coord_set.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: coord_set.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 18:28:31  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: coord_set.cpp,v 1000.2 2004/06/01 18:28:31 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 sets of coordinates for atoms and features
*
* ===========================================================================
*/

#ifdef _MSC_VER
#pragma warning(disable:4018)   // disable signed/unsigned mismatch warning in MSVC
#endif

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>

#include <objects/mmdb2/Model_coordinate_set.hpp>
#include <objects/mmdb2/Coordinates.hpp>
#include <objects/mmdb2/Surface_coordinates.hpp>
#include <objects/mmdb2/Model_descr.hpp>
#include <objects/mmdb3/Chem_graph_pntrs.hpp>
#include <objects/mmdb2/Surface_coordinates.hpp>

#include "coord_set.hpp"
#include "atom_set.hpp"
#include "object_3d.hpp"
#include "cn3d_tools.hpp"

USING_NCBI_SCOPE;
USING_SCOPE(objects);


BEGIN_SCOPE(Cn3D)

CoordSet::CoordSet(StructureBase *parent,
                   const CBiostruc_model::TModel_coordinates& modelCoords) :
    StructureBase(parent), atomSet(NULL)
{
    // iterate SEQUENCE OF Model-coordinate-set
    CBiostruc_model::TModel_coordinates::const_iterator j, je=modelCoords.end();
    for (j=modelCoords.begin(); j!=je; ++j) {
        const CModel_coordinate_set::C_Coordinates&
            coordSet = j->GetObject().GetCoordinates();
        if (coordSet.IsLiteral()) {
            const CCoordinates& coords = coordSet.GetLiteral();

            // coordinates of atoms
            if (coords.IsAtomic()) {
                if (!atomSet)
                    atomSet = new AtomSet(this, coords.GetAtomic());
                else
                    ERRORMSG("confused by multiple atomic coords");
            }

            // coordinates of 3d-objects
            else if (coords.IsSurface() && j->GetObject().IsSetDescr() &&
                j->GetObject().GetDescr().front().GetObject().IsOther_comment() &&
                coords.GetSurface().GetContents().IsResidues()) {

                const string& descr =
                    j->GetObject().GetDescr().front().GetObject().GetOther_comment();

                // helix cylinder
                if (descr == "helix" && coords.GetSurface().GetSurface().IsCylinder()) {
                    Helix3D *helix =
                        new Helix3D(this, coords.GetSurface().GetSurface().GetCylinder(),
                            coords.GetSurface().GetContents().GetResidues());
                    if (helix->moleculeID == Object3D::VALUE_NOT_SET) {
                        this->_RemoveChild(helix);
                        delete helix;
                        WARNINGMSG("bad helix");
                    } else
                        objectMap[helix->moleculeID].push_back(helix);

                // strand brick
                } else if (descr == "strand" && coords.GetSurface().GetSurface().IsBrick()) {
                    Strand3D *strand =
                        new Strand3D(this, coords.GetSurface().GetSurface().GetBrick(),
                            coords.GetSurface().GetContents().GetResidues());
                    if (strand->moleculeID == Object3D::VALUE_NOT_SET) {
                        this->_RemoveChild(strand);
                        delete strand;
                        WARNINGMSG("bad strand");
                    } else
                        objectMap[strand->moleculeID].push_back(strand);
                }
            }
        }
    }
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: coord_set.cpp,v $
* Revision 1000.2  2004/06/01 18:28:31  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
*
* Revision 1.15  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.14  2004/03/15 18:23:01  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.13  2004/02/19 17:04:54  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.12  2003/02/03 19:20:03  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.11  2001/05/31 18:54:21  thiessen
* TESTMSG moved
*
* Revision 1.10  2001/02/08 23:01:50  thiessen
* hook up C-toolkit stuff for threading; working PSSM calculation
*
* Revision 1.9  2000/08/27 18:52:21  thiessen
* extract sequence information
*
* Revision 1.8  2000/08/16 14:18:44  thiessen
* map 3-d objects to molecules
*
* Revision 1.7  2000/08/11 12:58:31  thiessen
* added worm; get 3d-object coords from asn1
*
* Revision 1.6  2000/08/07 00:21:17  thiessen
* add display list mechanism
*
* Revision 1.5  2000/08/03 15:12:23  thiessen
* add skeleton of style and show/hide managers
*
* Revision 1.4  2000/07/27 13:30:51  thiessen
* remove 'using namespace ...' from all headers
*
* Revision 1.3  2000/07/16 23:19:10  thiessen
* redo of drawing system
*
* Revision 1.2  2000/07/12 23:27:49  thiessen
* now draws basic CPK model
*
* Revision 1.1  2000/07/11 13:45:29  thiessen
* add modules to parse chemical graph; many improvements
*
*/