ccache = CompoundCacher('../cache/compounds.json')
groups_data = inchi2gv.init_groups_data()
group_list = groups_data.GetGroupNames()
group_names = groups_data.GetGroupNames()
decomposer = inchi2gv.InChIDecomposer(groups_data)
# test the decomposition of ATP into groups
ATP_inchi = ccache.get_compound('C00002').inchi
group_def = decomposer.inchi_to_groupvec(ATP_inchi)
for j, group_name in enumerate(group_names):
if group_def[j] != 0:
print group_name, ' x %d' % group_def[j]
patterns = ['c~[O;+0]', 'c~[O;+1]', 'c~[n;+1]~c', 'c~[n;+0]~c', 'c~[n;-1]~c']
for cid in ['C00255', 'C01007']:
comp = ccache.get_compound(cid)
print "-" * 50, '\n%s' % cid
inchi = comp.inchi
mol = Molecule.FromInChI(inchi)
print mol.ToSmiles()
print mol.FindSmarts("c~[n;+1]~c")
try:
groupvec = decomposer.inchi_to_groupvec(inchi)
sys.stdout.write(str(groupvec) + '\n')
except inchi2gv.GroupDecompositionError as e:
sys.stderr.write(str(e) + '\n')
sys.stderr.write(e.GetDebugTable())
'z': z,
'nMg': 0
}
yield d
if __name__ == '__main__':
import sys, json
logger = logging.getLogger('')
logger.setLevel(logging.DEBUG)
from compound_cacher import CompoundCacher, CompoundEncoder
from molecule import Molecule, OpenBabelError
ccache = CompoundCacher(cache_fname=None)
for compound_id in ['C00087', 'C00282', 'C00237']:
comp = Compound.from_kegg(compound_id)
try:
mol = Molecule.FromInChI(str(comp.inchi))
sys.stderr.write(
'%s : formula = %s, nE = %s' %
(str(comp.inchi), mol.GetFormula(), mol.GetNumElectrons()))
except OpenBabelError:
pass
ccache.add(comp)
sys.stderr.write(
'\ncompound id = %s, nH = %s, z = %s, pKa = %s, bag = %s\n\n\n' %
(compound_id, str(comp.nHs), str(comp.zs), str(
comp.pKas), str(comp.atom_bag)))
ccache.dump()
