Chemical Data Processing Library C++ API - Version 1.2.0
Namespaces | Functions
Chem/MolecularGraphFunctions.hpp File Reference

Declaration of functions that operate on Chem::MolecularGraph instances. More...

#include <string>
#include <cstddef>
#include <cstdint>
#include <ctime>
#include "CDPL/Chem/APIPrefix.hpp"
#include "CDPL/Chem/Fragment.hpp"
#include "CDPL/Chem/FragmentList.hpp"
#include "CDPL/Chem/ElectronSystemList.hpp"
#include "CDPL/Chem/MatchConstraintList.hpp"
#include "CDPL/Chem/MatchExpression.hpp"
#include "CDPL/Chem/StringDataBlock.hpp"
#include "CDPL/Chem/AtomPropertyFlag.hpp"
#include "CDPL/Chem/BondPropertyFlag.hpp"
#include "CDPL/Chem/ControlParameterDefault.hpp"
#include "CDPL/Math/Matrix.hpp"
#include "CDPL/Math/Vector.hpp"
#include "CDPL/Math/VectorArray.hpp"
#include "CDPL/Util/BitSet.hpp"

Go to the source code of this file.

Namespaces

 CDPL
 The namespace of the Chemical Data Processing Library.
 
 CDPL::Chem
 Contains classes and functions related to chemistry.
 

Functions

CDPL_CHEM_API const std::string & CDPL::Chem::getName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setName (MolecularGraph &molgraph, const std::string &name)
 
CDPL_CHEM_API void CDPL::Chem::clearName (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::time_t CDPL::Chem::getTimestamp (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setTimestamp (MolecularGraph &molgraph, std::time_t time)
 
CDPL_CHEM_API void CDPL::Chem::clearTimestamp (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasTimestamp (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & CDPL::Chem::getComment (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setComment (MolecularGraph &molgraph, const std::string &comment)
 
CDPL_CHEM_API void CDPL::Chem::clearComment (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasComment (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const MatchConstraintList::SharedPointer & CDPL::Chem::getMatchConstraints (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr)
 
CDPL_CHEM_API void CDPL::Chem::clearMatchConstraints (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMatchConstraints (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const MatchExpression< MolecularGraph >::SharedPointer & CDPL::Chem::getMatchExpression (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMatchExpression (MolecularGraph &molgraph, const MatchExpression< MolecularGraph >::SharedPointer &expr)
 
CDPL_CHEM_API void CDPL::Chem::clearMatchExpression (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMatchExpression (const MolecularGraph &molgraph)
 
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer CDPL::Chem::generateMatchExpression (const MolecularGraph &molgraph)
 
CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer CDPL::Chem::generateMatchExpression (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointer & CDPL::Chem::getRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setRings (MolecularGraph &molgraph, const FragmentList::SharedPointer &rings)
 
CDPL_CHEM_API void CDPL::Chem::clearRings (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveRings (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointer & CDPL::Chem::getSSSR (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setSSSR (MolecularGraph &molgraph, const FragmentList::SharedPointer &sssr)
 
CDPL_CHEM_API void CDPL::Chem::clearSSSR (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasSSSR (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveSSSR (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveSSSR (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::extractSSSRSubset (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::extractSSSRSubset (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
 
CDPL_CHEM_API const Fragment::SharedPointer & CDPL::Chem::getCyclicSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setCyclicSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
 
CDPL_CHEM_API void CDPL::Chem::clearCyclicSubstructure (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasCyclicSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveCyclicSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveCyclicSubstructure (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointer & CDPL::Chem::getComponents (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setComponents (MolecularGraph &molgraph, const FragmentList::SharedPointer &comps)
 
CDPL_CHEM_API void CDPL::Chem::clearComponents (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasComponents (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponents (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponents (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const FragmentList::SharedPointer & CDPL::Chem::getComponentGroups (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setComponentGroups (MolecularGraph &molgraph, const FragmentList::SharedPointer &comp_groups)
 
CDPL_CHEM_API void CDPL::Chem::clearComponentGroups (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasComponentGroups (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::perceiveComponentGroups (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API std::size_t CDPL::Chem::getConformationIndex (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setConformationIndex (MolecularGraph &molgraph, std::size_t index)
 
CDPL_CHEM_API void CDPL::Chem::clearConformationIndex (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasConformationIndex (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const Util::DArray::SharedPointer & CDPL::Chem::getConformerEnergies (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setConformerEnergies (MolecularGraph &molgraph, const Util::DArray::SharedPointer &energies)
 
CDPL_CHEM_API void CDPL::Chem::clearConformerEnergies (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasConformerEnergies (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setConformation (MolecularGraph &molgraph, std::size_t conf_idx, const Math::Vector3DArray &coords, double energy)
 
CDPL_CHEM_API void CDPL::Chem::addConformation (MolecularGraph &molgraph, const Math::Vector3DArray &coords, double energy)
 
CDPL_CHEM_API double CDPL::Chem::getConformationEnergy (const MolecularGraph &molgraph, std::size_t conf_idx)
 
