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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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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) |
| Returns the Chem::MolecularGraphProperty::NAME property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setName (MolecularGraph &molgraph, const std::string &name) |
| Sets the Chem::MolecularGraphProperty::NAME property of molgraph to name. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearName (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::NAME property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasName (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::NAME property. More... | |
| CDPL_CHEM_API std::time_t | CDPL::Chem::getTimestamp (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::TIMESTAMP property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setTimestamp (MolecularGraph &molgraph, std::time_t time) |
| Sets the Chem::MolecularGraphProperty::TIMESTAMP property of molgraph to time. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearTimestamp (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::TIMESTAMP property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasTimestamp (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::TIMESTAMP property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getComment (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::COMMENT property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setComment (MolecularGraph &molgraph, const std::string &comment) |
| Sets the Chem::MolecularGraphProperty::COMMENT property of molgraph to comment. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearComment (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::COMMENT property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasComment (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::COMMENT property. More... | |
| CDPL_CHEM_API const MatchConstraintList::SharedPointer & | CDPL::Chem::getMatchConstraints (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr) |
| Sets the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property of molgraph to constr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchConstraints (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchConstraints (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MATCH_CONSTRAINTS property. More... | |
| CDPL_CHEM_API const MatchExpression< MolecularGraph >::SharedPointer & | CDPL::Chem::getMatchExpression (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MATCH_EXPRESSION property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchExpression (MolecularGraph &molgraph, const MatchExpression< MolecularGraph >::SharedPointer &expr) |
| Sets the Chem::MolecularGraphProperty::MATCH_EXPRESSION property of molgraph to expr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchExpression (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MATCH_EXPRESSION property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchExpression (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MATCH_EXPRESSION property. More... | |
| CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer | CDPL::Chem::generateMatchExpression (const MolecularGraph &molgraph) |
| Builds a top-level match expression from the match-constraint list attached to molgraph. More... | |
| CDPL_CHEM_API MatchExpression< MolecularGraph >::SharedPointer | CDPL::Chem::generateMatchExpression (MolecularGraph &molgraph, bool overwrite) |
| Builds and (optionally) stores the top-level match expression of molgraph. More... | |
| CDPL_CHEM_API const FragmentList::SharedPointer & | CDPL::Chem::getRings (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::RINGS property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setRings (MolecularGraph &molgraph, const FragmentList::SharedPointer &rings) |
| Sets the Chem::MolecularGraphProperty::RINGS property of molgraph to rings. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearRings (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::RINGS property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasRings (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::RINGS property. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveRings (const MolecularGraph &molgraph) |
| Perceives the full set of rings of molgraph without modifying it. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveRings (MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the full set of rings of molgraph. More... | |
| CDPL_CHEM_API const FragmentList::SharedPointer & | CDPL::Chem::getSSSR (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::SSSR property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setSSSR (MolecularGraph &molgraph, const FragmentList::SharedPointer &sssr) |
| Sets the Chem::MolecularGraphProperty::SSSR property of molgraph to sssr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearSSSR (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::SSSR property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasSSSR (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::SSSR property. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveSSSR (const MolecularGraph &molgraph) |
| Perceives the Smallest Set of Smallest Rings of molgraph without modifying it. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveSSSR (MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the Smallest Set of Smallest Rings of molgraph. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::extractSSSRSubset (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph) |
| Extracts the subset of the SSSR of src_molgraph whose rings consist of atoms and bonds of tgt_molgraph. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::extractSSSRSubset (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite) |
| Extracts the SSSR subset of src_molgraph that fits within tgt_molgraph and (optionally) stores it on the latter. More... | |
