def checkFEP(self):
if len(self.mutation[0]) == 1:
AA_from = IO.AA(self.mutation[0])
else:
AA_from = self.mutation[0]
AA_to = IO.AA(self.mutation[2])
mutation = '{}{}{}'.format(*self.mutation)
FEPdir = s.FF_DIR + '/.FEP/' + self.forcefield + '/' + AA_from + '_' + AA_to
if not os.path.exists(FEPdir):
if self.dual == True:
'Generating dual topology inputfiles'
self.FEPlist = ['FEP1.fep']
self.FEPdir = None
else:
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 checkFEP(self):
if len(self.mutation[0]) == 1:
AA_from = IO.AA(self.mutation[0])
else:
AA_from = self.mutation[0]
AA_to = IO.AA(self.mutation[2])
mutation = '{}{}{}'.format(*self.mutation)
FEPdir = s.FF_DIR + '/.FEP/' + AA_from + '_' + AA_to
if self.forcefield == 'OPLS2005':
FEPdir = FEPdir + '-aa'
if 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 General(self):
for atom in self.top:
if len(atom[0]) != 6:
continue
try:
IO.AA(atom[4])
self.protein.append(atom[1])
except:
if atom[4] == 'LIG':
self.ligand.append(atom[1])
else:
continue
self.commands = [self.eq_top, '1', str(self.protein[0])+' '+str(self.protein[-1]),
str(self.ligand[0])+' '+str(self.ligand[-1]), 'end', 'go', self.MD, '.']
with open(self.inp, 'w') as outfile:
for line in self.commands:
outfile.write(line+'\n')
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 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)
