Biomol/AtomFunctions.hpp File Reference

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 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 atom to name. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearResidueAtomName (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_ATOM_NAME property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasResidueAtomName (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_ATOM_NAME property. 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 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 atom to name. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearResidueAltAtomName (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasResidueAltAtomName (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_ALT_ATOM_NAME property. 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 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 atom to leaving. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearResidueLeavingAtomFlag (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasResidueLeavingAtomFlag (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_LEAVING_ATOM_FLAG property. 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 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 atom to linking. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearResidueLinkingAtomFlag (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasResidueLinkingAtomFlag (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_LINKING_ATOM_FLAG property. 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 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 atom to code. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearResidueCode (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_CODE property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasResidueCode (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_CODE property. More...
CDPL_BIOMOL_API long	CDPL::Biomol::getResidueSequenceNumber (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property of 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 atom to seq_no. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearResidueSequenceNumber (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasResidueSequenceNumber (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_SEQUENCE_NUMBER property. More...
CDPL_BIOMOL_API char	CDPL::Biomol::getResidueInsertionCode (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property of 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 atom to code. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearResidueInsertionCode (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::RESIDUE_INSERTION_CODE property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasResidueInsertionCode (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::RESIDUE_INSERTION_CODE property. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::getHeteroAtomFlag (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::HETERO_ATOM_FLAG property of 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 atom to is_het. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearHeteroAtomFlag (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::HETERO_ATOM_FLAG property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasHeteroAtomFlag (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::HETERO_ATOM_FLAG property. 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 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 atom to id. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearChainID (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::CHAIN_ID property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasChainID (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::CHAIN_ID property. More...
CDPL_BIOMOL_API char	CDPL::Biomol::getAltLocationID (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::ALT_LOCATION_ID property of 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 atom to id. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearAltLocationID (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::ALT_LOCATION_ID property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasAltLocationID (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::ALT_LOCATION_ID property. 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 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 atom to id. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearEntityID (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::ENTITY_ID property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasEntityID (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::ENTITY_ID property. 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 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 atom to model_no. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearModelNumber (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::MODEL_NUMBER property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasModelNumber (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::MODEL_NUMBER property. More...
CDPL_BIOMOL_API long	CDPL::Biomol::getSerialNumber (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::SERIAL_NUMBER property of 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 atom to serial_no. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearSerialNumber (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::SERIAL_NUMBER property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasSerialNumber (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::SERIAL_NUMBER property. More...
CDPL_BIOMOL_API double	CDPL::Biomol::getOccupancy (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::OCCUPANCY property of atom. More...
CDPL_BIOMOL_API void	CDPL::Biomol::setOccupancy (Chem::Atom &atom, double occupancy)
	Sets the value of the Biomol::AtomProperty::OCCUPANCY property of atom to occupancy. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearOccupancy (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::OCCUPANCY property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasOccupancy (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::OCCUPANCY property. More...
CDPL_BIOMOL_API double	CDPL::Biomol::getBFactor (const Chem::Atom &atom)
	Returns the value of the Biomol::AtomProperty::B_FACTOR property of 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 atom to factor. More...
CDPL_BIOMOL_API void	CDPL::Biomol::clearBFactor (Chem::Atom &atom)
	Removes the Biomol::AtomProperty::B_FACTOR property from atom. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::hasBFactor (const Chem::Atom &atom)
	Tells whether atom carries an explicit Biomol::AtomProperty::B_FACTOR property. More...
CDPL_BIOMOL_API bool	CDPL::Biomol::isPDBBackboneAtom (const Chem::Atom &atom)
	Tells whether atom is a backbone atom of a PDB-style 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-identity attributes of 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 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 atom belongs to into res_substruct. More...

Detailed Description

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