.directory + '/inputfiles/' + self.MUTresn + '.lib'
headers =['[options]',
'[atom_types]',
'[bonds]',
'[angles]',
'[torsions]',
'[impropers]'
]
# Write tmp qprep.inp and prm file
if self.nonAA == True:
prmfile.append(self.mutation[2] + '.prm')
prms = IO.read_prm(prmfile)
prm_tmp = self.directory + '/inputfiles/tmp.prm'
qprep_tmp = self.directory + '/inputfiles/tmp.inp'
pdb_tmp = self.directory + '/inputfiles/tmp.pdb'
# Write out PDB file
with open(pdb_tmp, 'w') as outfile:
mutPDB = self.PDB[int(self.PDB2Q[self.mutation[1]])]
for atom in mutPDB:
outfile.write(IO.pdb_parse_out(atom) + '\n')
with open(prm_tmp, 'w') as outfile:
for key in headers:
outfile.write(key + '\n')
for line in prms[key]:
outfile.write(line)
with open(qprep_tmp, 'w') as outfile:
outfile.write('rl {}\n'.format(libfile.split('/')[-1]))
outfile.write('rprm {}\n'.format(prm_tmp.split('/')[-1]))
outfile.write('rp {}\n'.format(pdb_tmp.split('/')[-1]))
outfile.write('boundary 1 {} {} {} {}\n'.format(self.sphere[0],
self.sphere[1],
self.sphere[2],
self.radius))
outfile.write('maketop tmp.top\n'.format(pdb_tmp))
outfile.write('q')
# run qprep to get bonded parameters to be set to zero
os.chdir(self.directory + '/inputfiles/')
qprep = s.Q_DIR[self.preplocation] + 'qprep'
options = ' < tmp.inp > tmp.out'
# Somehow Q is very annoying with this < > input style so had to implement
# another function that just calls os.system instead of using the preferred
# subprocess module....
IO.run_command(qprep, options, string = True)
with open('tmp.out') as infile:
for line in infile:
line = line.split()
if len(line) < 3:
continue
if line[1] != 'Missing':
continue
# Create zero fk angles
if line[2] == 'angle':
angle_prm = '{:11}{:11}{:11}{: 8.2f}{:>12.7}\n'.format(line[-3],
line[-2],
line[-1],
0.0,
110.0)
self.zerofk['[angles]'].append(angle_prm)
# Create zero fk torsions
if line[2] == 'torsion':
torsion_prm='{:11}{:11}{:11}{:11}{:<10.3f}{: d}.000{:>10s}{:>10s}\n'.format(line[-4],
line[-3],
line[-2],
line[-1],
0.0,
1,
'0.000',
'1')
self.zerofk['[torsions]'].append(torsion_prm)
# ADD REMOVE FUNCTIONS FOR TMP FILES HERE
# for tmp in glob.glob('tmp*'):
# os.remove(tmp)
os.chdir('../../')
def merge_prm(self):
headers =['[options]',
'[atom_types]',
'[bonds]',
'[angles]',
'[torsions]',
'[impropers]'
]
prmfiles = [s.FF_DIR + '/' + self.forcefield + '.prm']
if self.cofactor[0] != None:
for filename in self.cofactor:
prmfiles.append(filename + '.prm')
if self.nonAA == True:
prmfiles.append(self.mutation[2] + '.prm')
prms = IO.read_prm(prmfiles)
prm_merged = self.directory + '/inputfiles/' + self.forcefield + '_merged.prm'
self.prm_merged = self.forcefield + '_merged.prm'
with open (prm_merged, 'w') as outfile:
for key in headers:
outfile.write(key + '\n')
for line in prms[key]:
outfile.write(line)
if self.dual == True:
if key in self.zerofk:
outfile.write('! Zero order bonds dual topology\n')
for line in self.zerofk[key]:
outfile.write(line)
outfile.write('\n')
def write_pdb(self):
PDBout = self.directory + '/inputfiles/complex.pdb'
self.PDBout = 'complex.pdb'
with open(PDBout, 'w') as outfile:
for key in self.PDB:
for line in self.PDB[key]:
outline = IO.pdb_parse_out(line) + '\n'
outfile.write(outline)
def select_waters(self):
src = 'water.pdb'
tgt = self.directory + '/inputfiles/water.pdb'
cofactor_coordinates = []
waters_remove = []
waters = {}
if self.cofactor[0] != None:
for line in self.cofactor:
with open(line + '.pdb') as infile:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
cofactor_coordinates.append([line[8], line[9], line[10]])
with open (src) as infile, open (tgt, 'w') as outfile:
