# # # Copyright (C) from 2009 to Present EPAM Systems. # # This file is part of Indigo toolkit. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import os import platform import sys import warnings from array import array from ctypes import (CDLL, POINTER, RTLD_GLOBAL, c_byte, c_char_p, c_double, c_float, c_int, c_ulonglong, pointer) DECODE_ENCODING = "utf-8" ENCODE_ENCODING = "utf-8" class IndigoException(Exception): def __init__(self, value): if sys.version_info > (3, 0) and not isinstance(value, str): self.value = value.decode(DECODE_ENCODING) else: self.value = value def __str__(self): return self.value class IndigoObject(object): """Docstring for class IndigoObject.""" def __init__(self, dispatcher, id, parent=None): self.id = id self.dispatcher = dispatcher self.parent = parent def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.dispatcher._setSessionId() self.dispatcher._lib.indigoClose(self.id) def __del__(self): self.dispose() def dispose(self): if self.id >= 0: if getattr(Indigo, "_lib", None) is not None: self.dispatcher._setSessionId() Indigo._lib.indigoFree(self.id) self.id = -1 def __iter__(self): return self def _next(self): self.dispatcher._setSessionId() newobj = self.dispatcher._checkResult(Indigo._lib.indigoNext(self.id)) if newobj == 0: return None else: return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) def __next__(self): obj = self._next() if obj == None: raise StopIteration return obj def next(self): return self.__next__() def oneBitsList(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoOneBitsList(self.id) ) def mdlct(self): buf = self.dispatcher.writeBuffer() self.dispatcher._setSessionId() self.dispatcher._checkResult( Indigo._lib.indigoSaveMDLCT(self.id, buf.id) ) return buf.toBuffer() def xyz(self): self.dispatcher._setSessionId() xyz = Indigo._lib.indigoXYZ(self.id) if xyz is None: raise IndigoException(Indigo._lib.indigoGetLastError()) return [xyz[0], xyz[1], xyz[2]] def coords(self): self.dispatcher._setSessionId() xyz = Indigo._lib.indigoCoords(self.id) if xyz is None: raise IndigoException(Indigo._lib.indigoGetLastError()) return [xyz[0], xyz[1]] def alignAtoms(self, atom_ids, desired_xyz): if len(atom_ids) * 3 != len(desired_xyz): raise IndigoException( "alignAtoms(): desired_xyz[] must be exactly 3 times bigger than atom_ids[]" ) atoms = (c_int * len(atom_ids))() for i in range(len(atoms)): atoms[i] = atom_ids[i] xyz = (c_float * len(desired_xyz))() for i in range(len(desired_xyz)): xyz[i] = desired_xyz[i] self.dispatcher._setSessionId() return self.dispatcher._checkResultFloat( self.dispatcher._lib.indigoAlignAtoms( self.id, len(atoms), atoms, xyz ) ) def addStereocenter(self, type, v1, v2, v3, v4=-1): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddStereocenter(self.id, type, v1, v2, v3, v4) ) def clone(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult(Indigo._lib.indigoClone(self.id)), ) def check(self, props=""): if props is None: props = "" self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoCheck(self.id, props.encode(ENCODE_ENCODING)) ) def close(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoClose(self.id)) def hasNext(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult(Indigo._lib.indigoHasNext(self.id)) ) def index(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoIndex(self.id)) def remove(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoRemove(self.id)) def saveMolfile(self, filename): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSaveMolfileToFile( self.id, filename.encode(ENCODE_ENCODING) ) ) def molfile(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoMolfile(self.id) ) def saveCml(self, filename): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSaveCmlToFile( self.id, filename.encode(ENCODE_ENCODING) ) ) def cml(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoCml(self.id) ) def saveCdxml(self, filename): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSaveCdxmlToFile( self.id, filename.encode(ENCODE_ENCODING) ) ) def cdxml(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoCdxml(self.id) ) def json(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoJson(self.id) ) def saveMDLCT(self, output): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSaveMDLCT(self.id, output.id) ) def addReactant(self, molecule): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddReactant(self.id, molecule.id) ) def addProduct(self, molecule): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddProduct(self.id, molecule.id) ) def addCatalyst(self, molecule): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddCatalyst(self.id, molecule.id) ) def countReactants(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountReactants(self.id) ) def countProducts(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountProducts(self.id) ) def countCatalysts(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountCatalysts(self.id) ) def countMolecules(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountMolecules(self.id) ) def getMolecule(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetMolecule(self.id, index) ), ) def iterateReactants(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateReactants(self.id) ), ) def iterateProducts(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateProducts(self.id) ), ) def iterateCatalysts(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateCatalysts(self.id) ), ) def iterateMolecules(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateMolecules(self.id) ), ) def saveRxnfile(self, filename): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSaveRxnfileToFile( self.id, filename.encode(ENCODE_ENCODING) ) ) def rxnfile(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoRxnfile(self.id) ) def optimize(self, options=""): if options is None: options = "" self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoOptimize( self.id, options.encode(ENCODE_ENCODING) ) ) def normalize(self, options=""): if options is None: options = "" self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult( Indigo._lib.indigoNormalize( self.id, options.encode(ENCODE_ENCODING) ) ) ) def standardize(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoStandardize(self.id) ) def ionize(self, pH, pH_toll): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoIonize(self.id, pH, pH_toll) ) def getAcidPkaValue(self, atom, level, min_level): self.dispatcher._setSessionId() result = self.dispatcher._checkResultPtr( Indigo._lib.indigoGetAcidPkaValue( self.id, atom.id, level, min_level ) ) return result[0] def getBasicPkaValue(self, atom, level, min_level): self.dispatcher._setSessionId() result = self.dispatcher._checkResultPtr( Indigo._lib.indigoGetBasicPkaValue( self.id, atom.id, level, min_level ) ) return result[0] def automap(self, mode=""): if mode is None: mode = "" self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAutomap(self.id, mode.encode(ENCODE_ENCODING)) ) def atomMappingNumber(self, reaction_atom): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetAtomMappingNumber(self.id, reaction_atom.id) ) def setAtomMappingNumber(self, reaction_atom, number): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetAtomMappingNumber( self.id, reaction_atom.id, number ) ) def reactingCenter(self, reaction_bond): value = c_int() self.dispatcher._setSessionId() res = self.dispatcher._checkResult( Indigo._lib.indigoGetReactingCenter( self.id, reaction_bond.id, pointer(value) ) ) if res == 0: return None return value.value def setReactingCenter(self, reaction_bond, rc): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetReactingCenter(self.id, reaction_bond.id, rc) ) def clearAAM(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoClearAAM(self.id) ) def correctReactingCenters(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCorrectReactingCenters(self.id) ) def iterateAtoms(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateAtoms(self.id) ), ) def iteratePseudoatoms(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIteratePseudoatoms(self.id) ), ) def iterateRSites(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateRSites(self.id) ), ) def iterateStereocenters(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateStereocenters(self.id) ), ) def iterateAlleneCenters(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateAlleneCenters(self.id) ), ) def iterateRGroups(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateRGroups(self.id) ), ) def countRGroups(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountRGroups(self.id) ) def isPseudoatom(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult( Indigo._lib.indigoIsPseudoatom(self.id) ) ) def isRSite(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult(Indigo._lib.indigoIsRSite(self.id)) ) def isTemplateAtom(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult( Indigo._lib.indigoIsTemplateAtom(self.id) ) ) def stereocenterType(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoStereocenterType(self.id) ) def stereocenterGroup(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoStereocenterGroup(self.id) ) def setStereocenterGroup(self, group): self.dispatcher._setSessionId() self.dispatcher._checkResult( Indigo._lib.indigoSetStereocenterGroup(self.id, group) ) def changeStereocenterType(self, type): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoChangeStereocenterType(self.id, type) ) def validateChirality(self): self.dispatcher._setSessionId() self.dispatcher._checkResult( Indigo._lib.indigoValidateChirality(self.id) ) def singleAllowedRGroup(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSingleAllowedRGroup(self.id) ) def iterateRGroupFragments(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateRGroupFragments(self.id) ), ) def countAttachmentPoints(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountAttachmentPoints(self.id) ) def iterateAttachmentPoints(self, order): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateAttachmentPoints(self.id, order) ), ) def symbol(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoSymbol(self.id) ) def degree(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoDegree(self.id)) def charge(self): value = c_int() self.dispatcher._setSessionId() res = self.dispatcher._checkResult( Indigo._lib.indigoGetCharge(self.id, pointer(value)) ) if res == 0: return None return value.value def getExplicitValence(self): value = c_int() self.dispatcher._setSessionId() res = self.dispatcher._checkResult( Indigo._lib.indigoGetExplicitValence(self.id, pointer(value)) ) if res == 0: return None return value.value def setExplicitValence(self, valence): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetExplicitValence(self.id, valence) ) def radicalElectrons(self): value = c_int() self.dispatcher._setSessionId() res = self.dispatcher._checkResult( Indigo._lib.indigoGetRadicalElectrons(self.id, pointer(value)) ) if res == 0: return None return value.value def radical(self): value = c_int() self.dispatcher._setSessionId() res = self.dispatcher._checkResult( Indigo._lib.indigoGetRadical(self.id, pointer(value)) ) if res == 0: return None return value.value def setRadical(self, radical): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetRadical(self.id, radical) ) def atomicNumber(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAtomicNumber(self.id) ) def isotope(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoIsotope(self.id)) def valence(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoValence(self.id)) def checkValence(self): """ :: Since version 1.3.0 """ self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCheckValence(self.id) ) def checkQuery(self): """ :: Since version 1.3.0 """ self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCheckQuery(self.id) ) def checkRGroups(self): """ :: Since version 1.3.0 """ self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCheckRGroups(self.id) ) def checkChirality(self): """ :: Since version 1.3.0 """ self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCheckChirality(self.id) ) def check3DStereo(self): """ :: Since version 1.3.0 """ self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCheck3DStereo(self.id) ) def checkStereo(self): """ :: Since version 1.3.0 """ self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCheckStereo(self.id) ) def