| CDPL_CHEM_API const Fragment::SharedPointer & | CDPL::Chem::getCyclicSubstructure (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setCyclicSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct) |
| Sets the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property of molgraph to substruct. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearCyclicSubstructure (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasCyclicSubstructure (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::CYCLIC_SUBSTRUCTURE property. More... | |
| CDPL_CHEM_API Fragment::SharedPointer | CDPL::Chem::perceiveCyclicSubstructure (const MolecularGraph &molgraph) |
| Perceives the cyclic substructure (union of all rings) of molgraph without modifying it. More... | |
| CDPL_CHEM_API Fragment::SharedPointer | CDPL::Chem::perceiveCyclicSubstructure (MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the cyclic substructure of molgraph. More... | |
| CDPL_CHEM_API const FragmentList::SharedPointer & | CDPL::Chem::getComponents (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::COMPONENTS property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setComponents (MolecularGraph &molgraph, const FragmentList::SharedPointer &comps) |
| Sets the Chem::MolecularGraphProperty::COMPONENTS property of molgraph to comps. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearComponents (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::COMPONENTS property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasComponents (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::COMPONENTS property. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveComponents (const MolecularGraph &molgraph) |
| Perceives the connected components of molgraph without modifying it. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveComponents (MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the connected components of molgraph. More... | |
| CDPL_CHEM_API const FragmentList::SharedPointer & | CDPL::Chem::getComponentGroups (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::COMPONENT_GROUPS property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setComponentGroups (MolecularGraph &molgraph, const FragmentList::SharedPointer &comp_groups) |
| Sets the Chem::MolecularGraphProperty::COMPONENT_GROUPS property of molgraph to comp_groups. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearComponentGroups (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::COMPONENT_GROUPS property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasComponentGroups (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::COMPONENT_GROUPS property. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveComponentGroups (const MolecularGraph &molgraph) |
| Perceives the component groups of molgraph (from atom-level Chem::AtomProperty::COMPONENT_GROUP_ID values). More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::perceiveComponentGroups (MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the component groups of molgraph. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getConformationIndex (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::CONFORMATION_INDEX property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setConformationIndex (MolecularGraph &molgraph, std::size_t index) |
| Sets the Chem::MolecularGraphProperty::CONFORMATION_INDEX property of molgraph to index. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearConformationIndex (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::CONFORMATION_INDEX property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasConformationIndex (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::CONFORMATION_INDEX property. More... | |
| CDPL_CHEM_API const Util::DArray::SharedPointer & | CDPL::Chem::getConformerEnergies (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setConformerEnergies (MolecularGraph &molgraph, const Util::DArray::SharedPointer &energies) |
| Sets the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property of molgraph to energies. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearConformerEnergies (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasConformerEnergies (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::CONFORMER_ENERGIES property. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setConformation (MolecularGraph &molgraph, std::size_t conf_idx, const Math::Vector3DArray &coords, double energy) |
| Overwrites the conformation at index conf_idx with the supplied coordinates and energy. More... | |
| CDPL_CHEM_API void | CDPL::Chem::addConformation (MolecularGraph &molgraph, const Math::Vector3DArray &coords, double energy) |
| Appends a new conformation built from the supplied coordinates and energy. More... | |
| CDPL_CHEM_API double | CDPL::Chem::getConformationEnergy (const MolecularGraph &molgraph, std::size_t conf_idx) |
| Returns the energy of the conformation at index conf_idx. More... | |
| CDPL_CHEM_API std::uint64_t | CDPL::Chem::getHashCode (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::HASH_CODE property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setHashCode (MolecularGraph &molgraph, std::uint64_t hash_code) |
| Sets the Chem::MolecularGraphProperty::HASH_CODE property of molgraph to hash_code. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearHashCode (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::HASH_CODE property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasHashCode (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::HASH_CODE property. More... | |
| 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) |
| Computes a 64-bit hash code for molgraph taking into account the specified atom and bond properties. More... | |
| CDPL_CHEM_API void | CDPL::Chem::extractReactionCenter (const MolecularGraph &molgraph, Fragment &rxn_center) |
