def check_chem_comp_formula_weight(block):
for cc in block.find('_chem_comp.', ['id', 'formula', 'formula_weight']):
if cc.str(0) in ('UNX', 'UNL'): # unknown residue or ligand
continue
fdict = formula_to_dict(cc.str(1).title())
calc_weight = sum(n * Element(e).weight for (e, n) in fdict.items())
diff = calc_weight - cif.as_number(cc[2])
if not (abs(diff) < 0.1): # also true if diff is NaN
print('%s %s %-16s % 9.3f - %9s = %+.3f' %
(block.name, cc[0], cc.str(1), calc_weight, cc[2], diff))
def check_entity_formula_weight(block):
# read chem_comp weights from the file, e.g. THR: 119.120
cc_weights = {
cc.str(0): cif.as_number(cc[1])
for cc in block.find('_chem_comp.', ['id', 'formula_weight'])
}
# read polymer types from _entity_poly.type
poly_types = {
ep.str(0): ep.str(1)
for ep in block.find('_entity_poly.', ['entity_id', 'type'])
}
# read and sort sequences from _entity_poly_seq
entity_seq = collections.defaultdict(list)
for m in block.find('_entity_poly_seq.', ['entity_id', 'num', 'mon_id']):
entity_seq[m.str(0)].append((cif.as_int(m[1]), cif.as_string(m[2])))
for seq in entity_seq.values():
seq.sort(key=lambda p: p[0])
# read _entity.formula_weight values
f_weights = block.find('_entity.', ['id', 'formula_weight'])
entity_weights = {ent.str(0): cif.as_number(ent[1]) for ent in f_weights}
# calculate weight from sequences and compare with _entity.formula_weight
for ent, seq in entity_seq.items():
# in case of microheterogeneity take the first conformer
main_seq = [next(g) for _, g in itertools.groupby(seq, lambda p: p[0])]
weight = sum(cc_weights[mon_id] for (num, mon_id) in main_seq)
weight -= (len(main_seq) - 1) * H2O_MASS
if 'ribonucleotide' in poly_types[ent]: # DNA or RNA
weight -= PO2_MASS
diff = weight - entity_weights[ent]
if abs(diff) > max(0.1, 3e-5 * weight):
print('%4s entity_id: %2s %10.2f - %10.2f = %+8.3f' %
(block.name, ent, weight, entity_weights[ent], diff))