/* * =========================================================================== * PRODUCTION $Log: residue.hpp,v $ * PRODUCTION Revision 1000.1  2004/04/12 17:33:17  gouriano * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.20 * PRODUCTION * =========================================================================== *//*  $Id: residue.hpp,v 1000.1 2004/04/12 17:33:17 gouriano Exp $* ===========================================================================**                            PUBLIC DOMAIN NOTICE*               National Center for Biotechnology Information**  This software/database is a "United States Government Work" under the*  terms of the United States Copyright Act.  It was written as part of*  the author's official duties as a United States Government employee and*  thus cannot be copyrighted.  This software/database is freely available*  to the public for use. The National Library of Medicine and the U.S.*  Government have not placed any restriction on its use or reproduction.**  Although all reasonable efforts have been taken to ensure the accuracy*  and reliability of the software and data, the NLM and the U.S.*  Government do not and cannot warrant the performance or results that*  may be obtained by using this software or data. The NLM and the U.S.*  Government disclaim all warranties, express or implied, including*  warranties of performance, merchantability or fitness for any particular*  purpose.**  Please cite the author in any work or product based on this material.** ===========================================================================** Authors:  Paul Thiessen** File Description:*      Classes to hold residues** ===========================================================================*/#ifndef CN3D_RESIDUE__HPP#define CN3D_RESIDUE__HPP#include <corelib/ncbistl.hpp>#include <map>#include <string>#include <objects/mmdb1/Residue_graph.hpp>#include <objects/mmdb1/Residue.hpp>#include "structure_base.hpp"BEGIN_SCOPE(Cn3D)typedef std::list< ncbi::CRef< ncbi::objects::CResidue_graph > > ResidueGraphList;// a Residue is a set of bonds that connect one residue of a larger Molecule.// Its constructor is where most of the work of decoding the ASN1 graph is done,// based on the standard and local residue dictionaries. Each Residue also holds// information (AtomInfo) about the nature of the atoms it contains.class Bond;class Residue : public StructureBase{public:    Residue(StructureBase *parent,        const ncbi::objects::CResidue& residue, int moleculeID,        const ResidueGraphList& standardDictionary,        const ResidueGraphList& localDictionary);    ~Residue(void);    // public data    int id;    static const char NO_CODE;    char code;    std::string        nameGraph,  // 'name' field from residue-graph dictionary        namePDB;    // 'name' in Residue, supposed to correspond to PDB-assigned residue number    static const int NO_ALPHA_ID;    int alphaID; // ID of "alpha" atom (C-alpha or P)    // residue type    enum eType {        eDNA = ncbi::objects::CResidue_graph::eResidue_type_deoxyribonucleotide,        eRNA = ncbi::objects::CResidue_graph::eResidue_type_ribonucleotide,        eAminoAcid = ncbi::objects::CResidue_graph::eResidue_type_amino_acid,        eOther = ncbi::objects::CResidue_graph::eResidue_type_other    };    eType type;    // atom type    enum eAtomClassification {        eSideChainAtom,        eAlphaBackboneAtom,     // C-alpha or P        ePartialBackboneAtom,   // for unbranched backbone trace        eCompleteBackboneAtom,  // all backbone atoms        eUnknownAtom            // anything that's not known to be of an amino acid or nucleotide    };    typedef struct {        std::string name, code;        int atomicNumber;        eAtomClassification classification;        unsigned int glName;        const Residue *residue;  // convenient way to go from atom->residue        bool isIonizableProton;    } AtomInfo;    typedef std::list < const Bond * > BondList;    BondList bonds;    // public methods    bool HasCode(void) const { return (code != NO_CODE); }    bool HasName(void) const { return (!nameGraph.empty()); }    bool IsNucleotide(void) const { return (type == eDNA || type == eRNA); }    bool IsAminoAcid(void) const { return (type == eAminoAcid); }    bool Draw(const AtomSet *atomSet) const;    typedef std::map < int , const AtomInfo * > AtomInfoMap;private:    AtomInfoMap atomInfos;  // mapped by Atom-id    int nAtomsWithAnyCoords;public:    // # atoms in the graph for this residue    int NAtomsInGraph(void) const { return atomInfos.size(); }    // # atoms in this residue with real coordinates in any model    int NAtomsWithAnyCoords(void) const { return nAtomsWithAnyCoords; }    const AtomInfoMap& GetAtomInfos(void) const { return atomInfos; }    const AtomInfo * GetAtomInfo(int aID) const    {        AtomInfoMap::const_iterator info=atomInfos.find(aID);        if (info != atomInfos.end()) return (*info).second;        ERR_POST(ncbi::Warning << "Residue #" << id << ": can't find atom #" << aID);        return NULL;    }};END_SCOPE(Cn3D)#endif // CN3D_RESIDUE__HPP/** ---------------------------------------------------------------------------* $Log: residue.hpp,v $* Revision 1000.1  2004/04/12 17:33:17  gouriano* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.20** Revision 1.20  2004/02/19 17:05:05  thiessen* remove cn3d/ from include paths; add pragma to disable annoying msvc warning** Revision 1.19  2003/06/21 08:18:58  thiessen* show all atoms with coordinates, even if not in all coord sets** Revision 1.18  2003/02/03 19:20:05  thiessen* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros** Revision 1.17  2001/05/31 18:46:27  thiessen* add preliminary style dialog; remove LIST_TYPE; add thread single and delete all; misc tweaks** Revision 1.16  2001/05/15 23:49:20  thiessen* minor adjustments to compile under Solaris/wxGTK** Revision 1.15  2001/04/18 15:46:32  thiessen* show description, length, and PDB numbering in status line** Revision 1.14  2001/03/28 23:01:38  thiessen* first working full threading** Revision 1.13  2001/03/23 23:31:30  thiessen* keep atom info around even if coords not all present; mainly for disulfide parsing in virtual models** Revision 1.12  2000/10/04 17:40:46  thiessen* rearrange STL #includes** Revision 1.11  2000/08/30 19:49:04  thiessen* working sequence window** Revision 1.10  2000/08/24 18:43:15  thiessen* tweaks for transparent sphere display** Revision 1.9  2000/08/17 14:22:00  thiessen* added working StyleManager** Revision 1.8  2000/08/11 12:59:13  thiessen* added worm; get 3d-object coords from asn1** Revision 1.7  2000/08/04 22:49:11  thiessen* add backbone atom classification and selection feedback mechanism** Revision 1.6  2000/08/03 15:12:29  thiessen* add skeleton of style and show/hide managers** Revision 1.5  2000/07/27 13:30:10  thiessen* remove 'using namespace ...' from all headers** Revision 1.4  2000/07/17 11:58:58  thiessen* fix nucleotide virtual bonds** Revision 1.3  2000/07/17 04:21:10  thiessen* now does correct structure alignment transformation** Revision 1.2  2000/07/16 23:18:34  thiessen* redo of drawing system** Revision 1.1  2000/07/11 13:49:29  thiessen* add modules to parse chemical graph; many improvements**/