| Collects every atom and bond of molgraph that carries a reaction-center flag into the fragment rxn_center. More... | |
| CDPL_CHEM_API double | CDPL::Chem::getStoichiometricNumber (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setStoichiometricNumber (MolecularGraph &molgraph, double num) |
| Sets the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property of molgraph to num. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearStoichiometricNumber (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasStoichiometricNumber (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::STOICHIOMETRIC_NUMBER property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMDLUserInitials (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_USER_INITIALS property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLUserInitials (MolecularGraph &molgraph, const std::string &initials) |
| Sets the Chem::MolecularGraphProperty::MDL_USER_INITIALS property of molgraph to initials. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLUserInitials (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_USER_INITIALS property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLUserInitials (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_USER_INITIALS property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMDLProgramName (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLProgramName (MolecularGraph &molgraph, const std::string &name) |
| Sets the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property of molgraph to name. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLProgramName (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLProgramName (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_PROGRAM_NAME property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getMDLRegistryNumber (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLRegistryNumber (MolecularGraph &molgraph, std::size_t reg_no) |
| Sets the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property of molgraph to reg_no. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLRegistryNumber (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLRegistryNumber (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_REGISTRY_NUMBER property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getMDLCTABVersion (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of molgraph (see namespace Chem::MDLDataFormatVersion). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLCTABVersion (MolecularGraph &molgraph, unsigned int version) |
| Sets the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property of molgraph to version (see namespace Chem::MDLDataFormatVersion). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLCTABVersion (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLCTABVersion (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_CTAB_VERSION property. More... | |
| CDPL_CHEM_API const StringDataBlock::SharedPointer & | CDPL::Chem::getStructureData (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::STRUCTURE_DATA property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setStructureData (MolecularGraph &molgraph, const StringDataBlock::SharedPointer &data) |
| Sets the Chem::MolecularGraphProperty::STRUCTURE_DATA property of molgraph to data. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearStructureData (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::STRUCTURE_DATA property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasStructureData (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::STRUCTURE_DATA property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getMDLDimensionality (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLDimensionality (MolecularGraph &molgraph, std::size_t dim) |
| Sets the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property of molgraph to dim. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLDimensionality (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLDimensionality (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_DIMENSIONALITY property. More... | |
| CDPL_CHEM_API long | CDPL::Chem::getMDLScalingFactor1 (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLScalingFactor1 (MolecularGraph &molgraph, long factor) |
| Sets the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property of molgraph to factor. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLScalingFactor1 (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLScalingFactor1 (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR1 property. More... | |
| CDPL_CHEM_API double | CDPL::Chem::getMDLScalingFactor2 (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLScalingFactor2 (MolecularGraph &molgraph, double factor) |
| Sets the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property of molgraph to factor. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLScalingFactor2 (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLScalingFactor2 (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_SCALING_FACTOR2 property. More... | |
| CDPL_CHEM_API double | CDPL::Chem::getMDLEnergy (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_ENERGY property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLEnergy (MolecularGraph &molgraph, double energy) |
| Sets the Chem::MolecularGraphProperty::MDL_ENERGY property of molgraph to energy. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLEnergy (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_ENERGY property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLEnergy (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_ENERGY property. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getMDLChiralFlag (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLChiralFlag (MolecularGraph &molgraph, bool flag) |