CDPL_CHEM_API std::uint64_t CDPL::Chem::getHashCode (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setHashCode (MolecularGraph &molgraph, std::uint64_t hash_code)
 
CDPL_CHEM_API void CDPL::Chem::clearHashCode (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasHashCode (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::uint64_t CDPL::Chem::calcHashCode (const MolecularGraph &molgraph, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool ord_h_deplete=true)
 
CDPL_CHEM_API void CDPL::Chem::extractReactionCenter (const MolecularGraph &molgraph, Fragment &rxn_center)
 
CDPL_CHEM_API double CDPL::Chem::getStoichiometricNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setStoichiometricNumber (MolecularGraph &molgraph, double num)
 
CDPL_CHEM_API void CDPL::Chem::clearStoichiometricNumber (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasStoichiometricNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & CDPL::Chem::getMDLUserInitials (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLUserInitials (MolecularGraph &molgraph, const std::string &initials)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLUserInitials (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLUserInitials (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const std::string & CDPL::Chem::getMDLProgramName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLProgramName (MolecularGraph &molgraph, const std::string &name)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLProgramName (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLProgramName (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::size_t CDPL::Chem::getMDLRegistryNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLRegistryNumber (MolecularGraph &molgraph, std::size_t reg_no)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLRegistryNumber (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLRegistryNumber (const MolecularGraph &molgraph)
 
CDPL_CHEM_API unsigned int CDPL::Chem::getMDLCTABVersion (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLCTABVersion (MolecularGraph &molgraph, unsigned int version)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLCTABVersion (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLCTABVersion (const MolecularGraph &molgraph)
 
CDPL_CHEM_API const StringDataBlock::SharedPointer & CDPL::Chem::getStructureData (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setStructureData (MolecularGraph &molgraph, const StringDataBlock::SharedPointer &data)
 
CDPL_CHEM_API void CDPL::Chem::clearStructureData (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasStructureData (const MolecularGraph &molgraph)
 
CDPL_CHEM_API std::size_t CDPL::Chem::getMDLDimensionality (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLDimensionality (MolecularGraph &molgraph, std::size_t dim)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLDimensionality (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLDimensionality (const MolecularGraph &molgraph)
 
CDPL_CHEM_API long CDPL::Chem::getMDLScalingFactor1 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLScalingFactor1 (MolecularGraph &molgraph, long factor)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor1 (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor1 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API double CDPL::Chem::getMDLScalingFactor2 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLScalingFactor2 (MolecularGraph &molgraph, double factor)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLScalingFactor2 (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLScalingFactor2 (const MolecularGraph &molgraph)
 
CDPL_CHEM_API double CDPL::Chem::getMDLEnergy (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLEnergy (MolecularGraph &molgraph, double energy)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLEnergy (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLEnergy (const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::getMDLChiralFlag (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMDLChiralFlag (MolecularGraph &molgraph, bool flag)
 
CDPL_CHEM_API void CDPL::Chem::clearMDLChiralFlag (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMDLChiralFlag (const MolecularGraph &molgraph)
 
CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2MoleculeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMOL2MoleculeType (MolecularGraph &molgraph, unsigned int type)
 
CDPL_CHEM_API void CDPL::Chem::clearMOL2MoleculeType (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMOL2MoleculeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API unsigned int CDPL::Chem::getMOL2ChargeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setMOL2ChargeType (MolecularGraph &molgraph, unsigned int type)
 
CDPL_CHEM_API void CDPL::Chem::clearMOL2ChargeType (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasMOL2ChargeType (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::generateAdjacencyMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void CDPL::Chem::generateIncidenceMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void CDPL::Chem::generateBondMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void CDPL::Chem::generateBondElectronMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API void CDPL::Chem::generateBondAtomTypeMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx)
 
CDPL_CHEM_API const Math::ULMatrix::SharedPointer & CDPL::Chem::getTopologicalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setTopologicalDistanceMatrix (MolecularGraph &molgraph, const Math::ULMatrix::SharedPointer &mtx)
 
CDPL_CHEM_API void CDPL::Chem::clearTopologicalDistanceMatrix (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasTopologicalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Math::ULMatrix::SharedPointer CDPL::Chem::calcTopologicalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcTopologicalDistanceMatrix (const MolecularGraph &molgraph, Math::ULMatrix &mtx)
 
CDPL_CHEM_API Math::ULMatrix::SharedPointer CDPL::Chem::extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph, Math::ULMatrix &mtx)
 
CDPL_CHEM_API const Math::DMatrix::SharedPointer & CDPL::Chem::getGeometricalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setGeometricalDistanceMatrix (MolecularGraph &molgraph, const Math::DMatrix::SharedPointer &mtx)
 
CDPL_CHEM_API void CDPL::Chem::clearGeometricalDistanceMatrix (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasGeometricalDistanceMatrix (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Math::DMatrix::SharedPointer CDPL::Chem::calcGeometricalDistanceMatrix (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const Fragment::SharedPointer & CDPL::Chem::getAromaticSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setAromaticSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct)
 
