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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::Atom instances. More...
#include <cstddef>#include <string>#include <type_traits>#include "CDPL/Chem/APIPrefix.hpp"#include "CDPL/Chem/MatchExpression.hpp"#include "CDPL/Chem/MatchConstraintList.hpp"#include "CDPL/Chem/FragmentList.hpp"#include "CDPL/Chem/AtomPropertyFlag.hpp"#include "CDPL/Chem/AtomPriorityFunction.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 Atom &atom) |
| Returns the Chem::AtomProperty::NAME property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setName (Atom &atom, const std::string &name) |
| Sets the Chem::AtomProperty::NAME property of atom to name. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearName (Atom &atom) |
| Removes the Chem::AtomProperty::NAME property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasName (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::NAME property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getSymbol (const Atom &atom) |
| Returns the Chem::AtomProperty::SYMBOL property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setSymbol (Atom &atom, const std::string &symbol) |
| Sets the Chem::AtomProperty::SYMBOL property of atom to symbol. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearSymbol (Atom &atom) |
| Removes the Chem::AtomProperty::SYMBOL property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasSymbol (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::SYMBOL property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getSymbolForType (const Atom &atom) |
| Returns the element symbol that corresponds to the Chem::AtomProperty::TYPE of atom. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getType (const Atom &atom) |
| Returns the Chem::AtomProperty::TYPE property of atom (see namespace Chem::AtomType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setType (Atom &atom, unsigned int type) |
| Sets the Chem::AtomProperty::TYPE property of atom to type (see namespace Chem::AtomType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearType (Atom &atom) |
| Removes the Chem::AtomProperty::TYPE property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasType (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::TYPE property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getTypeForSymbol (const Atom &atom) |
| Returns the atom type that corresponds to the Chem::AtomProperty::SYMBOL of atom. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getGenericType (const Atom &atom) |
Returns the generic atom type (e.g. A, Q, X, ...) that the atom's Chem::AtomProperty::TYPE belongs to. More... | |
| CDPL_CHEM_API long | CDPL::Chem::getFormalCharge (const Atom &atom) |
| Returns the Chem::AtomProperty::FORMAL_CHARGE property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setFormalCharge (Atom &atom, long charge) |
| Sets the Chem::AtomProperty::FORMAL_CHARGE property of atom to charge. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearFormalCharge (Atom &atom) |
| Removes the Chem::AtomProperty::FORMAL_CHARGE property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasFormalCharge (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::FORMAL_CHARGE property. More... | |
| CDPL_CHEM_API long | CDPL::Chem::calcFormalCharge (const Atom &atom, const MolecularGraph &molgraph) |
| Computes the formal charge of atom from its valence environment in molgraph. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getIsotope (const Atom &atom) |
| Returns the Chem::AtomProperty::ISOTOPE property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setIsotope (Atom &atom, std::size_t isotope) |
| Sets the Chem::AtomProperty::ISOTOPE property of atom to isotope. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearIsotope (Atom &atom) |
| Removes the Chem::AtomProperty::ISOTOPE property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasIsotope (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::ISOTOPE property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getRadicalType (const Atom &atom) |
| Returns the Chem::AtomProperty::RADICAL_TYPE property of atom (see namespace Chem::RadicalType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setRadicalType (Atom &atom, unsigned int type) |
| Sets the Chem::AtomProperty::RADICAL_TYPE property of atom to type (see namespace Chem::RadicalType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearRadicalType (Atom &atom) |
| Removes the Chem::AtomProperty::RADICAL_TYPE property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasRadicalType (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::RADICAL_TYPE property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getHybridizationState (const Atom &atom) |
| Returns the Chem::AtomProperty::HYBRIDIZATION property of atom (see namespace Chem::HybridizationState). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setHybridizationState (Atom &atom, unsigned int state) |
| Sets the Chem::AtomProperty::HYBRIDIZATION property of atom to state (see namespace Chem::HybridizationState). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearHybridizationState (Atom &atom) |
| Removes the Chem::AtomProperty::HYBRIDIZATION property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasHybridizationState (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::HYBRIDIZATION property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::perceiveHybridizationState (const Atom &atom, const MolecularGraph &molgraph) |
| Derives the hybridization state of atom from its valence environment in molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getRingFlag (const Atom &atom) |
