chemical_graph.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: chemical_graph.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 17:31:17  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.19
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: chemical_graph.hpp,v 1000.1 2004/04/12 17:31:17 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 the graph of chemical bonds
*
* ===========================================================================
*/

#ifndef CN3D_CHEMICALGRAPH__HPP
#define CN3D_CHEMICALGRAPH__HPP

#include <corelib/ncbistl.hpp>

#include <map>
#include <string>

#include <objects/mmdb1/Biostruc_graph.hpp>
#include <objects/mmdb3/Biostruc_feature_set.hpp>
#include <objects/mmdb1/Atom_pntr.hpp>

#include "structure_base.hpp"
#include "molecule.hpp"
#include "residue.hpp"

BEGIN_SCOPE(Cn3D)

// to create and delete dictionary - should be called on program init/exit
void LoadStandardDictionary(const char *filename);
void DeleteStandardDictionary(void);


// The ChemicalGraph is the set of bonds that link the atoms (from CoordSets).
// The graph is divided into essentially physically separate molecules (e.g.,
// protein chains, hets, solvents), occasionally joined by inter-molecule
// bonds ("connections" in Cn3D jargon).

class Bond;
class AtomSet;
class StructureObject;
class Molecule;

typedef std::list< ncbi::CRef< ncbi::objects::CBiostruc_feature_set > > FeatureList;

class ChemicalGraph : public StructureBase
{
public:
    ChemicalGraph(StructureBase *parent, const ncbi::objects::CBiostruc_graph& graph,
        const FeatureList& features);

    // public data
    typedef std::map < int, const Molecule * > MoleculeMap;
    MoleculeMap molecules;
    typedef std::list < const Bond * > BondList;
    BondList interMoleculeBonds;    // includes inter-molecular disulfides

    // public methods

    void RedrawMolecule(int moleculeID) const;
    bool DrawAll(const AtomSet *atomSet = NULL) const;
    const Residue::AtomInfo * GetAtomInfo(const AtomPntr& atom) const
    {
        MoleculeMap::const_iterator info=molecules.find(atom.mID);
        if (info != molecules.end()) return (*info).second->GetAtomInfo(atom.rID, atom.aID);
        ERR_POST(ncbi::Warning << "Graph: can't find molecule #" << atom.mID);
        return NULL;
    }

    // check if a bond between the given atoms is a disulfide bond; if so, flag Bond as disulfide, and
    // add new virtual disulfide Bond for these residues to the given bond list. Returns true if
    // a virtual disulfide was added to the bondList, false otherwise. (*Not* true or false depending
    // on whether the bond is actually a disulfide!)
    bool CheckForDisulfide(const Molecule *molecule,
        const ncbi::objects::CAtom_pntr& atomPtr1,
        const ncbi::objects::CAtom_pntr& atomPtr2,
        std::list < const Bond * > *bondList, Bond *bond, StructureBase *parent);

private:
    typedef std::list < std::pair < AtomSet *, const std::string * > > AtomSetList;
    AtomSetList atomSetList;
    unsigned int displayListOtherStart;

    void UnpackDomainFeatures(const ncbi::objects::CBiostruc_feature_set& featureSet);
    void UnpackSecondaryStructureFeatures(const ncbi::objects::CBiostruc_feature_set& featureSet);
};

END_SCOPE(Cn3D)

#endif // CN3D_CHEMICALGRAPH__HPP

/*
* ---------------------------------------------------------------------------
* $Log: chemical_graph.hpp,v $
* Revision 1000.1  2004/04/12 17:31:17  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.19
*
* Revision 1.19  2004/02/19 17:04:46  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.18  2003/02/03 19:20:02  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 18:46:25  thiessen
* add preliminary style dialog; remove LIST_TYPE; add thread single and delete all; misc tweaks
*
* Revision 1.16  2001/05/15 23:49:19  thiessen
* minor adjustments to compile under Solaris/wxGTK
*
* Revision 1.15  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 1.14  2001/03/23 04:18:20  thiessen
* parse and display disulfides
*
* Revision 1.13  2000/12/20 23:47:52  thiessen
* load CDD's
*
* Revision 1.12  2000/11/30 15:49:07  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
* Revision 1.11  2000/10/04 17:40:45  thiessen
* rearrange STL #includes
*
* Revision 1.10  2000/09/14 14:55:26  thiessen
* add row reordering; misc fixes
*
* Revision 1.9  2000/08/27 18:50:55  thiessen
* extract sequence information
*
* Revision 1.8  2000/08/21 17:22:45  thiessen
* add primitive highlighting for testing
*
* Revision 1.7  2000/08/07 00:20:18  thiessen
* add display list 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  2000/07/16 23:18:33  thiessen
* redo of drawing system
*
* Revision 1.3  2000/07/12 23:28:27  thiessen
* now draws basic CPK model
*
* Revision 1.2  2000/07/12 02:00:39  thiessen
* add basic wxWindows GUI
*
* Revision 1.1  2000/07/11 13:49:27  thiessen
* add modules to parse chemical graph; many improvements
*
*/