|
typedef std::function< const Math::Vector3D &(const Chem::Atom &)> | Atom3DCoordinatesFunction |
| A generic wrapper class used to store a user-defined Chem::Atom 3D-coordinates function. More...
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typedef std::function< bool(const Chem::Atom &, const Chem::Atom &)> | AtomCompareFunction |
| A generic wrapper class used to store a user-defined atom compare function. More...
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typedef std::function< bool(const Chem::Atom &)> | AtomPredicate |
| A generic wrapper class used to store a user-defined atom predicate. More...
|
|
typedef std::function< std::size_t(const Chem::Atom &)> | AtomPriorityFunction |
| A generic wrapper class used to store a user-defined atom priority function. More...
|
|
typedef std::function< bool(const Chem::Bond &, const Chem::Bond &)> | BondCompareFunction |
| A generic wrapper class used to store a user-defined bond compare function. More...
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typedef std::function< bool(const Chem::Bond &)> | BondPredicate |
| A generic wrapper class used to store a user-defined bond predicate. More...
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typedef Util::DefaultDataOutputHandler< CDFBZ2MolecularGraphWriter, DataFormat::CDF_BZ2 > | CDFBZ2MolecularGraphOutputHandler |
| A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
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typedef Util::CompressedDataWriter< CDFMolecularGraphWriter, Util::BZip2OStream > | CDFBZ2MolecularGraphWriter |
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typedef Util::DefaultDataInputHandler< CDFBZ2MoleculeReader, DataFormat::CDF_BZ2 > | CDFBZ2MoleculeInputHandler |
| A handler for the input of bzip2-compressed molecule data in the native I/O format of the CDPL. More...
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typedef Util::CompressedDataReader< CDFMoleculeReader, Util::BZip2IStream > | CDFBZ2MoleculeReader |
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typedef Util::DefaultDataInputHandler< CDFBZ2ReactionReader, DataFormat::CDF_BZ2 > | CDFBZ2ReactionInputHandler |
| A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
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typedef Util::DefaultDataOutputHandler< CDFBZ2ReactionWriter, DataFormat::CDF_BZ2 > | CDFBZ2ReactionOutputHandler |
| A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
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typedef Util::CompressedDataReader< CDFReactionReader, Util::BZip2IStream > | CDFBZ2ReactionReader |
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typedef Util::CompressedDataWriter< CDFReactionWriter, Util::BZip2OStream > | CDFBZ2ReactionWriter |
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typedef Util::DefaultDataOutputHandler< CDFGZMolecularGraphWriter, DataFormat::CDF_GZ > | CDFGZMolecularGraphOutputHandler |
| A handler for the output of gzip-compressed molecular graph data in the native I/O format of the CDPL. More...
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typedef Util::CompressedDataWriter< CDFMolecularGraphWriter, Util::GZipOStream > | CDFGZMolecularGraphWriter |
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typedef Util::DefaultDataInputHandler< CDFGZMoleculeReader, DataFormat::CDF_GZ > | CDFGZMoleculeInputHandler |
| A handler for the input of gzip-compressed molecule data in the native I/O format of the CDPL. More...
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typedef Util::CompressedDataReader< CDFMoleculeReader, Util::GZipIStream > | CDFGZMoleculeReader |
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typedef Util::DefaultDataInputHandler< CDFGZReactionReader, DataFormat::CDF_GZ > | CDFGZReactionInputHandler |
| A handler for the input of gzip-compressed reaction data in the native I/O format of the CDPL. More...
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typedef Util::DefaultDataOutputHandler< CDFGZReactionWriter, DataFormat::CDF_GZ > | CDFGZReactionOutputHandler |
| A handler for the output of gzip-compressed reaction data in the native I/O format of the CDPL. More...
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typedef Util::CompressedDataReader< CDFReactionReader, Util::GZipIStream > | CDFGZReactionReader |
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typedef Util::CompressedDataWriter< CDFReactionWriter, Util::GZipOStream > | CDFGZReactionWriter |
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typedef Util::DefaultDataOutputHandler< CDFMolecularGraphWriter, DataFormat::CDF > | CDFMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the native I/O format of the CDPL. More...
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typedef Util::DefaultDataInputHandler< CDFMoleculeReader, DataFormat::CDF > | CDFMoleculeInputHandler |
| A handler for the input of molecule data in the native I/O format of the CDPL. More...
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typedef Util::DefaultDataInputHandler< CDFReactionReader, DataFormat::CDF > | CDFReactionInputHandler |
| A handler for the input of reaction data in the native I/O format of the CDPL. More...
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typedef Util::DefaultDataOutputHandler< CDFReactionWriter, DataFormat::CDF > | CDFReactionOutputHandler |
| A handler for the output of reaction data in the native I/O format of the CDPL. More...
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typedef std::function< const Math::Vector3D &(const Chem::Entity &)> | Entity3DCoordinatesFunction |
| A generic wrapper class used to store a user-defined Chem::Entity3D coordinates function. More...
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typedef Util::DefaultDataOutputHandler< INCHIMolecularGraphWriter, DataFormat::INCHI > | INCHIMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
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typedef Util::DefaultDataInputHandler< INCHIMoleculeReader, DataFormat::INCHI > | INCHIMoleculeInputHandler |
| A handler for the input of molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
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typedef Util::DefaultDataOutputHandler< JMEMolecularGraphWriter, DataFormat::JME > | JMEMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
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typedef Util::DefaultDataInputHandler< JMEMoleculeReader, DataFormat::JME > | JMEMoleculeInputHandler |
| A handler for the input of molecule data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
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typedef Util::DefaultDataInputHandler< JMEReactionReader, DataFormat::JME > | JMEReactionInputHandler |
| A handler for the input of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
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typedef Util::DefaultDataOutputHandler< JMEReactionWriter, DataFormat::JME > | JMEReactionOutputHandler |
| A handler for the output of reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...
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typedef Util::DefaultDataOutputHandler< MOL2BZ2MolecularGraphWriter, DataFormat::MOL2_BZ2 > | MOL2BZ2MolecularGraphOutputHandler |
| A handler for the output of bzip2-compressed molecular graph data in the Sybyl MOL2 format. More...
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typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::BZip2OStream > | MOL2BZ2MolecularGraphWriter |
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typedef Util::DefaultDataInputHandler< MOL2BZ2MoleculeReader, DataFormat::MOL2_BZ2 > | MOL2BZ2MoleculeInputHandler |
| A handler for the input of bzip2-compressed molecule data in the Sybyl MOL2 format. More...
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typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::BZip2IStream > | MOL2BZ2MoleculeReader |
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typedef Util::DefaultDataOutputHandler< MOL2GZMolecularGraphWriter, DataFormat::MOL2_GZ > | MOL2GZMolecularGraphOutputHandler |
| A handler for the output of gzip-compressed molecular graph data in the Sybyl MOL2 format. More...
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typedef Util::CompressedDataWriter< MOL2MolecularGraphWriter, Util::GZipOStream > | MOL2GZMolecularGraphWriter |
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typedef Util::DefaultDataInputHandler< MOL2GZMoleculeReader, DataFormat::MOL2_GZ > | MOL2GZMoleculeInputHandler |
| A handler for the input of gzip-compressed molecule data in the Sybyl MOL2 format. More...
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typedef Util::CompressedDataReader< MOL2MoleculeReader, Util::GZipIStream > | MOL2GZMoleculeReader |
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typedef Util::DefaultDataOutputHandler< MOL2MolecularGraphWriter, DataFormat::MOL2 > | MOL2MolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the Sybyl MOL2 format. More...
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typedef Util::DefaultDataInputHandler< MOL2MoleculeReader, DataFormat::MOL2 > | MOL2MoleculeInputHandler |
| A handler for the input of molecule data in the Sybyl MOL2 format. More...
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typedef Util::MultiFormatDataWriter< MolecularGraph > | MolecularGraphWriter |
| Writer for molecule data in any supported format. More...
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typedef Util::MultiFormatDataReader< Molecule > | MoleculeReader |
| Reader for molecule data in any supported format. More...
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typedef Util::DefaultDataOutputHandler< MOLMolecularGraphWriter, DataFormat::MOL > | MOLMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the MDL Mol-File [CTFILE] format. More...
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typedef Util::DefaultDataInputHandler< MOLMoleculeReader, DataFormat::MOL > | MOLMoleculeInputHandler |
| A handler for the input of molecule data in the MDL Mol-File [CTFILE] format. More...
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typedef Util::DefaultDataInputHandler< RDFBZ2ReactionReader, DataFormat::RDF_BZ2 > | RDFBZ2ReactionInputHandler |
| A handler for the input of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
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typedef Util::DefaultDataOutputHandler< RDFBZ2ReactionWriter, DataFormat::RDF_BZ2 > | RDFBZ2ReactionOutputHandler |
| A handler for the output of bzip2-compressed reaction data in the MDL RD-File [CTFILE] format. More...
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typedef Util::CompressedDataReader< RDFReactionReader, Util::BZip2IStream > | RDFBZ2ReactionReader |
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typedef Util::CompressedDataWriter< RDFReactionWriter, Util::BZip2OStream > | RDFBZ2ReactionWriter |
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typedef Util::DefaultDataInputHandler< RDFGZReactionReader, DataFormat::RDF_GZ > | RDFGZReactionInputHandler |
| A handler for the input of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
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typedef Util::DefaultDataOutputHandler< RDFGZReactionWriter, DataFormat::RDF_GZ > | RDFGZReactionOutputHandler |
| A handler for the output of gzip-compressed reaction data in the MDL RD-File [CTFILE] format. More...
