def __init__(self, config, num):
self.name, self.conformation, self.location = config['ligand'][num]
self.selection = 'name CA and not HETERO'
try:
pdb = Pdb(self.name, selection=self.selection)
atoms = pdb.atoms.models()[0]
atoms.update_sec(pdb.dssp())
except InvalidPdbCode:
seq = self.name.split(':')[0]
check_peptide_sequence(seq)
atoms = Atoms(self.name)
atoms.set_bfac(0.0)
Atoms.__init__(self, atoms)
# checks the input peptide sequence for non-standard amino acids.
rev_dct = dict(map(reversed, AA_NAMES.items()))
[
check_peptide_sequence(rev_dct[peptide.resname])
for peptide in atoms.atoms
]
def __init__(self, config):
name = config['receptor']
selection = 'name CA and not HETERO'
pdb = Pdb(name, selection=selection)
atoms = pdb.atoms.models()[0]
token = config.get('receptor_flexibility')
if token:
try:
bfac = float(token)
atoms.set_bfac(bfac)
except ValueError:
if token.lower() == 'bf':
pass
elif token.lower() == 'bfi':
for a in atoms:
if a.bfac > 1.:
a.bfac = 0.
else:
a.bfac = 1. - a.bfac
elif exists(token):
d, de = self.read_flexibility(token)
atoms.update_bfac(d, de)
elif exists(join(config['work_dir'], token)):
d, de = self.read_flexibility(
join(config['work_dir'], token))
atoms.update_bfac(d, de)
else:
raise Exception(
'Invalid receptor_flexibility setting in \'%s\'!!!' %
token)
else:
atoms.set_bfac(1.0)
self.old_ids = atoms.update_sec(
pdb.dssp(dssp_command=config['dssp_command'])).fix_broken_chains()
self.new_ids = {v: k for k, v in self.old_ids.items()}
Atoms.__init__(self, atoms)
self.center = self.cent_of_mass()
self.dimension = self.max_dimension()
self.patches = {}
self.check_residue_modifications()