| Returns the Chem::AtomProperty::RING_FLAG property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setRingFlag (Atom &atom, bool in_ring) |
| Sets the Chem::AtomProperty::RING_FLAG property of atom to in_ring. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearRingFlag (Atom &atom) |
| Removes the Chem::AtomProperty::RING_FLAG property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasRingFlag (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::RING_FLAG property. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::isInFragmentOfSize (const Atom &atom, const FragmentList &frag_list, std::size_t size) |
| Tells whether atom is a member of any fragment in frag_list whose size matches size. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getSizeOfSmallestContainingFragment (const Atom &atom, const FragmentList &frag_list) |
| Returns the size (in atoms) of the smallest fragment in frag_list that contains atom. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getSizeOfLargestContainingFragment (const Atom &atom, const FragmentList &frag_list) |
| Returns the size (in atoms) of the largest fragment in frag_list that contains atom. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getNumContainingFragments (const Atom &atom, const FragmentList &frag_list) |
| Returns the number of fragments in frag_list that contain atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::getContainingFragments (const Atom &atom, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false) |
| Collects the fragments in frag_list that contain atom into cont_frag_list. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getAromaticityFlag (const Atom &atom) |
| Returns the Chem::AtomProperty::AROMATICITY_FLAG property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAromaticityFlag (Atom &atom, bool aromatic) |
| Sets the Chem::AtomProperty::AROMATICITY_FLAG property of atom to aromatic. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearAromaticityFlag (Atom &atom) |
| Removes the Chem::AtomProperty::AROMATICITY_FLAG property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasAromaticityFlag (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::AROMATICITY_FLAG property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getUnpairedElectronCount (const Atom &atom) |
| Returns the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setUnpairedElectronCount (Atom &atom, std::size_t count) |
| Sets the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property of atom to count. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearUnpairedElectronCount (Atom &atom) |
| Removes the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasUnpairedElectronCount (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::UNPAIRED_ELECTRON_COUNT property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getImplicitHydrogenCount (const Atom &atom) |
| Returns the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setImplicitHydrogenCount (Atom &atom, std::size_t count) |
| Sets the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property of atom to count. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearImplicitHydrogenCount (Atom &atom) |
| Removes the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasImplicitHydrogenCount (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::IMPLICIT_HYDROGEN_COUNT property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::calcImplicitHydrogenCount (const Atom &atom, const MolecularGraph &molgraph) |
| Computes the implicit hydrogen count of atom from its valence environment in molgraph. More... | |
| CDPL_CHEM_API const Math::Vector2D & | CDPL::Chem::get2DCoordinates (const Atom &atom) |
| Returns the Chem::AtomProperty::COORDINATES_2D property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::set2DCoordinates (Atom &atom, const Math::Vector2D &coords) |
| Sets the Chem::AtomProperty::COORDINATES_2D property of atom to coords. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clear2DCoordinates (Atom &atom) |
| Removes the Chem::AtomProperty::COORDINATES_2D property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::has2DCoordinates (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::COORDINATES_2D property. More... | |
| CDPL_CHEM_API const Math::Vector3D & | CDPL::Chem::getConformer3DCoordinates (const Atom &atom, std::size_t conf_idx) |
| Returns the 3D coordinates of atom for conformer conf_idx (from the Chem::AtomProperty::COORDINATES_3D_ARRAY property). More... | |
| CDPL_CHEM_API const Math::Vector3DArray::SharedPointer & | CDPL::Chem::get3DCoordinatesArray (const Atom &atom) |
| Returns the Chem::AtomProperty::COORDINATES_3D_ARRAY property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::set3DCoordinatesArray (Atom &atom, const Math::Vector3DArray::SharedPointer &coords_array) |
| Sets the Chem::AtomProperty::COORDINATES_3D_ARRAY property of atom to coords_array. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clear3DCoordinatesArray (Atom &atom) |
| Removes the Chem::AtomProperty::COORDINATES_3D_ARRAY property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::has3DCoordinatesArray (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::COORDINATES_3D_ARRAY property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getMorganNumber (const Atom &atom) |
| Returns the Chem::AtomProperty::MORGAN_NUMBER property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMorganNumber (Atom &atom, std::size_t num) |
| Sets the Chem::AtomProperty::MORGAN_NUMBER property of atom to num. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMorganNumber (Atom &atom) |