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typedef Util::CompressedDataReader< RDFReactionReader, Util::GZipIStream > | RDFGZReactionReader |
|
typedef Util::CompressedDataWriter< RDFReactionWriter, Util::GZipOStream > | RDFGZReactionWriter |
|
typedef Util::DefaultDataInputHandler< RDFReactionReader, DataFormat::RDF > | RDFReactionInputHandler |
| A handler for the input of reaction data in the MDL RD-File [CTFILE] format. More...
|
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typedef Util::DefaultDataOutputHandler< RDFReactionWriter, DataFormat::RDF > | RDFReactionOutputHandler |
| A handler for the output of reaction data in the MDL RD-File [CTFILE] format. More...
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typedef Util::MultiFormatDataReader< Reaction > | ReactionReader |
| Reader for reaction data in any supported format. More...
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typedef Util::MultiFormatDataWriter< Reaction > | ReactionWriter |
| Writer for reaction data in any supported format. More...
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typedef Util::DefaultDataInputHandler< RXNReactionReader, DataFormat::RXN > | RXNReactionInputHandler |
| A handler for the input of reaction data in the MDL Rxn-File [CTFILE] format. More...
|
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typedef Util::DefaultDataOutputHandler< RXNReactionWriter, DataFormat::RXN > | RXNReactionOutputHandler |
| A handler for the output of reaction data in the MDL Rxn-File [CTFILE] format. More...
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typedef Util::DefaultDataOutputHandler< SDFBZ2MolecularGraphWriter, DataFormat::SDF_BZ2 > | SDFBZ2MolecularGraphOutputHandler |
| A handler for the output of bzip2-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
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typedef Util::CompressedDataWriter< SDFMolecularGraphWriter, Util::BZip2OStream > | SDFBZ2MolecularGraphWriter |
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typedef Util::DefaultDataInputHandler< SDFBZ2MoleculeReader, DataFormat::SDF_BZ2 > | SDFBZ2MoleculeInputHandler |
| A handler for the input of bzip2-compressed molecule data in the MDL SD-File [CTFILE] format. More...
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typedef Util::CompressedDataReader< SDFMoleculeReader, Util::BZip2IStream > | SDFBZ2MoleculeReader |
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typedef Util::DefaultDataOutputHandler< SDFGZMolecularGraphWriter, DataFormat::SDF_GZ > | SDFGZMolecularGraphOutputHandler |
| A handler for the output of gzip-compressed molecular graph data in the MDL SD-File [CTFILE] format. More...
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typedef Util::CompressedDataWriter< SDFMolecularGraphWriter, Util::GZipOStream > | SDFGZMolecularGraphWriter |
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typedef Util::DefaultDataInputHandler< SDFGZMoleculeReader, DataFormat::SDF_GZ > | SDFGZMoleculeInputHandler |
| A handler for the input of gzip-compressed molecule data in the MDL SD-File [CTFILE] format. More...
|
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typedef Util::CompressedDataReader< SDFMoleculeReader, Util::GZipIStream > | SDFGZMoleculeReader |
|
typedef Util::DefaultDataOutputHandler< SDFMolecularGraphWriter, DataFormat::SDF > | SDFMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the MDL SD-File [CTFILE] format. More...
|
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typedef Util::DefaultDataInputHandler< SDFMoleculeReader, DataFormat::SDF > | SDFMoleculeInputHandler |
| A handler for the input of molecule data in the MDL SD-File [CTFILE] format. More...
|
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typedef Util::DefaultDataOutputHandler< SMARTSMolecularGraphWriter, DataFormat::SMARTS > | SMARTSMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the Daylight SMARTS [SMARTS] format. More...
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typedef Util::DefaultDataInputHandler< SMARTSMoleculeReader, DataFormat::SMARTS > | SMARTSMoleculeInputHandler |
| A handler for the input of molecule data in the Daylight SMARTS [SMARTS] format. More...
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typedef Util::DefaultDataInputHandler< SMARTSReactionReader, DataFormat::SMARTS > | SMARTSReactionInputHandler |
| A handler for the input of reaction data in the Daylight SMARTS [SMARTS] format. More...
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typedef Util::DefaultDataOutputHandler< SMARTSReactionWriter, DataFormat::SMARTS > | SMARTSReactionOutputHandler |
| A handler for the output of reaction data in the Daylight SMARTS [SMARTS] format. More...
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typedef Util::DefaultDataOutputHandler< SMILESBZ2MolecularGraphWriter, DataFormat::SMILES_BZ2 > | SMILESBZ2MolecularGraphOutputHandler |
| A handler for the output of bzip2-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
|
|
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::BZip2OStream > | SMILESBZ2MolecularGraphWriter |
|
typedef Util::DefaultDataInputHandler< SMILESBZ2MoleculeReader, DataFormat::SMILES_BZ2 > | SMILESBZ2MoleculeInputHandler |
| A handler for the input of bzip2-compressed molecule data in the Daylight SMILES [SMILES] format. More...
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typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::BZip2IStream > | SMILESBZ2MoleculeReader |
|
typedef Util::DefaultDataInputHandler< SMILESBZ2ReactionReader, DataFormat::SMILES_BZ2 > | SMILESBZ2ReactionInputHandler |
| A handler for the input of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
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typedef Util::DefaultDataOutputHandler< SMILESBZ2ReactionWriter, DataFormat::SMILES_BZ2 > | SMILESBZ2ReactionOutputHandler |
| A handler for the output of bzip2-compressed reaction data in the Daylight SMILES [SMILES] format. More...
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typedef Util::CompressedDataReader< SMILESReactionReader, Util::BZip2IStream > | SMILESBZ2ReactionReader |
|
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::BZip2OStream > | SMILESBZ2ReactionWriter |
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typedef Util::DefaultDataOutputHandler< SMILESGZMolecularGraphWriter, DataFormat::SMILES_GZ > | SMILESGZMolecularGraphOutputHandler |
| A handler for the output of gzip-compressed molecular graph data in the Daylight SMILES [SMILES] format. More...
|
|
typedef Util::CompressedDataWriter< SMILESMolecularGraphWriter, Util::GZipOStream > | SMILESGZMolecularGraphWriter |
|
typedef Util::DefaultDataInputHandler< SMILESGZMoleculeReader, DataFormat::SMILES_GZ > | SMILESGZMoleculeInputHandler |
| A handler for the input of gzip-compressed molecule data in Daylight SMILES [SMILES] format. More...
|
|
typedef Util::CompressedDataReader< SMILESMoleculeReader, Util::GZipIStream > | SMILESGZMoleculeReader |
|
typedef Util::DefaultDataInputHandler< SMILESGZReactionReader, DataFormat::SMILES_GZ > | SMILESGZReactionInputHandler |
| A handler for the input of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
|
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typedef Util::DefaultDataOutputHandler< SMILESGZReactionWriter, DataFormat::SMILES_GZ > | SMILESGZReactionOutputHandler |
| A handler for the output of gzip-compressed reaction data in the Daylight SMILES [SMILES] format. More...
|
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typedef Util::CompressedDataReader< SMILESReactionReader, Util::GZipIStream > | SMILESGZReactionReader |
|
typedef Util::CompressedDataWriter< SMILESReactionWriter, Util::GZipOStream > | SMILESGZReactionWriter |
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typedef Util::DefaultDataOutputHandler< SMILESMolecularGraphWriter, DataFormat::SMILES > | SMILESMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the Daylight SMILES [SMILES] format. More...
|
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typedef Util::DefaultDataInputHandler< SMILESMoleculeReader, DataFormat::SMILES > | SMILESMoleculeInputHandler |
| A handler for the input of molecule data in the Daylight SMILES [SMILES] format. More...
|
|
typedef Util::DefaultDataInputHandler< SMILESReactionReader, DataFormat::SMILES > | SMILESReactionInputHandler |
| A handler for the input of reaction data in the Daylight SMILES [SMILES] format. More...
|
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typedef Util::DefaultDataOutputHandler< SMILESReactionWriter, DataFormat::SMILES > | SMILESReactionOutputHandler |
| A handler for the output of reaction data in the Daylight SMILES [SMILES] format. More...
|
|
typedef Util::DefaultDataOutputHandler< XYZBZ2MolecularGraphWriter, DataFormat::XYZ_BZ2 > | XYZBZ2MolecularGraphOutputHandler |
| A handler for the output of bzip2-compressed molecular graph data in the XYZ format. More...
|
|
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::BZip2OStream > | XYZBZ2MolecularGraphWriter |
|
typedef Util::DefaultDataInputHandler< XYZBZ2MoleculeReader, DataFormat::XYZ_BZ2 > | XYZBZ2MoleculeInputHandler |
| A handler for the input of bzip2-compressed molecule data in the XYZ format. More...
|
|
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::BZip2IStream > | XYZBZ2MoleculeReader |
|
typedef Util::DefaultDataOutputHandler< XYZGZMolecularGraphWriter, DataFormat::XYZ_GZ > | XYZGZMolecularGraphOutputHandler |
| A handler for the output of gzip-compressed molecular graph data in the XYZ format. More...
|
|
typedef Util::CompressedDataWriter< XYZMolecularGraphWriter, Util::GZipOStream > | XYZGZMolecularGraphWriter |
|
typedef Util::DefaultDataInputHandler< XYZGZMoleculeReader, DataFormat::XYZ_GZ > | XYZGZMoleculeInputHandler |
| A handler for the input of gzip-compressed molecule data in the XYZ format. More...
|
|
typedef Util::CompressedDataReader< XYZMoleculeReader, Util::GZipIStream > | XYZGZMoleculeReader |
|
typedef Util::DefaultDataOutputHandler< XYZMolecularGraphWriter, DataFormat::XYZ > | XYZMolecularGraphOutputHandler |
| A handler for the output of molecular graph data in the XYZ format. More...
