bond.hpp

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/*  $Id: bond.hpp 33815 2007-05-04 17:18:18Z kazimird $
* ===========================================================================
*
*                            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
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*
*  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