outfile.write('{} SPHERE\n'.format(self.radius))
for line in infile:
line = IO.pdb_parse_in(line)
coord_wat = [line[8], line[9], line[10]]
try:
waters[line[6]].append(line)
except:
waters[line[6]] = [line]
for coord_co in cofactor_coordinates:
if f.euclidian_overlap(coord_wat, coord_co, 1.6) == True:
waters_remove.append(line[6])
for key in waters:
if key not in waters_remove:
for water in waters[key]:
outfile.write(IO.pdb_parse_out(water) + '\n')
def write_qprep(self):
replacements = {'PRM':self.prm_merged,
'PDB':self.PDBout,
'CENTER':'{} {} {}'.format(*self.sphere),
'SPHERE':self.radius,
}
if self.system == 'protein':
replacements['SOLVENT'] = '4 water.pdb'
elif self.system == 'water':
replacements['SOLVENT'] = '1 HOH'
elif self.system == 'vacuum':
replacements['solvate']='!solvate'
src = s.INPUT_DIR + '/qprep_resFEP.inp'
self.qprep = self.directory + '/inputfiles/qprep.inp'
libraries = [self.forcefield + '.lib']
if self.cofactor[0] != None:
for filename in self.cofactor:
libraries.append(filename + '.lib')
with open(src) as infile, open(self.qprep, 'w') as outfile:
if self.dual == True:
outfile.write('rl ' + self.MUTresn + '.lib\n')
for line in infile:
line = IO.replace(line, replacements)
if line.split()[0] == '!Added':
for libraryfile in libraries:
outfile.write('rl ' + libraryfile + '\n')
continue
if line.split()[0] == '!addbond':
for CYX in self.CYX:
outline = 'addbond {}:SG {}:SG y\n'.format(*CYX)
outfile.write(outline)
continue
outfile.write(line)
def run_qprep(self):
os.chdir(self.directory + '/inputfiles/')
qprep = s.Q_DIR[self.preplocation] + 'qprep'
options = ' < qprep.inp > qprep.out'
# Somehow Q is very annoying with this < > input style so had to implement
# another function that just calls os.system instead of using the preferred
# subprocess module....
IO.run_command(qprep, options, string = True)
os.chdir('../../')
def get_lambdas(self):
self.lambdas = IO.get_lambdas(self.windows, self.sampling)
def write_EQ(self):
for line in self.PDB[int(self.PDB2Q[self.chain][self.mutation[1]])]:
if line[2] == 'CA' and self.system == 'water' \
or line[2] == 'CA' and self.system == 'vacuum': \
self.replacements['WATER_RESTRAINT'] = '{} {} 1.0 0 0'.format(line[1],
line[1])
self.replacements['ATOM_END'] = '{}'.format(self.systemsize)
for EQ_file in glob.glob(s.INPUT_DIR + '/eq*.inp'):
src = EQ_file
EQ_file = EQ_file.split('/')
tgt = self.directory + '/inputfiles/' + EQ_file[-1]
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
def write_MD(self):
# Get restraint for water and vacuum systems
#for line in self.PDB[int(self.PDB2Q[self.mutation[1]])]:
# if line[2] == 'CA' and self.system == 'water' \
# or line[2] == 'CA' and self.system == 'vacuum': \ self.replacements['WATER_RESTRAINT'] = '{} {} 1.0 0 0'.format(line[1],
# line[1])
if self.start == '1':
for i in range(0, int(self.windows) + 1):
j = int(self.windows) - i
lambda1 = self.lambdas[i].replace(".", "")
lambda2 = self.lambdas[j].replace(".", "")
if self.lambdas[i] == '1.000':
src = s.INPUT_DIR + '/md_1000_0000.inp'
else:
src = s.INPUT_DIR + '/md_XXXX_XXXX.inp'
self.replacements['FLOAT_LAMBDA1'] = self.lambdas[i]
self.replacements['FLOAT_LAMBDA2'] = self.lambdas[j]
tgt = self.directory + '/inputfiles/md_{}_{}.inp'.format(lambda1,
lambda2)
self.replacements['FILE'] = 'md_{}_{}'.format(lambda1,
lambda2)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
## Store previous file
self.replacements['FILE_N'] = 'md_{}_{}'.format(lambda1,
lambda2)
# This needs to be a function at one point
if self.start == '0.5':
self.mdfiles = ['md_0500_0500']
