coord_set.cpp
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- /*
- * ===========================================================================
- * 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
- *
- */
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