def make_residue(key, hydrogens=True):
""" returns a molecule object with
default geometry"""
if not library._aacids.has_key(key):
raise KeyError, "Residue %s not known" % key
m = Molecule()
m.unity = 'A'
m.resname = key
for i, entry in enumerate(library._aacids[key]):
if hydrogens == False and entry[0][0] == 'H':
continue
else:
a = Atom()
a.id = i + 1
a.name = entry[0]
a.symbol = a.name[0]
a.x = entry[1]
a.occ = 1.
a.resname = key
a.m = library._atommass[a.symbol]
a.unity = 'A'
m.atoms.append(a)
return m
def make_residue(key,hydrogens = True):
""" returns a molecule object with
default geometry"""
if not library._aacids.has_key(key):
raise KeyError, "Residue %s not known" % key
m = Molecule()
m.unity = 'A'
m.resname = key
for i, entry in enumerate(library._aacids[key]):
if hydrogens == False and entry[0][0] == 'H':
continue
else:
a = Atom()
a.id = i+1
a.name = entry[0]
a.symbol = a.name[0]
a.x = entry[1]
a.occ = 1.
a.resname = key
a.m = library._atommass[a.symbol]
a.unity = 'A'
m.atoms.append(a)
return m