| Sets the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property of molgraph to flag. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLChiralFlag (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLChiralFlag (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MDL_CHIRAL_FLAG property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getMOL2MoleculeType (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of molgraph (see namespace Chem::MOL2MoleculeType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2MoleculeType (MolecularGraph &molgraph, unsigned int type) |
| Sets the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property of molgraph to type (see namespace Chem::MOL2MoleculeType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2MoleculeType (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2MoleculeType (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MOL2_MOLECULE_TYPE property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getMOL2ChargeType (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of molgraph (see namespace Chem::MOL2ChargeType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2ChargeType (MolecularGraph &molgraph, unsigned int type) |
| Sets the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property of molgraph to type (see namespace Chem::MOL2ChargeType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2ChargeType (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2ChargeType (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::MOL2_CHARGE_TYPE property. More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateAdjacencyMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
Builds the adjacency matrix of molgraph (entry i and j). More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateIncidenceMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
Builds the atom/bond incidence matrix of molgraph (entry 1 if atom i is an endpoint of bond j). More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateBondMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
Builds the bond-order matrix of molgraph (entry i and j). More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateBondElectronMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
Builds the bond-electron-count matrix of molgraph (entry i and j). More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateBondAtomTypeMatrix (const MolecularGraph &molgraph, Math::SparseULMatrix &mtx) |
| Builds a matrix combining bond order and atom-type information of the endpoints of every bond in molgraph. More... | |
| CDPL_CHEM_API const Math::ULMatrix::SharedPointer & | CDPL::Chem::getTopologicalDistanceMatrix (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setTopologicalDistanceMatrix (MolecularGraph &molgraph, const Math::ULMatrix::SharedPointer &mtx) |
| Sets the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property of molgraph to mtx. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearTopologicalDistanceMatrix (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasTopologicalDistanceMatrix (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::TOPOLOGICAL_DISTANCE_MATRIX property. More... | |
| CDPL_CHEM_API Math::ULMatrix::SharedPointer | CDPL::Chem::calcTopologicalDistanceMatrix (MolecularGraph &molgraph, bool overwrite) |
| Computes and (optionally) stores the topological-distance matrix of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcTopologicalDistanceMatrix (const MolecularGraph &molgraph, Math::ULMatrix &mtx) |
| Computes the topological-distance matrix of molgraph into the supplied mtx. More... | |
| CDPL_CHEM_API Math::ULMatrix::SharedPointer | CDPL::Chem::extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, MolecularGraph &tgt_molgraph, bool overwrite) |
| Extracts the topological-distance sub-matrix of src_molgraph that covers the atoms of tgt_molgraph and (optionally) stores it on the latter. More... | |
| CDPL_CHEM_API void | CDPL::Chem::extractTopologicalDistanceSubMatrix (const MolecularGraph &src_molgraph, const MolecularGraph &tgt_molgraph, Math::ULMatrix &mtx) |
| Extracts the topological-distance sub-matrix of src_molgraph that covers the atoms of tgt_molgraph into the supplied mtx. More... | |
| CDPL_CHEM_API const Math::DMatrix::SharedPointer & | CDPL::Chem::getGeometricalDistanceMatrix (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setGeometricalDistanceMatrix (MolecularGraph &molgraph, const Math::DMatrix::SharedPointer &mtx) |
| Sets the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property of molgraph to mtx. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearGeometricalDistanceMatrix (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasGeometricalDistanceMatrix (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::GEOMETRICAL_DISTANCE_MATRIX property. More... | |
| CDPL_CHEM_API Math::DMatrix::SharedPointer | CDPL::Chem::calcGeometricalDistanceMatrix (MolecularGraph &molgraph, bool overwrite) |
| Computes and (optionally) stores the geometrical-distance matrix of molgraph from its 3D coordinates. More... | |
| CDPL_CHEM_API const Fragment::SharedPointer & | CDPL::Chem::getAromaticSubstructure (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAromaticSubstructure (MolecularGraph &molgraph, const Fragment::SharedPointer &substruct) |
| Sets the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property of molgraph to substruct. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearAromaticSubstructure (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasAromaticSubstructure (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::AROMATIC_SUBSTRUCTURE property. More... | |
| CDPL_CHEM_API Fragment::SharedPointer | CDPL::Chem::perceiveAromaticSubstructure (const MolecularGraph &molgraph) |
| Perceives the aromatic substructure of molgraph without modifying it. More... | |
| CDPL_CHEM_API Fragment::SharedPointer | CDPL::Chem::perceiveAromaticSubstructure (MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the aromatic substructure of molgraph. More... | |