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typedef Util::DefaultDataInputHandler< XYZMoleculeReader, DataFormat::XYZ > | XYZMoleculeInputHandler |
| A handler for the input of molecule data in the XYZ format. More...
|
|
|
CDPL_CHEM_API bool | hasCoordinates (const AtomContainer &cntnr, std::size_t dim) |
|
CDPL_CHEM_API void | get2DCoordinates (const AtomContainer &cntnr, Math::Vector2DArray &coords, bool append=false) |
|
CDPL_CHEM_API void | set2DCoordinates (AtomContainer &cntnr, const Math::Vector2DArray &coords) |
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CDPL_CHEM_API void | transform2DCoordinates (AtomContainer &cntnr, const Math::Matrix3D &mtx) |
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CDPL_CHEM_API void | get3DCoordinates (const AtomContainer &cntnr, Math::Vector3DArray &coords, const Atom3DCoordinatesFunction &coords_func, bool append=false) |
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CDPL_CHEM_API void | clearConformations (AtomContainer &cntnr) |
|
CDPL_CHEM_API std::size_t | getNumConformations (const AtomContainer &cntnr) |
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CDPL_CHEM_API void | applyConformation (AtomContainer &cntnr, std::size_t conf_idx) |
|
CDPL_CHEM_API void | getConformation (const AtomContainer &cntnr, std::size_t conf_idx, Math::Vector3DArray &coords, bool append=false) |
|
CDPL_CHEM_API void | setConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Vector3DArray &coords) |
|
CDPL_CHEM_API void | addConformation (AtomContainer &cntnr, const Math::Vector3DArray &coords) |
|
CDPL_CHEM_API void | transformConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Matrix4D &mtx) |
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CDPL_CHEM_API void | transformConformations (AtomContainer &cntnr, const Math::Matrix4D &mtx) |
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CDPL_CHEM_API bool | alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms, const Math::Vector3DArray &ref_coords) |
|
CDPL_CHEM_API bool | alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms, const Math::Vector3DArray &ref_coords) |
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CDPL_CHEM_API bool | alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms) |
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CDPL_CHEM_API bool | alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms) |
|
CDPL_CHEM_API std::size_t | getMaxComponentGroupID (const AtomContainer &cntnr) |
|
CDPL_CHEM_API std::size_t | getMaxAtomMappingID (const AtomContainer &cntnr) |
|
CDPL_CHEM_API std::size_t | createAtomTypeMask (const AtomContainer &cntnr, Util::BitSet &mask, unsigned int type, bool reset=true, bool strict=true) |
|
CDPL_CHEM_API void | copyAtomsIf (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false) |
|
CDPL_CHEM_API void | copyAtomsIf (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false) |
|
CDPL_CHEM_API void | copyAtomsIfNot (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false) |
|
CDPL_CHEM_API void | copyAtomsIfNot (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false) |
|
CDPL_CHEM_API bool | calcCenterOfMass (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr) |
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CDPL_CHEM_API bool | calcCentroid (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr) |
|
CDPL_CHEM_API void | calcBoundingBox (const AtomContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func, bool reset=true) |
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CDPL_CHEM_API bool | insideBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func) |
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CDPL_CHEM_API bool | intersectsBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func) |
|
CDPL_CHEM_API const std::string & | getName (const Atom &atom) |
|
CDPL_CHEM_API void | setName (Atom &atom, const std::string &name) |
|
CDPL_CHEM_API void | clearName (Atom &atom) |
|
CDPL_CHEM_API bool | hasName (const Atom &atom) |
|
CDPL_CHEM_API const std::string & | getSymbol (const Atom &atom) |
|
CDPL_CHEM_API void | setSymbol (Atom &atom, const std::string &symbol) |
|
CDPL_CHEM_API void | clearSymbol (Atom &atom) |
|
CDPL_CHEM_API bool | hasSymbol (const Atom &atom) |
|
CDPL_CHEM_API const std::string & | getSymbolForType (const Atom &atom) |
|
CDPL_CHEM_API unsigned int | getType (const Atom &atom) |
|
CDPL_CHEM_API void | setType (Atom &atom, unsigned int type) |
|
CDPL_CHEM_API void | clearType (Atom &atom) |
|
CDPL_CHEM_API bool | hasType (const Atom &atom) |
|
CDPL_CHEM_API unsigned int | getTypeForSymbol (const Atom &atom) |
|
CDPL_CHEM_API unsigned int | getGenericType (const Atom &atom) |
|
CDPL_CHEM_API long | getFormalCharge (const Atom &atom) |
|
CDPL_CHEM_API void | setFormalCharge (Atom &atom, long charge) |
|
CDPL_CHEM_API void | clearFormalCharge (Atom &atom) |
|
CDPL_CHEM_API bool | hasFormalCharge (const Atom &atom) |
|
CDPL_CHEM_API long | calcFormalCharge (const Atom &atom, const MolecularGraph &molgraph) |
|
CDPL_CHEM_API std::size_t | getIsotope (const Atom &atom) |
|
CDPL_CHEM_API void | setIsotope (Atom &atom, std::size_t isotope) |
|
CDPL_CHEM_API void | clearIsotope (Atom &atom) |
|
CDPL_CHEM_API bool | hasIsotope (const Atom &atom) |
|
CDPL_CHEM_API unsigned int | getRadicalType (const Atom &atom) |
|
CDPL_CHEM_API void | setRadicalType (Atom &atom, unsigned int type) |
|
CDPL_CHEM_API void | clearRadicalType (Atom &atom) |
|
CDPL_CHEM_API bool | hasRadicalType (const Atom &atom) |
|
CDPL_CHEM_API unsigned int | getHybridizationState (const Atom &atom) |
|
CDPL_CHEM_API void | setHybridizationState (Atom &atom, unsigned int state) |
|
CDPL_CHEM_API void | clearHybridizationState (Atom &atom) |
|
CDPL_CHEM_API bool | hasHybridizationState (const Atom &atom) |
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CDPL_CHEM_API unsigned int | perceiveHybridizationState (const Atom &atom, const MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | getRingFlag (const Atom &atom) |
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CDPL_CHEM_API void | setRingFlag (Atom &atom, bool in_ring) |
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CDPL_CHEM_API void | clearRingFlag (Atom &atom) |
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CDPL_CHEM_API bool | hasRingFlag (const Atom &atom) |
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CDPL_CHEM_API bool | isInFragmentOfSize (const Atom &atom, const FragmentList &frag_list, std::size_t size) |
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CDPL_CHEM_API std::size_t | getSizeOfSmallestContainingFragment (const Atom &atom, const FragmentList &frag_list) |
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CDPL_CHEM_API std::size_t | getSizeOfLargestContainingFragment (const Atom &atom, const FragmentList &frag_list) |
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CDPL_CHEM_API std::size_t | getNumContainingFragments (const Atom &atom, const FragmentList &frag_list) |
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CDPL_CHEM_API void | getContainingFragments (const Atom &atom, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false) |
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CDPL_CHEM_API bool | getAromaticityFlag (const Atom &atom) |
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CDPL_CHEM_API void | setAromaticityFlag (Atom &atom, bool aromatic) |
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CDPL_CHEM_API void | clearAromaticityFlag (Atom &atom) |
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CDPL_CHEM_API bool | hasAromaticityFlag (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getUnpairedElectronCount (const Atom &atom) |
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CDPL_CHEM_API void | setUnpairedElectronCount (Atom &atom, std::size_t count) |
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CDPL_CHEM_API void | clearUnpairedElectronCount (Atom &atom) |
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CDPL_CHEM_API bool | hasUnpairedElectronCount (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getImplicitHydrogenCount (const Atom &atom) |
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CDPL_CHEM_API void | setImplicitHydrogenCount (Atom &atom, std::size_t count) |
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CDPL_CHEM_API void | clearImplicitHydrogenCount (Atom &atom) |
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CDPL_CHEM_API bool | hasImplicitHydrogenCount (const Atom &atom) |
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CDPL_CHEM_API std::size_t | calcImplicitHydrogenCount (const Atom &atom, const MolecularGraph &molgraph) |
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CDPL_CHEM_API const Math::Vector2D & | get2DCoordinates (const Atom &atom) |
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CDPL_CHEM_API void | set2DCoordinates (Atom &atom, const Math::Vector2D &coords) |
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CDPL_CHEM_API void | clear2DCoordinates (Atom &atom) |
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CDPL_CHEM_API bool | has2DCoordinates (const Atom &atom) |
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CDPL_CHEM_API const Math::Vector3D & | getConformer3DCoordinates (const Atom &atom, std::size_t conf_idx) |
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CDPL_CHEM_API const Math::Vector3DArray::SharedPointer & | get3DCoordinatesArray (const Atom &atom) |
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CDPL_CHEM_API void | set3DCoordinatesArray (Atom &atom, const Math::Vector3DArray::SharedPointer &coords_array) |
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CDPL_CHEM_API void | clear3DCoordinatesArray (Atom &atom) |
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CDPL_CHEM_API bool | has3DCoordinatesArray (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getMorganNumber (const Atom &atom) |
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CDPL_CHEM_API void | setMorganNumber (Atom &atom, std::size_t num) |
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CDPL_CHEM_API void | clearMorganNumber (Atom &atom) |
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CDPL_CHEM_API bool | hasMorganNumber (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getCanonicalNumber (const Atom &atom) |
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CDPL_CHEM_API void | setCanonicalNumber (Atom &atom, std::size_t num) |
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CDPL_CHEM_API void | clearCanonicalNumber (Atom &atom) |
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CDPL_CHEM_API bool | hasCanonicalNumber (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getCIPPriority (const Atom &atom) |
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CDPL_CHEM_API void | setCIPPriority (Atom &atom, std::size_t priority) |
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CDPL_CHEM_API void | clearCIPPriority (Atom &atom) |
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CDPL_CHEM_API bool | hasCIPPriority (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getSymmetryClass (const Atom &atom) |
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CDPL_CHEM_API void | setSymmetryClass (Atom &atom, std::size_t class_id) |
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CDPL_CHEM_API void | clearSymmetryClass (Atom &atom) |
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CDPL_CHEM_API bool | hasSymmetryClass (const Atom &atom) |
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CDPL_CHEM_API unsigned int | getCIPConfiguration (const Atom &atom) |
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CDPL_CHEM_API void | setCIPConfiguration (Atom &atom, unsigned int config) |
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CDPL_CHEM_API void | clearCIPConfiguration (Atom &atom) |
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CDPL_CHEM_API bool | hasCIPConfiguration (const Atom &atom) |
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CDPL_CHEM_API const StereoDescriptor & | getStereoDescriptor (const Atom &atom) |
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CDPL_CHEM_API void | setStereoDescriptor (Atom &atom, const StereoDescriptor &descr) |
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CDPL_CHEM_API void | clearStereoDescriptor (Atom &atom) |
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CDPL_CHEM_API bool | hasStereoDescriptor (const Atom &atom) |
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CDPL_CHEM_API StereoDescriptor | calcStereoDescriptor (const Atom &atom, const MolecularGraph &molgraph, std::size_t dim=1) |
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CDPL_CHEM_API StereoDescriptor | calcStereoDescriptorFromMDLParity (const Atom &atom, const MolecularGraph &molgraph) |
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CDPL_CHEM_API unsigned int | calcConfiguration (const Atom &atom, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords) |
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CDPL_CHEM_API bool | getStereoCenterFlag (const Atom &atom) |
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CDPL_CHEM_API void | setStereoCenterFlag (Atom &atom, bool is_center) |
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CDPL_CHEM_API void | clearStereoCenterFlag (Atom &atom) |
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CDPL_CHEM_API bool | hasStereoCenterFlag (const Atom &atom) |
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CDPL_CHEM_API bool | isStereoCenter (const Atom &atom, const MolecularGraph &molgraph, bool check_asym=true, bool check_inv_n=true, bool check_quart_n=true, bool check_plan_n=true, bool check_amide_n=true, bool check_res_ctrs=true) |
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CDPL_CHEM_API unsigned int | getSybylType (const Atom &atom) |
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CDPL_CHEM_API void | setSybylType (Atom &atom, unsigned int type) |
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CDPL_CHEM_API void | clearSybylType (Atom &atom) |
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CDPL_CHEM_API bool | hasSybylType (const Atom &atom) |