countHydrogens(self): value = c_int() self.dispatcher._setSessionId() res = self.dispatcher._checkResult( Indigo._lib.indigoCountHydrogens(self.id, pointer(value)) ) if res == 0: return None return value.value def countImplicitHydrogens(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountImplicitHydrogens(self.id) ) def setXYZ(self, x, y, z): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetXYZ(self.id, x, y, z) ) def countSuperatoms(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountSuperatoms(self.id) ) def countDataSGroups(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountDataSGroups(self.id) ) def countRepeatingUnits(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountRepeatingUnits(self.id) ) def countMultipleGroups(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountMultipleGroups(self.id) ) def countGenericSGroups(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountGenericSGroups(self.id) ) def iterateDataSGroups(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateDataSGroups(self.id) ), ) def iterateSuperatoms(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateSuperatoms(self.id) ), ) def iterateGenericSGroups(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateGenericSGroups(self.id) ), ) def iterateRepeatingUnits(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateRepeatingUnits(self.id) ), ) def iterateMultipleGroups(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateMultipleGroups(self.id) ), ) def iterateSGroups(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateSGroups(self.id) ), ) def iterateTGroups(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateTGroups(self.id) ), ) def getSuperatom(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetSuperatom(self.id, index) ), ) def getDataSGroup(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetDataSGroup(self.id, index) ), ) def getGenericSGroup(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetGenericSGroup(self.id, index) ), ) def getMultipleGroup(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetMultipleGroup(self.id, index) ), ) def getRepeatingUnit(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetRepeatingUnit(self.id, index) ), ) def description(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoDescription(self.id) ) def data(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoData(self.id) ) def addDataSGroup(self, atoms, bonds, description, data): arr2 = (c_int * len(atoms))() for i in range(len(atoms)): arr2[i] = atoms[i] arr4 = (c_int * len(bonds))() for i in range(len(bonds)): arr4[i] = bonds[i] self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoAddDataSGroup( self.id, len(arr2), arr2, len(arr4), arr4, description.encode(ENCODE_ENCODING), data.encode(ENCODE_ENCODING), ) ), ) def addSuperatom(self, atoms, name): arr2 = (c_int * len(atoms))() for i in range(len(atoms)): arr2[i] = atoms[i] self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoAddSuperatom( self.id, len(arr2), arr2, name.encode(ENCODE_ENCODING) ) ), ) def setDataSGroupXY(self, x, y, options=""): self.dispatcher._setSessionId() if options is None: options = "" return self.dispatcher._checkResult( Indigo._lib.indigoSetDataSGroupXY( self.id, x, y, options.encode(ENCODE_ENCODING) ) ) def setSGroupData(self, data): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupData( self.id, data.encode(ENCODE_ENCODING) ) ) def setSGroupCoords(self, x, y): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupCoords(self.id, x, y) ) def setSGroupDescription(self, description): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupDescription( self.id, description.encode(ENCODE_ENCODING) ) ) def setSGroupFieldName(self, name): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupFieldName( self.id, name.encode(ENCODE_ENCODING) ) ) def setSGroupQueryCode(self, code): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupQueryCode( self.id, code.encode(ENCODE_ENCODING) ) ) def setSGroupQueryOper(self, oper): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupQueryOper( self.id, oper.encode(ENCODE_ENCODING) ) ) def setSGroupDisplay(self, option): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupDisplay( self.id, option.encode(ENCODE_ENCODING) ) ) def setSGroupLocation(self, option): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupLocation( self.id, option.encode(ENCODE_ENCODING) ) ) def setSGroupTag(self, tag): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupTag( self.id, tag.encode(ENCODE_ENCODING) ) ) def setSGroupTagAlign(self, tag_align): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupTagAlign(self.id, tag_align) ) def setSGroupDataType(self, data_type): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupDataType( self.id, data_type.encode(ENCODE_ENCODING) ) ) def setSGroupXCoord(self, x): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupXCoord(self.id, x) ) def setSGroupYCoord(self, y): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupYCoord(self.id, y) ) def createSGroup(self, sgtype, mapping, name): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoCreateSGroup( sgtype.encode(ENCODE_ENCODING), mapping.id, name.encode(ENCODE_ENCODING), ) ), ) def setSGroupClass(self, sgclass): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupClass( self.id, sgclass.encode(ENCODE_ENCODING) ) ) def setSGroupName(self, sgname): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupName( self.id, sgname.encode(ENCODE_ENCODING) ) ) def getSGroupClass(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoGetSGroupClass(self.id) ) def getSGroupName(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoGetSGroupName(self.id) ) def getSGroupNumCrossBonds(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupNumCrossBonds(self.id) ) def addSGroupAttachmentPoint(self, aidx, lvidx, apid): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddSGroupAttachmentPoint( self.id, aidx, lvidx, apid.encode(ENCODE_ENCODING) ) ) def deleteSGroupAttachmentPoint(self, apidx): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoDeleteSGroupAttachmentPoint(self.id, apidx) ) def getSGroupDisplayOption(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupDisplayOption(self.id) ) def setSGroupDisplayOption(self, option): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupDisplayOption(self.id, option) ) def getSGroupSeqId(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupSeqId(self.id) ) def getSGroupCoords(self): """ Returns: XY coordinates for Data sgroup :: Since 1.3.0 """ self.dispatcher._setSessionId() xyz = Indigo._lib.indigoGetSGroupCoords(self.id) if xyz is None: raise IndigoException(Indigo._lib.indigoGetLastError()) return [xyz[0], xyz[1]] def getRepeatingUnitSubscript(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoGetRepeatingUnitSubscript(self.id) ) def getRepeatingUnitConnectivity(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetRepeatingUnitConnectivity(self.id) ) def getSGroupMultiplier(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupMultiplier(self.id) ) def setSGroupMultiplier(self, mult): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupMultiplier(self.id, mult) ) def setSGroupBrackets(self, style, x1, y1, x2, y2, x3, y3, x4, y4): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupBrackets( self.id, style, x1, y1, x2, y2, x3, y3, x4, y4 ) ) def findSGroups(self, prop, val): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoFindSGroups( self.id, prop.encode(ENCODE_ENCODING), val.encode(ENCODE_ENCODING), ) ), ) def getSGroupType(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupType(self.id) ) def getSGroupIndex(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupIndex(self.id) ) def getSGroupOriginalId(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupOriginalId(self.id) ) def setSGroupOriginalId(self, original): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupOriginalId(self.id, original) ) def getSGroupParentId(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetSGroupParentId(self.id) ) def setSGroupParentId(self, parent): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetSGroupParentId(self.id, parent) ) def addTemplate(self, templates, name): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddTemplate( self.id, templates.id, name.encode(ENCODE_ENCODING) ) ) def removeTemplate(self, name): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoRemoveTemplate( self.id, name.encode(ENCODE_ENCODING) ) ) def findTemplate(self, name): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoFindTemplate( self.id, name.encode(ENCODE_ENCODING) ) ) def getTGroupClass(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoGetTGroupClass(self.id) ) def getTGroupName(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoGetTGroupName(self.id) ) def getTGroupAlias(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoGetTGroupAlias(self.id) ) def transformSCSRtoCTAB(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoTransformSCSRtoCTAB(self.id) ) def transformCTABtoSCSR(self, templates): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoTransformCTABtoSCSR(self.id, templates.id) ) def getTemplateAtomClass(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoGetTemplateAtomClass(self.id) ) def setTemplateAtomClass(self, name): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetTemplateAtomClass( self.id, name.encode(ENCODE_ENCODING) ) ) def clean2d(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoClean2d(self.id)) def resetCharge(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoResetCharge(self.id) ) def resetExplicitValence(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoResetExplicitValence(self.id) ) def resetRadical(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoResetRadical(self.id) ) def resetIsotope(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoResetIsotope(self.id) ) def setAttachmentPoint(self, order): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetAttachmentPoint(self.id, order) ) def clearAttachmentPoints(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoClearAttachmentPoints(self.id) ) def removeConstraints(self, type): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoRemoveConstraints( self.id, type.encode(ENCODE_ENCODING) ) ) def addConstraint(self, type, value): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddConstraint( self.id, type.encode(ENCODE_ENCODING), value.encode(ENCODE_ENCODING), ) ) def addConstraintNot(self, type, value): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddConstraintNot( self.id, type.encode(ENCODE_ENCODING), value.encode(ENCODE_ENCODING), ) ) def addConstraintOr(self, type, value): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddConstraintOr( self.id, type.encode(ENCODE_ENCODING), value.encode(ENCODE_ENCODING), ) ) def resetStereo(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoResetStereo(self.id) ) def invertStereo(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoInvertStereo(self.id) ) def countAtoms(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountAtoms(self.id) ) def countBonds(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountBonds(self.id) ) def countPseudoatoms(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountPseudoatoms(self.id) ) def countRSites(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountRSites(self.id) ) def iterateBonds(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateBonds(self.id) ), ) def bondOrder(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoBondOrder(self.id) ) def bondStereo(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoBondStereo(self.id) ) def topology(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoTopology(self.id) ) def iterateNeighbors(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateNeighbors(self.id) ), ) def bond(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult(Indigo._lib.indigoBond(self.id)), ) def getAtom(self, idx): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetAtom(self.id, idx) ), ) def getBond(self, idx): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetBond(self.id, idx) ), ) def source(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult(Indigo._lib.indigoSource(self.id)), ) def destination(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoDestination(self.id) ), ) def