| CDPL_CHEM_API const ElectronSystemList::SharedPointer & | CDPL::Chem::getPiElectronSystems (const MolecularGraph &molgraph) |
| Returns the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setPiElectronSystems (MolecularGraph &molgraph, const ElectronSystemList::SharedPointer &pi_systems) |
| Sets the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property of molgraph to pi_systems. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearPiElectronSystems (MolecularGraph &molgraph) |
| Removes the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property from molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasPiElectronSystems (const MolecularGraph &molgraph) |
| Tells whether molgraph carries the Chem::MolecularGraphProperty::PI_ELECTRON_SYSTEMS property. More... | |
| CDPL_CHEM_API ElectronSystemList::SharedPointer | CDPL::Chem::perceivePiElectronSystems (const MolecularGraph &molgraph) |
| Perceives the pi-electron systems of molgraph without modifying it. More... | |
| CDPL_CHEM_API ElectronSystemList::SharedPointer | CDPL::Chem::perceivePiElectronSystems (MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the pi-electron systems of molgraph. More... | |
| 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) |
| Generates a SMILES string for molgraph. More... | |
| 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) |
| Generates an InChI string for molgraph using the InChI C-API. More... | |
| CDPL_CHEM_API int | CDPL::Chem::generateINCHIKey (const MolecularGraph &molgraph, std::string &inchi_key) |
| Generates an InChIKey for molgraph using the InChI C-API. More... | |
| 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) |
| Reorders the atoms (and optionally their neighbors and bonds) of molgraph according to a user-supplied comparator. More... | |
| CDPL_CHEM_API void | CDPL::Chem::canonicalize (MolecularGraph &molgraph, bool atoms=true, bool atom_nbrs=true, bool bonds=true, bool bond_atoms=false) |
| Reorders the atoms (and optionally their neighbors and bonds) of molgraph according to the canonical-numbering attached to its atoms. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calc2DCoordinates (MolecularGraph &molgraph, bool overwrite) |
| Computes 2D atom coordinates for molgraph and stores them as Chem::AtomProperty::COORDINATES_2D. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::align2DCoordinates (MolecularGraph &molgraph, const AtomContainer &atoms, const Math::Vector2DArray &ref_coords, bool fix_bond_stereo=true) |
| Aligns molgraph's 2D coordinates so that the atoms of atoms come to lie at the reference coordinates ref_coords. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::align2DCoordinates (MolecularGraph &molgraph, const AtomMapping &ref_atom_mpg, bool fix_bond_stereo=true) |
| Aligns molgraph's 2D coordinates onto a reference atom mapping. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::align2DCoordinates (MolecularGraph &molgraph, const MolecularGraph &ref_molgraph, bool use_mcss, bool fix_bond_stereo=true) |
| Aligns molgraph's 2D coordinates onto those of ref_molgraph, using either a maximum-common-substructure search or substructure matching. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::align2DCoordinates (MolecularGraph &molgraph, const MolecularGraph &ref_molgraph, const MolecularGraph &substr_ptn, bool fix_bond_stereo=true) |
| Aligns molgraph's 2D coordinates onto those of ref_molgraph, using substr_ptn as the explicit substructure pattern. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcHydrogen3DCoordinates (MolecularGraph &molgraph, bool undef_only=true) |
| Computes 3D coordinates for the hydrogen atoms of molgraph from the geometry of their non-hydrogen neighbors. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcBond2DStereoFlags (MolecularGraph &molgraph, bool overwrite) |
| Derives 2D wedge/hash bond stereo flags for the bonds of molgraph from the atoms' stereo descriptors and 2D layout. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcCIPPriorities (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores CIP priorities for the atoms of molgraph. More... | |
| 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) |
| Computes and stores topological-symmetry classes for the atoms of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcCanonicalNumbering (MolecularGraph &molgraph, bool overwrite, unsigned int atom_flags=AtomPropertyFlag::DEFAULT, unsigned int bond_flags=BondPropertyFlag::DEFAULT) |
| Computes and stores canonical atom numbers for the atoms of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcMorganNumbering (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores Morgan numbers for the atoms of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcImplicitHydrogenCounts (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores implicit-hydrogen counts for the atoms of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcFormalCharges (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores formal charges for the atoms of molgraph from their valence environment. More... | |
| CDPL_CHEM_API void | CDPL::Chem::perceiveHybridizationStates (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores hybridization states for the atoms of molgraph from their valence environment. More... | |
| CDPL_CHEM_API void | CDPL::Chem::perceiveBondOrders (MolecularGraph &molgraph, bool overwrite) |
| Perceives bond orders for the bonds of molgraph from atom geometry and ligand environment. More... | |
| CDPL_CHEM_API void | CDPL::Chem::kekulizeBonds (MolecularGraph &molgraph) |
| Assigns Kekulé bond orders to the aromatic bonds of molgraph. More... | |
| 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) |
| Flags the atoms of molgraph that qualify as stereo centers under the supplied criteria. More... | |
| 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) |