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CDPL_CHEM_API unsigned int | perceiveSybylType (const Atom &atom, const MolecularGraph &molgraph) |
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CDPL_CHEM_API const std::string & | getMOL2Name (const Atom &atom) |
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CDPL_CHEM_API void | setMOL2Name (Atom &atom, const std::string &name) |
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CDPL_CHEM_API void | clearMOL2Name (Atom &atom) |
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CDPL_CHEM_API bool | hasMOL2Name (const Atom &atom) |
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CDPL_CHEM_API double | getMOL2Charge (const Atom &atom) |
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CDPL_CHEM_API void | setMOL2Charge (Atom &atom, double charge) |
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CDPL_CHEM_API void | clearMOL2Charge (Atom &atom) |
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CDPL_CHEM_API bool | hasMOL2Charge (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getMOL2SubstructureID (const Atom &atom) |
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CDPL_CHEM_API void | setMOL2SubstructureID (Atom &atom, std::size_t id) |
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CDPL_CHEM_API void | clearMOL2SubstructureID (Atom &atom) |
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CDPL_CHEM_API bool | hasMOL2SubstructureID (const Atom &atom) |
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CDPL_CHEM_API const std::string & | getMOL2SubstructureName (const Atom &atom) |
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CDPL_CHEM_API void | setMOL2SubstructureName (Atom &atom, const std::string &id) |
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CDPL_CHEM_API void | clearMOL2SubstructureName (Atom &atom) |
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CDPL_CHEM_API bool | hasMOL2SubstructureName (const Atom &atom) |
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CDPL_CHEM_API const std::string & | getMOL2SubstructureSubtype (const Atom &atom) |
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CDPL_CHEM_API void | setMOL2SubstructureSubtype (Atom &atom, const std::string &subtype) |
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CDPL_CHEM_API void | clearMOL2SubstructureSubtype (Atom &atom) |
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CDPL_CHEM_API bool | hasMOL2SubstructureSubtype (const Atom &atom) |
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CDPL_CHEM_API const std::string & | getMOL2SubstructureChain (const Atom &atom) |
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CDPL_CHEM_API void | setMOL2SubstructureChain (Atom &atom, const std::string &chain) |
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CDPL_CHEM_API void | clearMOL2SubstructureChain (Atom &atom) |
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CDPL_CHEM_API bool | hasMOL2SubstructureChain (const Atom &atom) |
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CDPL_CHEM_API unsigned int | getMDLParity (const Atom &atom) |
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CDPL_CHEM_API void | setMDLParity (Atom &atom, unsigned int parity) |
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CDPL_CHEM_API void | clearMDLParity (Atom &atom) |
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CDPL_CHEM_API bool | hasMDLParity (const Atom &atom) |
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CDPL_CHEM_API unsigned int | calcMDLParity (const Atom &atom, const MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | getMDLStereoCareFlag (const Atom &atom) |
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CDPL_CHEM_API void | setMDLStereoCareFlag (Atom &atom, bool flag) |
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CDPL_CHEM_API void | clearMDLStereoCareFlag (Atom &atom) |
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CDPL_CHEM_API bool | hasMDLStereoCareFlag (const Atom &atom) |
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CDPL_CHEM_API unsigned int | getReactionCenterStatus (const Atom &atom) |
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CDPL_CHEM_API void | setReactionCenterStatus (Atom &atom, unsigned int status) |
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CDPL_CHEM_API void | clearReactionCenterStatus (Atom &atom) |
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CDPL_CHEM_API bool | hasReactionCenterStatus (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getAtomMappingID (const Atom &atom) |
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CDPL_CHEM_API void | setAtomMappingID (Atom &atom, std::size_t id) |
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CDPL_CHEM_API void | clearAtomMappingID (Atom &atom) |
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CDPL_CHEM_API bool | hasAtomMappingID (const Atom &atom) |
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CDPL_CHEM_API std::size_t | getComponentGroupID (const Atom &atom) |
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CDPL_CHEM_API void | setComponentGroupID (Atom &atom, std::size_t id) |
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CDPL_CHEM_API void | clearComponentGroupID (Atom &atom) |
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CDPL_CHEM_API bool | hasComponentGroupID (const Atom &atom) |
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CDPL_CHEM_API const MatchConstraintList::SharedPointer & | getMatchConstraints (const Atom &atom) |
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CDPL_CHEM_API void | setMatchConstraints (Atom &atom, const MatchConstraintList::SharedPointer &constr) |
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CDPL_CHEM_API void | clearMatchConstraints (Atom &atom) |
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CDPL_CHEM_API bool | hasMatchConstraints (const Atom &atom) |
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CDPL_CHEM_API const MatchExpression< Atom, MolecularGraph >::SharedPointer & | getMatchExpression (const Atom &atom) |
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CDPL_CHEM_API void | setMatchExpression (Atom &atom, const MatchExpression< Atom, MolecularGraph >::SharedPointer &expr) |
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CDPL_CHEM_API void | clearMatchExpression (Atom &atom) |
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CDPL_CHEM_API bool | hasMatchExpression (const Atom &atom) |
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CDPL_CHEM_API MatchExpression< Atom, MolecularGraph >::SharedPointer | generateMatchExpression (const Atom &atom, const MolecularGraph &molgraph) |
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CDPL_CHEM_API const std::string & | getMatchExpressionString (const Atom &atom) |
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CDPL_CHEM_API void | setMatchExpressionString (Atom &atom, const std::string &expr_str) |
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CDPL_CHEM_API void | clearMatchExpressionString (Atom &atom) |
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CDPL_CHEM_API bool | hasMatchExpressionString (const Atom &atom) |
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CDPL_CHEM_API void | generateMatchExpressionString (const Atom &atom, const MolecularGraph &molgraph, std::string &expr_str) |
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CDPL_CHEM_API void | markReachableAtoms (const Atom &atom, const MolecularGraph &molgraph, Util::BitSet &atom_mask, bool reset=true) |
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CDPL_CHEM_API std::size_t | getTopologicalDistance (const Atom &atom1, const Atom &atom2, const MolecularGraph &molgraph) |
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CDPL_CHEM_API std::size_t | getEnvironment (const Atom &atom, const MolecularGraph &molgraph, std::size_t max_dist, Fragment &env, bool append=false) |
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template<typename AtomType , typename OutputIterator > |
std::size_t | getConnectedAtoms (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0) |
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template<typename AtomType , typename OutputIterator > |
std::size_t | getIncidentBonds (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0) |
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template<typename AtomType , typename AtomOutputIterator , typename BondOutputIterator > |
std::size_t | getConnectedAtomsAndBonds (AtomType &atom, const MolecularGraph &molgraph, AtomOutputIterator ao_it, BondOutputIterator bo_it, AtomType *excl_atom=0) |
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CDPL_CHEM_API std::size_t | getOrder (const Bond &bond) |
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CDPL_CHEM_API void | setOrder (Bond &bond, std::size_t order) |
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CDPL_CHEM_API void | clearOrder (Bond &bond) |
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CDPL_CHEM_API bool | hasOrder (const Bond &bond) |
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CDPL_CHEM_API bool | getRingFlag (const Bond &bond) |
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CDPL_CHEM_API void | setRingFlag (Bond &bond, bool in_ring) |
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CDPL_CHEM_API void | clearRingFlag (Bond &bond) |
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CDPL_CHEM_API bool | hasRingFlag (const Bond &bond) |
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CDPL_CHEM_API bool | isInFragmentOfSize (const Bond &bond, const FragmentList &frag_list, std::size_t size) |
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CDPL_CHEM_API std::size_t | getSizeOfSmallestContainingFragment (const Bond &bond, const FragmentList &frag_list) |
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CDPL_CHEM_API std::size_t | getSizeOfLargestContainingFragment (const Bond &bond, const FragmentList &frag_list) |
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CDPL_CHEM_API std::size_t | getNumContainingFragments (const Bond &bond, const FragmentList &frag_list) |
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CDPL_CHEM_API void | getContainingFragments (const Bond &bond, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false) |
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CDPL_CHEM_API bool | getAromaticityFlag (const Bond &bond) |
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CDPL_CHEM_API void | setAromaticityFlag (Bond &bond, bool aromatic) |
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CDPL_CHEM_API void | clearAromaticityFlag (Bond &bond) |
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CDPL_CHEM_API bool | hasAromaticityFlag (const Bond &bond) |
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CDPL_CHEM_API unsigned int | get2DStereoFlag (const Bond &bond) |
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CDPL_CHEM_API void | set2DStereoFlag (Bond &bond, unsigned int flag) |
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CDPL_CHEM_API void | clear2DStereoFlag (Bond &bond) |
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CDPL_CHEM_API bool | has2DStereoFlag (const Bond &bond) |
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CDPL_CHEM_API unsigned int | getCIPConfiguration (const Bond &bond) |
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CDPL_CHEM_API void | setCIPConfiguration (Bond &bond, unsigned int config) |
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CDPL_CHEM_API void | clearCIPConfiguration (Bond &bond) |
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CDPL_CHEM_API bool | hasCIPConfiguration (const Bond &bond) |
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CDPL_CHEM_API const StereoDescriptor & | getStereoDescriptor (const Bond &bond) |
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CDPL_CHEM_API void | setStereoDescriptor (Bond &bond, const StereoDescriptor &descr) |
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CDPL_CHEM_API void | clearStereoDescriptor (Bond &bond) |
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CDPL_CHEM_API bool | hasStereoDescriptor (const Bond &bond) |
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CDPL_CHEM_API StereoDescriptor | calcStereoDescriptor (const Bond &bond, const MolecularGraph &molgraph, std::size_t dim=1) |
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CDPL_CHEM_API unsigned int | calcConfiguration (const Bond &bond, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords) |
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CDPL_CHEM_API bool | getStereoCenterFlag (const Bond &bond) |
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CDPL_CHEM_API void | setStereoCenterFlag (Bond &bond, bool is_center) |
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CDPL_CHEM_API void | clearStereoCenterFlag (Bond &bond) |
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CDPL_CHEM_API bool | hasStereoCenterFlag (const Bond &bond) |
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CDPL_CHEM_API bool | isStereoCenter (const Bond &bond, const MolecularGraph &molgraph, bool check_asym=true, bool check_term_n=true, bool check_order=true, std::size_t min_ring_size=8) |
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CDPL_CHEM_API unsigned int | getDirection (const Bond &bond) |
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CDPL_CHEM_API void | setDirection (Bond &bond, unsigned int dir) |
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CDPL_CHEM_API void | clearDirection (Bond &bond) |
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CDPL_CHEM_API bool | hasDirection (const Bond &bond) |
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CDPL_CHEM_API unsigned int | getReactionCenterStatus (const Bond &bond) |
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CDPL_CHEM_API void | setReactionCenterStatus (Bond &bond, unsigned int status) |
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CDPL_CHEM_API void | clearReactionCenterStatus (Bond &bond) |
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CDPL_CHEM_API bool | hasReactionCenterStatus (const Bond &bond) |