CDPL_CHEM_API void CDPL::Chem::clearAromaticSubstructure (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasAromaticSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveAromaticSubstructure (const MolecularGraph &molgraph)
 
CDPL_CHEM_API Fragment::SharedPointer CDPL::Chem::perceiveAromaticSubstructure (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API const ElectronSystemList::SharedPointer & CDPL::Chem::getPiElectronSystems (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::setPiElectronSystems (MolecularGraph &molgraph, const ElectronSystemList::SharedPointer &pi_systems)
 
CDPL_CHEM_API void CDPL::Chem::clearPiElectronSystems (MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::hasPiElectronSystems (const MolecularGraph &molgraph)
 
CDPL_CHEM_API ElectronSystemList::SharedPointer CDPL::Chem::perceivePiElectronSystems (const MolecularGraph &molgraph)
 
CDPL_CHEM_API ElectronSystemList::SharedPointer CDPL::Chem::perceivePiElectronSystems (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API bool CDPL::Chem::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)
 
CDPL_CHEM_API int CDPL::Chem::generateINCHI (const MolecularGraph &molgraph, std::string &inchi, const std::string &options=ControlParameterDefault::INCHI_OUTPUT_OPTIONS, std::size_t dim=0)
 
CDPL_CHEM_API int CDPL::Chem::generateINCHIKey (const MolecularGraph &molgraph, std::string &inchi_key)
 
CDPL_CHEM_API void CDPL::Chem::canonicalize (MolecularGraph &molgraph, const AtomCompareFunction &func, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
 
CDPL_CHEM_API void CDPL::Chem::canonicalize (MolecularGraph &molgraph, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false)
 
CDPL_CHEM_API void CDPL::Chem::calc2DCoordinates (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcHydrogen3DCoordinates (MolecularGraph &molgraph, bool undef_only=true)
 
CDPL_CHEM_API void CDPL::Chem::calcBond2DStereoFlags (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcCIPPriorities (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::perceiveSymmetryClasses (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT, bool inc_impl_h=true)
 
CDPL_CHEM_API void CDPL::Chem::calcCanonicalNumbering (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT)
 
CDPL_CHEM_API void CDPL::Chem::calcMorganNumbering (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcImplicitHydrogenCounts (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcFormalCharges (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::perceiveHybridizationStates (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::perceiveBondOrders (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::kekulizeBonds (MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::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)
 
CDPL_CHEM_API void CDPL::Chem::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)
 
CDPL_CHEM_API void CDPL::Chem::calcMDLParities (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcAtomStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
 
CDPL_CHEM_API void CDPL::Chem::calcAtomStereoDescriptorsFromMDLParities (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcBondStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true)
 
CDPL_CHEM_API void CDPL::Chem::calcAtomCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::calcBondCIPConfigurations (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::setAtomMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::setBondMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::generateMatchExpressions (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::generateMatchExpressionStrings (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchQuery (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::initSubstructureSearchTarget (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::setAromaticityFlags (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::setRingFlags (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::setAtomTypesFromSymbols (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::setAtomSymbolsFromTypes (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API void CDPL::Chem::perceiveSybylAtomTypes (MolecularGraph &molgraph, bool overwrite)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticRings (const MolecularGraph &molgraph)
 
CDPL_CHEM_API FragmentList::SharedPointer CDPL::Chem::getAromaticSSSRSubset (const MolecularGraph &molgraph)
 
CDPL_CHEM_API bool CDPL::Chem::containsMolecularGraph (const MolecularGraph &molgraph, const MolecularGraph &sub_molgraph, bool atoms=true, bool bonds=true)
 
CDPL_CHEM_API void CDPL::Chem::getContainedFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true)
 
CDPL_CHEM_API void CDPL::Chem::getContainingFragments (const MolecularGraph &molgraph, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false, bool atoms=true, bool bonds=true)
 
CDPL_CHEM_API void CDPL::Chem::translateFragment (const MolecularGraph &src_molgraph, const Fragment &src_frag, const MolecularGraph &tgt_molgraph, Fragment &tgt_frag, bool append=false)
 
CDPL_CHEM_API void CDPL::Chem::translateFragments (const MolecularGraph &src_molgraph, const FragmentList &src_frag_list, const MolecularGraph &tgt_molgraph, FragmentList &tgt_frag_list, bool append=false)
 
CDPL_CHEM_API void CDPL::Chem::splitIntoFragments (const MolecularGraph &molgraph, FragmentList &frag_list, const Util::BitSet &split_bond_mask, bool append=false)
 
CDPL_CHEM_API std::size_t CDPL::Chem::getCompleteBondCount (const MolecularGraph &molgraph)
 
CDPL_CHEM_API void CDPL::Chem::calcBasicProperties (MolecularGraph &molgraph, bool overwrite)
 

Detailed Description

Declaration of functions that operate on Chem::MolecularGraph instances.

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