| Flags the bonds of molgraph that qualify as stereo centers under the supplied criteria. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcMDLParities (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores MDL parities for the atoms of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcAtomStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true) |
| Computes and stores stereo descriptors for the atoms of molgraph from their geometric layout. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcAtomStereoDescriptorsFromMDLParities (MolecularGraph &molgraph, bool overwrite) |
| Derives atom stereo descriptors of molgraph from previously-assigned MDL parities. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcBondStereoDescriptors (MolecularGraph &molgraph, bool overwrite, std::size_t dim=1, bool check_stc_flag=true) |
| Computes and stores stereo descriptors for the bonds of molgraph from their geometric layout. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcAtomCIPConfigurations (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores CIP configuration labels for the atoms of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcBondCIPConfigurations (MolecularGraph &molgraph, bool overwrite) |
| Computes and stores CIP configuration labels for the bonds of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAtomMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite) |
| Sets the atom-level match-constraint list constr on every atom of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setBondMatchConstraints (MolecularGraph &molgraph, const MatchConstraintList::SharedPointer &constr, bool overwrite) |
| Sets the bond-level match-constraint list constr on every bond of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateMatchExpressions (MolecularGraph &molgraph, bool overwrite) |
| Generates and stores match expressions for every atom, bond and the molecular graph itself. More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateMatchExpressionStrings (MolecularGraph &molgraph, bool overwrite) |
| Generates and stores textual representations of the match expressions of molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::initSubstructureSearchQuery (MolecularGraph &molgraph, bool overwrite) |
| Prepares molgraph for use as a substructure search query (precomputes match expressions and required cached properties). More... | |
| CDPL_CHEM_API void | CDPL::Chem::initSubstructureSearchTarget (MolecularGraph &molgraph, bool overwrite) |
| Prepares molgraph for use as a substructure search target (precomputes required cached properties). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAromaticityFlags (MolecularGraph &molgraph, bool overwrite) |
| Perceives aromaticity and sets the corresponding atom/bond aromaticity flags on molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setRingFlags (MolecularGraph &molgraph, bool overwrite) |
| Perceives ring membership and sets the corresponding atom/bond ring flags on molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAtomTypesFromSymbols (MolecularGraph &molgraph, bool overwrite) |
| Sets the atom types of molgraph from their element symbols. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAtomSymbolsFromTypes (MolecularGraph &molgraph, bool overwrite) |
| Sets the atom symbols of molgraph from their atom types. More... | |
| CDPL_CHEM_API void | CDPL::Chem::perceiveSybylAtomTypes (MolecularGraph &molgraph, bool overwrite) |
| Perceives Sybyl atom types for the atoms of molgraph. More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::getAromaticRings (const MolecularGraph &molgraph) |
| Returns the subset of the aromatic rings of molgraph (a fresh list, not stored on molgraph). More... | |
| CDPL_CHEM_API FragmentList::SharedPointer | CDPL::Chem::getAromaticSSSRSubset (const MolecularGraph &molgraph) |
| Returns the subset of the SSSR of molgraph that contains only aromatic rings (a fresh list, not stored on molgraph). More... | |
| CDPL_CHEM_API bool | CDPL::Chem::containsMolecularGraph (const MolecularGraph &molgraph, const MolecularGraph &sub_molgraph, bool atoms=true, bool bonds=true) |
| Tells whether molgraph contains the atoms and/or bonds of sub_molgraph. More... | |
| 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) |
| Collects the fragments in frag_list that are fully contained in molgraph into cont_frag_list. More... | |
| 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) |
| Collects the fragments in frag_list that contain molgraph into cont_frag_list. More... | |
| 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) |
| Translates the atoms/bonds of src_frag (a fragment of src_molgraph) to the corresponding atoms/bonds of tgt_molgraph and stores them in tgt_frag. More... | |
| 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) |
| Translates every fragment in src_frag_list (defined on src_molgraph) to the corresponding fragments on tgt_molgraph. More... | |
| CDPL_CHEM_API void | CDPL::Chem::splitIntoFragments (const MolecularGraph &molgraph, FragmentList &frag_list, const Util::BitSet &split_bond_mask, bool append=false) |
| Splits molgraph into connected fragments by removing the bonds flagged in split_bond_mask. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getCompleteBondCount (const MolecularGraph &molgraph) |
| Returns the number of bonds of molgraph that lie between two atoms of molgraph (i.e. no dangling cross-graph bonds). More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcBasicProperties (MolecularGraph &molgraph, bool overwrite) |
| Computes the basic per-atom/per-bond properties (aromaticity, ring info, etc.) of molgraph. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::editSubstructures (const MolecularGraph &molgraph, Molecule &result_mol, const std::string &search_ptns, const std::string &result_ptn, const std::string &exclude_ptns=std::string()) |
| Builds result_mol from molgraph by replacing all substructures matching the SMARTS patterns in search_ptns with result_ptn. More... | |
Declaration of functions that operate on Chem::MolecularGraph instances.
1.9.1