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CDPL_CHEM_API const MatchConstraintList::SharedPointer & | getMatchConstraints (const Bond &bond) |
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CDPL_CHEM_API void | setMatchConstraints (Bond &bond, const MatchConstraintList::SharedPointer &constr) |
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CDPL_CHEM_API void | clearMatchConstraints (Bond &bond) |
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CDPL_CHEM_API bool | hasMatchConstraints (const Bond &bond) |
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CDPL_CHEM_API const MatchExpression< Bond, MolecularGraph >::SharedPointer & | getMatchExpression (const Bond &bond) |
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CDPL_CHEM_API void | setMatchExpression (Bond &bond, const MatchExpression< Bond, MolecularGraph >::SharedPointer &expr) |
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CDPL_CHEM_API void | clearMatchExpression (Bond &bond) |
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CDPL_CHEM_API bool | hasMatchExpression (const Bond &bond) |
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CDPL_CHEM_API MatchExpression< Bond, MolecularGraph >::SharedPointer | generateMatchExpression (const Bond &bond, const MolecularGraph &molgraph) |
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CDPL_CHEM_API const std::string & | getMatchExpressionString (const Bond &bond) |
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CDPL_CHEM_API void | setMatchExpressionString (Bond &bond, const std::string &expr_str) |
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CDPL_CHEM_API void | clearMatchExpressionString (Bond &bond) |
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CDPL_CHEM_API bool | hasMatchExpressionString (const Bond &bond) |
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CDPL_CHEM_API void | generateMatchExpressionString (const Bond &bond, const MolecularGraph &molgraph, std::string &str) |
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CDPL_CHEM_API unsigned int | getSybylType (const Bond &bond) |
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CDPL_CHEM_API void | setSybylType (Bond &bond, unsigned int type) |
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CDPL_CHEM_API void | clearSybylType (Bond &bond) |
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CDPL_CHEM_API bool | hasSybylType (const Bond &bond) |
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CDPL_CHEM_API unsigned int | perceiveSybylType (const Bond &bond, const MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | getOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr, bool deplete) |
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CDPL_CHEM_API bool | hasOrdinaryHydrogenDepleteParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearOrdinaryHydrogenDepleteParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API std::size_t | getCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr, std::size_t dim) |
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CDPL_CHEM_API bool | hasCoordinatesDimensionParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearCoordinatesDimensionParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr, bool strict) |
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CDPL_CHEM_API bool | hasStrictErrorCheckingParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearStrictErrorCheckingParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API const std::string & | getRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setRecordSeparatorParameter (Base::ControlParameterContainer &cntnr, const std::string &sep) |
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CDPL_CHEM_API bool | hasRecordSeparatorParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearRecordSeparatorParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr, bool fix) |
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CDPL_CHEM_API bool | hasBondMemberSwapStereoFixParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearBondMemberSwapStereoFixParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setCheckLineLengthParameter (Base::ControlParameterContainer &cntnr, bool check) |
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CDPL_CHEM_API bool | hasCheckLineLengthParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearCheckLineLengthParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API unsigned int | getMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version) |
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CDPL_CHEM_API bool | hasMDLCTABVersionParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLCTABVersionParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr, bool ignore) |
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CDPL_CHEM_API bool | hasMDLIgnoreParityParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLIgnoreParityParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr, bool update) |
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CDPL_CHEM_API bool | hasMDLUpdateTimestampParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLUpdateTimestampParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr, bool trim) |
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CDPL_CHEM_API bool | hasMDLTrimStringsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLTrimStringsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr, bool trim) |
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CDPL_CHEM_API bool | hasMDLTrimLinesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLTrimLinesParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr, bool trunc) |
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CDPL_CHEM_API bool | hasMDLTruncateStringsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLTruncateStringsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr, bool trunc) |
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CDPL_CHEM_API bool | hasMDLTruncateLinesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLTruncateLinesParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API unsigned int | getMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr, unsigned int version) |
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CDPL_CHEM_API bool | hasMDLRXNFileVersionParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLRXNFileVersionParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr, bool output) |
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CDPL_CHEM_API bool | hasMDLOutputConfEnergyToEnergyFieldParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLOutputConfEnergyToEnergyFieldParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr, bool output) |
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CDPL_CHEM_API bool | hasMDLOutputConfEnergyAsSDEntryParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLOutputConfEnergyAsSDEntryParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API const std::string & | getMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr, const std::string &tag) |
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CDPL_CHEM_API bool | hasMDLConfEnergySDTagParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMDLConfEnergySDTagParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr, bool separate) |
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CDPL_CHEM_API bool | hasJMESeparateComponentsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearJMESeparateComponentsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API const std::string & | getSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr, const std::string &format) |
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CDPL_CHEM_API bool | hasSMILESRecordFormatParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESRecordFormatParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteCanonicalFormParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteCanonicalFormParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteCanonicalFormParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteCanonicalFormParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteKekuleFormParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteKekuleFormParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteKekuleFormParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteKekuleFormParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteAtomStereoParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteAtomStereoParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteAtomStereoParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteAtomStereoParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteBondStereoParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteBondStereoParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteBondStereoParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteBondStereoParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteRingBondStereoParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteRingBondStereoParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteRingBondStereoParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteRingBondStereoParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API std::size_t | getSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr, std::size_t min_size) |
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CDPL_CHEM_API bool | hasSMILESMinStereoBondRingSizeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESMinStereoBondRingSizeParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteIsotopeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteIsotopeParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteIsotopeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteIsotopeParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESMolWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESMolWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESMolWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESMolWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESRxnWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESRxnWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESRxnWriteAtomMappingIDParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESRxnWriteAtomMappingIDParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteSingleBondsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteSingleBondsParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteSingleBondsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteSingleBondsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESWriteAromaticBondsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESWriteAromaticBondsParameter (Base::ControlParameterContainer &cntnr, bool write) |
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CDPL_CHEM_API bool | hasSMILESWriteAromaticBondsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESWriteAromaticBondsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr, bool no_subset) |
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CDPL_CHEM_API bool | hasSMILESNoOrganicSubsetParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearSMILESNoOrganicSubsetParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API const std::string & | getINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts) |
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CDPL_CHEM_API bool | hasINCHIInputOptionsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearINCHIInputOptionsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API const std::string & | getINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr, const std::string &opts) |
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CDPL_CHEM_API bool | hasINCHIOutputOptionsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearINCHIOutputOptionsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMultiConfImportParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMultiConfImportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf) |
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CDPL_CHEM_API bool | hasMultiConfImportParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMultiConfImportParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMultiConfExportParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMultiConfExportParameter (Base::ControlParameterContainer &cntnr, bool multi_conf) |
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CDPL_CHEM_API bool | hasMultiConfExportParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMultiConfExportParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr, bool output) |
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CDPL_CHEM_API bool | hasOutputConfEnergyAsCommentParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearOutputConfEnergyAsCommentParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API const std::string & | getConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr, const std::string &pattern) |
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CDPL_CHEM_API bool | hasConfIndexNameSuffixPatternParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearConfIndexNameSuffixPatternParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API const MultiConfMoleculeInputProcessor::SharedPointer & | getMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr, const MultiConfMoleculeInputProcessor::SharedPointer &proc) |
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CDPL_CHEM_API bool | hasMultiConfInputProcessorParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMultiConfInputProcessorParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr, bool single_prec) |
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CDPL_CHEM_API bool | hasCDFWriteSinglePrecisionFloatsParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearCDFWriteSinglePrecisionFloatsParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr, bool enable) |
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CDPL_CHEM_API bool | hasMOL2EnableExtendedAtomTypesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMOL2EnableExtendedAtomTypesParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr, bool enable) |