clearCisTrans(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoClearCisTrans(self.id) ) def clearStereocenters(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoClearStereocenters(self.id) ) def countStereocenters(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountStereocenters(self.id) ) def clearAlleneCenters(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoClearAlleneCenters(self.id) ) def countAlleneCenters(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountAlleneCenters(self.id) ) def resetSymmetricCisTrans(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoResetSymmetricCisTrans(self.id) ) def resetSymmetricStereocenters(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoResetSymmetricStereocenters(self.id) ) def markEitherCisTrans(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoMarkEitherCisTrans(self.id) ) def markStereobonds(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoMarkStereobonds(self.id) ) def addAtom(self, symbol): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoAddAtom( self.id, symbol.encode(ENCODE_ENCODING) ) ), ) def resetAtom(self, symbol): self.dispatcher._setSessionId() self.dispatcher._checkResult( Indigo._lib.indigoResetAtom( self.id, symbol.encode(ENCODE_ENCODING) ) ) def addRSite(self, name): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoAddRSite( self.id, name.encode(ENCODE_ENCODING) ) ), ) def setRSite(self, name): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetRSite(self.id, name.encode(ENCODE_ENCODING)) ) def setCharge(self, charge): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetCharge(self.id, charge) ) def setIsotope(self, isotope): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetIsotope(self.id, isotope) ) def setImplicitHCount(self, impl_h): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetImplicitHCount(self.id, impl_h) ) def addBond(self, destination, order): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoAddBond(self.id, destination.id, order) ), ) def setBondOrder(self, order): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoSetBondOrder(self.id, order) ), ) def merge(self, what): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoMerge(self.id, what.id) ), ) def highlight(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoHighlight(self.id) ) def unhighlight(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoUnhighlight(self.id) ) def isHighlighted(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult( Indigo._lib.indigoIsHighlighted(self.id) ) ) def countComponents(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountComponents(self.id) ) def componentIndex(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoComponentIndex(self.id) ) def iterateComponents(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateComponents(self.id) ), ) def component(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoComponent(self.id, index) ), ) def countSSSR(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountSSSR(self.id) ) def iterateSSSR(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateSSSR(self.id) ), ) def iterateSubtrees(self, min_atoms, max_atoms): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateSubtrees( self.id, min_atoms, max_atoms ) ), ) def iterateRings(self, min_atoms, max_atoms): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateRings(self.id, min_atoms, max_atoms) ), ) def iterateEdgeSubmolecules(self, min_bonds, max_bonds): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateEdgeSubmolecules( self.id, min_bonds, max_bonds ) ), ) def countHeavyAtoms(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountHeavyAtoms(self.id) ) def grossFormula(self): self.dispatcher._setSessionId() gfid = self.dispatcher._checkResult( Indigo._lib.indigoGrossFormula(self.id) ) gf = self.dispatcher.IndigoObject(self.dispatcher, gfid) return self.dispatcher._checkResultString( Indigo._lib.indigoToString(gf.id) ) def molecularWeight(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultFloat( Indigo._lib.indigoMolecularWeight(self.id) ) def mostAbundantMass(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultFloat( Indigo._lib.indigoMostAbundantMass(self.id) ) def monoisotopicMass(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultFloat( Indigo._lib.indigoMonoisotopicMass(self.id) ) def massComposition(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoMassComposition(self.id) ) def canonicalSmiles(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoCanonicalSmiles(self.id) ) def canonicalSmarts(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoCanonicalSmarts(self.id) ) def layeredCode(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoLayeredCode(self.id) ) def symmetryClasses(self): c_size = c_int() self.dispatcher._setSessionId() c_buf = self.dispatcher._checkResultPtr( Indigo._lib.indigoSymmetryClasses(self.id, pointer(c_size)) ) res = array("i") for i in range(c_size.value): res.append(c_buf[i]) return res def hasCoord(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult(Indigo._lib.indigoHasCoord(self.id)) ) def hasZCoord(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult(Indigo._lib.indigoHasZCoord(self.id)) ) def isChiral(self): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult(Indigo._lib.indigoIsChiral(self.id)) ) def isPossibleFischerProjection(self, options): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult( Indigo._lib.indigoIsPossibleFischerProjection( self.id, options.encode(ENCODE_ENCODING) ) ) ) def createSubmolecule(self, vertices): arr2 = (c_int * len(vertices))() for i in range(len(vertices)): arr2[i] = vertices[i] self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoCreateSubmolecule(self.id, len(arr2), arr2) ), ) def createEdgeSubmolecule(self, vertices, edges): arr2 = (c_int * len(vertices))() for i in range(len(vertices)): arr2[i] = vertices[i] arr4 = (c_int * len(edges))() for i in range(len(edges)): arr4[i] = edges[i] self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoCreateEdgeSubmolecule( self.id, len(arr2), arr2, len(arr4), arr4 ) ), ) def getSubmolecule(self, vertices): arr2 = (c_int * len(vertices))() for i in range(len(vertices)): arr2[i] = vertices[i] self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoGetSubmolecule(self.id, len(arr2), arr2) ), self, ) def removeAtoms(self, vertices): arr2 = (c_int * len(vertices))() for i in range(len(vertices)): arr2[i] = vertices[i] self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoRemoveAtoms(self.id, len(arr2), arr2) ) def removeBonds(self, bonds): arr2 = (c_int * len(bonds))() for i in range(len(bonds)): arr2[i] = bonds[i] self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoRemoveBonds(self.id, len(arr2), arr2) ) def aromatize(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAromatize(self.id) ) def dearomatize(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoDearomatize(self.id) ) def foldHydrogens(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoFoldHydrogens(self.id) ) def unfoldHydrogens(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoUnfoldHydrogens(self.id) ) def layout(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoLayout(self.id)) def smiles(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoSmiles(self.id) ) def smarts(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoSmarts(self.id) ) def name(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoName(self.id) ) def setName(self, name): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetName(self.id, name.encode(ENCODE_ENCODING)) ) def serialize(self): c_size = c_int() c_buf = POINTER(c_byte)() self.dispatcher._setSessionId() self.dispatcher._checkResult( Indigo._lib.indigoSerialize( self.id, pointer(c_buf), pointer(c_size) ) ) res = array("b") for i in range(c_size.value): res.append(c_buf[i]) return res def hasProperty(self, prop): self.dispatcher._setSessionId() return bool( self.dispatcher._checkResult( Indigo._lib.indigoHasProperty(self.id, prop) ) ) def getProperty(self, prop): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoGetProperty( self.id, prop.encode(ENCODE_ENCODING) ) ) def setProperty(self, prop, value): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSetProperty( self.id, prop.encode(ENCODE_ENCODING), value.encode(ENCODE_ENCODING), ) ) def removeProperty(self, prop): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoRemoveProperty( self.id, prop.encode(ENCODE_ENCODING) ) ) def iterateProperties(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateProperties(self.id) ), ) def clearProperties(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoClearProperties(self.id) ) def checkBadValence(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoCheckBadValence(self.id) ) def checkAmbiguousH(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoCheckAmbiguousH(self.id) ) def fingerprint(self, type): self.dispatcher._setSessionId() newobj = self.dispatcher._checkResult( Indigo._lib.indigoFingerprint( self.id, type.encode(ENCODE_ENCODING) ) ) if newobj == 0: return None return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) def countBits(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountBits(self.id) ) def rawData(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoRawData(self.id) ) def tell(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoTell(self.id)) def sdfAppend(self, item): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSdfAppend(self.id, item.id) ) def smilesAppend(self, item): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoSmilesAppend(self.id, item.id) ) def rdfHeader(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoRdfHeader(self.id) ) def rdfAppend(self, item): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoRdfAppend(self.id, item.id) ) def cmlHeader(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCmlHeader(self.id) ) def cmlAppend(self, item): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCmlAppend(self.id, item.id) ) def cmlFooter(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCmlFooter(self.id) ) def append(self, object): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAppend(self.id, object.id) ) def arrayAdd(self, object): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoArrayAdd(self.id, object.id) ) def at(self, index): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult(Indigo._lib.indigoAt(self.id, index)), ) def count(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoCount(self.id)) def clear(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult(Indigo._lib.indigoClear(self.id)) def iterateArray(self): self.dispatcher._setSessionId() newobj = self.dispatcher._checkResult( Indigo._lib.indigoIterateArray(self.id) ) if newobj == 0: return None else: return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) def ignoreAtom(self, atom_object): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoIgnoreAtom(self.id, atom_object.id) ) def unignoreAtom(self, atom_object): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoUnignoreAtom(self.id, atom_object.id) ) def unignoreAllAtoms(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoUnignoreAllAtoms(self.id) ) def match(self, query): self.dispatcher._setSessionId() newobj = self.dispatcher._checkResult( Indigo._lib.indigoMatch(self.id, query.id) ) if newobj == 0: return None else: return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) def countMatches(self, query): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountMatches(self.id, query.id) ) def countMatchesWithLimit(self, query, embeddings_limit): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoCountMatchesWithLimit( self.id, query.id, embeddings_limit ) ) def iterateMatches(self, query): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateMatches(self.id, query.id) ), ) def highlightedTarget(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoHighlightedTarget(self.id) ), ) def mapAtom(self, atom): self.dispatcher._setSessionId() newobj = self.dispatcher._checkResult( Indigo._lib.indigoMapAtom(self.id, atom.id) ) if newobj == 0: return None else: return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) def mapBond(self, bond): self.dispatcher._setSessionId() newobj = self.dispatcher._checkResult( Indigo._lib.indigoMapBond(self.id, bond.id) ) if newobj == 0: return None else: return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) def mapMolecule(self, molecule): self.dispatcher._setSessionId() newobj = self.dispatcher._checkResult( Indigo._lib.indigoMapMolecule(self.id, molecule.id) ) if newobj == 0: return None else: return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) def allScaffolds(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoAllScaffolds(self.id) ), ) def decomposedMoleculeScaffold(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoDecomposedMoleculeScaffold(self.id) ), ) def iterateDecomposedMolecules(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateDecomposedMolecules(self.id) ), ) def decomposedMoleculeHighlighted(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoDecomposedMoleculeHighlighted(self.id) ), ) def decomposedMoleculeWithRGroups(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoDecomposedMoleculeWithRGroups(self.id) ), ) def decomposeMolecule(self, mol): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoDecomposeMolecule(self.id, mol.id) ), ) def iterateDecompositions(self): self.dispatcher._setSessionId() return self.dispatcher.IndigoObject( self.dispatcher, self.dispatcher._checkResult( Indigo._lib.indigoIterateDecompositions(self.id) ), ) def addDecomposition(self, q_match): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoAddDecomposition(self.id, q_match.id) ) def toString(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoToString(self.id) ) def toBuffer(self): c_size = c_int() c_buf = POINTER(c_byte)() self.dispatcher._setSessionId() self.dispatcher._checkResult( Indigo._lib.indigoToBuffer( self.id, pointer(c_buf), pointer(c_size) ) ) res = array("b") for i in range(c_size.value): res.append(c_buf[i]) return res def stereocenterPyramid(self): self.dispatcher._setSessionId() ptr = self.dispatcher._checkResultPtr( Indigo._lib.indigoStereocenterPyramid(self.id) ) res = [0] * 4 for i in range(4): res[i] = ptr[i] return res def expandAbbreviations(self): self.dispatcher._setSessionId() return self.dispatcher._checkResult( Indigo._lib.indigoExpandAbbreviations(self.id) ) def dbgInternalType(self): self.dispatcher._setSessionId() return self.dispatcher._checkResultString( Indigo._lib.indigoDbgInternalType(self.id) ) class Indigo(object): ABS = 1 OR = 2 AND = 3 EITHER = 4 UP = 5 DOWN = 6 CIS = 7 TRANS = 8 CHAIN = 9 RING = 10 ALLENE = 11 SINGLET = 101 DOUBLET = 102 TRIPLET = 103 RC_NOT_CENTER = -1 RC_UNMARKED = 0 RC_CENTER = 1 RC_UNCHANGED = 2 RC_MADE_OR_BROKEN = 4 RC_ORDER_CHANGED = 8 SG_TYPE_GEN = 0 SG_TYPE_DAT = 1 SG_TYPE_SUP = 2 SG_TYPE_SRU = 3 SG_TYPE_MUL = 4 SG_TYPE_MON = 5 SG_TYPE_MER = 6 SG_TYPE_COP = 7 SG_TYPE_CRO = 8 SG_TYPE_MOD = 9 SG_TYPE_GRA = 10 SG_TYPE_COM = 11 SG_TYPE_MIX = 12 SG_TYPE_FOR = 13 SG_TYPE_ANY = 14 _crt = None _crtp = None _lib = None # Python embeds path into .pyc code if method is marked with @staticmethod # This causes an error when Indigo is loaded from different places by relative path def _initStatic(self, path=None): def cdll_if_exists(cdll_path_): if os.path.exists(cdll_path_): return CDLL(cdll_path_) return None paths = [] if not path: cur_file = os.path.abspath(__file__) paths = [ os.path.join(os.path.dirname(cur_file), "lib"), os.path.join( os.path.dirname(os.path.dirname(cur_file)), "lib" ), ] else: paths.append(path) indigoFound = False for path in paths: if ( os.name == "posix" and not platform.mac_ver()[0] and not platform.system().startswith("CYGWIN") ): arch = platform.architecture()[0] path = os.path.join(path, "Linux") if arch == "32bit": path = os.path.join(path, "x86") elif arch == "64bit": path = os.path.join(path, "x64") else: raise IndigoException("unknown platform " + arch) if os.path.exists(os.path.join(path, "libindigo.so")): Indigo._lib = CDLL( os.path.join(path, "libindigo.so"), mode=RTLD_GLOBAL ) indigoFound = True Indigo.dllpath = path elif os.name == "nt" or platform.system().startswith("CYGWIN"): arch = platform.architecture()[0] path = os.path.join(path, "Win") if arch == "32bit": path = os.path.join(path, "x86") elif arch == "64bit": path = os.path.join(path, "x64") else: raise IndigoException("unknown platform " + arch) if os.path.exists(os.path.join(path, "indigo.dll")): Indigo._crt = cdll_if_exists( os.path.join(path, "vcruntime140.dll") ) Indigo._crt_1 = cdll_if_exists( os.path.join(path, "vcruntime140_1.dll") ) Indigo._crtp = cdll_if_exists( os.path.join(path, "msvcp140.dll") ) Indigo._crtc = cdll_if_exists( os.path.join(path, "concrt140.dll") ) Indigo._lib = CDLL(os.path.join(path, "indigo.dll")) indigoFound = True Indigo.dllpath = path elif platform.mac_ver()[0]: path = os.path.join(path, "Mac") mac_ver = ".".join(platform.mac_ver()[0].split(".")[:2]) current_mac_ver = int(mac_ver.split(".")[1]) using_mac_ver = None for version in reversed(range(5, current_mac_ver + 1)): if os.path.exists( os.path.join(path, "10." + str(version)) ): using_mac_ver = str(version) break if using_mac_ver: path = os.path.join(path, "10." + using_mac_ver) Indigo._lib = CDLL( os.path.join(path, "libindigo.dylib"), mode=RTLD_GLOBAL ) indigoFound = True Indigo.dllpath = path else: raise IndigoException("unsupported OS: " + os.name) if not indigoFound: raise IndigoException( "Could not find native libraries for target OS in search directories: {}".format( os.pathsep.join(paths) ) ) def _setSessionId(self): Indigo._lib.indigoSetSessionId(self._sid) def __init__(self, path=None): if Indigo._lib is None: self._initStatic(path) self._sid = Indigo._lib.indigoAllocSessionId() # Capture a reference to the _lib to access it in the __del__ method because # at interpreter shutdown, the module's global variables are set to None self._lib = Indigo._lib self._setSessionId() self.IndigoObject = IndigoObject Indigo._lib.indigoVersion.restype = c_char_p Indigo._lib.indigoVersion.argtypes = None Indigo._lib.indigoAllocSessionId.restype = c_ulonglong Indigo._lib.indigoAllocSessionId.argtypes = None Indigo._lib.indigoSetSessionId.restype = None Indigo._lib.indigoSetSessionId.argtypes = [c_ulonglong] Indigo._lib.indigoReleaseSessionId.restype = None Indigo._lib.indigoReleaseSessionId.argtypes = [c_ulonglong] Indigo._lib.indigoGetLastError.restype = c_char_p Indigo._lib.indigoGetLastError.argtypes = None Indigo._lib.indigoFree.restype = c_int Indigo._lib.indigoFree.argtypes = [c_int] Indigo._lib.indigoCountReferences.restype = c_int Indigo._lib.indigoCountReferences.argtypes = None Indigo._lib.indigoFreeAllObjects.restype = c_int Indigo._lib.indigoFreeAllObjects.argtypes = None Indigo._lib.indigoSetOption.restype = c_int Indigo._lib.indigoSetOption.argtypes = [c_char_p, c_char_p] Indigo._lib.indigoSetOptionInt.restype = c_int Indigo._lib.indigoSetOptionInt.argtypes = [c_char_p, c_int] Indigo._lib.indigoSetOptionBool.restype = c_int Indigo._lib.indigoSetOptionBool.argtypes = [c_char_p, c_int] Indigo._lib.indigoSetOptionFloat.restype = c_int Indigo._lib.indigoSetOptionFloat.argtypes = [c_char_p, c_float] Indigo._lib.indigoSetOptionColor.restype = c_int Indigo._lib.indigoSetOptionColor.argtypes = [ c_char_p, c_float, c_float, c_float, ] Indigo._lib.indigoSetOptionXY.restype = c_int Indigo._lib.indigoSetOptionXY.argtypes = [c_char_p, c_int, c_int] Indigo._lib.indigoGetOption.restype = c_char_p Indigo._lib.indigoGetOption.argtypes = [c_char_p] Indigo._lib.indigoGetOptionInt.restype = c_int Indigo._lib.indigoGetOptionInt.argtypes = [c_char_p, POINTER(c_int)] Indigo._lib.indigoGetOptionBool.argtypes = [c_char_p, POINTER(c_int)] Indigo._lib.indigoGetOptionBool.restype = c_int Indigo._lib.indigoGetOptionFloat.argtypes = [ c_char_p, POINTER(c_float), ] Indigo._lib.indigoGetOptionFloat.restype = c_int Indigo._lib.indigoGetOptionColor.argtypes = [ c_char_p, POINTER(c_float), POINTER(c_float), POINTER(c_float), ] Indigo._lib.indigoGetOptionColor.restype = c_int Indigo._lib.indigoGetOptionXY.argtypes = [ c_char_p, POINTER(c_int), POINTER(c_int), ] Indigo._lib.indigoGetOptionXY.restype = c_int Indigo._lib.indigoGetOptionType.restype = c_char_p Indigo._lib.indigoGetOptionType.argtypes = [c_char_p] Indigo._lib.indigoReadFile.restype = c_int Indigo._lib.indigoReadFile.argtypes = [c_char_p] Indigo._lib.indigoLoadString.restype = c_int Indigo._lib.indigoLoadString.argtypes = [c_char_p] Indigo._lib.indigoLoadBuffer.restype = c_int Indigo._lib.indigoLoadBuffer.argtypes = [POINTER(c_byte), c_int] Indigo._lib.indigoWriteFile.restype = c_int Indigo._lib.indigoWriteFile.argtypes = [c_char_p] Indigo._lib.indigoWriteBuffer.restype = c_int Indigo._lib.indigoWriteBuffer.argtypes = None Indigo._lib.indigoCreateMolecule.restype = c_int Indigo._lib.indigoCreateMolecule.argtypes = None Indigo._lib.indigoCreateQueryMolecule.restype = c_int Indigo._lib.indigoCreateQueryMolecule.argtypes = None Indigo._lib.indigoLoadMoleculeFromString.restype = c_int Indigo._lib.indigoLoadMoleculeFromString.argtypes = [c_char_p] Indigo._lib.indigoLoadMoleculeFromFile.restype = c_int Indigo._lib.indigoLoadMoleculeFromFile.argtypes = [c_char_p] Indigo._lib.indigoLoadMoleculeFromBuffer.restype = c_int Indigo._lib.indigoLoadMoleculeFromBuffer.argtypes = [ POINTER(c_byte), c_int, ] Indigo._lib.indigoLoadQueryMoleculeFromString.restype = c_int Indigo._lib.indigoLoadQueryMoleculeFromString.argtypes = [c_char_p] Indigo._lib.indigoLoadQueryMoleculeFromFile.restype = c_int Indigo._lib.indigoLoadQueryMoleculeFromFile.argtypes = [c_char_p] Indigo._lib.indigoLoadSmartsFromString.restype = c_int Indigo._lib.indigoLoadSmartsFromString.argtypes = [c_char_p] Indigo._lib.indigoLoadSmartsFromFile.restype = c_int Indigo._lib.indigoLoadSmartsFromFile.argtypes = [c_char_p] Indigo._lib.indigoLoadReactionFromString.restype = c_int Indigo._lib.indigoLoadReactionFromString.argtypes = [c_char_p] Indigo._lib.indigoLoadReactionFromFile.restype = c_int Indigo._lib.indigoLoadReactionFromFile.argtypes = [c_char_p] Indigo._lib.indigoLoadQueryReactionFromString.restype = c_int Indigo._lib.indigoLoadQueryReactionFromString.argtypes = [c_char_p] Indigo._lib.indigoLoadQueryReactionFromFile.restype = c_int Indigo._lib.indigoLoadQueryReactionFromFile.argtypes = [c_char_p] Indigo._lib.indigoLoadReactionSmartsFromString.restype = c_int Indigo._lib.indigoLoadReactionSmartsFromString.argtypes = [c_char_p] Indigo._lib.indigoLoadReactionSmartsFromFile.restype = c_int Indigo._lib.indigoLoadReactionSmartsFromFile.argtypes = [c_char_p] Indigo._lib.indigoLoadStructureFromString.restype = c_int Indigo._lib.indigoLoadStructureFromString.argtypes = [ c_char_p, c_char_p, ] Indigo._lib.indigoLoadStructureFromBuffer.restype = c_int Indigo._lib.indigoLoadStructureFromBuffer.argtypes = [ POINTER(c_byte), c_int, c_char_p, ] Indigo._lib.indigoLoadStructureFromFile.restype = c_int Indigo._lib.indigoLoadStructureFromFile.argtypes = [c_char_p, c_char_p] Indigo._lib.indigoCreateReaction.restype = c_int Indigo._lib.indigoCreateReaction.argtypes = None Indigo._lib.indigoCreateQueryReaction.restype = c_int Indigo._lib.indigoCreateQueryReaction.argtypes = None Indigo._lib.indigoExactMatch.restype = c_int Indigo._lib.indigoExactMatch.argtypes = [c_int, c_int, c_char_p] Indigo._lib.indigoSetTautomerRule.restype = c_int Indigo._lib.indigoSetTautomerRule.argtypes = [ c_int, c_char_p, c_char_p, ] Indigo._lib.indigoRemoveTautomerRule.restype = c_int Indigo._lib.indigoRemoveTautomerRule.argtypes = [c_int] Indigo._lib.indigoClearTautomerRules.restype = c_int Indigo._lib.indigoClearTautomerRules.argtypes = None Indigo._lib.indigoUnserialize.restype = c_int Indigo._lib.indigoUnserialize.argtypes = [POINTER(c_byte), c_int] Indigo._lib.indigoCommonBits.restype = c_int Indigo._lib.indigoCommonBits.argtypes = [c_int, c_int] Indigo._lib.indigoSimilarity.restype = c_float Indigo._lib.indigoSimilarity.argtypes = [c_int, c_int, c_char_p] Indigo._lib.indigoIterateSDF.restype = c_int Indigo._lib.indigoIterateSDF.argtypes = [c_int] Indigo._lib.indigoIterateRDF.restype = c_int Indigo._lib.indigoIterateRDF.argtypes = [c_int] Indigo._lib.indigoIterateSmiles.restype = c_int Indigo._lib.indigoIterateSmiles.argtypes = [c_int] Indigo._lib.indigoIterateCML.restype = c_int Indigo._lib.indigoIterateCML.argtypes = [c_int] Indigo._lib.indigoIterateCDX.restype = c_int Indigo._lib.indigoIterateCDX.argtypes = [c_int] Indigo._lib.indigoIterateSDFile.restype = c_int Indigo._lib.indigoIterateSDFile.argtypes = [c_char_p] Indigo._lib.indigoIterateRDFile.restype = c_int