def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oegraphsim.OEConfigureFingerPrint(
itf, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
if not oechem.OEParseCommandLine(itf, argv):
return 1
ifname = itf.GetString("-in")
ffname = itf.GetString("-fpdb")
if oechem.OEGetFileExtension(ffname) != "fpbin":
oechem.OEThrow.Fatal(
"Fingerprint database file should have '.fpbin' file extension!")
idxfname = oechem.OEGetMolDatabaseIdxFileName(ifname)
if not os.path.exists(idxfname):
if not oechem.OECreateMolDatabaseIdx(ifname):
oechem.OEThrow.Warning("Unable to create %s molecule index file" %
idxfname)
oechem.OEThrow.Info("Using %s index molecule file" % idxfname)
moldb = oechem.OEMolDatabase()
if not moldb.Open(ifname):
oechem.OEThrow.Fatal("Cannot open molecule database file!")
nrmols = moldb.GetMaxMolIdx()
fptype = oegraphsim.OESetupFingerPrint(itf)
oechem.OEThrow.Info("Using fingerprint type %s" % fptype.GetFPTypeString())
opts = oegraphsim.OECreateFastFPDatabaseOptions(fptype)
opts.SetTracer(oechem.OEDots(100000, 1000, "fingerprints"))
oechem.OEThrow.Info("Generating fingerprints with %d threads" %
opts.GetNumProcessors())
timer = oechem.OEWallTimer()
if not oegraphsim.OECreateFastFPDatabaseFile(ffname, ifname, opts):
oechem.OEThrow.Fatal("Cannot create fingerprint database file!")
oechem.OEThrow.Info("%5.2f secs to generate %d fingerprints" %
(timer.Elapsed(), nrmols))
return 0
def GetFragments(mol, minbonds, maxbonds):
from openeye import oegraphsim
frags = []
fptype = oegraphsim.OEGetFPType("Tree,ver=2.0.0,size=4096,bonds=%d-%d,atype=AtmNum,btype=Order"
% (minbonds, maxbonds))
for abset in oegraphsim.OEGetFPCoverage(mol, fptype, True):
fragatompred = oechem.OEIsAtomMember(abset.GetAtoms())
frag = oechem.OEGraphMol()
adjustHCount = True
oechem.OESubsetMol(frag, mol, fragatompred, adjustHCount)
oechem.OEFindRingAtomsAndBonds(frag)
frags.append(oechem.OEGraphMol(frag))
return frags
def __createOeFastFingerPrintDatabase(self,
oeMolDbFilePath,
oeFpDbFilePath,
fpType="TREE"):
"""Create fast search fingerprint database from the input molecular database.
Args:
oeMolDbFilePath (str): path to the input molecular database
oeFpDbFilePath (str): path to the output fingerprint database
fpType (str): finger print type
Returns:
bool: True for success or False otherwise
Supports:
OEFPType_Circular
OEFPType_Path
OEFPType_Tree
Not currently supported by OE fp search -
OEFPType_MACCS166
OEFPType_Lingo
"""
startTime = time.time()
ok = False
try:
_ = fpType
fpD = {
"TREE": oegraphsim.OEFPType_Tree,
"CIRCULAR": oegraphsim.OEFPType_Circular,
"PATH": oegraphsim.OEFPType_Path
}
myFpType = fpD[
fpType] if fpType in fpD else oegraphsim.OEFPType_Tree
opts = oegraphsim.OECreateFastFPDatabaseOptions(
oegraphsim.OEGetFPType(myFpType))
ok = oegraphsim.OECreateFastFPDatabaseFile(oeFpDbFilePath,
oeMolDbFilePath, opts)
except Exception as e:
logger.exception("Failing with %s", str(e))
endTime = time.time()
logger.info("Completed operation at %s (%.4f seconds)",
time.strftime("%Y %m %d %H:%M:%S", time.localtime()),
endTime - startTime)
return ok
def visualize_mols(smiles,
fname,
rows,
cols,
bond_idx,
wbos,
colors,
align_to=0):
"""
Visualize molecules with highlighted bond and labeled with WBO
Parameters
----------
smiles : list of SMILES to visualize.