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CDPL_CHEM_API bool | hasMOL2EnableAromaticBondTypesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMOL2EnableAromaticBondTypesParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc) |
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CDPL_CHEM_API bool | hasMOL2CalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMOL2CalcFormalChargesParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API unsigned int | getMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type) |
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CDPL_CHEM_API bool | hasMOL2ChargeTypeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMOL2ChargeTypeParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API unsigned int | getMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr, unsigned int type) |
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CDPL_CHEM_API bool | hasMOL2MoleculeTypeParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMOL2MoleculeTypeParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr, bool output) |
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CDPL_CHEM_API bool | hasMOL2OutputSubstructuresParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearMOL2OutputSubstructuresParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr, bool is_name) |
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CDPL_CHEM_API bool | hasXYZCommentIsNameParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearXYZCommentIsNameParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr, bool perceive) |
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CDPL_CHEM_API bool | hasXYZPerceiveConnectivityParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearXYZPerceiveConnectivityParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr, bool perceive) |
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CDPL_CHEM_API bool | hasXYZPerceiveBondOrdersParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearXYZPerceiveBondOrdersParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API bool | getXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | setXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr, bool calc) |
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CDPL_CHEM_API bool | hasXYZCalcFormalChargesParameter (const Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | clearXYZCalcFormalChargesParameter (Base::ControlParameterContainer &cntnr) |
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CDPL_CHEM_API void | calcGeometricalDistanceMatrix (const Entity3DContainer &cntnr, Math::DMatrix &mtx) |
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CDPL_CHEM_API void | get3DCoordinates (const Entity3DContainer &cntnr, Math::Vector3DArray &coords, bool append=false) |
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CDPL_CHEM_API void | set3DCoordinates (Entity3DContainer &cntnr, const Math::Vector3DArray &coords) |
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CDPL_CHEM_API void | transform3DCoordinates (Entity3DContainer &cntnr, const Math::Matrix4D &mtx) |
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CDPL_CHEM_API bool | align3DCoordinates (Entity3DContainer &cntnr, const Entity3DContainer &ref_entities, const Math::Vector3DArray &ref_coords) |
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CDPL_CHEM_API bool | calcCentroid (const Entity3DContainer &cntnr, Math::Vector3D &ctr) |
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CDPL_CHEM_API void | calcBoundingBox (const Entity3DContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, bool reset=true) |
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CDPL_CHEM_API bool | insideBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max) |
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CDPL_CHEM_API bool | intersectsBoundingBox (const Entity3DContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max) |
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CDPL_CHEM_API const Math::Vector3D & | get3DCoordinates (const Entity3D &entity) |
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CDPL_CHEM_API void | set3DCoordinates (Entity3D &entity, const Math::Vector3D &coords) |
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CDPL_CHEM_API void | clear3DCoordinates (Entity3D &entity) |
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CDPL_CHEM_API bool | has3DCoordinates (const Entity3D &entity) |
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CDPL_CHEM_API bool | makeHydrogenDeplete (Fragment &frag) |
| Removes all explicit hydrogen atoms from the fragment frag. More...
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CDPL_CHEM_API bool | makeOrdinaryHydrogenDeplete (Fragment &frag, unsigned int flags) |
| Removes all explicit ordinary hydrogen atoms from the fragment frag. More...
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CDPL_CHEM_API void | removeAtomsIf (Fragment &frag, const AtomPredicate &pred) |
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CDPL_CHEM_API void | removeAtomsIfNot (Fragment &frag, const AtomPredicate &pred) |
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CDPL_CHEM_API const std::string & | getName (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setName (MolecularGraph &molgraph, const std::string &name) |
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CDPL_CHEM_API void | clearName (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasName (const MolecularGraph &molgraph) |
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CDPL_CHEM_API std::time_t | getTimestamp (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setTimestamp (MolecularGraph &molgraph, std::time_t time) |
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CDPL_CHEM_API void | clearTimestamp (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasTimestamp (const MolecularGraph &molgraph) |
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CDPL_CHEM_API const std::string & | getComment (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setComment (MolecularGraph &molgraph, const std::string &comment) |
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CDPL_CHEM_API void | clearComment (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasComment (const MolecularGraph &molgraph) |
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CDPL_CHEM_API const MatchConstraintList::SharedPointer & | getMatchConstraints (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr) |
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CDPL_CHEM_API void | clearMatchConstraints (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMatchConstraints (const MolecularGraph &molgraph) |
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CDPL_CHEM_API const MatchExpression< MolecularGraph >::SharedPointer & | getMatchExpression (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMatchExpression (MolecularGraph &molgraph, const MatchExpression< MolecularGraph >::SharedPointer &expr) |
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CDPL_CHEM_API void | clearMatchExpression (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMatchExpression (const MolecularGraph &molgraph) |
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CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer | generateMatchExpression (const MolecularGraph &molgraph) |
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CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer | generateMatchExpression (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API const FragmentList::SharedPointer & | getRings (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setRings (MolecularGraph &molgraph, const FragmentList::SharedPointer &rings) |
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CDPL_CHEM_API void | clearRings (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasRings (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveRings (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveRings (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API const FragmentList::SharedPointer & | getSSSR (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setSSSR (MolecularGraph &molgraph, const FragmentList::SharedPointer &sssr) |
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CDPL_CHEM_API void | clearSSSR (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasSSSR (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveSSSR (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveSSSR (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API FragmentList::SharedPointer | extractSSSRSubset (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | extractSSSRSubset (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite) |
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CDPL_CHEM_API const Fragment::SharedPointer & | getCyclicSubstructure (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setCyclicSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct) |
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CDPL_CHEM_API void | clearCyclicSubstructure (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasCyclicSubstructure (const MolecularGraph &molgraph) |
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CDPL_CHEM_API Fragment::SharedPointer | perceiveCyclicSubstructure (const MolecularGraph &molgraph) |
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CDPL_CHEM_API Fragment::SharedPointer | perceiveCyclicSubstructure (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API const FragmentList::SharedPointer & | getComponents (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setComponents (MolecularGraph &molgraph, const FragmentList::SharedPointer &comps) |
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CDPL_CHEM_API void | clearComponents (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasComponents (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveComponents (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveComponents (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API const FragmentList::SharedPointer & | getComponentGroups (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setComponentGroups (MolecularGraph &molgraph, const FragmentList::SharedPointer &comp_groups) |
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CDPL_CHEM_API void | clearComponentGroups (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasComponentGroups (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveComponentGroups (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveComponentGroups (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API std::size_t | getConformationIndex (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setConformationIndex (MolecularGraph &molgraph, std::size_t index) |
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CDPL_CHEM_API void | clearConformationIndex (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasConformationIndex (const MolecularGraph &molgraph) |
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CDPL_CHEM_API const Util::DArray::SharedPointer & | getConformerEnergies (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setConformerEnergies (MolecularGraph &molgraph, const Util::DArray::SharedPointer &energies) |
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CDPL_CHEM_API void | clearConformerEnergies (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasConformerEnergies (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setConformation (MolecularGraph &molgraph, std::size_t conf_idx, const Math::Vector3DArray &coords, double energy) |
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CDPL_CHEM_API void | addConformation (MolecularGraph &molgraph, const Math::Vector3DArray &coords, double energy) |
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CDPL_CHEM_API double | getConformationEnergy (const MolecularGraph &molgraph, std::size_t conf_idx) |
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CDPL_CHEM_API std::uint64_t | getHashCode (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setHashCode (MolecularGraph &molgraph, std::uint64_t hash_code) |
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CDPL_CHEM_API void | clearHashCode (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasHashCode (const MolecularGraph &molgraph) |
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CDPL_CHEM_API std::uint64_t | calcHashCode (const MolecularGraph &molgraph, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool ord_h_deplete=true) |
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CDPL_CHEM_API void | extractReactionCenter (const MolecularGraph &molgraph, Fragment &rxn_center) |
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CDPL_CHEM_API double | getStoichiometricNumber (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setStoichiometricNumber (MolecularGraph &molgraph, double num) |
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CDPL_CHEM_API void | clearStoichiometricNumber (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasStoichiometricNumber (const MolecularGraph &molgraph) |
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CDPL_CHEM_API const std::string & | getMDLUserInitials (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLUserInitials (MolecularGraph &molgraph, const std::string &initials) |
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CDPL_CHEM_API void | clearMDLUserInitials (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLUserInitials (const MolecularGraph &molgraph) |
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CDPL_CHEM_API const std::string & | getMDLProgramName (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLProgramName (MolecularGraph &molgraph, const std::string &name) |
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CDPL_CHEM_API void | clearMDLProgramName (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLProgramName (const MolecularGraph &molgraph) |
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CDPL_CHEM_API std::size_t | getMDLRegistryNumber (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLRegistryNumber (MolecularGraph &molgraph, std::size_t reg_no) |
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CDPL_CHEM_API void | clearMDLRegistryNumber (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLRegistryNumber (const MolecularGraph &molgraph) |
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CDPL_CHEM_API unsigned int | getMDLCTABVersion (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLCTABVersion (MolecularGraph &molgraph, unsigned int version) |
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CDPL_CHEM_API void | clearMDLCTABVersion (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLCTABVersion (const MolecularGraph &molgraph) |
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CDPL_CHEM_API const StringDataBlock::SharedPointer & | getStructureData (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setStructureData (MolecularGraph &molgraph, const StringDataBlock::SharedPointer &data) |
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CDPL_CHEM_API void | clearStructureData (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasStructureData (const MolecularGraph &molgraph) |
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CDPL_CHEM_API std::size_t | getMDLDimensionality (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLDimensionality (MolecularGraph &molgraph, std::size_t dim) |
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CDPL_CHEM_API void | clearMDLDimensionality (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLDimensionality (const MolecularGraph &molgraph) |
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CDPL_CHEM_API long | getMDLScalingFactor1 (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLScalingFactor1 (MolecularGraph &molgraph, long factor) |
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CDPL_CHEM_API void | clearMDLScalingFactor1 (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLScalingFactor1 (const MolecularGraph &molgraph) |
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CDPL_CHEM_API double | getMDLScalingFactor2 (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLScalingFactor2 (MolecularGraph &molgraph, double factor) |
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CDPL_CHEM_API void | clearMDLScalingFactor2 (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLScalingFactor2 (const MolecularGraph &molgraph) |
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CDPL_CHEM_API double | getMDLEnergy (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLEnergy (MolecularGraph &molgraph, double energy) |
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CDPL_CHEM_API void | clearMDLEnergy (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLEnergy (const MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | getMDLChiralFlag (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMDLChiralFlag (MolecularGraph &molgraph, bool flag) |
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CDPL_CHEM_API void | clearMDLChiralFlag (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMDLChiralFlag (const MolecularGraph &molgraph) |
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CDPL_CHEM_API unsigned int | getMOL2MoleculeType (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMOL2MoleculeType (MolecularGraph &molgraph, unsigned int type) |
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CDPL_CHEM_API void | clearMOL2MoleculeType (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMOL2MoleculeType (const MolecularGraph &molgraph) |
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CDPL_CHEM_API unsigned int | getMOL2ChargeType (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setMOL2ChargeType (MolecularGraph &molgraph, unsigned int type) |
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CDPL_CHEM_API void | clearMOL2ChargeType (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasMOL2ChargeType (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | generateAdjacencyMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
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CDPL_CHEM_API void | generateIncidenceMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
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CDPL_CHEM_API void | generateBondMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
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CDPL_CHEM_API void | generateBondElectronMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
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CDPL_CHEM_API void | generateBondAtomTypeMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
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CDPL_CHEM_API const Math::ULMatrix::SharedPointer & | getTopologicalDistanceMatrix (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setTopologicalDistanceMatrix (MolecularGraph &molgraph, const Math::ULMatrix::SharedPointer &mtx) |
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CDPL_CHEM_API void | clearTopologicalDistanceMatrix (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasTopologicalDistanceMatrix (const MolecularGraph &molgraph) |
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CDPL_CHEM_API Math::ULMatrix::SharedPointer | calcTopologicalDistanceMatrix (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcTopologicalDistanceMatrix (const MolecularGraph &molgraph, Math::ULMatrix &mtx) |
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CDPL_CHEM_API Math::ULMatrix::SharedPointer | extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite) |
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CDPL_CHEM_API void | extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph, Math::ULMatrix &mtx) |
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CDPL_CHEM_API const Math::DMatrix::SharedPointer & | getGeometricalDistanceMatrix (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setGeometricalDistanceMatrix (MolecularGraph &molgraph, const Math::DMatrix::SharedPointer &mtx) |
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CDPL_CHEM_API void | clearGeometricalDistanceMatrix (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasGeometricalDistanceMatrix (const MolecularGraph &molgraph) |
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CDPL_CHEM_API Math::DMatrix::SharedPointer | calcGeometricalDistanceMatrix (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API const Fragment::SharedPointer & | getAromaticSubstructure (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setAromaticSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct) |
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CDPL_CHEM_API void | clearAromaticSubstructure (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasAromaticSubstructure (const MolecularGraph &molgraph) |
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CDPL_CHEM_API Fragment::SharedPointer | perceiveAromaticSubstructure (const MolecularGraph &molgraph) |
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CDPL_CHEM_API Fragment::SharedPointer | perceiveAromaticSubstructure (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API const ElectronSystemList::SharedPointer & | getPiElectronSystems (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | setPiElectronSystems (MolecularGraph &molgraph, const ElectronSystemList::SharedPointer &pi_systems) |
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CDPL_CHEM_API void | clearPiElectronSystems (MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | hasPiElectronSystems (const MolecularGraph &molgraph) |
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CDPL_CHEM_API ElectronSystemList::SharedPointer | perceivePiElectronSystems (const MolecularGraph &molgraph) |
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CDPL_CHEM_API ElectronSystemList::SharedPointer | perceivePiElectronSystems (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API bool | generateSMILES (const MolecularGraph &molgraph, std::string &smiles, bool canonical=false, bool ord_h_deplete=true, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT) |
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CDPL_CHEM_API int | generateINCHI (const MolecularGraph &molgraph, std::string &inchi, const std::string &options=ControlParameterDefault::INCHI_OUTPUT_OPTIONS, std::size_t dim=0) |
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CDPL_CHEM_API int | generateINCHIKey (const MolecularGraph &molgraph, std::string &inchi_key) |
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CDPL_CHEM_API void | canonicalize (MolecularGraph &molgraph, const AtomCompareFunction &func, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false) |
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CDPL_CHEM_API void | canonicalize (MolecularGraph &molgraph, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false) |
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CDPL_CHEM_API void | calc2DCoordinates (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcHydrogen3DCoordinates (MolecularGraph &molgraph, bool undef_only=true) |
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CDPL_CHEM_API void | calcBond2DStereoFlags (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcCIPPriorities (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | perceiveSymmetryClasses (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool inc_impl_h=true) |
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CDPL_CHEM_API void | calcCanonicalNumbering (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT) |
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CDPL_CHEM_API void | calcMorganNumbering (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcImplicitHydrogenCounts (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcFormalCharges (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | perceiveHybridizationStates (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | perceiveBondOrders (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | kekulizeBonds (MolecularGraph &molgraph) |
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CDPL_CHEM_API void | perceiveAtomStereoCenters (MolecularGraph &molgraph, bool overwrite, bool check_asym=true, bool check_inv_n=true, bool check_quart_n=true, bool check_plan_n=true, bool check_amide_n=true, bool check_res_ctrs=true) |
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CDPL_CHEM_API void | perceiveBondStereoCenters (MolecularGraph &molgraph, bool overwrite, bool check_asym=true, bool check_term_n=true, bool check_order=true, std::size_t min_ring_size=8) |
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CDPL_CHEM_API void | calcMDLParities (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcAtomStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true) |
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CDPL_CHEM_API void | calcAtomStereoDescriptorsFromMDLParities (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcBondStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true) |
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CDPL_CHEM_API void | calcAtomCIPConfigurations (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | calcBondCIPConfigurations (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | setAtomMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite) |
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CDPL_CHEM_API void | setBondMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite) |
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CDPL_CHEM_API void | generateMatchExpressions (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | generateMatchExpressionStrings (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | initSubstructureSearchQuery (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | initSubstructureSearchTarget (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | setAromaticityFlags (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | setRingFlags (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | setAtomTypesFromSymbols (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | setAtomSymbolsFromTypes (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API void | perceiveSybylAtomTypes (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API FragmentList::SharedPointer | getAromaticRings (const MolecularGraph &molgraph) |
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CDPL_CHEM_API FragmentList::SharedPointer | getAromaticSSSRSubset (const MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | containsMolecularGraph (const MolecularGraph &molgraph, const MolecularGraph &sub_molgraph, bool atoms=true, bool bonds=true) |
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CDPL_CHEM_API void | getContainedFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true) |
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CDPL_CHEM_API void | getContainingFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true) |
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CDPL_CHEM_API void | translateFragment (const MolecularGraph &src_molgraph, const Fragment &src_frag, const MolecularGraph &tgt_molgraph, Fragment &tgt_frag, bool append=false) |
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CDPL_CHEM_API void | translateFragments (const MolecularGraph &src_molgraph, const FragmentList &src_frag_list, const MolecularGraph &tgt_molgraph, FragmentList &tgt_frag_list, bool append=false) |
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CDPL_CHEM_API void | splitIntoFragments (const MolecularGraph &molgraph, FragmentList &frag_list, const Util::BitSet &split_bond_mask, bool append=false) |
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CDPL_CHEM_API std::size_t | getCompleteBondCount (const MolecularGraph &molgraph) |
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CDPL_CHEM_API void | calcBasicProperties (MolecularGraph &molgraph, bool overwrite) |
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CDPL_CHEM_API bool | makeHydrogenDeplete (Molecule &mol, bool corr_impl_h_count=true) |
| Removes all explicit hydrogen atoms from the molecule mol. More...
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CDPL_CHEM_API bool | makeOrdinaryHydrogenDeplete (Molecule &mol, unsigned int flags, bool corr_impl_h_count=true) |
| Removes all explicit ordinary hydrogen atoms from the molecule mol. More...
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CDPL_CHEM_API bool | makeHydrogenComplete (Molecule &mol, bool corr_impl_h_count=true) |
| Converts all implicit hydrogens of the molecule mol to explicit hydrogen atoms. More...
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CDPL_CHEM_API void | connectAtoms (Molecule &mol, double dist_tol=0.3, std::size_t atom_idx_offs=0) |
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CDPL_CHEM_API void | connectAtoms (Molecule &mol, const Atom3DCoordinatesFunction &coords_func, double dist_tol=0.3, std::size_t atom_idx_offs=0) |
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CDPL_CHEM_API void | removeAtomsIf (Molecule &mol, const AtomPredicate &pred) |
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CDPL_CHEM_API void | removeAtomsIfNot (Molecule &mol, const AtomPredicate &pred) |
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CDPL_CHEM_API const std::string & | getName (const Reaction &rxn) |
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CDPL_CHEM_API void | setName (Reaction &rxn, const std::string &name) |
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CDPL_CHEM_API void | clearName (Reaction &rxn) |
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CDPL_CHEM_API bool | hasName (const Reaction &rxn) |
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CDPL_CHEM_API std::time_t | getTimestamp (const Reaction &rxn) |
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CDPL_CHEM_API void | setTimestamp (Reaction &rxn, std::time_t time) |
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CDPL_CHEM_API void | clearTimestamp (Reaction &rxn) |
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CDPL_CHEM_API bool | hasTimestamp (const Reaction &rxn) |
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CDPL_CHEM_API const std::string & | getComment (const Reaction &rxn) |
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CDPL_CHEM_API void | setComment (Reaction &rxn, const std::string &comment) |
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CDPL_CHEM_API void | clearComment (Reaction &rxn) |
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CDPL_CHEM_API bool | hasComment (const Reaction &rxn) |
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CDPL_CHEM_API const MatchExpression< Reaction >::SharedPointer & | getMatchExpression (const Reaction &rxn) |
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CDPL_CHEM_API void | setMatchExpression (Reaction &rxn, const MatchExpression< Reaction >::SharedPointer &expr) |
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CDPL_CHEM_API void | clearMatchExpression (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMatchExpression (const Reaction &rxn) |
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CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer | generateMatchExpression (const Reaction &rxn) |
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CDPL_CHEM_API MatchExpression< Reaction >::SharedPointer | generateMatchExpression (Reaction &rxn, bool overwrite) |
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CDPL_CHEM_API const MatchConstraintList::SharedPointer & | getMatchConstraints (const Reaction &rxn) |
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CDPL_CHEM_API void | setMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr) |
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CDPL_CHEM_API void | clearMatchConstraints (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMatchConstraints (const Reaction &rxn) |
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CDPL_CHEM_API const FragmentList::SharedPointer & | getComponentGroups (const Reaction &rxn) |
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CDPL_CHEM_API void | setComponentGroups (Reaction &rxn, const FragmentList::SharedPointer &comp_groups) |
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CDPL_CHEM_API void | clearComponentGroups (Reaction &rxn) |
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CDPL_CHEM_API bool | hasComponentGroups (const Reaction &rxn) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveComponentGroups (const Reaction &rxn) |
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CDPL_CHEM_API FragmentList::SharedPointer | perceiveComponentGroups (Reaction &rxn, bool overwrite) |
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CDPL_CHEM_API const AtomMapping::SharedPointer & | getAtomMapping (const Reaction &rxn) |
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CDPL_CHEM_API void | setAtomMapping (Reaction &rxn, const AtomMapping::SharedPointer &mapping) |
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CDPL_CHEM_API void | clearAtomMapping (Reaction &rxn) |
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CDPL_CHEM_API bool | hasAtomMapping (const Reaction &rxn) |
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CDPL_CHEM_API AtomMapping::SharedPointer | perceiveAtomMapping (const Reaction &rxn) |
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CDPL_CHEM_API AtomMapping::SharedPointer | perceiveAtomMapping (Reaction &rxn, bool overwrite) |
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CDPL_CHEM_API bool | generateSMILES (const Reaction &rxn, std::string &smiles, bool canonical=false, bool ord_h_deplete=true, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT) |
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CDPL_CHEM_API std::uint64_t | calcHashCode (const Reaction &rxn, unsigned int role_mask=ReactionRole::ALL, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool ord_h_deplete=true) |
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CDPL_CHEM_API const std::string & | getMDLUserInitials (const Reaction &rxn) |
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CDPL_CHEM_API void | setMDLUserInitials (Reaction &rxn, const std::string &initials) |
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CDPL_CHEM_API void | clearMDLUserInitials (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMDLUserInitials (const Reaction &rxn) |
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CDPL_CHEM_API const std::string & | getMDLProgramName (const Reaction &rxn) |
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CDPL_CHEM_API void | setMDLProgramName (Reaction &rxn, const std::string &name) |
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CDPL_CHEM_API void | clearMDLProgramName (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMDLProgramName (const Reaction &rxn) |
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CDPL_CHEM_API std::size_t | getMDLRegistryNumber (const Reaction &rxn) |
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CDPL_CHEM_API void | setMDLRegistryNumber (Reaction &rxn, std::size_t reg_no) |
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CDPL_CHEM_API void | clearMDLRegistryNumber (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMDLRegistryNumber (const Reaction &rxn) |
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CDPL_CHEM_API const StringDataBlock::SharedPointer & | getReactionData (const Reaction &rxn) |
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CDPL_CHEM_API void | setReactionData (Reaction &rxn, const StringDataBlock::SharedPointer &data) |
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CDPL_CHEM_API void | clearReactionData (Reaction &rxn) |
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CDPL_CHEM_API bool | hasReactionData (const Reaction &rxn) |
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CDPL_CHEM_API const Molecule::SharedPointer & | getMDLMoleculeRecord (const Reaction &rxn) |
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CDPL_CHEM_API void | setMDLMoleculeRecord (Reaction &rxn, const Molecule::SharedPointer &mol_rec) |
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CDPL_CHEM_API void | clearMDLMoleculeRecord (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMDLMoleculeRecord (const Reaction &rxn) |
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CDPL_CHEM_API const std::string & | getMDLInternalRegistryNumber (const Reaction &rxn) |
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CDPL_CHEM_API void | setMDLInternalRegistryNumber (Reaction &rxn, const std::string ®_no) |
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CDPL_CHEM_API void | clearMDLInternalRegistryNumber (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMDLInternalRegistryNumber (const Reaction &rxn) |
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CDPL_CHEM_API const std::string & | getMDLExternalRegistryNumber (const Reaction &rxn) |
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CDPL_CHEM_API void | setMDLExternalRegistryNumber (Reaction &rxn, const std::string ®_no) |
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CDPL_CHEM_API void | clearMDLExternalRegistryNumber (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMDLExternalRegistryNumber (const Reaction &rxn) |
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CDPL_CHEM_API unsigned int | getMDLRXNFileVersion (const Reaction &rxn) |
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CDPL_CHEM_API void | setMDLRXNFileVersion (Reaction &rxn, unsigned int version) |
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CDPL_CHEM_API void | clearMDLRXNFileVersion (Reaction &rxn) |
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CDPL_CHEM_API bool | hasMDLRXNFileVersion (const Reaction &rxn) |
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CDPL_CHEM_API std::size_t | getMaxComponentGroupID (const Reaction &rxn) |
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CDPL_CHEM_API std::size_t | getMaxAtomMappingID (const Reaction &rxn) |
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CDPL_CHEM_API void | setAtomMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite) |
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CDPL_CHEM_API void | setBondMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite) |
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CDPL_CHEM_API void | setComponentMatchConstraints (Reaction &rxn, const MatchConstraintList::SharedPointer &constr, bool overwrite) |
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CDPL_CHEM_API void | generateMatchExpressions (Reaction &rxn, bool overwrite) |
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CDPL_CHEM_API void | initSubstructureSearchQuery (Reaction &rxn, bool overwrite) |
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CDPL_CHEM_API void | initSubstructureSearchTarget (Reaction &rxn, bool overwrite) |
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CDPL_CHEM_API void | calcBasicProperties (Reaction &rxn, bool overwrite) |
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CDPL_CHEM_API Molecule::SharedPointer | parseSMARTS (const std::string &smarts, bool init_qry=true) |
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CDPL_CHEM_API bool | parseSMARTS (const std::string &smarts, Molecule &mol, bool init_qry=true) |
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CDPL_CHEM_API Molecule::SharedPointer | parseSMILES (const std::string &smiles) |
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CDPL_CHEM_API bool | parseSMILES (const std::string &smiles, Molecule &mol) |
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CDPL_CHEM_API void | extendBoundingBox (Math::Vector3D &min, Math::Vector3D &max, const Math::Vector3D &coords, bool reset=false) |
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CDPL_CHEM_API bool | insideBoundingBox (const Math::Vector3D &min, const Math::Vector3D &max, const Math::Vector3D &coords) |
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CDPL_CHEM_API bool | isAromatic (const Fragment &ring, const MolecularGraph &molgraph, const Util::BitSet &arom_bond_mask) |
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CDPL_CHEM_API bool | isNotAromatic (const Fragment &ring, const MolecularGraph &molgraph) |
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CDPL_CHEM_API bool | containsFragmentWithBond (const FragmentList &frag_list, const Bond &bond) |
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CDPL_CHEM_API bool | containsFragmentWithMinSize (const FragmentList &frag_list, std::size_t min_size) |
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CDPL_CHEM_API bool | atomTypesMatch (unsigned int qry_type, unsigned int tgt_type) |
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CDPL_CHEM_API unsigned int | sybylToAtomType (unsigned int sybyl_type) |
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CDPL_CHEM_API const std::string & | getSybylAtomTypeString (unsigned int sybyl_type) |
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CDPL_CHEM_API const std::string & | getSybylBondTypeString (unsigned int sybyl_type) |
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