Indigo._lib.indigoIterateRDFile.argtypes = [c_char_p] Indigo._lib.indigoIterateSmilesFile.restype = c_int Indigo._lib.indigoIterateSmilesFile.argtypes = [c_char_p] Indigo._lib.indigoIterateCMLFile.restype = c_int Indigo._lib.indigoIterateCMLFile.argtypes = [c_char_p] Indigo._lib.indigoIterateCDXFile.restype = c_int Indigo._lib.indigoIterateCDXFile.argtypes = [c_char_p] Indigo._lib.indigoCreateSaver.restype = c_int Indigo._lib.indigoCreateSaver.argtypes = [c_int, c_char_p] Indigo._lib.indigoCreateFileSaver.restype = c_int Indigo._lib.indigoCreateFileSaver.argtypes = [c_char_p, c_char_p] Indigo._lib.indigoCreateArray.restype = c_int Indigo._lib.indigoCreateArray.argtypes = None Indigo._lib.indigoSubstructureMatcher.restype = c_int Indigo._lib.indigoSubstructureMatcher.argtypes = [c_int, c_char_p] Indigo._lib.indigoExtractCommonScaffold.restype = c_int Indigo._lib.indigoExtractCommonScaffold.argtypes = [c_int, c_char_p] Indigo._lib.indigoDecomposeMolecules.restype = c_int Indigo._lib.indigoDecomposeMolecules.argtypes = [c_int, c_int] Indigo._lib.indigoRGroupComposition.restype = c_int Indigo._lib.indigoRGroupComposition.argtypes = [c_int, c_char_p] Indigo._lib.indigoGetFragmentedMolecule.restype = c_int Indigo._lib.indigoGetFragmentedMolecule.argtypes = [c_int, c_char_p] Indigo._lib.indigoCreateDecomposer.restype = c_int Indigo._lib.indigoCreateDecomposer.argtypes = [c_int] Indigo._lib.indigoReactionProductEnumerate.restype = c_int Indigo._lib.indigoReactionProductEnumerate.argtypes = [c_int, c_int] Indigo._lib.indigoTransform.restype = c_int Indigo._lib.indigoTransform.argtypes = [c_int, c_int] Indigo._lib.indigoDbgBreakpoint.restype = None Indigo._lib.indigoDbgBreakpoint.argtypes = None Indigo._lib.indigoClone.restype = c_int Indigo._lib.indigoClone.argtypes = [c_int] Indigo._lib.indigoCheck.restype = c_char_p Indigo._lib.indigoCheck.argtypes = [c_int, c_char_p] Indigo._lib.indigoCheckStructure.restype = c_char_p Indigo._lib.indigoCheckStructure.argtypes = [c_char_p, c_char_p] Indigo._lib.indigoClose.restype = c_int Indigo._lib.indigoClose.argtypes = [c_int] Indigo._lib.indigoNext.restype = c_int Indigo._lib.indigoNext.argtypes = [c_int] Indigo._lib.indigoHasNext.restype = c_int Indigo._lib.indigoHasNext.argtypes = [c_int] Indigo._lib.indigoIndex.restype = c_int Indigo._lib.indigoIndex.argtypes = [c_int] Indigo._lib.indigoRemove.restype = c_int Indigo._lib.indigoRemove.argtypes = [c_int] Indigo._lib.indigoSaveMolfileToFile.restype = c_int Indigo._lib.indigoSaveMolfileToFile.argtypes = [c_int, c_char_p] Indigo._lib.indigoMolfile.restype = c_char_p Indigo._lib.indigoMolfile.argtypes = [c_int] Indigo._lib.indigoSaveCmlToFile.restype = c_int Indigo._lib.indigoSaveCmlToFile.argtypes = [c_int, c_char_p] Indigo._lib.indigoCml.restype = c_char_p Indigo._lib.indigoCml.argtypes = [c_int] Indigo._lib.indigoSaveCdxmlToFile.restype = c_int Indigo._lib.indigoSaveCdxmlToFile.argtypes = [c_int, c_char_p] Indigo._lib.indigoCdxml.restype = c_char_p Indigo._lib.indigoCdxml.argtypes = [c_int] Indigo._lib.indigoJson.restype = c_char_p Indigo._lib.indigoJson.argtypes = [c_int] Indigo._lib.indigoSaveMDLCT.restype = c_int Indigo._lib.indigoSaveMDLCT.argtypes = [c_int, c_int] Indigo._lib.indigoAddReactant.restype = c_int Indigo._lib.indigoAddReactant.argtypes = [c_int, c_int] Indigo._lib.indigoAddProduct.restype = c_int Indigo._lib.indigoAddProduct.argtypes = [c_int, c_int] Indigo._lib.indigoAddCatalyst.restype = c_int Indigo._lib.indigoAddCatalyst.argtypes = [c_int, c_int] Indigo._lib.indigoCountReactants.restype = c_int Indigo._lib.indigoCountReactants.argtypes = [c_int] Indigo._lib.indigoCountProducts.restype = c_int Indigo._lib.indigoCountProducts.argtypes = [c_int] Indigo._lib.indigoCountCatalysts.restype = c_int Indigo._lib.indigoCountCatalysts.argtypes = [c_int] Indigo._lib.indigoCountMolecules.restype = c_int Indigo._lib.indigoCountMolecules.argtypes = [c_int] Indigo._lib.indigoGetMolecule.restype = c_int Indigo._lib.indigoGetMolecule.argtypes = [c_int, c_int] Indigo._lib.indigoIterateReactants.restype = c_int Indigo._lib.indigoIterateReactants.argtypes = [c_int] Indigo._lib.indigoIterateProducts.restype = c_int Indigo._lib.indigoIterateProducts.argtypes = [c_int] Indigo._lib.indigoIterateCatalysts.restype = c_int Indigo._lib.indigoIterateCatalysts.argtypes = [c_int] Indigo._lib.indigoIterateMolecules.restype = c_int Indigo._lib.indigoIterateMolecules.argtypes = [c_int] Indigo._lib.indigoSaveRxnfileToFile.restype = c_int Indigo._lib.indigoSaveRxnfileToFile.argtypes = [c_int, c_char_p] Indigo._lib.indigoRxnfile.restype = c_char_p Indigo._lib.indigoRxnfile.argtypes = [c_int] Indigo._lib.indigoOptimize.restype = c_int Indigo._lib.indigoOptimize.argtypes = [c_int, c_char_p] Indigo._lib.indigoNormalize.restype = c_int Indigo._lib.indigoNormalize.argtypes = [c_int, c_char_p] Indigo._lib.indigoStandardize.restype = c_int Indigo._lib.indigoStandardize.argtypes = [c_int] Indigo._lib.indigoIonize.restype = c_int Indigo._lib.indigoIonize.argtypes = [c_int, c_float, c_float] Indigo._lib.indigoBuildPkaModel.restype = c_int Indigo._lib.indigoBuildPkaModel.argtypes = [c_int, c_float, c_char_p] Indigo._lib.indigoGetAcidPkaValue.restype = POINTER(c_float) Indigo._lib.indigoGetAcidPkaValue.argtypes = [ c_int, c_int, c_int, c_int, ] Indigo._lib.indigoGetBasicPkaValue.restype = POINTER(c_float) Indigo._lib.indigoGetBasicPkaValue.argtypes = [ c_int, c_int, c_int, c_int, ] Indigo._lib.indigoAutomap.restype = c_int Indigo._lib.indigoAutomap.argtypes = [c_int, c_char_p] Indigo._lib.indigoGetAtomMappingNumber.restype = c_int Indigo._lib.indigoGetAtomMappingNumber.argtypes = [c_int, c_int] Indigo._lib.indigoSetAtomMappingNumber.restype = c_int Indigo._lib.indigoSetAtomMappingNumber.argtypes = [c_int, c_int, c_int] Indigo._lib.indigoGetReactingCenter.restype = c_int Indigo._lib.indigoGetReactingCenter.argtypes = [ c_int, c_int, POINTER(c_int), ] Indigo._lib.indigoSetReactingCenter.restype = c_int Indigo._lib.indigoSetReactingCenter.argtypes = [c_int, c_int, c_int] Indigo._lib.indigoClearAAM.restype = c_int Indigo._lib.indigoClearAAM.argtypes = [c_int] Indigo._lib.indigoCorrectReactingCenters.restype = c_int Indigo._lib.indigoCorrectReactingCenters.argtypes = [c_int] Indigo._lib.indigoIterateAtoms.restype = c_int Indigo._lib.indigoIterateAtoms.argtypes = [c_int] Indigo._lib.indigoIteratePseudoatoms.restype = c_int Indigo._lib.indigoIteratePseudoatoms.argtypes = [c_int] Indigo._lib.indigoIterateRSites.restype = c_int Indigo._lib.indigoIterateRSites.argtypes = [c_int] Indigo._lib.indigoIterateStereocenters.restype = c_int Indigo._lib.indigoIterateStereocenters.argtypes = [c_int] Indigo._lib.indigoIterateAlleneCenters.restype = c_int Indigo._lib.indigoIterateAlleneCenters.argtypes = [c_int] Indigo._lib.indigoIterateRGroups.restype = c_int Indigo._lib.indigoIterateRGroups.argtypes = [c_int] Indigo._lib.indigoCountRGroups.restype = c_int Indigo._lib.indigoCountRGroups.argtypes = [c_int] Indigo._lib.indigoIsPseudoatom.restype = c_int Indigo._lib.indigoIsPseudoatom.argtypes = [c_int] Indigo._lib.indigoIsRSite.restype = c_int Indigo._lib.indigoIsRSite.argtypes = [c_int] Indigo._lib.indigoIsTemplateAtom.restype = c_int Indigo._lib.indigoIsTemplateAtom.argtypes = [c_int] Indigo._lib.indigoStereocenterType.restype = c_int Indigo._lib.indigoStereocenterType.argtypes = [c_int] Indigo._lib.indigoStereocenterGroup.restype = c_int Indigo._lib.indigoStereocenterGroup.argtypes = [c_int] Indigo._lib.indigoSetStereocenterGroup.restype = c_int Indigo._lib.indigoSetStereocenterGroup.argtypes = [c_int, c_int] Indigo._lib.indigoChangeStereocenterType.restype = c_int Indigo._lib.indigoChangeStereocenterType.argtypes = [c_int, c_int] Indigo._lib.indigoValidateChirality.restype = c_int Indigo._lib.indigoValidateChirality.argtypes = [c_int] Indigo._lib.indigoSingleAllowedRGroup.restype = c_int Indigo._lib.indigoSingleAllowedRGroup.argtypes = [c_int] Indigo._lib.indigoAddStereocenter.restype = c_int Indigo._lib.indigoAddStereocenter.argtypes = [ c_int, c_int, c_int, c_int, c_int, c_int, ] Indigo._lib.indigoIterateRGroupFragments.restype = c_int Indigo._lib.indigoIterateRGroupFragments.argtypes = [c_int] Indigo._lib.indigoCountAttachmentPoints.restype = c_int Indigo._lib.indigoCountAttachmentPoints.argtypes = [c_int] Indigo._lib.indigoIterateAttachmentPoints.restype = c_int Indigo._lib.indigoIterateAttachmentPoints.argtypes = [c_int, c_int] Indigo._lib.indigoSymbol.restype = c_char_p Indigo._lib.indigoSymbol.argtypes = [c_int] Indigo._lib.indigoDegree.restype = c_int Indigo._lib.indigoDegree.argtypes = [c_int] Indigo._lib.indigoGetCharge.restype = c_int Indigo._lib.indigoGetCharge.argtypes = [c_int, POINTER(c_int)] Indigo._lib.indigoGetExplicitValence.restype = c_int Indigo._lib.indigoGetExplicitValence.argtypes = [c_int, POINTER(c_int)] Indigo._lib.indigoSetExplicitValence.restype = c_int Indigo._lib.indigoSetExplicitValence.argtypes = [c_int, c_int] Indigo._lib.indigoGetRadicalElectrons.restype = c_int Indigo._lib.indigoGetRadicalElectrons.argtypes = [ c_int, POINTER(c_int), ] Indigo._lib.indigoGetRadical.restype = c_int Indigo._lib.indigoGetRadical.argtypes = [c_int, POINTER(c_int)] Indigo._lib.indigoSetRadical.restype = c_int Indigo._lib.indigoSetRadical.argtypes = [c_int, c_int] Indigo._lib.indigoAtomicNumber.restype = c_int Indigo._lib.indigoAtomicNumber.argtypes = [c_int] Indigo._lib.indigoIsotope.restype = c_int Indigo._lib.indigoIsotope.argtypes = [c_int] Indigo._lib.indigoValence.restype = c_int Indigo._lib.indigoValence.argtypes = [c_int] Indigo._lib.indigoCheckValence.restype = c_int Indigo._lib.indigoCheckValence.argtypes = [c_int] Indigo._lib.indigoCheckQuery.restype = c_int Indigo._lib.indigoCheckQuery.argtypes = [c_int] Indigo._lib.indigoCheckRGroups.restype = c_int Indigo._lib.indigoCheckRGroups.argtypes = [c_int] Indigo._lib.indigoCountHydrogens.restype = c_int Indigo._lib.indigoCountHydrogens.argtypes = [c_int, POINTER(c_int)] Indigo._lib.indigoCountImplicitHydrogens.restype = c_int Indigo._lib.indigoCountImplicitHydrogens.argtypes = [c_int] Indigo._lib.indigoXYZ.restype = POINTER(c_float) Indigo._lib.indigoXYZ.argtypes = [c_int] Indigo._lib.indigoCoords.restype = POINTER(c_float) Indigo._lib.indigoCoords.argtypes = [c_int] Indigo._lib.indigoSetXYZ.restype = c_int Indigo._lib.indigoSetXYZ.argtypes = [c_int, c_float, c_float, c_float] Indigo._lib.indigoCountSuperatoms.restype = c_int Indigo._lib.indigoCountSuperatoms.argtypes = [c_int] Indigo._lib.indigoCountDataSGroups.restype = c_int Indigo._lib.indigoCountDataSGroups.argtypes = [c_int] Indigo._lib.indigoCountRepeatingUnits.restype = c_int Indigo._lib.indigoCountRepeatingUnits.argtypes = [c_int] Indigo._lib.indigoCountMultipleGroups.restype = c_int Indigo._lib.indigoCountMultipleGroups.argtypes = [c_int] Indigo._lib.indigoCountGenericSGroups.restype = c_int Indigo._lib.indigoCountGenericSGroups.argtypes = [c_int] Indigo._lib.indigoIterateDataSGroups.restype = c_int Indigo._lib.indigoIterateDataSGroups.argtypes = [c_int] Indigo._lib.indigoIterateSuperatoms.restype = c_int Indigo._lib.indigoIterateSuperatoms.argtypes = [c_int] Indigo._lib.indigoIterateGenericSGroups.restype = c_int Indigo._lib.indigoIterateGenericSGroups.argtypes = [c_int] Indigo._lib.indigoIterateRepeatingUnits.restype = c_int Indigo._lib.indigoIterateRepeatingUnits.argtypes = [c_int] Indigo._lib.indigoIterateMultipleGroups.restype = c_int Indigo._lib.indigoIterateMultipleGroups.argtypes = [c_int] Indigo._lib.indigoIterateSGroups.restype = c_int Indigo._lib.indigoIterateSGroups.argtypes = [c_int] Indigo._lib.indigoIterateTGroups.restype = c_int Indigo._lib.indigoIterateTGroups.argtypes = [c_int] Indigo._lib.indigoGetSuperatom.restype = c_int Indigo._lib.indigoGetSuperatom.argtypes = [c_int, c_int] Indigo._lib.indigoGetDataSGroup.restype = c_int Indigo._lib.indigoGetDataSGroup.argtypes = [c_int, c_int] Indigo._lib.indigoGetGenericSGroup.restype = c_int Indigo._lib.indigoGetGenericSGroup.argtypes = [c_int, c_int] Indigo._lib.indigoGetMultipleGroup.restype = c_int Indigo._lib.indigoGetMultipleGroup.argtypes = [c_int, c_int] Indigo._lib.indigoGetRepeatingUnit.restype = c_int Indigo._lib.indigoGetRepeatingUnit.argtypes = [c_int, c_int] Indigo._lib.indigoDescription.restype = c_char_p Indigo._lib.indigoDescription.argtypes = [c_int] Indigo._lib.indigoData.restype = c_char_p Indigo._lib.indigoData.argtypes = [c_int] Indigo._lib.indigoAddDataSGroup.restype = c_int Indigo._lib.indigoAddDataSGroup.argtypes = [ c_int, c_int, POINTER(c_int), c_int, POINTER(c_int), c_char_p, c_char_p, ] Indigo._lib.indigoAddSuperatom.restype = c_int Indigo._lib.indigoAddSuperatom.argtypes = [ c_int, c_int, POINTER(c_int), c_char_p, ] Indigo._lib.indigoSetDataSGroupXY.restype = c_int Indigo._lib.indigoSetDataSGroupXY.argtypes = [ c_int, c_float, c_float, c_char_p, ] Indigo._lib.indigoSetSGroupData.restype = c_int Indigo._lib.indigoSetSGroupData.