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