def is_protein(self, ff=''):
'''
Returns true if standard amino acid residues are present
'''
aa = util.get_available_res(ff).intersection(self.mol_data['resname'])
return len(aa) > 0
assert args.water_model in ['opc', 'tip3p', 'spce',
'tip4'], 'Unknown water \
model %s\n' % args.water_model
if args.water_model == 'opc':
args.water_model = 'leaprc.water.opc'
elif args.water_model == 'tip3p':
args.water_model = 'leaprc.water.tip3p'
elif args.water_model == 'spce':
args.water_model = 'leaprc.water.spce'
elif args.water_model == 'tip4':
args.water_model = 'leaprc.water.tip4pew'
#do we have nonstandard residues?
mol_data = {}
nonstandard_res = {}
standard_res = util.get_available_res(ff)
#pdb4amber seems to delete mercury (HG) along with hydrogens; for now my
#hacky fix is to store the relevant atom info if mercury is present and add
#the mercury back in after stripping...I'm preemptively doing this for
#hafnium too
metal_info = {}
#if any structure was not provided in PDB format, we will attempt to create
#one from what was provided using obabel, choosing a filename that will not
#overwrite anything in the directory (optionally)
for structure in args.structures:
net_charge = None
#the "structure" string in the args.structure list will be updated so
#that it corresponds to the PDB we should use for subsequent steps
assert os.path.isfile(structure), '%s does not exist\n' % structure
#"base" is the base filename (no extension) from which others will be derived
assert args.water_model in ['opc', 'tip3p', 'spce',
'tip4'], 'Unknown water \
model %s\n' % args.water_model
if args.water_model == 'opc':
args.water_model = 'leaprc.water.opc'
elif args.water_model == 'tip3p':
args.water_model = 'leaprc.water.tip3p'
elif args.water_model == 'spce':
args.water_model = 'leaprc.water.spce'
elif args.water_model == 'tip4':
args.water_model = 'leaprc.water.tip4pew'
#do we have nonstandard residues?
mol_data = {}
nonstandard_res = {}
standard_res = util.get_available_res(ff)
ff = [ff]
if nff:
standard_res = standard_res.union(util.get_available_res(nff))
ff = ff.append(nff)
#pdb4amber seems to delete mercury (HG) along with hydrogens; for now my
#hacky fix is to store the relevant atom info if mercury is present and add
#the mercury back in after stripping...I'm preemptively doing this for
#hafnium too
metal_info = {}
#if any structure was not provided in PDB format, we will attempt to create
#one from what was provided using obabel, choosing a filename that will not
#overwrite anything in the directory (optionally)
for structure in args.structures:
net_charge = None