bond atoms should have map indices
fname : str
filename
rows : int
cols : int
bond_idx : tuple of atom maps of bond to highlight.
wbos : list of floats
colors : list of hex values for colors
align_to: int, optional, default 0
index for which molecule to align to. If zero, will align to first molecules in SMILES list
"""
itf = oechem.OEInterface()
ropts = oedepict.OEReportOptions(rows, cols)
ropts.SetHeaderHeight(25)
ropts.SetFooterHeight(25)
ropts.SetCellGap(2)
ropts.SetPageMargins(10)
report = oedepict.OEReport(ropts)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
opts = oedepict.OE2DMolDisplayOptions(cellwidth, cellheight,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
# align to chosen molecule
ref_mol = oechem.OEGraphMol()
oechem.OESmilesToMol(ref_mol, smiles[align_to])
oedepict.OEPrepareDepiction(ref_mol)
mols = []
minscale = float("inf")
for s in smiles:
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, s)
mols.append(mol)
oedepict.OEPrepareDepiction(mol, False, True)
minscale = min(minscale, oedepict.OEGetMoleculeScale(mol, opts))
print(minscale)
print(minscale)
opts.SetScale(minscale)
for i, mol in enumerate(mols):
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, False, True)
bond = get_bond(mol, bond_idx)
atom_bond_set = oechem.OEAtomBondSet()
atom_bond_set.AddAtoms([bond.GetBgn(), bond.GetEnd()])
atom_bond_set.AddBond(bond)
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(*colors[i])
overlaps = oegraphsim.OEGetFPOverlap(
ref_mol, mol, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(mol, ref_mol, overlaps)
#opts.SetBondPropLabelFontScale(4.0)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_set)
#font = oedepict.OEFont(oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Bold, 12,
# oedepict.OEAlignment_Default, oechem.OEBlack)
bond_label = oedepict.OEHighlightLabel("{:.2f}".format((wbos[i])),
hcolor)
bond_label.SetFontScale(1.4)
#bond_label.SetFont(font)
oedepict.OEAddLabel(disp, bond_label, atom_bond_set)
oedepict.OERenderMolecule(cell, disp)
# oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
return (oedepict.OEWriteReport(fname, report))
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oegraphsim
# @ <SNIPPET-PATH-DEFAULT-PARAMS>
fptype = oegraphsim.OEGetFPType(oegraphsim.OEFPType_Path)
print(fptype.GetFPTypeString())
# @ </SNIPPET-PATH-DEFAULT-PARAMS>
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oegraphsim
# @ <SNIPPET-FPOVERLAP>
pmol = oechem.OEGraphMol()
oechem.OESmilesToMol(pmol, "c1cnc2c(c1)CC(CC2O)CF")
tmol = oechem.OEGraphMol()
oechem.OESmilesToMol(tmol, "c1cc2c(cc1)CC(CCl)CC2N")
fptype = oegraphsim.OEGetFPType("Tree,ver=2.0.0,size=4096,bonds=5-5,"
"atype=AtmNum|HvyDeg|EqHalo,btype=Order")
for idx, match in enumerate(oegraphsim.OEGetFPOverlap(pmol, tmol, fptype)):
ostring = "match %2d: " % (idx + 1)
for mpair in match.GetAtoms():
p = mpair.pattern
t = mpair.target
ostring += "%d%s-%d%s " % (
p.GetIdx(), oechem.OEGetAtomicSymbol(p.GetAtomicNum()), t.GetIdx(),
oechem.OEGetAtomicSymbol(t.GetAtomicNum()))
print(ostring)
# @ </SNIPPET-FPOVERLAP>
def to_pdf(molecules, bond_map_idx, fname, rows=3, cols=2, align=None):
"""
Generate PDF of list of oemols or SMILES
Parameters
----------
molecules : list of OEMols
These mols need to have map indices on bond of interest and WBO attached to that bond's data
fname : str
Name of PDF
rows : int
How many rows of molecules per page
cols : int
How many columns of molecule per page
bond_map_idx : tuple of bond to highlight
align: oemol
molecule to align all other molecules in the list
"""
itf = oechem.OEInterface()
ropts = oedepict.OEReportOptions(rows, cols)
ropts.SetHeaderHeight(25)
ropts.SetFooterHeight(25)