| Removes the Chem::AtomProperty::MORGAN_NUMBER property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMorganNumber (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MORGAN_NUMBER property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getCanonicalNumber (const Atom &atom) |
| Returns the Chem::AtomProperty::CANONICAL_NUMBER property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setCanonicalNumber (Atom &atom, std::size_t num) |
| Sets the Chem::AtomProperty::CANONICAL_NUMBER property of atom to num. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearCanonicalNumber (Atom &atom) |
| Removes the Chem::AtomProperty::CANONICAL_NUMBER property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasCanonicalNumber (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::CANONICAL_NUMBER property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getCIPPriority (const Atom &atom) |
| Returns the Chem::AtomProperty::CIP_PRIORITY property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setCIPPriority (Atom &atom, std::size_t priority) |
| Sets the Chem::AtomProperty::CIP_PRIORITY property of atom to priority. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearCIPPriority (Atom &atom) |
| Removes the Chem::AtomProperty::CIP_PRIORITY property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasCIPPriority (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::CIP_PRIORITY property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getSymmetryClass (const Atom &atom) |
| Returns the Chem::AtomProperty::SYMMETRY_CLASS property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setSymmetryClass (Atom &atom, std::size_t class_id) |
| Sets the Chem::AtomProperty::SYMMETRY_CLASS property of atom to class_id. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearSymmetryClass (Atom &atom) |
| Removes the Chem::AtomProperty::SYMMETRY_CLASS property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasSymmetryClass (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::SYMMETRY_CLASS property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getCIPConfiguration (const Atom &atom) |
| Returns the Chem::AtomProperty::CIP_CONFIGURATION property of atom (see namespace Chem::CIPDescriptor). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setCIPConfiguration (Atom &atom, unsigned int config) |
| Sets the Chem::AtomProperty::CIP_CONFIGURATION property of atom to config (see namespace Chem::CIPDescriptor). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearCIPConfiguration (Atom &atom) |
| Removes the Chem::AtomProperty::CIP_CONFIGURATION property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasCIPConfiguration (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::CIP_CONFIGURATION property. More... | |
| CDPL_CHEM_API const StereoDescriptor & | CDPL::Chem::getStereoDescriptor (const Atom &atom) |
| Returns the Chem::AtomProperty::STEREO_DESCRIPTOR property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setStereoDescriptor (Atom &atom, const StereoDescriptor &descr) |
| Sets the Chem::AtomProperty::STEREO_DESCRIPTOR property of atom to descr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearStereoDescriptor (Atom &atom) |
| Removes the Chem::AtomProperty::STEREO_DESCRIPTOR property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasStereoDescriptor (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::STEREO_DESCRIPTOR property. More... | |
| CDPL_CHEM_API StereoDescriptor | CDPL::Chem::calcStereoDescriptor (const Atom &atom, const MolecularGraph &molgraph, std::size_t dim=1) |
| Computes the stereo descriptor for atom based on the geometry of molgraph. More... | |
| CDPL_CHEM_API StereoDescriptor | CDPL::Chem::calcStereoDescriptorFromMDLParity (const Atom &atom, const MolecularGraph &molgraph) |
| Derives the stereo descriptor of atom from its MDL parity in molgraph. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::calcConfiguration (const Atom &atom, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords) |
| Derives the atom configuration label from the supplied descriptor and 3D coordinates. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getStereoCenterFlag (const Atom &atom) |
| Returns the Chem::AtomProperty::STEREO_CENTER_FLAG property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setStereoCenterFlag (Atom &atom, bool is_center) |
| Sets the Chem::AtomProperty::STEREO_CENTER_FLAG property of atom to is_center. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearStereoCenterFlag (Atom &atom) |
| Removes the Chem::AtomProperty::STEREO_CENTER_FLAG property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasStereoCenterFlag (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::STEREO_CENTER_FLAG property. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::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) |
| Tells whether atom qualifies as a stereo center in the context of molgraph. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getSybylType (const Atom &atom) |
| Returns the Chem::AtomProperty::SYBYL_TYPE property of atom (see namespace Chem::SybylAtomType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setSybylType (Atom &atom, unsigned int type) |
| Sets the Chem::AtomProperty::SYBYL_TYPE property of atom to type (see namespace Chem::SybylAtomType). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearSybylType (Atom &atom) |
| Removes the Chem::AtomProperty::SYBYL_TYPE property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasSybylType (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::SYBYL_TYPE property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::perceiveSybylType (const Atom &atom, const MolecularGraph &molgraph) |
