def write_qprep(self, writedir):
replacements = {}
center = f.COG(self.lig1 + '.pdb')
center = '{:} {:} {:}'.format(center[0], center[1], center[2])
qprep_in = s.ROOT_DIR + '/INPUTS/qprep.inp'
qprep_out = writedir + '/qprep.inp'
replacements['FF_LIB'] = s.ROOT_DIR + '/FF/' + self.FF + '.lib'
replacements['LIG1'] = self.lig1 + '.lib'
replacements['LIG2'] = self.lig2 + '_renumber.lib'
replacements[
'LIGPRM'] = self.FF + '_' + self.lig1 + '_' + self.lig2 + '_merged.prm'
replacements['LIGPDB'] = self.lig1 + '_' + self.lig2 + '.pdb'
replacements['CENTER'] = center
replacements['SPHERE'] = self.sphereradius
if self.system == 'vacuum':
replacements['solvate'] = '!solvate'
if self.system == 'water':
replacements['SOLVENT'] = '1 HOH'
if self.system == 'protein':
replacements['SOLVENT'] = '4 water.pdb'
with open(qprep_in) as infile, open(qprep_out, 'w') as outfile:
for line in infile:
line = run.replace(line, replacements)
if line == '!addbond at1 at2 y\n' and self.cysbond != None:
cysbond = self.cysbond.split(',')
for cys in cysbond:
at1 = cys.split('_')[0]
at2 = cys.split('_')[1]
outfile.write('addbond ' + at1 + ' ' + at2 + ' y \n')
continue
outfile.write(line)
def __init__(self, ligand, cofactor, forcefield, include, system,
preplocation, cluster, temperature, replicates,
radius,
*args, **kwargs):
# Argparse arguments
self.ligand = ligand
self.cofactor = [ligand]
self.forcefield = forcefield
self.system = system
self.preplocation = preplocation
self.cluster = cluster
if temperature == None:
self.temperature = s.TEMPERATURE
else:
self.temperature = temperature
if replicates == None:
self.replicates = s.REPLICATES
else:
self.replicates = replicates
# Constructs for local variables
self.include = include
self.replacements = {'TEMP_VAR':self.temperature,
'RUN_VAR':self.replicates,
'RUNFILE':'run' + self.cluster + '.sh'
}
self.CYX = []
self.PDB2Q = {}
self.PDB = {}
self.systemsize = 0
# Add cofactors to list for further pdb/prm parsing
if cofactor != None:
self.cofactor.append(cofactor)
if self.system == 'water' or self.system == 'vacuum':
self.sphere = f.COG(self.ligand +'.pdb')
self.radius = radius