def main(argv=[__name__]):
if len(argv) != 4:
oechem.OEThrow.Usage("%s <refmol> <fitmol> <outfile>" % argv[0])
reffs = oechem.oemolistream()
if not reffs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
if not oechem.OEIs3DFormat(reffs.GetFormat()):
oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates")
refmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(reffs, refmol):
oechem.OEThrow.Fatal("Unable to read molecule in %s" % argv[1])
if not refmol.GetDimension() == 3:
oechem.OEThrow.Fatal("%s doesn't have 3D coordinates" % refmol.GetTitle())
fitfs = oechem.oemolistream()
if not fitfs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[2])
if not oechem.OEIs3DFormat(fitfs.GetFormat()):
oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates")
ofs = oechem.oemolostream()
if not ofs.open(argv[3]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[3])
if not oechem.OEIs3DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates")
oechem.OEWriteConstMolecule(ofs, refmol)
oechem.OESuppressHydrogens(refmol)
for fitmol in fitfs.GetOEGraphMols():
if not fitmol.GetDimension() == 3:
oechem.OEThrow.Warning("%s doesn't have 3D coordinates" % fitmol.GetTitle())
continue
MCSAlign(refmol, fitmol, ofs)
def main(argv=[__name__]):
if len(argv) != 5:
oechem.OEThrow.Usage("%s <refmol> <fitmol> <outfile> <smarts>" %
argv[0])
reffs = oechem.oemolistream()
if not reffs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
if not oechem.OEIs3DFormat(reffs.GetFormat()):
oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates")
refmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(reffs, refmol):
oechem.OEThrow.Fatal("Unable to read molecule in %s" % argv[1])
if not refmol.GetDimension() == 3:
oechem.OEThrow.Fatal("%s doesn't have 3D coordinates" %
refmol.GetTitle())
fitfs = oechem.oemolistream()
if not fitfs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[2])
if not oechem.OEIs3DFormat(fitfs.GetFormat()):
oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates")
ofs = oechem.oemolostream()
if not ofs.open(argv[3]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[3])
if not oechem.OEIs3DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates")
oechem.OEWriteConstMolecule(ofs, refmol)
ss = oechem.OESubSearch()
if not ss.Init(argv[4]):
oechem.OEThrow.Fatal("Unable to parse SMARTS: %s" % argv[4])
oechem.OEPrepareSearch(refmol, ss)
if not ss.SingleMatch(refmol):
oechem.OEThrow.Fatal("SMARTS fails to match refmol")
for fitmol in fitfs.GetOEGraphMols():
if not fitmol.GetDimension() == 3:
oechem.OEThrow.Warning("%s doesn't have 3D coordinates" %
fitmol.GetTitle())
continue
oechem.OEPrepareSearch(fitmol, ss)
if not ss.SingleMatch(fitmol):
oechem.OEThrow.Warning("SMARTS fails to match fitmol %s" %
fitmol.GetTitle())
continue
SmartsAlign(refmol, fitmol, ss, ofs)
def main(argv=[__name__]):
if len(argv) != 3:
oechem.OEThrow.Usage("%s <infile> <outfile>" % argv[0])
ifs = oechem.oemolistream()
if not ifs.open(argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])
ofs = oechem.oemolostream()
if not ofs.open(argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[2])
if not oechem.OEIs3DFormat(ofs.GetFormat()):
oechem.OEThrow.Fatal("Invalid output file format for 3D coordinates!")
omegaOpts = oeomega.OEMacrocycleOmegaOptions()
mcomega = oeomega.OEMacrocycleOmega(omegaOpts)
for mol in ifs.GetOEMols():
oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
ret_code = mcomega.Build(mol)
if ret_code == oeomega.OEOmegaReturnCode_Success:
oechem.OEWriteMolecule(ofs, mol)
else:
oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))
return 0
def ReadMolecule(filename):
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(filename):
oechem.OEThrow.Fatal("Unable to open %s for reading", filename)
if not oechem.OEIs3DFormat(ifs.GetFormat()):
oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates")
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Unable to read a molecule from %s", filename)
return mol
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
# @ <SNIPPET-ALTLOCFACT-FLAVOR>
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
# @ </SNIPPET-ALTLOCFACT-FLAVOR>
inputFile = itf.GetString("-in")
if not ims.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading." % inputFile)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % inputFile)
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read %s." % inputFile)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
# @ <SNIPPET-ALTLOCFACT-PRIMARY>
alf = oechem.OEAltLocationFactory(mol)
if alf.GetGroupCount() != 0:
alf.MakePrimaryAltMol(mol)
# @ </SNIPPET-ALTLOCFACT-PRIMARY>
# @ <SNIPPET-PLACE-HYDROGENS-BASIC>
if oechem.OEPlaceHydrogens(mol):
