bond.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: bond.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 17:30:59  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.8
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: bond.hpp,v 1000.1 2004/04/12 17:30:59 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 chemical bonds
*
* ===========================================================================
*/

#ifndef CN3D_BOND__HPP
#define CN3D_BOND__HPP

#include <objects/mmdb1/Inter_residue_bond.hpp>
#include <objects/mmdb1/Atom_pntr.hpp>

#include "structure_base.hpp"

BEGIN_SCOPE(Cn3D)

class AtomSet;

// A Bond is a link between two atoms, referenced by Atom-pntr (molecule,
// residue, and atom IDs).

class Bond : public StructureBase
{
public:
    enum eBondOrder {
        eSingle = ncbi::objects::CInter_residue_bond::eBond_order_single,
        ePartialDouble = ncbi::objects::CInter_residue_bond::eBond_order_partial_double,
        eAromatic = ncbi::objects::CInter_residue_bond::eBond_order_aromatic,
        eDouble = ncbi::objects::CInter_residue_bond::eBond_order_double,
        eTriple = ncbi::objects::CInter_residue_bond::eBond_order_triple,
        eOther = ncbi::objects::CInter_residue_bond::eBond_order_other,
        eUnknown = ncbi::objects::CInter_residue_bond::eBond_order_unknown,
        eVirtual,           // special identifier for virtual bonds (no "normal" bond order)
        eRealDisulfide,     // special flag for real disulfides (bonds between cysteine sulfur atoms)
        eVirtualDisulfide   // virtual disulfide - links C-alphas with disulfide color when bb trace
    };

    Bond(StructureBase *parent);

    // public data
    AtomPntr atom1, atom2;
    eBondOrder order;
    const Bond *previousVirtual, *nextVirtual;

    // public methods
    bool Draw(const AtomSet *data) const;
};

const Bond* MakeBond(StructureBase *parent,
    const ncbi::objects::CAtom_pntr& atomPtr1, const ncbi::objects::CAtom_pntr& atomPtr2,
    int bondOrder = Bond::eUnknown);
const Bond* MakeBond(StructureBase *parent,
    int mID1, int rID1, int aID1, int mID2, int rID2, int aID2,
    int bondOrder = Bond::eUnknown);

END_SCOPE(Cn3D)

#endif // CN3D_BOND__HPP

/*
* ---------------------------------------------------------------------------
* $Log: bond.hpp,v $
* Revision 1000.1  2004/04/12 17:30:59  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.8
*
* Revision 1.8  2004/02/19 17:04:44  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.7  2003/02/03 19:20:01  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.6  2001/03/23 04:18:20  thiessen
* parse and display disulfides
*
* Revision 1.5  2000/08/11 12:59:13  thiessen
* added worm; get 3d-object coords from asn1
*
* Revision 1.4  2000/08/03 15:12:29  thiessen
* add skeleton of style and show/hide managers
*
* Revision 1.3  2000/07/27 13:30:10  thiessen
* remove 'using namespace ...' from all headers
*
* Revision 1.2  2000/07/16 23:18:33  thiessen
* redo of drawing system
*
* Revision 1.1  2000/07/11 13:49:26  thiessen
* add modules to parse chemical graph; many improvements
*
*/