| Derives the Sybyl atom type of atom from its valence environment in molgraph. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMOL2Name (const Atom &atom) |
| Returns the Chem::AtomProperty::MOL2_NAME property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2Name (Atom &atom, const std::string &name) |
| Sets the Chem::AtomProperty::MOL2_NAME property of atom to name. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2Name (Atom &atom) |
| Removes the Chem::AtomProperty::MOL2_NAME property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2Name (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MOL2_NAME property. More... | |
| CDPL_CHEM_API double | CDPL::Chem::getMOL2Charge (const Atom &atom) |
| Returns the Chem::AtomProperty::MOL2_CHARGE property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2Charge (Atom &atom, double charge) |
| Sets the Chem::AtomProperty::MOL2_CHARGE property of atom to charge. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2Charge (Atom &atom) |
| Removes the Chem::AtomProperty::MOL2_CHARGE property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2Charge (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MOL2_CHARGE property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getMOL2SubstructureID (const Atom &atom) |
| Returns the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2SubstructureID (Atom &atom, std::size_t id) |
| Sets the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property of atom to id. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2SubstructureID (Atom &atom) |
| Removes the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2SubstructureID (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MOL2_SUBSTRUCTURE_ID property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMOL2SubstructureName (const Atom &atom) |
| Returns the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2SubstructureName (Atom &atom, const std::string &id) |
| Sets the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property of atom to id. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2SubstructureName (Atom &atom) |
| Removes the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2SubstructureName (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MOL2_SUBSTRUCTURE_NAME property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMOL2SubstructureSubtype (const Atom &atom) |
| Returns the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2SubstructureSubtype (Atom &atom, const std::string &subtype) |
| Sets the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property of atom to subtype. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2SubstructureSubtype (Atom &atom) |
| Removes the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2SubstructureSubtype (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MOL2_SUBSTRUCTURE_SUBTYPE property. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMOL2SubstructureChain (const Atom &atom) |
| Returns the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMOL2SubstructureChain (Atom &atom, const std::string &chain) |
| Sets the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property of atom to chain. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMOL2SubstructureChain (Atom &atom) |
| Removes the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMOL2SubstructureChain (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MOL2_SUBSTRUCTURE_CHAIN property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getMDLParity (const Atom &atom) |
| Returns the Chem::AtomProperty::MDL_PARITY property of atom (see namespace Chem::MDLParity). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLParity (Atom &atom, unsigned int parity) |
| Sets the Chem::AtomProperty::MDL_PARITY property of atom to parity (see namespace Chem::MDLParity). More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLParity (Atom &atom) |
| Removes the Chem::AtomProperty::MDL_PARITY property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLParity (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MDL_PARITY property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::calcMDLParity (const Atom &atom, const MolecularGraph &molgraph) |
| Computes the MDL parity of atom from its 2D layout and stereo flags in molgraph. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getMDLStereoCareFlag (const Atom &atom) |
| Returns the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMDLStereoCareFlag (Atom &atom, bool flag) |
| Sets the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property of atom to flag. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMDLStereoCareFlag (Atom &atom) |
| Removes the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMDLStereoCareFlag (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MDL_DB_STEREO_CARE_FLAG property. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getReactionCenterStatus (const Atom &atom) |
| Returns the Chem::AtomProperty::REACTION_CENTER_STATUS property of atom (see namespace Chem::ReactionCenterStatus). More... | |
| CDPL_CHEM_API void | CDPL::Chem::setReactionCenterStatus (Atom &atom, unsigned int status) |
| Sets the Chem::AtomProperty::REACTION_CENTER_STATUS property of atom to status. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearReactionCenterStatus (Atom &atom) |
| Removes the Chem::AtomProperty::REACTION_CENTER_STATUS property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasReactionCenterStatus (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::REACTION_CENTER_STATUS property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getAtomMappingID (const Atom &atom) |
