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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::Bond instances. More...
#include <cstddef>#include <string>#include "CDPL/Chem/APIPrefix.hpp"#include "CDPL/Chem/MatchExpression.hpp"#include "CDPL/Chem/MatchConstraintList.hpp"#include "CDPL/Chem/FragmentList.hpp"#include "CDPL/Math/VectorArray.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 std::size_t | CDPL::Chem::getOrder (const Bond &bond) |
| Returns the value of the Chem::BondProperty::ORDER property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setOrder (Bond &bond, std::size_t order) |
| Sets the value of the Chem::BondProperty::ORDER property of the bond bond to order. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearOrder (Bond &bond) |
| Clears the value of the Chem::BondProperty::ORDER property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasOrder (const Bond &bond) |
| Tells whether the Chem::BondProperty::ORDER property of the bond bond is set. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getRingFlag (const Bond &bond) |
| Returns the value of the Chem::BondProperty::RING_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setRingFlag (Bond &bond, bool in_ring) |
| Sets the value of the Chem::BondProperty::RING_FLAG property of the bond bond to in_ring. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearRingFlag (Bond &bond) |
| Clears the value of the Chem::BondProperty::RING_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasRingFlag (const Bond &bond) |
| Tells whether the Chem::BondProperty::RING_FLAG property of the bond bond is set. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::isInFragmentOfSize (const Bond &bond, const FragmentList &frag_list, std::size_t size) |
| Tells whether the bond bond is a member of any fragment in frag_list whose size matches size. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getSizeOfSmallestContainingFragment (const Bond &bond, const FragmentList &frag_list) |
| Returns the size (in atoms) of the smallest fragment in frag_list that contains the bond bond. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getSizeOfLargestContainingFragment (const Bond &bond, const FragmentList &frag_list) |
| Returns the size (in atoms) of the largest fragment in frag_list that contains the bond bond. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getNumContainingFragments (const Bond &bond, const FragmentList &frag_list) |
| Returns the number of fragments in frag_list that contain the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::getContainingFragments (const Bond &bond, const FragmentList &frag_list, FragmentList &cont_frag_list, bool append=false) |
| Collects the fragments in frag_list that contain the bond bond into cont_frag_list. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getAromaticityFlag (const Bond &bond) |
| Returns the value of the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setAromaticityFlag (Bond &bond, bool aromatic) |
| Sets the value of the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond to aromatic. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearAromaticityFlag (Bond &bond) |
| Clears the value of the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasAromaticityFlag (const Bond &bond) |
| Tells whether the Chem::BondProperty::AROMATICITY_FLAG property of the bond bond is set. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::get2DStereoFlag (const Bond &bond) |
| Returns the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::set2DStereoFlag (Bond &bond, unsigned int flag) |
| Sets the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond to flag. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clear2DStereoFlag (Bond &bond) |
| Clears the value of the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::has2DStereoFlag (const Bond &bond) |
| Tells whether the Chem::BondProperty::STEREO_2D_FLAG property of the bond bond is set. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getCIPConfiguration (const Bond &bond) |
| Returns the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setCIPConfiguration (Bond &bond, unsigned int config) |
| Sets the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond to config. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearCIPConfiguration (Bond &bond) |
| Clears the value of the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasCIPConfiguration (const Bond &bond) |
| Tells whether the Chem::BondProperty::CIP_CONFIGURATION property of the bond bond is set. More... | |
| CDPL_CHEM_API const StereoDescriptor & | CDPL::Chem::getStereoDescriptor (const Bond &bond) |
| Returns the value of the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setStereoDescriptor (Bond &bond, const StereoDescriptor &descr) |
| Sets the value of the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond to descr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearStereoDescriptor (Bond &bond) |
| Clears the value of the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasStereoDescriptor (const Bond &bond) |
| Tells whether the Chem::BondProperty::STEREO_DESCRIPTOR property of the bond bond is set. More... | |
| CDPL_CHEM_API StereoDescriptor | CDPL::Chem::calcStereoDescriptor (const Bond &bond, const MolecularGraph &molgraph, std::size_t dim=1) |
| Computes the stereo descriptor for the bond bond based on the geometry of the molecular graph molgraph. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::calcConfiguration (const Bond &bond, const MolecularGraph &molgraph, const StereoDescriptor &descr, const Math::Vector3DArray &coords) |
| Derives the bond configuration label from the supplied descriptor and 3D coordinates. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::getStereoCenterFlag (const Bond &bond) |
