Biomol/AtomFunctions.hpp

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/* 
 * AtomFunctions.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_BIOMOL_ATOMFUNCTIONS_HPP
#define CDPL_BIOMOL_ATOMFUNCTIONS_HPP
 
#include <cstddef>
#include <string>
 
#include "CDPL/Biomol/APIPrefix.hpp"
#include "CDPL/Biomol/ProcessingFlags.hpp"
#include "CDPL/Biomol/AtomPropertyFlag.hpp"
 
 
namespace CDPL
{
 
    namespace Chem
    {
 
        class Atom;
        class MolecularGraph;
        class Fragment;
    } // namespace Chem
 
    namespace Biomol
    {
 
        CDPL_BIOMOL_API const std::string& getResidueAtomName(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setResidueAtomName(Chem::Atom& atom, const std::string& name);
 
        CDPL_BIOMOL_API void clearResidueAtomName(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasResidueAtomName(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API const std::string& getResidueAltAtomName(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setResidueAltAtomName(Chem::Atom& atom, const std::string& name);
 
        CDPL_BIOMOL_API void clearResidueAltAtomName(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasResidueAltAtomName(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API bool getResidueLeavingAtomFlag(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setResidueLeavingAtomFlag(Chem::Atom& atom, bool leaving);
 
        CDPL_BIOMOL_API void clearResidueLeavingAtomFlag(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasResidueLeavingAtomFlag(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API bool getResidueLinkingAtomFlag(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setResidueLinkingAtomFlag(Chem::Atom& atom, bool linking);
 
        CDPL_BIOMOL_API void clearResidueLinkingAtomFlag(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasResidueLinkingAtomFlag(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API const std::string& getResidueCode(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setResidueCode(Chem::Atom& atom, const std::string& code);
 
        CDPL_BIOMOL_API void clearResidueCode(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasResidueCode(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API long getResidueSequenceNumber(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setResidueSequenceNumber(Chem::Atom& atom, long seq_no);
 
        CDPL_BIOMOL_API void clearResidueSequenceNumber(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasResidueSequenceNumber(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API char getResidueInsertionCode(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setResidueInsertionCode(Chem::Atom& atom, char code);
 
        CDPL_BIOMOL_API void clearResidueInsertionCode(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasResidueInsertionCode(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API bool getHeteroAtomFlag(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setHeteroAtomFlag(Chem::Atom& atom, bool is_het);
 
        CDPL_BIOMOL_API void clearHeteroAtomFlag(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasHeteroAtomFlag(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API const std::string& getChainID(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setChainID(Chem::Atom& atom, const std::string& id);
 
        CDPL_BIOMOL_API void clearChainID(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasChainID(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API char getAltLocationID(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setAltLocationID(Chem::Atom& atom, char id);
 
        CDPL_BIOMOL_API void clearAltLocationID(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasAltLocationID(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API const std::string& getEntityID(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setEntityID(Chem::Atom& atom, const std::string& id);
 
        CDPL_BIOMOL_API void clearEntityID(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasEntityID(const Chem::Atom& atom);
 
        
        CDPL_BIOMOL_API std::size_t getModelNumber(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setModelNumber(Chem::Atom& atom, std::size_t model_no);
 
        CDPL_BIOMOL_API void clearModelNumber(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasModelNumber(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API long getSerialNumber(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setSerialNumber(Chem::Atom& atom, long serial_no);
 
        CDPL_BIOMOL_API void clearSerialNumber(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasSerialNumber(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API double getOccupancy(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setOccupancy(Chem::Atom& atom, double occupancy);
 
        CDPL_BIOMOL_API void clearOccupancy(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasOccupancy(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API double getBFactor(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API void setBFactor(Chem::Atom& atom, double factor);
 
        CDPL_BIOMOL_API void clearBFactor(Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool hasBFactor(const Chem::Atom& atom);
 
 
        CDPL_BIOMOL_API bool isPDBBackboneAtom(const Chem::Atom& atom);
 
        CDPL_BIOMOL_API bool 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);
 
        CDPL_BIOMOL_API bool areInSameResidue(const Chem::Atom& atom1, const Chem::Atom& atom2, unsigned int flags = AtomPropertyFlag::DEFAULT);
 
        CDPL_BIOMOL_API void 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);
    } // namespace Biomol
} // namespace CDPL
 
#endif // CDPL_BIOMOL_ATOMFUNCTIONS_HPP