# ...
# @ </SNIPPET-PLACE-HYDROGENS-BASIC>
print("success")
# @ <SNIPPET-PLACE-HYDROGENS-OPTIONS>
opt = oechem.OEPlaceHydrogensOptions()
opt.SetStandardizeBondLen(False)
# @ </SNIPPET-PLACE-HYDROGENS-OPTIONS>
# @ <SNIPPET-PLACE-HYDROGENS-DETAILS>
# given molecule mol and OEPlaceHydrogensOptions opt...
details = oechem.OEPlaceHydrogensDetails()
if oechem.OEPlaceHydrogens(mol, details, opt):
print(details.Describe())
# @ </SNIPPET-PLACE-HYDROGENS-DETAILS>
ims.close()
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_ALTLOC)
inputFile = itf.GetString("-in")
if not ims.open(inputFile):
oechem.OEThrow.Fatal("Unable to open %s for reading." % inputFile)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % inputFile)
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, mol):
oechem.OEThrow.Fatal("Unable to read %s." % inputFile)
if not oechem.OEHasResidues(mol):
oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
alf = oechem.OEAltLocationFactory(mol)
if alf.GetGroupCount() != 0:
alf.MakePrimaryAltMol(mol)
# in our example, we will select the first histidine
selectedResidue = oechem.OEResidue()
for atom in mol.GetAtoms():
res = oechem.OEAtomGetResidue(atom)
if oechem.OEGetResidueIndex(res) == oechem.OEResidueIndex_HIS:
selectedResidue = res
break
# @ <SNIPPET-PLACE-HYDROGENS-PRED>
# given predicate IsSameResidue, residue selectedResidue and molecule mol...
opt = oechem.OEPlaceHydrogensOptions()
opt.SetNoFlipPredicate(IsSameResidue(selectedResidue))
if oechem.OEPlaceHydrogens(mol, opt):
# selectedResidue will not be flipped...
# @ </SNIPPET-PLACE-HYDROGENS-PRED>
print("success")
ims.close()
def __init__(self, ipf, keepAlts=F, verbose=T):
self.ipf = ipf
self.keepAlts = keepAlts
self.verbose = verbose
flavor = oechem.OEIFlavor_PDB_Default
ims = oechem.oemolistream()
ims.SetFlavor(oechem.OEFormat_PDB, flavor)
if not ims.open(self.ipf):
oechem.OEThrow.Fatal("Unable to open %s for reading." % self.ipf)
if not oechem.OEIs3DFormat(ims.GetFormat()):
oechem.OEThrow.Fatal("%s is not in a 3D format." % self.ipf)
iftp = oechem.OEGetFileType(oechem.OEGetFileExtension(self.ipf))
if (iftp == oechem.OEFormat_PDB) and not self.keepAlts:
oechem.OEThrow.Verbose(
"Default processing of alt locations (keep just 'A' and ' ').")
inmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ims, inmol):
oechem.OEThrow.Fatal("Unable to read %s." % self.ipf)
ims.close()
if (inmol.NumAtoms() == 0):
oechem.OEThrow.Fatal("Input molecule %s contains no atoms." %
self.ipf)
if inmol.GetTitle() == "":
inmol.SetTitle(ipf[:-4])
oechem.OEThrow.Verbose("Processing %s." % inmol.GetTitle())
if not oechem.OEHasResidues(inmol):
oechem.OEPerceiveResidues(inmol, oechem.OEPreserveResInfo_All)
self.inmol = inmol
self.mol = inmol.CreateCopy()
# or its use.
from __future__ import print_function
import sys
from openeye import oechem
from openeye import oezap
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <molfile>" % sys.argv[0])
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream()
if not ifs.open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading", sys.argv[1])
if not oechem.OEIs3DFormat(ifs.GetFormat()):
oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates")
oechem.OEReadMolecule(ifs, mol)
oechem.OEAssignBondiVdWRadii(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
# @ <SNIPPET-GetArea-Molecule>
area = oezap.OEArea()
a = area.GetArea(mol)
print("Molecule area =", a)
# @ </SNIPPET-GetArea-Molecule>
# @ <SNIPPET-GetArea-Atoms>
atomArea = oechem.OEFloatArray(mol.GetMaxAtomIdx())