bond.hpp
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- /*
- * ===========================================================================
- * 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
- *
- */