prx = select([md_tab.c.molecule_design_id, ssd_tab.c.modification,
ssd_tab.c.sequence],
where_clause,
from_obj=md_tab.outerjoin(ssd_tab)).execute()
elif mt_id == 'COMPOUND':
cmp_tab = metadata.tables['compound']
prx = select([md_tab.c.molecule_design_id, cmp_tab.c.smiles],
where_clause,
from_obj=md_tab.outerjoin(cmp_tab)).execute()
cch = dict([(row[0], row[1:]) for row in prx.fetchall()])
print 'Fetching molecule designs.'
print
mt = sess.query(MoleculeType).filter_by(molecule_type_id=mt_id).one()
new_structs = set()
mds = sess.query(MoleculeDesign).filter_by(molecule_type=mt).all()
for idx, md in enumerate(mds):
print '%s: %d (%3d %%)' % (md.molecule_type_id,
md.molecule_design_id,
int((idx + 1) * 100 / len(mds)))
process_design(md, cch[md.molecule_design_id], new_structs)
sess.add_all(new_structs)
if COMMIT and len(WARNINGS) == 0:
sess.commit()
else:
if WARNINGS:
print 'Warnings occurred - rolling back transaction.'
print 'Warning messages:'
print '\n'.join(WARNINGS)
sess.rollback()