half = int((len(self.lambdas)-1)/2)
lambda1 = self.lambdas[0:half]
lambda2 = self.lambdas[half+1:]
# Write out the middle file
self.replacements['FILE_N'] = 'md_0500_0500'
src = s.INPUT_DIR + '/md_0500_0500.inp'
tgt = self.directory + '/inputfiles/md_0500_0500.inp'
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
# Write out part 1 of the out files
src = s.INPUT_DIR + '/md_XXXX_XXXX.inp'
for i in range(0, len(lambda1)):
l1 = lambda1[(half - i) - 1].replace(".", "")
l2 = lambda2[i].replace(".", "")
self.replacements['FLOAT_LAMBDA1'] = lambda1[(half - i) - 1]
self.replacements['FLOAT_LAMBDA2'] = lambda2[i]
tgt = self.directory + '/inputfiles/md_{}_{}.inp'.format(l1,
l2)
self.replacements['FILE'] = 'md_{}_{}'.format(l1,
l2)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
## Store previous file
self.replacements['FILE_N'] = 'md_{}_{}'.format(l1,
l2)
self.mdfiles.append('md_{}_{}'.format(l1,l2))
# And part 2
self.replacements['FILE_N'] = 'md_0500_0500'
for i in range(0, len(lambda1)):
l1 = lambda2[i].replace(".", "")
l2 = lambda1[(half - i) - 1].replace(".", "")
self.replacements['FLOAT_LAMBDA1'] = lambda2[i]
self.replacements['FLOAT_LAMBDA2'] = lambda1[(half - i) - 1]
tgt = self.directory + '/inputfiles/md_{}_{}.inp'.format(l1,
l2)
self.replacements['FILE'] = 'md_{}_{}'.format(l1,
l2)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
## Store previous file
self.replacements['FILE_N'] = 'md_{}_{}'.format(l1,
l2)
self.mdfiles.append('md_{}_{}'.format(l1,l2))
def write_runfile(self):
ntasks = getattr(s, self.cluster)['NTASKS']
src = s.INPUT_DIR + '/run.sh'
tgt = self.directory + '/inputfiles/run' + self.cluster + '.sh'
EQ_files = sorted(glob.glob(self.directory + '/inputfiles/eq*.inp'))
if self.start == '1':
MD_files = reversed(sorted(glob.glob(self.directory + '/inputfiles/md*.inp')))
elif self.start == '0.5':
MD_files = self.mdfiles[1:]
half = int((len(MD_files)/2))
md_1 = MD_files[0:half]
md_2 = MD_files[half:]
replacements = IO.merge_two_dicts(self.replacements, getattr(s, self.cluster))
replacements['FEPS'] = ' '.join(self.FEPlist)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
if line.strip() == '#SBATCH -A ACCOUNT':
try:
replacements['ACCOUNT']
except:
line = ''
outline = IO.replace(line, replacements)
outfile.write(outline)
if line.strip() == '#EQ_FILES':
for line in EQ_files:
file_base = line.split('/')[-1][:-4]
outline = 'time mpirun -np {} $qdyn {}.inp' \
' > {}.log\n'.format(ntasks,
file_base,
file_base)
outfile.write(outline)
if line.strip() == '#RUN_FILES':
if self.start == '1':
for line in MD_files:
file_base = line.split('/')[-1][:-4]
outline = 'time mpirun -np {} $qdyn {}.inp' \
' > {}.log\n'.format(ntasks,
file_base,
file_base)
outfile.write(outline)
elif self.start == '0.5':
outline = 'time mpirun -np {} $qdyn {}.inp' \
' > {}.log\n\n'.format(ntasks,
'md_0500_0500',
'md_0500_0500')
outfile.write(outline)
for i, md in enumerate(md_1):
outline1 = 'time mpirun -np {:d} $qdyn {}.inp' \
' > {}.log &\n'.format(int(int(ntasks)/2),
md_1[i],
md_1[i])
outline2 = 'time mpirun -np {:d} $qdyn {}.inp' \
' > {}.log\n'.format(int(int(ntasks)/2),
md_2[i],
md_2[i])
outfile.write(outline1)
outfile.write(outline2)
outfile.write('\n')
def write_submitfile(self):
IO.write_submitfile(self.directory, self.replacements)
def write_FEPfile(self):
if self.dual == True:
run.write_dualFEPfile()
if self.dual == False:
run.write_singleFEPfile()
def write_singleFEPfile(self):
RES_list = self.PDB[int(self.PDB2Q[self.chain][self.mutation[1]])]
RES_dic = {}
block = 0
empty = ['[change_charges]',
'[FEP]',
'[atom_types]',
