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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 "CDPL/Biomol/APIPrefix.hpp"#include "CDPL/Biomol/ProcessingFlags.hpp"#include "CDPL/Biomol/AtomPropertyFlag.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. | |
| CDPL::Biomol | |
| Contains classes and functions related to biological macromolecules. | |
Functions | |
| CDPL_BIOMOL_API const std::string & | CDPL::Biomol::getResidueAtomName (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setResidueAtomName (Chem::Atom &atom, const std::string &name) |
| Sets the value of the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of the atom atom to name. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearResidueAtomName (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasResidueAtomName (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::RESIDUE_ATOM_NAME property of the atom atom is set. More... | |
| CDPL_BIOMOL_API const std::string & | CDPL::Biomol::getResidueAltAtomName (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setResidueAltAtomName (Chem::Atom &atom, const std::string &name) |
| Sets the value of the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of the atom atom to name. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearResidueAltAtomName (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasResidueAltAtomName (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property of the atom atom is set. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::getResidueLeavingAtomFlag (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setResidueLeavingAtomFlag (Chem::Atom &atom, bool leaving) |
| Sets the value of the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of the atom atom to leaving. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearResidueLeavingAtomFlag (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasResidueLeavingAtomFlag (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property of the atom atom is set. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::getResidueLinkingAtomFlag (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setResidueLinkingAtomFlag (Chem::Atom &atom, bool linking) |
| Sets the value of the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of the atom atom to linking. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearResidueLinkingAtomFlag (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasResidueLinkingAtomFlag (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property of the atom atom is set. More... | |
| CDPL_BIOMOL_API const std::string & | CDPL::Biomol::getResidueCode (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::RESIDUE_CODE property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setResidueCode (Chem::Atom &atom, const std::string &code) |
| Sets the value of the Biomol::AtomProperty::RESIDUE_CODE property of the atom atom to code. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearResidueCode (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::RESIDUE_CODE property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasResidueCode (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::RESIDUE_CODE property of the atom atom is set. More... | |
| CDPL_BIOMOL_API long | CDPL::Biomol::getResidueSequenceNumber (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setResidueSequenceNumber (Chem::Atom &atom, long seq_no) |
| Sets the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of the atom atom to seq_no. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearResidueSequenceNumber (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasResidueSequenceNumber (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of the atom atom is set. More... | |
| CDPL_BIOMOL_API char | CDPL::Biomol::getResidueInsertionCode (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setResidueInsertionCode (Chem::Atom &atom, char code) |
| Sets the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of the atom atom to code. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearResidueInsertionCode (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasResidueInsertionCode (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of the atom atom is set. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::getHeteroAtomFlag (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setHeteroAtomFlag (Chem::Atom &atom, bool is_het) |
| Sets the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of the atom atom to is_het. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearHeteroAtomFlag (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasHeteroAtomFlag (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::HETERO_ATOM_FLAG property of the atom atom is set. More... | |
| CDPL_BIOMOL_API const std::string & | CDPL::Biomol::getChainID (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::CHAIN_ID property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setChainID (Chem::Atom &atom, const std::string &id) |
| Sets the value of the Biomol::AtomProperty::CHAIN_ID property of the atom atom to id. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearChainID (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::CHAIN_ID property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasChainID (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::CHAIN_ID property of the atom atom is set. More... | |
| CDPL_BIOMOL_API char | CDPL::Biomol::getAltLocationID (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setAltLocationID (Chem::Atom &atom, char id) |
| Sets the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of the atom atom to id. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearAltLocationID (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasAltLocationID (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::ALT_LOCATION_ID property of the atom atom is set. More... | |
| CDPL_BIOMOL_API const std::string & | CDPL::Biomol::getEntityID (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::ENTITY_ID property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setEntityID (Chem::Atom &atom, const std::string &id) |
| Sets the value of the Biomol::AtomProperty::ENTITY_ID property of the atom atom to id. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearEntityID (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::ENTITY_ID property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasEntityID (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::ENTITY_ID property of the atom atom is set. More... | |
| CDPL_BIOMOL_API std::size_t | CDPL::Biomol::getModelNumber (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::MODEL_NUMBER property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setModelNumber (Chem::Atom &atom, std::size_t model_no) |
| Sets the value of the Biomol::AtomProperty::MODEL_NUMBER property of the atom atom to model_no. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearModelNumber (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::MODEL_NUMBER property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasModelNumber (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::MODEL_NUMBER property of the atom atom is set. More... | |
| CDPL_BIOMOL_API long | CDPL::Biomol::getSerialNumber (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::SERIAL_NUMBER property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setSerialNumber (Chem::Atom &atom, long serial_no) |
| Sets the value of the Biomol::AtomProperty::SERIAL_NUMBER property of the atom atom to serial_no. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearSerialNumber (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::SERIAL_NUMBER property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasSerialNumber (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::SERIAL_NUMBER property of the atom atom is set. More... | |
| CDPL_BIOMOL_API double | CDPL::Biomol::getOccupancy (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::OCCUPANCY property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setOccupancy (Chem::Atom &atom, double occupancy) |
| Sets the value of the Biomol::AtomProperty::OCCUPANCY property of the atom atom to occupancy. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearOccupancy (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::OCCUPANCY property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasOccupancy (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::OCCUPANCY property of the atom atom is set. More... | |
| CDPL_BIOMOL_API double | CDPL::Biomol::getBFactor (const Chem::Atom &atom) |
| Returns the value of the Biomol::AtomProperty::B_FACTOR property of the atom atom. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::setBFactor (Chem::Atom &atom, double factor) |
| Sets the value of the Biomol::AtomProperty::B_FACTOR property of the atom atom to factor. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::clearBFactor (Chem::Atom &atom) |
| Clears the value of the Biomol::AtomProperty::B_FACTOR property of the atom atom. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::hasBFactor (const Chem::Atom &atom) |
| Tells whether the Biomol::AtomProperty::B_FACTOR property of the atom atom is set. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::isPDBBackboneAtom (const Chem::Atom &atom) |
| Tells whether the atom atom is a backbone atom of an amino acid or nucleotide residue. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::matchesResidueInfo (const Chem::Atom &atom, const char *res_code=0, const char *chain_id=0, long res_seq_no=IGNORE_SEQUENCE_NO, char ins_code=0, std::size_t model_no=0, const char *atom_name=0, long serial_no=IGNORE_SERIAL_NO) |
| Tells whether the residue attributes of the atom atom match the given filter values. More... | |
| CDPL_BIOMOL_API bool | CDPL::Biomol::areInSameResidue (const Chem::Atom &atom1, const Chem::Atom &atom2, unsigned int flags=AtomPropertyFlag::DEFAULT) |
| Tells whether the atoms atom1 and atom2 belong to the same residue, comparing the atom properties selected by flags. More... | |
| CDPL_BIOMOL_API void | CDPL::Biomol::extractResidueSubstructure (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, Chem::Fragment &res_substruct, bool cnctd_only=false, unsigned int flags=AtomPropertyFlag::DEFAULT, bool append=false) |
| Extracts the substructure of the residue the atom atom belongs to into res_substruct. More... | |
Declaration of functions that operate on Chem::Atom instances.
1.9.1