def main(argv=[__name__]):
if len(argv) != 2:
oechem.OEThrow.Usage("%s <infile>" % argv[0])
ifs = oechem.oemolistream(argv[1])
for mol in ifs.GetOEGraphMols():
oechem.OEThrow.Info(" Title: %s" % mol.GetTitle())
oechem.OEThrow.Info(" Volume: %8.2f" %
oeshape.OECalcVolume(mol))
oechem.OEThrow.Info("Volume: (without H): %8.2f\n" %
oeshape.OECalcVolume(mol, False))
smult = oeshape.OECalcShapeMultipoles(mol)
oechem.OEThrow.Info(" Steric multipoles:")
oechem.OEThrow.Info(" monopole: %8.2f" % smult[0])
oechem.OEThrow.Info(" quadrupoles: %8.2f %8.2f %8.2f" %
(smult[1], smult[2], smult[3]))
oechem.OEThrow.Info(" octopoles:")
oechem.OEThrow.Info(
" xxx: %8.2f yyy: %8.2f zzz: %8.2f" %
(smult[4], smult[5], smult[6]))
oechem.OEThrow.Info(
" xxy: %8.2f xxz: %8.2f yyx: %8.2f" %
(smult[7], smult[8], smult[9]))
oechem.OEThrow.Info(
" yyz: %8.2f zzx: %8.2f zzy: %8.2f" %
(smult[10], smult[11], smult[12]))
oechem.OEThrow.Info(" xyz: %8.2f\n" % smult[13])
for molecule in tqdm(docked_molecules):
shapeFunc.SetupRef(molecule)
# Compute overlaps
score = 0.0
result = oeshape.OEOverlapResults()
overlapping_fragments = list()
for fragment_name, fragment in fragments.items():
#overlap, volume = compute_fragment_overlap(molecule, fragment)
shapeFunc.Overlap(fragment, result)
# Compute overlap
overlap = result.GetTanimoto()
if overlap > max_overlap:
max_overlap = overlap
# Compute volume
volume = oeshape.OECalcVolume(fragment)
# Accumulate score
score += volume * overlap
# Store fragment
if overlap > OVERLAP_THRESHOLD:
overlapping_fragments.append(fragment_name)
# DEBUG
#print(f' {fragment_name} {overlap:8.3f} {volume:10.3f}')
# Correct for fragment-fragment overlap
n_overlapping_fragments = len(overlapping_fragments)
#print(f'{directory:16} {index:6} {molecule.GetTitle():18} {covalent_id:8} {score:10.3f} {overlapping_fragments}')
# Attach scores
oechem.OESetSDData(molecule, 'number_of_overlapping_fragments',
# Store it
fragments[fragment_name] = fragment.CreateCopy()
print(f'{len(fragments)} fragments loaded.')
# Get appropriate function to calculate analytic shape
prep = oeshape.OEOverlapPrep()
result = oeshape.OEOverlapResults()
fragment_func = oeshape.OEExactColorFunc()
print('Computing overlap scores...')
for molecule in tqdm(docked_molecules):
# Compute overlap with merged query
refmol = molecule.CreateCopy()
prep.Prep(refmol)
fragment_func.SetupRef(refmol)
volume = oeshape.OECalcVolume(molecule)
# Compute overlaps
overlapping_fragments = list()
fragment_overlap_scores = dict()
score = 0.0
inspiration_fragment_names = oechem.OEGetSDData(molecule, 'fragments').split(',')
for fragment_name in inspiration_fragment_names:
if fragment_name not in fragments:
continue
fragment = fragments[fragment_name]
fitmol = fragment.CreateCopy()
prep.Prep(fitmol)
fragment_func.Overlap(fitmol, result)
# Compute overlap (fraction of the fragment covered)
fragment_overlap = result.GetRefTverskyCombo()