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupCoords.restype = c_int Indigo._lib.indigoSetSGroupCoords.argtypes = [c_int, c_float, c_float] Indigo._lib.indigoSetSGroupDescription.restype = c_int Indigo._lib.indigoSetSGroupDescription.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupFieldName.restype = c_int Indigo._lib.indigoSetSGroupFieldName.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupQueryCode.restype = c_int Indigo._lib.indigoSetSGroupQueryCode.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupQueryOper.restype = c_int Indigo._lib.indigoSetSGroupQueryOper.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupDisplay.restype = c_int Indigo._lib.indigoSetSGroupDisplay.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupLocation.restype = c_int Indigo._lib.indigoSetSGroupLocation.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupTag.restype = c_int Indigo._lib.indigoSetSGroupTag.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupTagAlign.restype = c_int Indigo._lib.indigoSetSGroupTagAlign.argtypes = [c_int, c_int] Indigo._lib.indigoSetSGroupDataType.restype = c_int Indigo._lib.indigoSetSGroupDataType.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupXCoord.restype = c_int Indigo._lib.indigoSetSGroupXCoord.argtypes = [c_int, c_float] Indigo._lib.indigoSetSGroupYCoord.restype = c_int Indigo._lib.indigoSetSGroupYCoord.argtypes = [c_int, c_float] Indigo._lib.indigoCreateSGroup.restype = c_int Indigo._lib.indigoCreateSGroup.argtypes = [c_char_p, c_int, c_char_p] Indigo._lib.indigoSetSGroupClass.restype = c_int Indigo._lib.indigoSetSGroupClass.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetSGroupName.restype = c_int Indigo._lib.indigoSetSGroupName.argtypes = [c_int, c_char_p] Indigo._lib.indigoGetSGroupClass.restype = c_char_p Indigo._lib.indigoGetSGroupClass.argtypes = [c_int] Indigo._lib.indigoGetSGroupName.restype = c_char_p Indigo._lib.indigoGetSGroupName.argtypes = [c_int] Indigo._lib.indigoGetSGroupNumCrossBonds.restype = c_int Indigo._lib.indigoGetSGroupNumCrossBonds.argtypes = [c_int] Indigo._lib.indigoAddSGroupAttachmentPoint.restype = c_int Indigo._lib.indigoAddSGroupAttachmentPoint.argtypes = [ c_int, c_int, c_int, c_char_p, ] Indigo._lib.indigoDeleteSGroupAttachmentPoint.restype = c_int Indigo._lib.indigoDeleteSGroupAttachmentPoint.argtypes = [c_int, c_int] Indigo._lib.indigoGetSGroupDisplayOption.restype = c_int Indigo._lib.indigoGetSGroupDisplayOption.argtypes = [c_int] Indigo._lib.indigoSetSGroupDisplayOption.restype = c_int Indigo._lib.indigoSetSGroupDisplayOption.argtypes = [c_int, c_int] Indigo._lib.indigoGetSGroupSeqId.restype = c_int Indigo._lib.indigoGetSGroupSeqId.argtypes = [c_int] Indigo._lib.indigoGetSGroupCoords.restype = POINTER(c_float) Indigo._lib.indigoGetSGroupCoords.argtypes = [c_int] Indigo._lib.indigoGetRepeatingUnitSubscript.restype = c_char_p Indigo._lib.indigoGetRepeatingUnitSubscript.argtypes = [c_int] Indigo._lib.indigoGetRepeatingUnitConnectivity.restype = c_int Indigo._lib.indigoGetRepeatingUnitConnectivity.argtypes = [c_int] Indigo._lib.indigoGetSGroupMultiplier.restype = c_int Indigo._lib.indigoGetSGroupMultiplier.argtypes = [c_int] Indigo._lib.indigoSetSGroupMultiplier.restype = c_int Indigo._lib.indigoSetSGroupMultiplier.argtypes = [c_int, c_int] Indigo._lib.indigoSetSGroupBrackets.restype = c_int Indigo._lib.indigoSetSGroupBrackets.argtypes = [ c_int, c_int, c_float, c_float, c_float, c_float, c_float, c_float, c_float, c_float, ] Indigo._lib.indigoFindSGroups.restype = c_int Indigo._lib.indigoFindSGroups.argtypes = [c_int, c_char_p, c_char_p] Indigo._lib.indigoGetSGroupType.restype = c_int Indigo._lib.indigoGetSGroupType.argtypes = [c_int] Indigo._lib.indigoGetSGroupIndex.restype = c_int Indigo._lib.indigoGetSGroupIndex.argtypes = [c_int] Indigo._lib.indigoGetSGroupOriginalId.restype = c_int Indigo._lib.indigoGetSGroupOriginalId.argtypes = [c_int] Indigo._lib.indigoSetSGroupOriginalId.restype = c_int Indigo._lib.indigoSetSGroupOriginalId.argtypes = [c_int, c_int] Indigo._lib.indigoGetSGroupParentId.restype = c_int Indigo._lib.indigoGetSGroupParentId.argtypes = [c_int] Indigo._lib.indigoSetSGroupParentId.restype = c_int Indigo._lib.indigoSetSGroupParentId.argtypes = [c_int, c_int] Indigo._lib.indigoAddTemplate.restype = c_int Indigo._lib.indigoAddTemplate.argtypes = [c_int, c_int, c_char_p] Indigo._lib.indigoRemoveTemplate.restype = c_int Indigo._lib.indigoRemoveTemplate.argtypes = [c_int, c_char_p] Indigo._lib.indigoFindTemplate.restype = c_int Indigo._lib.indigoFindTemplate.argtypes = [c_int, c_char_p] Indigo._lib.indigoGetTGroupClass.restype = c_char_p Indigo._lib.indigoGetTGroupClass.argtypes = [c_int] Indigo._lib.indigoGetTGroupName.restype = c_char_p Indigo._lib.indigoGetTGroupName.argtypes = [c_int] Indigo._lib.indigoGetTGroupAlias.restype = c_char_p Indigo._lib.indigoGetTGroupAlias.argtypes = [c_int] Indigo._lib.indigoTransformSCSRtoCTAB.restype = c_int Indigo._lib.indigoTransformSCSRtoCTAB.argtypes = [c_int] Indigo._lib.indigoTransformCTABtoSCSR.restype = c_int Indigo._lib.indigoTransformCTABtoSCSR.argtypes = [c_int, c_int] Indigo._lib.indigoTransformHELMtoSCSR.restype = c_int Indigo._lib.indigoTransformHELMtoSCSR.argtypes = [c_int] Indigo._lib.indigoGetTemplateAtomClass.restype = c_char_p Indigo._lib.indigoGetTemplateAtomClass.argtypes = [c_int] Indigo._lib.indigoSetTemplateAtomClass.restype = c_int Indigo._lib.indigoSetTemplateAtomClass.argtypes = [c_int, c_char_p] Indigo._lib.indigoResetCharge.restype = c_int Indigo._lib.indigoResetCharge.argtypes = [c_int] Indigo._lib.indigoResetExplicitValence.restype = c_int Indigo._lib.indigoResetExplicitValence.argtypes = [c_int] Indigo._lib.indigoResetRadical.restype = c_int Indigo._lib.indigoResetRadical.argtypes = [c_int] Indigo._lib.indigoResetIsotope.restype = c_int Indigo._lib.indigoResetIsotope.argtypes = [c_int] Indigo._lib.indigoSetAttachmentPoint.restype = c_int Indigo._lib.indigoSetAttachmentPoint.argtypes = [c_int, c_int] Indigo._lib.indigoClearAttachmentPoints.restype = c_int Indigo._lib.indigoClearAttachmentPoints.argtypes = [c_int] Indigo._lib.indigoRemoveConstraints.restype = c_int Indigo._lib.indigoRemoveConstraints.argtypes = [c_int, c_char_p] Indigo._lib.indigoAddConstraint.restype = c_int Indigo._lib.indigoAddConstraint.argtypes = [c_int, c_char_p, c_char_p] Indigo._lib.indigoAddConstraintNot.restype = c_int Indigo._lib.indigoAddConstraintNot.argtypes = [ c_int, c_char_p, c_char_p, ] Indigo._lib.indigoAddConstraintOr.restype = c_int Indigo._lib.indigoAddConstraintOr.argtypes = [ c_int, c_char_p, c_char_p, ] Indigo._lib.indigoResetStereo.restype = c_int Indigo._lib.indigoResetStereo.argtypes = [c_int] Indigo._lib.indigoInvertStereo.restype = c_int Indigo._lib.indigoInvertStereo.argtypes = [c_int] Indigo._lib.indigoCountAtoms.restype = c_int Indigo._lib.indigoCountAtoms.argtypes = [c_int] Indigo._lib.indigoCountBonds.restype = c_int Indigo._lib.indigoCountBonds.argtypes = [c_int] Indigo._lib.indigoCountPseudoatoms.restype = c_int Indigo._lib.indigoCountPseudoatoms.argtypes = [c_int] Indigo._lib.indigoCountRSites.restype = c_int Indigo._lib.indigoCountRSites.argtypes = [c_int] Indigo._lib.indigoIterateBonds.restype = c_int Indigo._lib.indigoIterateBonds.argtypes = [c_int] Indigo._lib.indigoBondOrder.restype = c_int Indigo._lib.indigoBondOrder.argtypes = [c_int] Indigo._lib.indigoBondStereo.restype = c_int Indigo._lib.indigoBondStereo.argtypes = [c_int] Indigo._lib.indigoTopology.restype = c_int Indigo._lib.indigoTopology.argtypes = [c_int] Indigo._lib.indigoIterateNeighbors.restype = c_int Indigo._lib.indigoIterateNeighbors.argtypes = [c_int] Indigo._lib.indigoBond.restype = c_int Indigo._lib.indigoBond.argtypes = [c_int] Indigo._lib.indigoGetAtom.restype = c_int Indigo._lib.indigoGetAtom.argtypes = [c_int, c_int] Indigo._lib.indigoGetBond.restype = c_int Indigo._lib.indigoGetBond.argtypes = [c_int, c_int] Indigo._lib.indigoSource.restype = c_int Indigo._lib.indigoSource.argtypes = [c_int] Indigo._lib.indigoDestination.restype = c_int Indigo._lib.indigoDestination.argtypes = [c_int] Indigo._lib.indigoClearCisTrans.restype = c_int Indigo._lib.indigoClearCisTrans.argtypes = [c_int] Indigo._lib.indigoClearStereocenters.restype = c_int Indigo._lib.indigoClearStereocenters.argtypes = [c_int] Indigo._lib.indigoCountStereocenters.restype = c_int Indigo._lib.indigoCountStereocenters.argtypes = [c_int] Indigo._lib.indigoClearAlleneCenters.restype = c_int Indigo._lib.indigoClearAlleneCenters.argtypes = [c_int] Indigo._lib.indigoCountAlleneCenters.restype = c_int Indigo._lib.indigoCountAlleneCenters.argtypes = [c_int] Indigo._lib.indigoResetSymmetricCisTrans.restype = c_int Indigo._lib.indigoResetSymmetricCisTrans.argtypes = [c_int] Indigo._lib.indigoResetSymmetricStereocenters.restype = c_int Indigo._lib.indigoResetSymmetricStereocenters.argtypes = [c_int] Indigo._lib.indigoMarkEitherCisTrans.restype = c_int Indigo._lib.indigoMarkEitherCisTrans.argtypes = [c_int] Indigo._lib.indigoMarkStereobonds.restype = c_int Indigo._lib.indigoMarkStereobonds.argtypes = [c_int] Indigo._lib.indigoAddAtom.restype = c_int Indigo._lib.indigoAddAtom.argtypes = [c_int, c_char_p] Indigo._lib.indigoResetAtom.restype = c_int Indigo._lib.indigoResetAtom.argtypes = [c_int, c_char_p] Indigo._lib.indigoAddRSite.restype = c_int Indigo._lib.indigoAddRSite.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetRSite.restype = c_int Indigo._lib.indigoSetRSite.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetCharge.restype = c_int Indigo._lib.indigoSetCharge.argtypes = [c_int, c_int] Indigo._lib.indigoSetIsotope.restype = c_int Indigo._lib.indigoSetIsotope.argtypes = [c_int, c_int] Indigo._lib.indigoSetImplicitHCount.restype = c_int Indigo._lib.indigoSetImplicitHCount.argtypes = [c_int, c_int] Indigo._lib.indigoAddBond.restype = c_int Indigo._lib.indigoAddBond.argtypes = [c_int, c_int, c_int] Indigo._lib.indigoSetBondOrder.restype = c_int Indigo._lib.indigoSetBondOrder.argtypes = [c_int, c_int] Indigo._lib.indigoMerge.restype = c_int Indigo._lib.indigoMerge.argtypes = [c_int, c_int] Indigo._lib.indigoHighlight.restype = c_int Indigo._lib.indigoHighlight.argtypes = [c_int] Indigo._lib.indigoUnhighlight.restype = c_int Indigo._lib.indigoUnhighlight.argtypes = [c_int] Indigo._lib.indigoIsHighlighted.restype = c_int Indigo._lib.indigoIsHighlighted.argtypes = [c_int] Indigo._lib.indigoCountComponents.restype = c_int Indigo._lib.indigoCountComponents.argtypes = [c_int] Indigo._lib.indigoComponentIndex.restype = c_int Indigo._lib.indigoComponentIndex.argtypes = [c_int] Indigo._lib.indigoIterateComponents.restype = c_int Indigo._lib.indigoIterateComponents.argtypes = [c_int] Indigo._lib.indigoComponent.restype = c_int Indigo._lib.indigoComponent.argtypes = [c_int, c_int] Indigo._lib.indigoCountSSSR.restype = c_int Indigo._lib.indigoCountSSSR.argtypes = [c_int] Indigo._lib.indigoIterateSSSR.restype = c_int Indigo._lib.indigoIterateSSSR.argtypes = [c_int] Indigo._lib.indigoIterateSubtrees.restype = c_int Indigo._lib.indigoIterateSubtrees.argtypes = [c_int, c_int, c_int] Indigo._lib.indigoIterateRings.restype = c_int Indigo._lib.indigoIterateRings.argtypes = [c_int, c_int, c_int] Indigo._lib.indigoIterateEdgeSubmolecules.restype = c_int Indigo._lib.indigoIterateEdgeSubmolecules.argtypes = [ c_int, c_int, c_int, ] Indigo._lib.indigoCountHeavyAtoms.restype = c_int Indigo._lib.indigoCountHeavyAtoms.argtypes = [c_int] Indigo._lib.indigoGrossFormula.restype = c_int Indigo._lib.indigoGrossFormula.argtypes = [c_int] Indigo._lib.indigoMolecularWeight.restype = c_double Indigo._lib.indigoMolecularWeight.argtypes = [c_int] Indigo._lib.indigoMostAbundantMass.restype = c_double Indigo._lib.indigoMostAbundantMass.argtypes = [c_int] Indigo._lib.indigoMonoisotopicMass.restype = c_double Indigo._lib.indigoMonoisotopicMass.argtypes = [c_int] Indigo._lib.indigoMassComposition.restype = c_char_p Indigo._lib.indigoMassComposition.argtypes = [c_int] Indigo._lib.indigoCanonicalSmiles.restype = c_char_p Indigo._lib.indigoCanonicalSmiles.argtypes = [c_int] Indigo._lib.indigoCanonicalSmarts.restype = c_char_p Indigo._lib.indigoCanonicalSmarts.argtypes = [c_int] Indigo._lib.indigoLayeredCode.restype = c_char_p Indigo._lib.indigoLayeredCode.argtypes = [c_int] Indigo._lib.indigoSymmetryClasses.restype = POINTER(c_int) Indigo._lib.indigoSymmetryClasses.argtypes = [c_int, POINTER(c_int)] Indigo._lib.indigoHasCoord.restype = c_int Indigo._lib.indigoHasCoord.argtypes = [c_int] Indigo._lib.indigoHasZCoord.restype = c_int Indigo._lib.indigoHasZCoord.argtypes = [c_int] Indigo._lib.indigoIsChiral.restype = c_int Indigo._lib.indigoIsChiral.argtypes = [c_int] Indigo._lib.indigoIsPossibleFischerProjection.restype = c_int Indigo._lib.indigoIsPossibleFischerProjection.argtypes = [ c_int, c_char_p, ] Indigo._lib.indigoCreateSubmolecule.restype = c_int Indigo._lib.indigoCreateSubmolecule.argtypes = [ c_int, c_int, POINTER(c_int), ] Indigo._lib.indigoCreateEdgeSubmolecule.restype = c_int Indigo._lib.indigoCreateEdgeSubmolecule.argtypes = [ c_int, c_int, POINTER(c_int), c_int, POINTER(c_int), ] Indigo._lib.indigoGetSubmolecule.restype = c_int Indigo._lib.indigoGetSubmolecule.argtypes = [ c_int, c_int, POINTER(c_int), ] Indigo._lib.indigoRemoveAtoms.restype = c_int Indigo._lib.indigoRemoveAtoms.argtypes = [c_int, c_int, POINTER(c_int)] Indigo._lib.indigoRemoveBonds.restype = c_int Indigo._lib.indigoRemoveBonds.argtypes = [c_int, c_int, POINTER(c_int)] Indigo._lib.indigoAlignAtoms.restype = c_float Indigo._lib.indigoAlignAtoms.argtypes = [ c_int, c_int, POINTER(c_int), POINTER(c_float), ] Indigo._lib.indigoAromatize.restype = c_int Indigo._lib.indigoAromatize.argtypes = [c_int] Indigo._lib.indigoDearomatize.restype = c_int Indigo._lib.indigoDearomatize.argtypes = [c_int] Indigo._lib.indigoFoldHydrogens.restype = c_int Indigo._lib.indigoFoldHydrogens.argtypes = [c_int] Indigo._lib.indigoUnfoldHydrogens.restype = c_int Indigo._lib.indigoUnfoldHydrogens.argtypes = [c_int] Indigo._lib.indigoLayout.restype = c_int Indigo._lib.indigoLayout.argtypes = [c_int] Indigo._lib.indigoClean2d.restype = c_int Indigo._lib.indigoClean2d.argtypes = [c_int] Indigo._lib.indigoSmiles.restype = c_char_p Indigo._lib.indigoSmiles.argtypes = [c_int] Indigo._lib.indigoSmarts.restype = c_char_p Indigo._lib.indigoSmarts.argtypes = [c_int] Indigo._lib.indigoName.restype = c_char_p Indigo._lib.indigoName.argtypes = [c_int] Indigo._lib.indigoSetName.restype = c_int Indigo._lib.indigoSetName.argtypes = [c_int, c_char_p] Indigo._lib.indigoSerialize.restype = c_int Indigo._lib.indigoSerialize.argtypes = [ c_int, POINTER(POINTER(c_byte)), POINTER(c_int), ] Indigo._lib.indigoHasProperty.restype = c_int Indigo._lib.indigoHasProperty.argtypes = [c_int, c_char_p] Indigo._lib.indigoGetProperty.restype = c_char_p Indigo._lib.indigoGetProperty.argtypes = [c_int, c_char_p] Indigo._lib.indigoSetProperty.restype = c_int Indigo._lib.indigoSetProperty.argtypes = [c_int, c_char_p, c_char_p] Indigo._lib.indigoRemoveProperty.restype = c_int Indigo._lib.indigoRemoveProperty.argtypes = [c_int, c_char_p] Indigo._lib.indigoIterateProperties.restype = c_int Indigo._lib.indigoIterateProperties.argtypes = [c_int] Indigo._lib.indigoClearProperties.restype = c_int Indigo._lib.indigoClearProperties.argtypes = [c_int] Indigo._lib.indigoCheckBadValence.restype = c_char_p Indigo._lib.indigoCheckBadValence.argtypes = [c_int] Indigo._lib.indigoCheckAmbiguousH.restype = c_char_p Indigo._lib.indigoCheckAmbiguousH.argtypes = [c_int] Indigo._lib.indigoCheckChirality.restype = c_int Indigo._lib.indigoCheckChirality.argtypes = [c_int] Indigo._lib.indigoCheck3DStereo.restype = c_int Indigo._lib.indigoCheck3DStereo.argtypes = [c_int] Indigo._lib.indigoCheckStereo.restype = c_int Indigo._lib.indigoCheckStereo.argtypes = [c_int] Indigo._lib.indigoFingerprint.restype = c_int Indigo._lib.indigoFingerprint.argtypes = [c_int, c_char_p] Indigo._lib.indigoLoadFingerprintFromBuffer.restype = c_int Indigo._lib.indigoLoadFingerprintFromBuffer.argtypes = [ POINTER(c_byte), c_int, ] Indigo._lib.indigoLoadFingerprintFromDescriptors.restype = c_int Indigo._lib.indigoLoadFingerprintFromDescriptors.argtypes = [ POINTER(c_double), c_int, c_int, c_double, ] Indigo._lib.indigoCountBits.restype = c_int Indigo._lib.indigoCountBits.argtypes = [c_int] Indigo._lib.indigoRawData.restype = c_char_p Indigo._lib.indigoRawData.argtypes = [c_int] Indigo._lib.indigoTell.restype = c_int Indigo._lib.indigoTell.argtypes = [c_int] Indigo._lib.indigoSdfAppend.restype = c_int Indigo._lib.indigoSdfAppend.argtypes = [c_int, c_int] Indigo._lib.indigoSmilesAppend.restype = c_int Indigo._lib.indigoSmilesAppend.argtypes = [c_int, c_int] Indigo._lib.indigoRdfHeader.restype = c_int Indigo._lib.indigoRdfHeader.argtypes = [c_int] Indigo._lib.indigoRdfAppend.restype = c_int Indigo._lib.indigoRdfAppend.argtypes = [c_int, c_int] Indigo._lib.indigoCmlHeader.restype = c_int Indigo._lib.indigoCmlHeader.argtypes = [c_int] Indigo._lib.indigoCmlAppend.restype = c_int Indigo._lib.indigoCmlAppend.argtypes = [c_int, c_int] Indigo._lib.indigoCmlFooter.restype = c_int Indigo._lib.indigoCmlFooter.argtypes = [c_int] Indigo._lib.indigoAppend.restype = c_int Indigo._lib.indigoAppend.argtypes = [c_int, c_int] Indigo._lib.indigoArrayAdd.restype = c_int Indigo._lib.indigoArrayAdd.argtypes = [c_int, c_int] Indigo._lib.indigoAt.restype = c_int Indigo._lib.indigoAt.argtypes = [c_int, c_int] Indigo._lib.indigoCount.restype = c_int Indigo._lib.indigoCount.argtypes = [c_int] Indigo._lib.indigoClear.restype = c_int Indigo._lib.indigoClear.argtypes = [c_int] Indigo._lib.indigoIterateArray.restype = c_int Indigo._lib.indigoIterateArray.argtypes = [c_int] Indigo._lib.indigoIgnoreAtom.restype = c_int Indigo._lib.indigoIgnoreAtom.argtypes = [c_int, c_int] Indigo._lib.indigoUnignoreAtom.restype = c_int Indigo._lib.indigoUnignoreAtom.argtypes = [c_int, c_int] Indigo._lib.indigoUnignoreAllAtoms.restype = c_int Indigo._lib.indigoUnignoreAllAtoms.argtypes = [c_int] Indigo._lib.indigoMatch.restype = c_int Indigo._lib.indigoMatch.argtypes = [c_int, c_int] Indigo._lib.indigoCountMatches.restype = c_int Indigo._lib.indigoCountMatches.argtypes = [c_int, c_int] Indigo._lib.indigoCountMatchesWithLimit.restype = c_int Indigo._lib.indigoCountMatchesWithLimit.argtypes = [ c_int, c_int, c_int, ] Indigo._lib.indigoIterateMatches.restype = c_int Indigo._lib.indigoIterateMatches.argtypes = [c_int, c_int] Indigo._lib.indigoHighlightedTarget.restype = c_int Indigo._lib.indigoHighlightedTarget.argtypes = [c_int] Indigo._lib.indigoMapAtom.restype = c_int Indigo._lib.indigoMapAtom.argtypes = [c_int, c_int] Indigo._lib.indigoMapBond.restype = c_int Indigo._lib.indigoMapBond.argtypes = [c_int, c_int] Indigo._lib.indigoMapMolecule.restype = c_int Indigo._lib.indigoMapMolecule.argtypes = [c_int, c_int] Indigo._lib.indigoIterateTautomers.restype = c_int Indigo._lib.indigoIterateTautomers.argtypes = [c_int, c_char_p] Indigo._lib.indigoAllScaffolds.restype = c_int Indigo._lib.indigoAllScaffolds.argtypes = [c_int] Indigo._lib.indigoDecomposedMoleculeScaffold.restype = c_int Indigo._lib.indigoDecomposedMoleculeScaffold.argtypes = [c_int] Indigo._lib.indigoIterateDecomposedMolecules.restype = c_int Indigo._lib.indigoIterateDecomposedMolecules.argtypes = [c_int] Indigo._lib.indigoDecomposedMoleculeHighlighted.restype = c_int Indigo._lib.indigoDecomposedMoleculeHighlighted.argtypes = [c_int] Indigo._lib.indigoDecomposedMoleculeWithRGroups.restype = c_int Indigo._lib.indigoDecomposedMoleculeWithRGroups.argtypes = [c_int] Indigo._lib.indigoDecomposeMolecule.restype = c_int Indigo._lib.indigoDecomposeMolecule.argtypes = [c_int, c_int] Indigo._lib.indigoIterateDecompositions.restype = c_int Indigo._lib.indigoIterateDecompositions.argtypes = [c_int] Indigo._lib.indigoAddDecomposition.restype = c_int Indigo._lib.indigoAddDecomposition.argtypes = [c_int, c_int] Indigo._lib.indigoToString.restype = c_char_p Indigo._lib.indigoToString.argtypes = [c_int] Indigo._lib.indigoOneBitsList.restype = c_char_p Indigo._lib.indigoOneBitsList.argtypes = [c_int] Indigo._lib.indigoToBuffer.restype = c_int Indigo._lib.indigoToBuffer.argtypes = [ c_int, POINTER(POINTER(c_byte)), POINTER(c_int), ] Indigo._lib.indigoStereocenterPyramid.restype = POINTER(c_int) Indigo._lib.indigoStereocenterPyramid.argtypes = [c_int] Indigo._lib.indigoExpandAbbreviations.restype = c_int Indigo._lib.indigoExpandAbbreviations.argtypes = [c_int] Indigo._lib.indigoDbgInternalType.restype = c_char_p Indigo._lib.indigoDbgInternalType.argtypes = [c_int] Indigo._lib.indigoNameToStructure.restype = c_int Indigo._lib.indigoNameToStructure.argtypes = [c_char_p, c_char_p] Indigo._lib.indigoResetOptions.restype = c_int Indigo._lib.indigoResetOptions.argtypes = None def __del__(self): if hasattr(self, "_lib"): self._lib.indigoReleaseSessionId(self._sid) def deserialize(self, arr): values = (c_byte * len(arr))() for i in range(len(arr)): values[i] = arr[i] self._setSessionId() res = Indigo._lib.indigoUnserialize(values, len(arr)) return self.IndigoObject(self, self._checkResult(res)) def unserialize(self, arr): warnings.warn( "unserialize() is deprecated, use deserialize() instead", DeprecationWarning, ) return self.deserialize(arr) def setOption(self, option, value1, value2=None, value3=None): self._setSessionId() if ( ( type(value1).__name__ == "str" or type(value1).__name__ == "unicode" ) and value2 is None and value3 is None ): self._checkResult( Indigo._lib.indigoSetOption( option.encode(ENCODE_ENCODING), value1.encode(ENCODE_ENCODING), ) ) elif ( type(value1).__name__ == "int" and value2 is None and value3 is None ): self._checkResult( Indigo._lib.indigoSetOptionInt( option.encode(ENCODE_ENCODING), value1 ) ) elif ( type(value1).__name__ == "float" and value2 is None and value3 is None ): self._checkResult( Indigo._lib.indigoSetOptionFloat( option.encode(ENCODE_ENCODING), value1 ) ) elif ( type(value1).__name__ == "bool" and value2 is None and value3 is None ): value1_b = 0 if value1: value1_b = 1 self._checkResult( Indigo._lib.indigoSetOptionBool( option.encode(ENCODE_ENCODING), value1_b ) ) elif ( type(value1).__name__ == "int" and value2 and type(value2).__name__ == "int" and value3 is None ): self._checkResult( Indigo._lib.indigoSetOptionXY( option.encode(ENCODE_ENCODING), value1, value2 ) ) elif ( type(value1).__name__ == "float" and value2 and type(value2).__name__ == "float" and value3 and type(value3).