def main(argv=[__name__]):
if len(argv) != 5:
oechem.OEThrow.Usage("%s <reffile> <fitfile> <out.sdf> <keepsize>" %
argv[0])
reffs = oechem.oemolistream(argv[1])
fitfs = oechem.oemolistream(argv[2])
outfs = oechem.oemolostream(argv[3])
keepsize = int(argv[4])
refmol = oechem.OEMol()
oechem.OEReadMolecule(reffs, refmol)
print("Ref. Title:", refmol.GetTitle(), "Num Confs:", refmol.NumConfs())
# Prepare reference molecule for calculation
# With default options this will remove any explicit
# hydrogens present and add color atoms
prep = oeshape.OEOverlapPrep()
prep.Prep(refmol)
overlay = oeshape.OEMultiRefOverlay()
overlay.SetupRef(refmol)
for fitmol in fitfs.GetOEMols():
print("Fit Title:", fitmol.GetTitle(), "Num Confs:", fitmol.NumConfs())
prep.Prep(fitmol)
resCount = 0
# Sort all scores according to highest tanimoto
scoreiter = oeshape.OEBestOverlayScoreIter()
oeshape.OESortOverlayScores(scoreiter, overlay.Overlay(fitmol),
oeshape.OEHighestTanimoto())
for score in scoreiter:
outmol = oechem.OEGraphMol(
fitmol.GetConf(oechem.OEHasConfIdx(score.GetFitConfIdx())))
score.Transform(outmol)
oechem.OESetSDData(outmol, "RefConfIdx",
"%-d" % score.GetRefConfIdx())
oechem.OESetSDData(outmol, "tanimoto combo",
"%-.3f" % score.GetTanimotoCombo())
oechem.OEWriteMolecule(
outfs,
refmol.GetConf(oechem.OEHasConfIdx(score.GetRefConfIdx())))
oechem.OEWriteMolecule(outfs, outmol)
resCount += 1
# Break at the user specified size
if resCount == keepsize:
break
print(resCount, "results returned")
def get_oe_mol_positions(molecule, conformer_idx=0):
from openeye import oechem
# Extract correct conformer
if conformer_idx > 0:
try:
if molecule.NumConfs() <= conformer_idx:
raise UnboundLocalError # same error message
molecule = oechem.OEGraphMol(
molecule.GetConf(oechem.OEHasConfIdx(conformer_idx)))
except UnboundLocalError:
raise ValueError(
'conformer_idx {} out of range'.format(conformer_idx))
# Extract positions
oe_coords = oechem.OEFloatArray(3)
molecule_pos = np.zeros((molecule.NumAtoms(), 3))
for i, atom in enumerate(molecule.GetAtoms()):
molecule.GetCoords(atom, oe_coords)
molecule_pos[i] = oe_coords
return molecule_pos
def overlay_molecules(
reference_molecule: oechem.OEGraphMol,
fit_molecule: oechem.OEMol,
return_overlay: bool = True,
) -> (int, List[oechem.OEGraphMol]):
"""
Overlay two molecules and calculate TanimotoCombo score.
Parameters
----------
reference_molecule: oechem.OEGraphMol
An OpenEye molecule holding the reference molecule for overlay.
fit_molecule: oechem.OEMol
An OpenEye multi-conformer molecule holding the fit molecule for overlay.
return_overlay: bool
If the best scored overlay of molecules should be returned.
Returns
-------
: int or int and list of oechem.OEGraphMol
The TanimotoCombo score of the best overlay and the overlay if score_only is set False.
"""
from openeye import oechem, oeshape
prep = oeshape.OEOverlapPrep()
prep.Prep(reference_molecule)
overlay = oeshape.OEOverlay()
overlay.SetupRef(reference_molecule)
prep.Prep(fit_molecule)
score = oeshape.OEBestOverlayScore()
overlay.BestOverlay(score, fit_molecule, oeshape.OEHighestTanimoto())
if not return_overlay:
return score.GetTanimotoCombo()
else:
overlay = [reference_molecule]
fit_molecule = oechem.OEGraphMol(
fit_molecule.GetConf(oechem.OEHasConfIdx(score.GetFitConfIdx())))
score.Transform(fit_molecule)
overlay.append(fit_molecule)
return score.GetTanimotoCombo(), overlay
def read_oe_molecule(file_path, conformer_idx=None):
from openeye import oechem
# Open input file stream
ifs = oechem.oemolistream()
if not ifs.open(file_path):
oechem.OEThrow.Fatal('Unable to open {}'.format(file_path))
# Read all conformations
for mol in ifs.GetOEMols():
try:
molecule.NewConf(mol)
except UnboundLocalError:
molecule = oechem.OEMol(mol)
# Select conformation of interest
if conformer_idx is not None:
if molecule.NumConfs() <= conformer_idx:
raise ValueError(
'conformer_idx {} out of range'.format(conformer_idx))
molecule = oechem.OEGraphMol(
molecule.GetConf(oechem.OEHasConfIdx(conformer_idx)))
return molecule
def main(argv=[__name__]):
parser = argparse.ArgumentParser()
# positional arguments retaining backward compatibility
parser.add_argument(
'database',
help='File containing the database molecules to be search \
(format not restricted to *.oeb).')
parser.add_argument(
'query',
default=[],
nargs='+',
help='File containing the query molecule(s) to be search \
(format not restricted to *.oeb).')
parser.add_argument(
'--nHits',
dest='nHits',
type=int,
default=100,
help='Number of hits to return (default = number of database mols).')
parser.add_argument('--cutoff',
dest='cutoff',
type=float,
default=argparse.SUPPRESS,
help='Specify a cutoff criteria for scores.')
parser.add_argument(
'--tversky',
dest='tversky',
action='store_true',
default=argparse.SUPPRESS,
help='Switch to Tversky similarity scoring (default = Tanimoto).')
args = parser.parse_args()
dbname = args.database
if not oefastrocs.OEFastROCSIsGPUReady():
oechem.OEThrow.Info("No supported GPU available!")
return 0
# set options
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetLimit(args.nHits)
print("Number of hits set to %u" % opts.GetLimit())
if hasattr(args, 'cutoff') is not False:
opts.SetCutoff(args.cutoff)
print("Cutoff set to %f" % args.cutoff)
if hasattr(args, 'tversky') is not False:
opts.SetSimFunc(args.tversky)
print("Tversky similarity scoring set.")
# read in database
ifs = oechem.oemolistream()
if not ifs.open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
print("\nOpening database file %s ..." % dbname)
timer = oechem.OEWallTimer()
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(ifs):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
dots.Total()
print("%f seconds to load database\n" % timer.Elapsed())
for qfname in args.query:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % qfname)
mcmol = oechem.OEMol()
if not oechem.OEReadMolecule(qfs, mcmol):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % qfname)
qfs.rewind()
ext = oechem.OEGetFileExtension(qfname)
qmolidx = 0
while oechem.OEReadMolecule(qfs, mcmol):
# write out to file name based on molecule title
ofs = oechem.oemolostream()
moltitle = mcmol.GetTitle()
if len(moltitle) == 0:
moltitle = str(qmolidx)
ofname = moltitle + "_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
print("Searching for %s of %s (%s conformers)" %
(moltitle, qfname, mcmol.NumConfs()))
qconfidx = 0
for conf in mcmol.GetConfs():
for score in dbase.GetSortedScores(conf, opts):
dbmol = oechem.OEMol()
dbmolidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, dbmolidx):
print(
"Unable to retrieve molecule '%u' from the database"
% dbmolidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "QueryConfidx", "%s" % qconfidx)
oechem.OESetSDData(mol, "ShapeTanimoto",
"%.4f" % score.GetShapeTanimoto())
oechem.OESetSDData(mol, "ColorTanimoto",
"%.4f" % score.GetColorTanimoto())
oechem.OESetSDData(mol, "TanimotoCombo",
"%.4f" % score.GetTanimotoCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
qconfidx += 1
print("%s conformers processed" % qconfidx)
print("Wrote results to %s\n" % ofname)
qmolidx += 1
return 0
def main(argv=[__name__]):
if len(argv) < 3:
oechem.OEThrow.Usage("%s <database> [<queries> ... ]" % argv[0])
return 0
# check system
if not oefastrocs.OEFastROCSIsGPUReady():
oechem.OEThrow.Info("No supported GPU available!")
return 0
# read in database
dbname = argv[1]
print("Opening database file %s ..." % dbname)
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
# customize search options
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetLimit(5)
for qfname in argv[2:]:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % qfname)
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(qfs, query):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % qfname)
ext = oechem.OEGetFileExtension(qfname)
base = qfname[:-(len(ext) + 1)]
# write out everthing to a similary named file
ofs = oechem.oemolostream()
ofname = base + "_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
oechem.OEWriteMolecule(ofs, query)
print("Searching for %s" % qfname)
for score in dbase.GetSortedScores(query, opts):
print("Score for mol %u(conf %u) %f shape %f color" %
(score.GetMolIdx(), score.GetConfIdx(),
score.GetShapeTanimoto(), score.GetColorTanimoto()))
dbmol = oechem.OEMol()
molidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, molidx):
print("Unable to retrieve molecule '%u' from the database" %
molidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "ShapeTanimoto",
"%.4f" % score.GetShapeTanimoto())
oechem.OESetSDData(mol, "ColorTanimoto",
"%.4f" % score.GetColorTanimoto())
oechem.OESetSDData(mol, "TanimotoCombo",
"%.4f" % score.GetTanimotoCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
print("Wrote results to %s" % ofname)
return 0
def GetBestOverlays(self, querymolstr, options, iformat, oformat):
""" Return a string of the format specified by 'oformat'
containing nhits overlaid confomers using querymolstr as the
query interpretted as iformat.
querymolstr - a string containing a molecule to use as the query
options - an instance of OEShapeDatabaseOptions
iformat - a string representing the file extension to parse the querymolstr as.
Note: old clients could be passing .sq files, so
iformat == '.oeb' will try to interpret the file as
a .sq file.
oformat - file format to write the results as
"""
timer = oechem.OEWallTimer()
# make sure to wait for the load to finish
blocking = True
loaded = self.IsLoaded(blocking)
assert loaded
if iformat.startswith(".sq"):
query = ReadShapeQuery(querymolstr)
else:
# read in query
qfs = oechem.oemolistream()
qfs = SetupStream(qfs, iformat)
if not qfs.openstring(querymolstr):
raise ValueError("Unable to open input molecule string")
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(qfs, query):
if iformat == ".oeb": # could be an old client trying to send a .sq file.
query = ReadShapeQuery(querymolstr)
else:
raise ValueError(
"Unable to read a molecule from the string of format '%s'"
% iformat)
ofs = oechem.oemolostream()
ofs = SetupStream(ofs, oformat)
if not ofs.openstring():
raise ValueError("Unable to openstring for output")
# do we only want shape based results?
# this is a "Write" lock to be paranoid and not overload the GPU
self.rwlock.AcquireWriteLock()
try:
# do search
scores = self.shapedb.GetSortedScores(query, options)
sys.stderr.write("%f seconds to do search\n" % timer.Elapsed())
finally:
self.rwlock.ReleaseWriteLock()
timer.Start()
# write results
for score in scores:
mcmol = oechem.OEMol()
if not self.moldb.GetMolecule(mcmol, score.GetMolIdx()):
oechem.OEThrow.Warning(
"Can't retrieve molecule %i from the OEMolDatabase, "
"skipping..." % score.GetMolIdx())
continue
# remove hydrogens to make output smaller, this also
# ensures OEPrepareFastROCSMol will have the same output
oechem.OESuppressHydrogens(mcmol)
mol = oechem.OEGraphMol(
mcmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OECopySDData(mol, mcmol)
if options.GetSimFunc() == oefastrocs.OEShapeSimFuncType_Tanimoto:
oechem.OESetSDData(mol, "ShapeTanimoto",
"%.4f" % score.GetShapeTanimoto())
oechem.OESetSDData(mol, "ColorTanimoto",
"%.4f" % score.GetColorTanimoto())
oechem.OESetSDData(mol, "TanimotoCombo",
"%.4f" % score.GetTanimotoCombo())
else:
oechem.OESetSDData(mol, "ShapeTversky",
"%.4f" % score.GetShapeTversky())
oechem.OESetSDData(mol, "ColorTversky",
"%.4f" % score.GetColorTversky())
oechem.OESetSDData(mol, "TverskyCombo",
"%.4f" % score.GetTverskyCombo())
if options.GetInitialOrientation(
) != oefastrocs.OEFastROCSOrientation_Inertial:
oechem.OEAddSDData(
mol, "Opt. Starting Pos.",
GetAltStartsString(options.GetInitialOrientation()))
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
output = ofs.GetString()
sys.stderr.write("%f seconds to write hitlist\n" % timer.Elapsed())
sys.stderr.flush()
ofs.close()
return output
def main(argv=[__name__]):
if len(argv) < 3:
oechem.OEThrow.Usage("%s <database> [<queries> ... ]" % argv[0])
return 0
# check system
if not oefastrocs.OEFastROCSIsGPUReady():
oechem.OEThrow.Info("No supported GPU available!")
return 0
# read in database
dbname = argv[1]
print("Opening database file %s ..." % dbname)
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
# customize search options
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetInitialOrientation(
oefastrocs.OEFastROCSOrientation_UserInertialStarts)
opts.SetLimit(5)
for qfname in argv[2:]:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % qfname)
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(qfs, query):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % qfname)
ext = oechem.OEGetFileExtension(qfname)
base = qfname[:-(len(ext) + 1)]
# write out everthing to a similary named file
ofs = oechem.oemolostream()
ofname = base + "_user_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
oechem.OEWriteMolecule(ofs, query)
startsCoords = oechem.OEFloatVector()
atomIdx = 1
xyz = query.GetCoords()[atomIdx]
for x in xyz:
startsCoords.append(x)
if not len(startsCoords) % 3 == 0:
oechem.OEThrow.Fatal(
"Something went wrong whilst reading in user-starts coordinates"
)
opts.SetUserStarts(oechem.OEFloatVector(startsCoords),
int(len(startsCoords) / 3))
opts.SetMaxOverlays(opts.GetNumInertialStarts() *
opts.GetNumUserStarts())
if opts.GetInitialOrientation(
) == oefastrocs.OEFastROCSOrientation_UserInertialStarts:
numStarts = opts.GetNumUserStarts()
print("This example will use %u starts" % numStarts)
print("Searching for %s" % qfname)
for score in dbase.GetSortedScores(query, opts):
print("Score for mol %u(conf %u) %f shape %f color" %
(score.GetMolIdx(), score.GetConfIdx(),
score.GetShapeTanimoto(), score.GetColorTanimoto()))
dbmol = oechem.OEMol()
molidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, molidx):
print("Unable to retrieve molecule '%u' from the database" %
molidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "ShapeTanimoto",
"%.4f" % score.GetShapeTanimoto())
oechem.OESetSDData(mol, "ColorTanimoto",
"%.4f" % score.GetColorTanimoto())
oechem.OESetSDData(mol, "TanimotoCombo",
"%.4f" % score.GetTanimotoCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
print("Wrote results to %s" % ofname)
return 0
omega.SetSampleHydrogens(
True
) # Word to the wise: skipping this step can lead to significantly different charges!
omega.SetEnergyWindow(15.0)
omega.SetRMSThreshold(
1.0
) # Word to the wise: skipping this step can lead to significantly different charges!