| Returns the Chem::AtomProperty::ATOM_MAPPING_ID property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAtomMappingID (Atom &atom, std::size_t id) |
| Sets the Chem::AtomProperty::ATOM_MAPPING_ID property of atom to id. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearAtomMappingID (Atom &atom) |
| Removes the Chem::AtomProperty::ATOM_MAPPING_ID property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasAtomMappingID (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::ATOM_MAPPING_ID property. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getComponentGroupID (const Atom &atom) |
| Returns the Chem::AtomProperty::COMPONENT_GROUP_ID property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setComponentGroupID (Atom &atom, std::size_t id) |
| Sets the Chem::AtomProperty::COMPONENT_GROUP_ID property of atom to id. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearComponentGroupID (Atom &atom) |
| Removes the Chem::AtomProperty::COMPONENT_GROUP_ID property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasComponentGroupID (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::COMPONENT_GROUP_ID property. More... | |
| CDPL_CHEM_API const MatchConstraintList::SharedPointer & | CDPL::Chem::getMatchConstraints (const Atom &atom) |
| Returns the Chem::AtomProperty::MATCH_CONSTRAINTS property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchConstraints (Atom &atom, const MatchConstraintList::SharedPointer &constr) |
| Sets the Chem::AtomProperty::MATCH_CONSTRAINTS property of atom to constr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchConstraints (Atom &atom) |
| Removes the Chem::AtomProperty::MATCH_CONSTRAINTS property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchConstraints (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MATCH_CONSTRAINTS property. More... | |
| CDPL_CHEM_API const MatchExpression< Atom, MolecularGraph >::SharedPointer & | CDPL::Chem::getMatchExpression (const Atom &atom) |
| Returns the Chem::AtomProperty::MATCH_EXPRESSION property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchExpression (Atom &atom, const MatchExpression< Atom, MolecularGraph >::SharedPointer &expr) |
| Sets the Chem::AtomProperty::MATCH_EXPRESSION property of atom to expr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchExpression (Atom &atom) |
| Removes the Chem::AtomProperty::MATCH_EXPRESSION property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchExpression (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MATCH_EXPRESSION property. More... | |
| CDPL_CHEM_API MatchExpression< Atom, MolecularGraph >::SharedPointer | CDPL::Chem::generateMatchExpression (const Atom &atom, const MolecularGraph &molgraph) |
| Builds an atom-level match expression from the match-constraint list attached to atom. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMatchExpressionString (const Atom &atom) |
| Returns the Chem::AtomProperty::MATCH_EXPRESSION_STRING property of atom. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchExpressionString (Atom &atom, const std::string &expr_str) |
| Sets the Chem::AtomProperty::MATCH_EXPRESSION_STRING property of atom to expr_str. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchExpressionString (Atom &atom) |
| Removes the Chem::AtomProperty::MATCH_EXPRESSION_STRING property from atom. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchExpressionString (const Atom &atom) |
| Tells whether atom carries the Chem::AtomProperty::MATCH_EXPRESSION_STRING property. More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateMatchExpressionString (const Atom &atom, const MolecularGraph &molgraph, std::string &expr_str) |
| Writes a textual representation of the atom-level match expression of atom into expr_str. More... | |
| CDPL_CHEM_API void | CDPL::Chem::markReachableAtoms (const Atom &atom, const MolecularGraph &molgraph, Util::BitSet &atom_mask, bool reset=true) |
| Sets bits in atom_mask for every atom of molgraph that is reachable from atom through the bonds of molgraph. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getTopologicalDistance (const Atom &atom1, const Atom &atom2, const MolecularGraph &molgraph) |
| Returns the topological distance (number of edges along the shortest path) between two atoms of molgraph. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getEnvironment (const Atom &atom, const MolecularGraph &molgraph, std::size_t max_dist, Fragment &env, bool append=false) |
| Collects every atom of molgraph that is within max_dist bonds of atom into the fragment env. More... | |
| template<typename AtomType , typename OutputIterator > | |
| std::size_t | CDPL::Chem::getConnectedAtoms (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0) |
| Writes every neighbor of atom (with bonds belonging to molgraph) into it, skipping excl_atom. More... | |
| template<typename AtomType , typename OutputIterator > | |
| std::size_t | CDPL::Chem::getIncidentBonds (AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0) |
| Writes every bond incident to atom (with both endpoints belonging to molgraph) into it, skipping bonds to excl_atom. More... | |
| template<typename AtomType , typename AtomOutputIterator , typename BondOutputIterator > | |
| std::size_t | CDPL::Chem::getConnectedAtomsAndBonds (AtomType &atom, const MolecularGraph &molgraph, AtomOutputIterator ao_it, BondOutputIterator bo_it, AtomType *excl_atom=0) |
| Writes every neighbor of atom and the corresponding incident bond (both filtered by molgraph) into the supplied output iterators. More... | |
Declaration of functions that operate on Chem::Atom instances.
1.9.1