| Returns the value of the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setStereoCenterFlag (Bond &bond, bool is_center) |
| Sets the value of the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond to is_center. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearStereoCenterFlag (Bond &bond) |
| Clears the value of the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasStereoCenterFlag (const Bond &bond) |
| Tells whether the Chem::BondProperty::STEREO_CENTER_FLAG property of the bond bond is set. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::isStereoCenter (const Bond &bond, const MolecularGraph &molgraph, bool check_asym=true, bool check_term_n=true, bool check_order=true, std::size_t min_ring_size=8) |
| Tells whether the bond bond qualifies as a stereo center in the context of the molecular graph molgraph. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getDirection (const Bond &bond) |
| Returns the value of the Chem::BondProperty::DIRECTION property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setDirection (Bond &bond, unsigned int dir) |
| Sets the value of the Chem::BondProperty::DIRECTION property of the bond bond to dir. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearDirection (Bond &bond) |
| Clears the value of the Chem::BondProperty::DIRECTION property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasDirection (const Bond &bond) |
| Tells whether the Chem::BondProperty::DIRECTION property of the bond bond is set. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getReactionCenterStatus (const Bond &bond) |
| Returns the value of the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setReactionCenterStatus (Bond &bond, unsigned int status) |
| Sets the value of the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond to status. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearReactionCenterStatus (Bond &bond) |
| Clears the value of the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasReactionCenterStatus (const Bond &bond) |
| Tells whether the Chem::BondProperty::REACTION_CENTER_STATUS property of the bond bond is set. More... | |
| CDPL_CHEM_API const MatchConstraintList::SharedPointer & | CDPL::Chem::getMatchConstraints (const Bond &bond) |
| Returns the value of the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchConstraints (Bond &bond, const MatchConstraintList::SharedPointer &constr) |
| Sets the value of the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond to constr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchConstraints (Bond &bond) |
| Clears the value of the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchConstraints (const Bond &bond) |
| Tells whether the Chem::BondProperty::MATCH_CONSTRAINTS property of the bond bond is set. More... | |
| CDPL_CHEM_API const MatchExpression< Bond, MolecularGraph >::SharedPointer & | CDPL::Chem::getMatchExpression (const Bond &bond) |
| Returns the value of the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchExpression (Bond &bond, const MatchExpression< Bond, MolecularGraph >::SharedPointer &expr) |
| Sets the value of the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond to expr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchExpression (Bond &bond) |
| Clears the value of the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchExpression (const Bond &bond) |
| Tells whether the Chem::BondProperty::MATCH_EXPRESSION property of the bond bond is set. More... | |
| CDPL_CHEM_API MatchExpression< Bond, MolecularGraph >::SharedPointer | CDPL::Chem::generateMatchExpression (const Bond &bond, const MolecularGraph &molgraph) |
| Builds a bond-level match expression from the match constraint list attached to the bond bond. More... | |
| CDPL_CHEM_API const std::string & | CDPL::Chem::getMatchExpressionString (const Bond &bond) |
| Returns the value of the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setMatchExpressionString (Bond &bond, const std::string &expr_str) |
| Sets the value of the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond to expr_str. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearMatchExpressionString (Bond &bond) |
| Clears the value of the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasMatchExpressionString (const Bond &bond) |
| Tells whether the Chem::BondProperty::MATCH_EXPRESSION_STRING property of the bond bond is set. More... | |
| CDPL_CHEM_API void | CDPL::Chem::generateMatchExpressionString (const Bond &bond, const MolecularGraph &molgraph, std::string &str) |
| Writes a textual representation of the bond-level match expression of the bond bond into str. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::getSybylType (const Bond &bond) |
| Returns the value of the Chem::BondProperty::SYBYL_TYPE property of the bond bond. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setSybylType (Bond &bond, unsigned int type) |
| Sets the value of the Chem::BondProperty::SYBYL_TYPE property of the bond bond to type. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearSybylType (Bond &bond) |
| Clears the value of the Chem::BondProperty::SYBYL_TYPE property of the bond bond. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::hasSybylType (const Bond &bond) |
| Tells whether the Chem::BondProperty::SYBYL_TYPE property of the bond bond is set. More... | |
| CDPL_CHEM_API unsigned int | CDPL::Chem::perceiveSybylType (const Bond &bond, const MolecularGraph &molgraph) |
| Derives the Sybyl MOL2 bond type of the bond bond from its bond order, aromaticity and ligand environment in the molecular graph molgraph. More... | |
Declaration of functions that operate on Chem::Bond instances.
1.9.1