if omega(mol_multiconf): # generate conformation
# Generate am1bcc partial charges
oequacpac.OEAssignCharges(mol_multiconf,
oequacpac.OEAM1BCCELF10Charges())
# Get total charge
conf = mol_multiconf.GetConf(oechem.OEHasConfIdx(0))
absFCharge = 0
sumFCharge = 0
sumPCharge = 0.0
for atm in mol_multiconf.GetAtoms():
sumFCharge += atm.GetFormalCharge()
absFCharge += abs(atm.GetFormalCharge())
sumPCharge += atm.GetPartialCharge()
oechem.OEThrow.Info(
"%s: %d formal charges give total charge %d ; Sum of Partial Charges %5.4f"
% (mol_multiconf.GetTitle(), absFCharge, sumFCharge, sumPCharge))
# Output file
ofs = oechem.oemolostream(charged_FN)
ofs.SetFormat(oechem.OEFormat_MOL2H)
oechem.OEWriteMolecule(ofs, conf)
# Convert to OEMol molecule
mol_oemol = smiles_to_oemol(smiles_str)
mol_oemol.SetTitle(ligand_name)
# Use OpenEye Omega toolkit to generate lowest energy structure
omega = oeomega.OEOmega()
omega.SetCanonOrder(False)
omega.SetMaxConfs(OMEGA_MAX_CONFS)
omega(mol_oemol)
# Generate protonation/tautomeric states with epik and charge molecule
valid_structure = False
with working_directory(temp_dir):
for i in range(mol_oemol.GetMaxConfIdx()):
try:
confomer = mol_oemol.GetConf(oechem.OEHasConfIdx(i))
mk_single_conformer_epik(ligand_name, confomer, pH=PH)
valid_structure = True
break
except ValueError:
print "WARNING: Omega structure #{:d} discarded.".format(i)
# Copy to output directory final file
if valid_structure:
mol2_file_name = ligand_name + '.mol2'
src_path = os.path.join(temp_dir, mol2_file_name)
dst_path = os.path.join(LIGANDS_DIR_PATH, mol2_file_name)
shutil.copyfile(src_path, dst_path)
smiles_file.close()
def save_charged_mol(mol, ofs):
"""Write conformer 0 of `mol` into output file stream `ofs`"""
conf = mol.GetConf(oechem.OEHasConfIdx(0))
oechem.OEWriteMolecule(ofs, conf)
def main(argv=[__name__]):
if len(argv) < 3:
oechem.OEThrow.Usage("%s <database> [<queries> ... ]" % argv[0])
dbname = argv[1]
# read in database
ifs = oechem.oemolistream()
if not ifs.open(dbname):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
print("Opening database file %s ..." % dbname)
timer = oechem.OEWallTimer()
dbase = oefastrocs.OEShapeDatabase()
moldb = oechem.OEMolDatabase()
if not moldb.Open(ifs):
oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)
dots = oechem.OEThreadedDots(10000, 200, "conformers")
if not dbase.Open(moldb, dots):
oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" %
dbname)
dots.Total()
print("%s seconds to load database" % timer.Elapsed())
opts = oefastrocs.OEShapeDatabaseOptions()
opts.SetSimFunc(oefastrocs.OEShapeSimFuncType_Tversky)
numHits = moldb.NumMols()
opts.SetLimit(numHits)
for qfname in argv[2:]:
# read in query
qfs = oechem.oemolistream()
if not qfs.open(qfname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[1])
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(qfs, query):
oechem.OEThrow.Fatal("Unable to read query from '%s'" % argv[1])
ext = oechem.OEGetFileExtension(qfname)
base = qfname[:-(len(ext) + 1)]
# write out everthing to a similary named file
ofs = oechem.oemolostream()
ofname = base + "_results." + ext
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])
print("Searching for %s" % qfname)
for score in dbase.GetSortedScores(query, opts):
dbmol = oechem.OEMol()
molidx = score.GetMolIdx()
if not moldb.GetMolecule(dbmol, molidx):
print("Unable to retrieve molecule '%u' from the database" %
molidx)
continue
mol = oechem.OEGraphMol(
dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))
oechem.OESetSDData(mol, "ShapeTversky",
"%.4f" % score.GetShapeTversky())
oechem.OESetSDData(mol, "ColorTversky",
"%.4f" % score.GetColorTversky())
oechem.OESetSDData(mol, "TverskyCombo",
"%.4f" % score.GetTverskyCombo())
score.Transform(mol)
oechem.OEWriteMolecule(ofs, mol)
print("Wrote results to %s" % ofname)
return 0