ropts.SetCellGap(2)
ropts.SetPageMargins(10)
report = oedepict.OEReport(ropts)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
opts = oedepict.OE2DMolDisplayOptions(cellwidth, cellheight,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
if align:
if isinstance(align, str):
ref_mol = oechem.OEGraphMol()
oechem.OESmilesToMol(ref_mol, align)
elif isinstance(align,
(oechem.OEMol, oechem.OEMolBase, oechem.OEGraphMol)):
ref_mol = align
oedepict.OEPrepareDepiction(ref_mol)
for i, mol in enumerate(molecules):
cell = report.NewCell()
mol_copy = oechem.OEMol(mol)
oedepict.OEPrepareDepiction(mol_copy, False, True)
atom_bond_set = oechem.OEAtomBondSet()
a1 = mol_copy.GetAtom(oechem.OEHasMapIdx(bond_map_idx[0]))
a2 = mol_copy.GetAtom(oechem.OEHasMapIdx(bond_map_idx[1]))
b = mol_copy.GetBond(a1, a2)
opts.SetBondPropertyFunctor(fragmenter.chemi.LabelWibergBondOrder())
atom_bond_set.AddAtom(a1)
atom_bond_set.AddAtom(a2)
atom_bond_set.AddBond(b)
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
overlaps = oegraphsim.OEGetFPOverlap(
ref_mol, mol_copy,
oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(mol_copy, ref_mol, overlaps)
disp = oedepict.OE2DMolDisplay(mol_copy, opts)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_set)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteReport(fname, report)
# @ <SNIPPET-FINGERPRINT-ALIGN>
refmol = oechem.OEGraphMol()
oechem.OESmilesToMol(refmol, "C[C@H](C(=O)N1CCC[C@H]1C(=O)O)OC(=O)[C@@H](Cc2ccccc2)S")
oedepict.OEPrepareDepiction(refmol)
fitmol = oechem.OEGraphMol()
oechem.OESmilesToMol(fitmol, "C[C@H](C(=O)N1CCC[C@H]1C(=O)O)NC(=O)[C@@H](Cc2ccccn2)S")
oedepict.OEPrepareDepiction(fitmol)
image = oedepict.OEImage(500, 300)
rows, cols = 1, 2
grid = oedepict.OEImageGrid(image, rows, cols)
overlaps = oegraphsim.OEGetFPOverlap(refmol, fitmol,
oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(fitmol, refmol, overlaps)
opts = oedepict.OE2DMolDisplayOptions(grid.GetCellWidth(), grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
refscale = oedepict.OEGetMoleculeScale(refmol, opts)
fitscale = oedepict.OEGetMoleculeScale(fitmol, opts)
opts.SetScale(min(refscale, fitscale))
refdisp = oedepict.OE2DMolDisplay(refmol, opts)
fitdisp = oedepict.OE2DMolDisplay(fitmol, opts)
refcell = grid.GetCell(1, 1)
oedepict.OERenderMolecule(refcell, refdisp)
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oegraphsim
# @ <SNIPPET-FPPATTERN>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "NCC(=O)[O-]")
fptype = oegraphsim.OEGetFPType("Tree,ver=2.0.0,size=4096,bonds=0-4,"
"atype=AtmNum|Arom|FCharge|HvyDeg,btype=Order")
for idx, pattern in enumerate(oegraphsim.OEGetFPPatterns(mol, fptype)):
atomstr = " ".join([str(a) for a in pattern.GetAtoms()])
print("%2d %5d %50s %s" %
((idx + 1), pattern.GetBit(), pattern.GetSmarts(), atomstr))
# @ </SNIPPET-FPPATTERN>
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oegraphsim
# @ <SNIPPET-CIRCULAR-DEFAULT-PARAMS>
fptype = oegraphsim.OEGetFPType(oegraphsim.OEFPType_Circular)
print(fptype.GetFPTypeString())
# @ </SNIPPET-CIRCULAR-DEFAULT-PARAMS>
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
defopts = oegraphsim.OEFPDatabaseOptions(10,
oegraphsim.OESimMeasure_Tanimoto)
oegraphsim.OEConfigureFPDatabaseOptions(itf, defopts)
oegraphsim.OEConfigureFingerPrint(
itf, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
if not oechem.OEParseCommandLine(itf, argv):
return 0
qfname = itf.GetString("-query")
mfname = itf.GetString("-molfname")
ofname = itf.GetString("-out")
# initialize databases
timer = oechem.OEWallTimer()
timer.Start()
ifs = oechem.oemolistream()
if not ifs.open(qfname):
oechem.OEThrow.Fatal("Cannot open input file!")
query = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, query):
oechem.OEThrow.Fatal("Cannot read query molecule!")
moldb = oechem.OEMolDatabase()
if not moldb.Open(mfname):
oechem.OEThrow.Fatal("Cannot open molecule database!")
ofs = oechem.oemolostream()
if not ofs.open(ofname):
oechem.OEThrow.Fatal("Cannot open output file!")
fptype = oegraphsim.OESetupFingerPrint(itf)
oechem.OEThrow.Info("Using fingerprint type %s" % fptype.GetFPTypeString())
fpdb = oegraphsim.OEFPDatabase(fptype)
emptyfp = oegraphsim.OEFingerPrint()
emptyfp.SetFPTypeBase(fptype)
nrmols = moldb.GetMaxMolIdx()
mol = oechem.OEGraphMol()
for idx in range(0, nrmols):
if moldb.GetMolecule(mol, idx):
fpdb.AddFP(mol)
else:
fpdb.AddFP(emptyfp)
nrfps = fpdb.NumFingerPrints()
oechem.OEThrow.Info("%5.2f sec to initialize databases" % timer.Elapsed())
opts = oegraphsim.OEFPDatabaseOptions()
oegraphsim.OESetupFPDatabaseOptions(opts, itf)
# search fingerprint database
timer.Start()
scores = fpdb.GetSortedScores(query, opts)
oechem.OEThrow.Info("%5.2f sec to search %d fingerprints" %
(timer.Elapsed(), nrfps))
timer.Start()
hit = oechem.OEGraphMol()
for si in scores:
if moldb.GetMolecule(hit, si.GetIdx()):
oechem.OEWriteMolecule(ofs, hit)
oechem.OEThrow.Info("%5.2f sec to write %d hits" %
(timer.Elapsed(), opts.GetLimit()))
return 0
from openeye import oegraphsim
# @ <SNIPPET-SDF2FP>
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <infile>" % sys.argv[0])
ifs = oechem.oemolistream()
if not ifs.open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % sys.argv[1])
if ifs.GetFormat() != oechem.OEFormat_SDF:
oechem.OEThrow.Fatal("%s input file has to be an SDF file" % sys.argv[1])
molcounter = 0
fpcounter = 0
for mol in ifs.GetOEGraphMols():
molcounter += 1
for dp in oechem.OEGetSDDataPairs(mol):
if oegraphsim.OEIsValidFPTypeString(dp.GetTag()):
fpcounter += 1
fptypestr = dp.GetTag()
fphexdata = dp.GetValue()
fp = oegraphsim.OEFingerPrint()
fptype = oegraphsim.OEGetFPType(fptypestr)
fp.SetFPTypeBase(fptype)
fp.FromHexString(fphexdata)
print("Number of molecules = %d" % molcounter)
print("Number of fingerprints = %d" % fpcounter)
# @ </SNIPPET-SDF2FP>