'[change_atoms]',
'[softcore]',
'[bond_types]'
]
atom_map = {}
print(RES_list)
for line in RES_list:
RES_dic[line[2].strip()] = line
for src in sorted(glob.glob(self.FEPdir + '/FEP*.fep')):
tgt = self.directory + '/inputfiles/' + src.split('/')[-1]
with open (src) as infile, open (tgt, 'w') as outfile:
for line in infile:
if line.strip() == '[atoms]':
outfile.write(line)
block = 1
if line.strip() == '[change_bonds]':
outfile.write(line)
block = 2
if line.strip() in empty:
block = 0
if block == 0:
outfile.write(line)
if block == 1:
if line.strip() != '[atoms]':
line = line.split()
if len(line) > 1 and line[0] != '!charge':
atnr = RES_dic[line[3]][1]
atom_map[line[0]] = atnr
try:
comment = line[4]
except:
comment = ' '
outline = ('{:7s}{:<7d}{:5s}{:5s}{:5s}\n'.format(line[1],
atnr,
'!',
line[3],
comment))
outfile.write(outline)
else:
outfile.write('\n')
if block == 2:
if line.strip != '[change_bonds]':
line = line.split()
if len(line) > 1 and line[0] != '!charge':
at_1 = atom_map[line[0]]
at_2 = atom_map[line[1]]
outline = '{:<7d}{:<7d}{:5s}{:5s}\n'.format(at_1,
at_2,
line[2],
line[3])
outfile.write(outline)
else:
outfile.write('\n')
def write_dualFEPfile(self):
# The vdW paramers need to be extracted from the reference .prm file
prmfiles = [s.FF_DIR + '/' + self.forcefield + '.prm']
if self.nonAA == True:
prmfiles.append(self.mutation[2] + '.prm')
vdw_prms = IO.read_prm(prmfiles)['[atom_types]']
## Next, we start to construct the FEP file
with open(self.directory + '/inputfiles/FEP1.fep', 'w') as outfile:
# First create the file header
outfile.write('! Dual topology QresFEP: ' + self.MUTresn + '\n\n')
outfile.write('[FEP]\n')
outfile.write('states 2\n')
outfile.write('softcore_use_max_potential on \n\n')
# Write out [atoms] section
outfile.write('[atoms]\n')
cnt = 0
res_ID = int(self.PDB2Q[self.mutation[1]])
for line in self.PDB[res_ID]:
cnt += 1
outfile.write('{:4d} {:4d} ! {:<4s}\n'.format(cnt, line[1], line[2]))
outfile.write('\n')
# Write out [change_charges] section
cnt = 0
outfile.write('[change_charges]\n')
for line in self.merged_lib['[atoms]']:
cnt += 1
line = line.split()
if line[1][0].islower() == False:
if line[1] in self.backbone:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
line[3],
line[3]))
else:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
line[3],
'0.0000'))
else:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
'0.0000',
line[3]))
outfile.write('\n')
# Write out [atom_types] section
outfile.write('[atom_types]\n')
for line in vdw_prms:
line = line.split()
if len(line) >= 7:
outfile.write('{:<8s}{:>10s}{:>10s}{:>10s}'\
'{:>10s}{:>10s}{:>10s}{:>10s}\n'.format(line[0],
line[1],
line[3],
'0.0000',
'0.0000',
line[4],
line[5],
line[6],
))
# Write out DUM entry
outfile.write('{:<8s}{:>10s}{:>10s}{:>10s}'\
'{:>10s}{:>10s}{:>10s}{:>10s}\n'.format('DUM',
'0.0000',
'0.0000',
'0.0000',
'0.0000',
'0.0000',
'0.0000',
'1.0080',
))
outfile.write('\n')
# Write out [change_atoms] section
outfile.write('[change_atoms]\n')
cnt = 0
for line in self.merged_lib['[atoms]']:
cnt += 1
line = line.split()
if line[1][0].islower() == False:
if line[1] in self.backbone:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
line[2],
line[2]))
else:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
line[2],
'DUM'))
else:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
'DUM',
line[2]))
outfile.write('\n')
# Write out [softcore] section
outfile.write('[softcore]\n')
cnt = 0
for line in self.merged_lib['[atoms]']:
cnt += 1
line = line.split()
if line[1][0].islower() == False:
if line[1] in self.backbone: