def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData, argv)
if not itf.HasString("-smirks") and not itf.HasString("-rxn"):
oechem.OEThrow.Fatal(
"Please provide SMIRKS string or MDL reaction file")
if itf.HasString("-smirks") and itf.HasString("-rxn"):
oechem.OEThrow.Fatal(
"Please provide only SMIRKS string or MDL reaction file")
reaction = oechem.OEQMol()
if itf.HasString("-smirks"):
smirks = itf.GetString("-smirks")
if not oechem.OEParseSmirks(reaction, smirks):
oechem.OEThrow.Fatal("Unable to parse SMIRKS: %s" % smirks)
else:
rxn = itf.GetString("-rxn")
rfile = oechem.oemolistream(rxn)
opt = oechem.OEMDLQueryOpts_ReactionQuery | oechem.OEMDLQueryOpts_SuppressExplicitH
if not oechem.OEReadMDLReactionQueryFile(rfile, reaction, opt):
oechem.OEThrow.Fatal("Unable to read reaction file: %s" % rxn)
relax = itf.GetBool("-relax")
unique = itf.GetBool("-unique")
implicitH = itf.GetBool("-implicitH")
valcorrect = itf.GetBool("-valence")
isomeric = itf.GetBool("-isomeric")
libgen = oechem.OELibraryGen()
if not libgen.Init(reaction, not relax):
oechem.OEThrow.Fatal("failed to initialize library generator")
libgen.SetValenceCorrection(valcorrect)
libgen.SetExplicitHydrogens(not implicitH)
libgen.SetClearCoordinates(True)
ofs = oechem.oemolostream(".smi")
if itf.HasString("-product"):
ofs.open(itf.GetString("-product"))
nrReacts = 0
while itf.HasString("-reactants", nrReacts):
fileName = itf.GetString("-reactants", nrReacts)
if nrReacts >= libgen.NumReactants():
oechem.OEThrow.Fatal("Number of reactant files exceeds number of \
reactants specified in reaction")
ifs = oechem.oemolistream()
if not ifs.open(fileName):
oechem.OEThrow.Fatal("Unable to read %s reactant file" % fileName)
for mol in ifs.GetOEGraphMols():
libgen.AddStartingMaterial(mol, nrReacts, unique)
nrReacts += 1
if nrReacts != libgen.NumReactants():
oechem.OEThrow.Fatal("Reactions requires %d reactant files!" %
libgen.NumReactants())
LibGen(libgen, ofs, unique, isomeric)
rfile = oechem.oemolistream("amide.rxn")
reaction = oechem.OEQMol()
# reading reaction
# @ <SNIPPET-RXN-OPT>
opt = oechem.OEMDLQueryOpts_ReactionQuery | oechem.OEMDLQueryOpts_SuppressExplicitH
# @ </SNIPPET-RXN-OPT>
# @ <SNIPPET-READREACTION>
oechem.OEReadMDLReactionQueryFile(rfile, reaction, opt)
# @ </SNIPPET-READREACTION>
# @ <SNIPPET-RXN-ATOMS>
printatoms("Reactant atoms:", reaction.GetQAtoms(oechem.OEAtomIsInReactant()))
printatoms("Product atoms :", reaction.GetQAtoms(oechem.OEAtomIsInProduct()))
# @ </SNIPPET-RXN-ATOMS>
# initializing library generator
libgen = oechem.OELibraryGen()
libgen.Init(reaction)
# @ <SNIPPET-RXN-EXPH>
libgen.SetExplicitHydrogens(False)
# @ </SNIPPET-RXN-EXPH>
# @ <SNIPPET-RXN-VCORRECT>
libgen.SetValenceCorrection(True)
# @ </SNIPPET-RXN-VCORRECT>
# adding reactants
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1ccc(cc1)C(=O)O")
libgen.AddStartingMaterial(mol, 0)
mol.Clear()
oechem.OESmilesToMol(mol, "CC(C)CN")
libgen.AddStartingMaterial(mol, 1)
# accessing generated products
# 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.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
libgen = oechem.OELibraryGen("[O:1]=[C:2][Cl:3].[N:4]>>[O:1]=[C:2][N:4]")
libgen.SetExplicitHydrogens(False)
libgen.SetValenceCorrection(True)
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "CC(=O)Cl")
libgen.SetStartingMaterial(mol, 0)
mol.Clear()
oechem.OESmilesToMol(mol, "NCC")
libgen.SetStartingMaterial(mol, 1)
for product in libgen.GetProducts():
print("product smiles =", oechem.OEMolToSmiles(product))
# @ </SNIPPET>
# 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.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
lg = oechem.OELibraryGen()
lg.Init(
"[N:3][c:4]1[n:2][c:7][c:6][c:5][n:1]1>>[c:6]1[c:7][n:2][c:4]2[n:3]cc[n:1]2[c:5]1"
)
lg.SetExplicitHydrogens(False)
lg.SetValenceCorrection(True)
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cnc(nc1O)N")
matches = lg.AddStartingMaterial(mol, 0, False)
print("number of matches =", matches)
for product in lg.GetProducts():
print("product smiles =", oechem.OEMolToSmiles(product))
# @ </SNIPPET>