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None | clearChainID (Chem.Atom atom) |
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bool | hasChainID (Chem.Atom atom) |
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str | getChainID (Chem.Atom atom) |
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None | setChainID (Chem.Atom atom, str id) |
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None | clearAltLocationID (Chem.Atom atom) |
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bool | hasAltLocationID (Chem.Atom atom) |
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str | getAltLocationID (Chem.Atom atom) |
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None | setAltLocationID (Chem.Atom atom, str id) |
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None | clearResidueCode (Chem.Atom atom) |
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bool | hasResidueCode (Chem.Atom atom) |
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str | getResidueCode (Chem.Atom atom) |
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None | setResidueCode (Chem.Atom atom, str code) |
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None | clearResidueInsertionCode (Chem.Atom atom) |
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bool | hasResidueInsertionCode (Chem.Atom atom) |
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str | getResidueInsertionCode (Chem.Atom atom) |
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None | setResidueInsertionCode (Chem.Atom atom, str code) |
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None | clearResidueAtomName (Chem.Atom atom) |
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bool | hasResidueAtomName (Chem.Atom atom) |
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str | getResidueAtomName (Chem.Atom atom) |
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None | setResidueAtomName (Chem.Atom atom, str name) |
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None | clearResidueAltAtomName (Chem.Atom atom) |
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bool | hasResidueAltAtomName (Chem.Atom atom) |
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str | getResidueAltAtomName (Chem.Atom atom) |
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None | setResidueAltAtomName (Chem.Atom atom, str name) |
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None | extractResidueSubstructure (Chem.Atom atom, Chem.MolecularGraph molgraph, Chem.Fragment res_substruct, bool cnctd_only=False, int flags=2147483648, bool append=False) |
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bool | areInSameResidue (Chem.Atom atom1, Chem.Atom atom2, int flags=2147483648) |
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None | clearResidueLinkingAtomFlag (Chem.Atom atom) |
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bool | hasResidueLinkingAtomFlag (Chem.Atom atom) |
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bool | getResidueLinkingAtomFlag (Chem.Atom atom) |
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None | setResidueLinkingAtomFlag (Chem.Atom atom, bool linking) |
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None | clearResidueLeavingAtomFlag (Chem.Atom atom) |
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bool | hasResidueLeavingAtomFlag (Chem.Atom atom) |
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bool | getResidueLeavingAtomFlag (Chem.Atom atom) |
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None | setResidueLeavingAtomFlag (Chem.Atom atom, bool leaving) |
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None | clearHeteroAtomFlag (Chem.Atom atom) |
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bool | hasHeteroAtomFlag (Chem.Atom atom) |
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bool | getHeteroAtomFlag (Chem.Atom atom) |
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None | setHeteroAtomFlag (Chem.Atom atom, bool is_het) |
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bool | isPDBBackboneAtom (Chem.Atom atom) |
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bool | matchesResidueInfo (Chem.Atom atom, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0, str atom_name='', int serial_no=-9223372036854775808) |
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None | clearResidueSequenceNumber (Chem.Atom atom) |
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bool | hasResidueSequenceNumber (Chem.Atom atom) |
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int | getResidueSequenceNumber (Chem.Atom atom) |
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None | setResidueSequenceNumber (Chem.Atom atom, int seq_no) |
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None | clearSerialNumber (Chem.Atom atom) |
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bool | hasSerialNumber (Chem.Atom atom) |
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int | getSerialNumber (Chem.Atom atom) |
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None | setSerialNumber (Chem.Atom atom, int serial_no) |
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None | clearModelNumber (Chem.Atom atom) |
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bool | hasModelNumber (Chem.Atom atom) |
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int | getModelNumber (Chem.Atom atom) |
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None | setModelNumber (Chem.Atom atom, int model_no) |
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None | clearBFactor (Chem.Atom atom) |
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bool | hasBFactor (Chem.Atom atom) |
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float | getBFactor (Chem.Atom atom) |
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None | setBFactor (Chem.Atom atom, float factor) |
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None | clearOccupancy (Chem.Atom atom) |
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bool | hasOccupancy (Chem.Atom atom) |
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float | getOccupancy (Chem.Atom atom) |
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None | setOccupancy (Chem.Atom atom, float occupancy) |
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None | clearPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBIgnoreFormalChargeFieldParameter (Base.ControlParameterContainer cntnr, bool ignore) |
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None | clearPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBEvaluateMASTERRecordParameter (Base.ControlParameterContainer cntnr, bool evaluate) |
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None | clearStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr) |
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bool | hasStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr) |
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bool | getStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr) |
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None | setStrictErrorCheckingParameter (Base.ControlParameterContainer cntnr, bool strict) |
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None | clearCheckLineLengthParameter (Base.ControlParameterContainer cntnr) |
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bool | hasCheckLineLengthParameter (Base.ControlParameterContainer cntnr) |
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bool | getCheckLineLengthParameter (Base.ControlParameterContainer cntnr) |
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None | setCheckLineLengthParameter (Base.ControlParameterContainer cntnr, bool check) |
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None | clearPDBFormatVersionParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBFormatVersionParameter (Base.ControlParameterContainer cntnr) |
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int | getPDBFormatVersionParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBFormatVersionParameter (Base.ControlParameterContainer cntnr, int ver) |
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None | clearPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBWriteCONECTRecordsReflectingBondOrderParameter (Base.ControlParameterContainer cntnr, bool write) |
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None | clearPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBWriteCONECTRecordsForAllBondsParameter (Base.ControlParameterContainer cntnr, bool write) |
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None | clearPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBWriteCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool write) |
