def _parse_fragment_tree(self, el):
fragments = []
for el_fragments in el.findall('fragments'):
for el_f in el_fragments:
fragments.append(self._parse_fragment_tree(el_f))
atoms = []
for el_atoms in el.findall('atoms'):
for el_a in el_atoms:
atom_classes = {"dummy": im.dummy,
"unknown": im.unknown,
"element": im.element}
descr = atom_classes[el_a.get('type')](el_a.get('name'))
atoms.append((el_a.get('label'),
im.atom(descr, int(el_a.get('nsites', '1')))))
bonds = []
for el_bonds in el.findall('bonds'):
for el_b in el_bonds:
a1, a2 = el_b.get('atoms').split()
bonds.append((a1, a2, el_b.get('order')))
label = el.get('label')
species = el.get('species')
polymer_type = el.get('polymer_type', None)
if polymer_type is None:
return label, im.fragment(species, fragments, atoms, bonds)
else:
assert len(atoms) == 0
return label, im.polymer(species, fragments, bonds, polymer_type)
def _make_molecule(self):
C = M.element('C')
H = M.element('H')
N = M.element('N')
O = M.element('O')
peptide_group = M.fragment('peptide',
(),
(('CA', M.atom(C)),
('HA', M.atom(H)),
('H', M.atom(H)),
('N', M.atom(N)),
('C', M.atom(C)),
('O', M.atom(O))),
(('N', 'H', "single"),
('N', 'CA', "single"),
('CA', 'HA', "single"),
('CA', 'C', "single"),
('C', 'O', "double")))
ala_sidechain = M.fragment('ala_sidechain',
(),
(('CB', M.atom(C)),
('HB1', M.atom(H)),
('HB2', M.atom(H)),
('HB3', M.atom(H))),
(('CB', 'HB1', "single"),
('CB', 'HB2', "single"),
('CB', 'HB3', "single"),))
ala = M.fragment('alanine',
(('peptide', peptide_group),
('sidechain', ala_sidechain)),
(),
(('peptide.CA', 'sidechain.CB', "single"),))
return M.polymer('alanine_dipeptide',
(('ALA1', ala),
('ALA2', ala)),
(('ALA1.peptide.C', 'ALA2.peptide.N', "single"),),
'polypeptide')