__name__ == "float" ): self._checkResult( Indigo._lib.indigoSetOptionColor( option.encode(ENCODE_ENCODING), value1, value2, value3 ) ) else: raise IndigoException("bad option") def getOption(self, option): self._setSessionId() return self._checkResultString( Indigo._lib.indigoGetOption(option.encode(ENCODE_ENCODING)) ) def getOptionInt(self, option): self._setSessionId() value = c_int() self._checkResult( Indigo._lib.indigoGetOptionInt( option.encode(ENCODE_ENCODING), pointer(value) ) ) return value.value def getOptionBool(self, option): self._setSessionId() value = c_int() self._checkResult( Indigo._lib.indigoGetOptionBool( option.encode(ENCODE_ENCODING), pointer(value) ) ) if value.value == 1: return True return False def getOptionFloat(self, option): self._setSessionId() value = c_float() self._checkResult( Indigo._lib.indigoGetOptionFloat( option.encode(ENCODE_ENCODING), pointer(value) ) ) return value.value def getOptionType(self, option): self._setSessionId() return self._checkResultString( Indigo._lib.indigoGetOptionType(option.encode(ENCODE_ENCODING)) ) def resetOptions(self): self._setSessionId() self._checkResult(Indigo._lib.indigoResetOptions()) def _checkResult(self, result): if result < 0: raise IndigoException(Indigo._lib.indigoGetLastError()) return result def _checkResultFloat(self, result): if result < -0.5: raise IndigoException(Indigo._lib.indigoGetLastError()) return result def _checkResultPtr(self, result): if result is None: raise IndigoException(Indigo._lib.indigoGetLastError()) return result def _checkResultString(self, result): return self._checkResultPtr(result).decode(DECODE_ENCODING) def convertToArray(self, iteratable): if isinstance(iteratable, IndigoObject): return iteratable try: some_object_iterator = iter(iteratable) res = self.createArray() for obj in some_object_iterator: res.arrayAdd(self.convertToArray(obj)) return res except TypeError: raise IndigoException( "Cannot convert object %s to an array" % (iteratable) ) def dbgBreakpoint(self): self._setSessionId() return Indigo._lib.indigoDbgBreakpoint() def version(self): self._setSessionId() return self._checkResultString(Indigo._lib.indigoVersion()) def countReferences(self): self._setSessionId() return self._checkResult(Indigo._lib.indigoCountReferences()) def writeFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoWriteFile(filename.encode(ENCODE_ENCODING)) ), ) def writeBuffer(self): self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoWriteBuffer()) ) def createMolecule(self): self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoCreateMolecule()) ) def createQueryMolecule(self): self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoCreateQueryMolecule()) ) def loadMolecule(self, string): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadMoleculeFromString( string.encode(ENCODE_ENCODING) ) ), ) def loadMoleculeFromFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadMoleculeFromFile( filename.encode(ENCODE_ENCODING) ) ), ) def loadMoleculeFromBuffer(self, data): """ Loads molecule from given buffer. Automatically detects input format Args: * buf - byte array Usage: ``` with open (..), 'rb') as f: m = indigo.loadMoleculeFromBuffer(f.read()) ``` Raises: Exception if structure format is incorrect :: Since version 1.3.0 """ if sys.version_info[0] < 3: buf = map(ord, data) else: buf = data values = (c_byte * len(buf))() for i in range(len(buf)): values[i] = buf[i] self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadMoleculeFromBuffer(values, len(buf)) ), ) def loadQueryMolecule(self, string): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadQueryMoleculeFromString( string.encode(ENCODE_ENCODING) ) ), ) def loadQueryMoleculeFromFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadQueryMoleculeFromFile( filename.encode(ENCODE_ENCODING) ) ), ) def loadSmarts(self, string): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadSmartsFromString( string.encode(ENCODE_ENCODING) ) ), ) def loadSmartsFromFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadSmartsFromFile( filename.encode(ENCODE_ENCODING) ) ), ) def loadReaction(self, string): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadReactionFromString( string.encode(ENCODE_ENCODING) ) ), ) def loadReactionFromFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadReactionFromFile( filename.encode(ENCODE_ENCODING) ) ), ) def loadQueryReaction(self, string): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadQueryReactionFromString( string.encode(ENCODE_ENCODING) ) ), ) def loadQueryReactionFromFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadQueryReactionFromFile( filename.encode(ENCODE_ENCODING) ) ), ) def loadReactionSmarts(self, string): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadReactionSmartsFromString( string.encode(ENCODE_ENCODING) ) ), ) def loadReactionSmartsFromFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadReactionSmartsFromFile( filename.encode(ENCODE_ENCODING) ) ), ) def loadStructure(self, structureStr, parameter=None): self._setSessionId() parameter = "" if parameter is None else parameter return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadStructureFromString( structureStr.encode(ENCODE_ENCODING), parameter.encode(ENCODE_ENCODING), ) ), ) def loadStructureFromBuffer(self, structureData, parameter=None): if sys.version_info[0] < 3: buf = map(ord, structureData) else: buf = structureData values = (c_byte * len(buf))() for i in range(len(buf)): values[i] = buf[i] self._setSessionId() parameter = "" if parameter is None else parameter return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadStructureFromBuffer( values, len(buf), parameter.encode(ENCODE_ENCODING) ) ), ) def loadStructureFromFile(self, filename, parameter=None): self._setSessionId() parameter = "" if parameter is None else parameter return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadStructureFromFile( filename.encode(ENCODE_ENCODING), parameter.encode(ENCODE_ENCODING), ) ), ) def checkStructure(self, structure, props=""): if props is None: props = "" self._setSessionId() return self._checkResultString( Indigo._lib.indigoCheckStructure( structure.encode(ENCODE_ENCODING), props.encode(ENCODE_ENCODING), ) ) def loadFingerprintFromBuffer(self, buffer): """Creates a fingerprint from the supplied binary data :param buffer: a list of bytes :return: a fingerprint object Since version 1.3.0 """ self._setSessionId() length = len(buffer) values = (c_byte * length)() for i in range(length): values[i] = buffer[i] return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadFingerprintFromBuffer(values, length) ), ) def loadFingerprintFromDescriptors(self, descriptors, size, density): """Packs a list of molecule descriptors into a fingerprint object :param descriptors: list of normalized numbers (roughly) between 0.0 and 1.0 :param size: size of the fingerprint in bytes :param density: approximate density of '1's vs `0`s in the fingerprint :return: a fingerprint object Since version 1.3.0 """ self._setSessionId() length = len(descriptors) descr_arr = (c_double * length)() for i in range(length): descr_arr[i] = descriptors[i] result = Indigo._lib.indigoLoadFingerprintFromDescriptors( descr_arr, length, size, density ) return self.IndigoObject(self, self._checkResult(result)) def createReaction(self): self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoCreateReaction()) ) def createQueryReaction(self): self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoCreateQueryReaction()) ) def exactMatch(self, item1, item2, flags=""): if flags is None: flags = "" self._setSessionId() newobj = self._checkResult( Indigo._lib.indigoExactMatch( item1.id, item2.id, flags.encode(ENCODE_ENCODING) ) ) if newobj == 0: return None else: return self.IndigoObject(self, newobj, [item1, item2, self]) def setTautomerRule(self, id, beg, end): self._setSessionId() return self._checkResult( Indigo._lib.indigoSetTautomerRule( id, beg.encode(ENCODE_ENCODING), end.encode(ENCODE_ENCODING) ) ) def removeTautomerRule(self, id): self._setSessionId() return self._checkResult(Indigo._lib.indigoRemoveTautomerRule(id)) def clearTautomerRules(self): self._setSessionId() return self._checkResult(Indigo._lib.indigoClearTautomerRules()) def commonBits(self, fingerprint1, fingerprint2): self._setSessionId() return self._checkResult( Indigo._lib.indigoCommonBits(fingerprint1.id, fingerprint2.id) ) def similarity(self, item1, item2, metrics=""): if metrics is None: metrics = "" self._setSessionId() return self._checkResultFloat( Indigo._lib.indigoSimilarity( item1.id, item2.id, metrics.encode(ENCODE_ENCODING) ) ) def iterateSDFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoIterateSDFile( filename.encode(ENCODE_ENCODING) ) ), ) def iterateRDFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoIterateRDFile( filename.encode(ENCODE_ENCODING) ) ), ) def iterateSmilesFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoIterateSmilesFile( filename.encode(ENCODE_ENCODING) ) ), ) def iterateCMLFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoIterateCMLFile( filename.encode(ENCODE_ENCODING) ) ), ) def iterateCDXFile(self, filename): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoIterateCDXFile( filename.encode(ENCODE_ENCODING) ) ), ) def createFileSaver(self, filename, format): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoCreateFileSaver( filename.encode(ENCODE_ENCODING), format.encode(ENCODE_ENCODING), ) ), ) def createSaver(self, obj, format): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoCreateSaver( obj.id, format.encode(ENCODE_ENCODING) ) ), ) def createArray(self): self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoCreateArray()) ) def substructureMatcher(self, target, mode=""): if mode is None: mode = "" self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoSubstructureMatcher( target.id, mode.encode(ENCODE_ENCODING) ) ), target, ) def extractCommonScaffold(self, structures, options=""): structures = self.convertToArray(structures) if options is None: options = "" self._setSessionId() newobj = self._checkResult( Indigo._lib.indigoExtractCommonScaffold( structures.id, options.encode(ENCODE_ENCODING) ) ) if newobj == 0: return None else: return self.IndigoObject(self, newobj, self) def decomposeMolecules(self, scaffold, structures): structures = self.convertToArray(structures) self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoDecomposeMolecules( scaffold.id, structures.id ) ), scaffold, ) def rgroupComposition(self, molecule, options=""): if options is None: options = "" self._setSessionId() newobj = self._checkResult( Indigo._lib.indigoRGroupComposition( molecule.id, options.encode(ENCODE_ENCODING) ) ) if newobj == 0: return None else: return self.IndigoObject(self, newobj, self) def getFragmentedMolecule(self, elem, options=""): if options is None: options = "" self._setSessionId() newobj = self._checkResult( Indigo._lib.indigoGetFragmentedMolecule( elem.id, options.encode(ENCODE_ENCODING) ) ) if newobj == 0: return None else: return self.IndigoObject(self, newobj, self) def createDecomposer(self, scaffold): self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoCreateDecomposer(scaffold.id)), scaffold, ) def reactionProductEnumerate(self, replacedaction, monomers): self._setSessionId() monomers = self.convertToArray(monomers) return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoReactionProductEnumerate( replacedaction.id, monomers.id ) ), replacedaction, ) def transform(self, reaction, monomers): self._setSessionId() newobj = self._checkResult( Indigo._lib.indigoTransform(reaction.id, monomers.id) ) if newobj == 0: return None else: return self.IndigoObject(self, newobj, self) def loadBuffer(self, buf): buf = list(buf) values = (c_byte * len(buf))() for i in range(len(buf)): values[i] = buf[i] self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoLoadBuffer(values, len(buf))), ) def loadString(self, string): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoLoadString(string.encode(ENCODE_ENCODING)) ), ) def iterateSDF(self, reader): self._setSessionId() result = self._checkResult(Indigo._lib.indigoIterateSDF(reader.id)) if not result: return None return self.IndigoObject(self, result, reader) def iterateSmiles(self, reader): self._setSessionId() result = self._checkResult(Indigo._lib.indigoIterateSmiles(reader.id)) if not result: return None return self.IndigoObject(self, result, reader) def iterateCML(self, reader): self._setSessionId() result = self._checkResult(Indigo._lib.indigoIterateCML(reader.id)) if not result: return None return self.IndigoObject(self, result, reader) def iterateCDX(self, reader): self._setSessionId() result = self._checkResult(Indigo._lib.indigoIterateCDX(reader.id)) if not result: return None return self.IndigoObject(self, result, reader) def iterateRDF(self, reader): self._setSessionId() result = self._checkResult(Indigo._lib.indigoIterateRDF(reader.id)) if not result: return None return self.IndigoObject(self, result, reader) def iterateTautomers(self, molecule, params): self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoIterateTautomers( molecule.id, params.encode(ENCODE_ENCODING) ) ), molecule, ) def nameToStructure(self, name, params=None): """ Converts a chemical name into a corresponding structure Args: * name - a name to parse * params - a string containing parsing options or nullptr if no options are changed Raises: Exception if parsing fails or no structure is found :: Since version 1.3.0 """ if params is None: params = "" self._setSessionId() return self.IndigoObject( self, self._checkResult( Indigo._lib.indigoNameToStructure( name.encode(ENCODE_ENCODING), params.encode(ENCODE_ENCODING), ) ), ) def buildPkaModel(self, level, threshold, filename): self._setSessionId() return self._checkResult( Indigo._lib.indigoBuildPkaModel( level, threshold, filename.encode(ENCODE_ENCODING) ) ) def transformHELMtoSCSR(self, item): """ :: Since version 1.3.0 """ self._setSessionId() return self.IndigoObject( self, self._checkResult(Indigo._lib.indigoTransformHELMtoSCSR(item.id)), )