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None | clearPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBDeduceBondOrdersFromCONECTRecordsParameter (Base.ControlParameterContainer cntnr, bool deduce) |
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None | clearPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBIgnoreConectRecordsParameter (Base.ControlParameterContainer cntnr, bool ignore) |
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None | clearPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBWriteFormalChargesParameter (Base.ControlParameterContainer cntnr, bool write) |
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None | clearPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBCalcMissingFormalChargesParameter (Base.ControlParameterContainer cntnr, bool calc) |
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None | clearPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBApplyDictFormalAtomChargesParameter (Base.ControlParameterContainer cntnr, bool apply) |
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None | clearPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBTruncateLinesParameter (Base.ControlParameterContainer cntnr, bool trunc) |
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None | clearPDBApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBApplyDictAtomTypesParameter (Base.ControlParameterContainer cntnr, bool apply) |
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None | clearCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr) |
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bool | getCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr) |
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None | setCombineInterferingResidueCoordinatesParameter (Base.ControlParameterContainer cntnr, bool comb) |
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None | clearPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBApplyDictAtomBondingToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply) |
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None | clearPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBApplyDictBondOrdersToNonStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply) |
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None | clearPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBApplyDictAtomBondingToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply) |
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None | clearPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBApplyDictBondOrdersToStdResiduesParameter (Base.ControlParameterContainer cntnr, bool apply) |
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None | clearPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr) |
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bool | getPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBPerceiveMissingBondOrdersParameter (Base.ControlParameterContainer cntnr, bool perceive) |
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None | clearPDBResidueDictionaryParameter (Base.ControlParameterContainer cntnr) |
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bool | hasPDBResidueDictionaryParameter (Base.ControlParameterContainer cntnr) |
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ResidueDictionary | getPDBResidueDictionaryParameter (Base.ControlParameterContainer cntnr) |
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None | setPDBResidueDictionaryParameter (Base.ControlParameterContainer cntnr, ResidueDictionary dict) |
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None | clearChainID (Chem.MolecularGraph molgraph) |
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bool | hasChainID (Chem.MolecularGraph molgraph) |
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str | getChainID (Chem.MolecularGraph molgraph) |
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None | setChainID (Chem.MolecularGraph molgraph, str id) |
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None | clearPDBData (Chem.MolecularGraph molgraph) |
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bool | hasPDBData (Chem.MolecularGraph molgraph) |
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PDBData | getPDBData (Chem.MolecularGraph molgraph) |
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None | setPDBData (Chem.MolecularGraph molgraph, PDBData data) |
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None | clearResidueCode (Chem.MolecularGraph molgraph) |
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bool | hasResidueCode (Chem.MolecularGraph molgraph) |
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str | getResidueCode (Chem.MolecularGraph molgraph) |
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None | setResidueCode (Chem.MolecularGraph molgraph, str code) |
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None | clearResidueInsertionCode (Chem.MolecularGraph molgraph) |
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bool | hasResidueInsertionCode (Chem.MolecularGraph molgraph) |
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str | getResidueInsertionCode (Chem.MolecularGraph molgraph) |
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None | setResidueInsertionCode (Chem.MolecularGraph molgraph, str code) |
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None | setHydrogenResidueSequenceInfo (Chem.MolecularGraph molgraph, bool overwrite, int flags=2147483648) |
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None | convertMOL2ToPDBResidueInfo (Chem.MolecularGraph molgraph, bool override) |
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bool | matchesResidueInfo (Chem.MolecularGraph molgraph, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0) |
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None | clearResidueSequenceNumber (Chem.MolecularGraph molgraph) |
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bool | hasResidueSequenceNumber (Chem.MolecularGraph molgraph) |
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int | getResidueSequenceNumber (Chem.MolecularGraph molgraph) |
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None | setResidueSequenceNumber (Chem.MolecularGraph molgraph, int seq_no) |
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None | clearModelNumber (Chem.MolecularGraph molgraph) |
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bool | hasModelNumber (Chem.MolecularGraph molgraph) |
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int | getModelNumber (Chem.MolecularGraph molgraph) |
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None | setModelNumber (Chem.MolecularGraph molgraph, int model_no) |
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None | extractResidueSubstructures (Chem.MolecularGraph molgraph, Chem.MolecularGraph parent_molgraph, Chem.Fragment res_substructs, bool cnctd_only=False, int flags=2147483648, bool append=False) |
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None | extractEnvironmentResidues (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_residues, float max_dist, bool append=False) |
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None | extractEnvironmentResidues (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_residues, Chem.Atom3DCoordinatesFunction coords_func, float max_dist, bool append=False) |
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None | extractProximalAtoms (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_atoms, float max_dist, bool inc_core_atoms=False, bool append=False) |
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None | extractProximalAtoms (Chem.MolecularGraph core, Chem.MolecularGraph macromol, Chem.Fragment env_atoms, Chem.Atom3DCoordinatesFunction coords_func, float max_dist, bool inc_core_atoms=False, bool append=False) |
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bool | combineInterferingResidueCoordinates (Chem.Molecule mol, float max_ctr_dist=1.0) |
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int | findResidue (object cntnr, int idx, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0, str atom_name='', int serial_no=-9223372036854775808) |
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int | findResidueAtom (object cntnr, int idx, str res_code='', str chain_id='', int res_seq_no=-9223372036854775808, str ins_code='\x00', int model_no=0, str atom_name='', int serial_no=-9223372036854775808) |
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Contains classes and functions related to biological macromolecules.