structure_set.hpp

ncbi源码

    // min and max atomic temperatures
    static const double NO_TEMPERATURE;
    double minTemperature, maxTemperature;

    // map of internal domainID -> Molecule and MMDB-assigned id
    typedef std::map < int, const Molecule * > DomainMap;
    DomainMap domainMap;
    typedef std::map < int, int > DomainIDMap;
    DomainIDMap domainID2MMDB;

    // public methods

    typedef std::map < const Residue *, const Molecule * > ResidueMap;
    void SelectByDistance(double cutoff, bool biopolymersOnly, bool otherMoleculesOnly,
        ResidueMap *selectedResidues) const;

    // set transform based on asn1 data
    bool SetTransformToMaster(const ncbi::objects::CBiostruc_annot_set& annot, int masterMMDBID);

    // set transform based on rigid body fit of given coordinates
    void RealignStructure(int nCoords,
        const Vector * const *masterCoords, const Vector * const *slaveCoords,
        const double *weights, int slaveRow);

    bool IsMaster(void) const { return isMaster; }
    bool IsSlave(void) const { return !isMaster; }
    int NDomains(void) const { return domainMap.size(); }
};

END_SCOPE(Cn3D)

#endif // CN3D_STRUCTURESET__HPP

/*
* ---------------------------------------------------------------------------
* $Log: structure_set.hpp,v $
* Revision 1000.2  2004/06/01 18:29:31  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.79
*
* Revision 1.79  2004/05/21 17:29:51  thiessen
* allow conversion of mime to cdd data
*
* Revision 1.78  2004/02/19 17:05:15  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.77  2003/07/17 20:13:51  thiessen
* don't ask for filename on save/termination with -f; add eAnyAlignmentData flag
*
* Revision 1.76  2003/07/17 16:52:34  thiessen
* add FileSaved message with edit typing
*
* Revision 1.75  2003/07/14 18:37:08  thiessen
* change GetUngappedAlignedBlocks() param types; other syntax changes
*
* Revision 1.74  2003/02/03 19:20:07  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.73  2003/01/27 15:52:22  thiessen
* merge after highlighted row; show rejects; trim rejects from new reject list
*
* Revision 1.72  2002/11/21 15:26:33  thiessen
* fix style dictionary loading bug
*
* Revision 1.71  2002/11/19 21:19:44  thiessen
* more const changes for objects; fix user vs default style bug
*
* Revision 1.70  2002/11/06 00:18:10  thiessen
* fixes for new CRef/const rules in objects
*
* Revision 1.69  2002/09/26 17:32:13  thiessen
* show distance between picked atoms; show RMS for structure alignments
*
* Revision 1.68  2002/09/19 12:51:08  thiessen
* fix block aligner / update bug; add distance select for other molecules only
*
* Revision 1.67  2002/09/14 17:03:07  thiessen
* center initial view on aligned residues
*
* Revision 1.66  2002/06/05 17:50:09  thiessen
* title tweaks
*
* Revision 1.65  2002/04/10 13:16:29  thiessen
* new selection by distance algorithm
*
* Revision 1.64  2002/02/19 14:59:40  thiessen
* add CDD reject and purge sequence
*
* Revision 1.63  2002/02/12 17:19:22  thiessen
* first working structure import
*
* Revision 1.62  2002/01/03 16:18:40  thiessen
* add distance selection
*
* Revision 1.61  2001/12/06 23:13:46  thiessen
* finish import/align new sequences into single-structure data; many small tweaks
*
* Revision 1.60  2001/11/27 16:26:10  thiessen
* major update to data management system
*
* Revision 1.59  2001/10/17 17:46:27  thiessen
* save camera setup and rotation center in files
*
* Revision 1.58  2001/10/09 18:57:27  thiessen
* add CDD references editing dialog
*
* Revision 1.57  2001/10/08 00:00:02  thiessen
* estimate threader N random starts; edit CDD name
*
* Revision 1.56  2001/10/01 16:03:58  thiessen
* make CDD annotation window non-modal; add SetWindowTitle to viewers
*
* Revision 1.55  2001/09/27 15:36:48  thiessen
* decouple sequence import and BLAST
*
* Revision 1.54  2001/09/18 03:09:38  thiessen
* add preliminary sequence import pipeline
*
* Revision 1.53  2001/08/15 20:53:58  juran
* Heed warnings.
*
* Revision 1.52  2001/08/13 22:30:52  thiessen
* add structure window mouse drag/zoom; add highlight option to render settings
*
* Revision 1.51  2001/07/12 17:34:23  thiessen
* change domain mapping ; add preliminary cdd annotation GUI
*
* Revision 1.50  2001/07/10 16:39:34  thiessen
* change selection control keys; add CDD name/notes dialogs
*
* Revision 1.49  2001/07/04 19:38:55  thiessen
* finish user annotation system
*
* Revision 1.48  2001/06/14 17:44:46  thiessen
* progress in styles<->asn ; add structure limits
*
* Revision 1.47  2001/06/14 00:33:23  thiessen
* asn additions
*
* Revision 1.46  2001/06/05 13:21:17  thiessen
* fix structure alignment list problems
*
* Revision 1.45  2001/05/31 18:46:27  thiessen
* add preliminary style dialog; remove LIST_TYPE; add thread single and delete all; misc tweaks
*
* Revision 1.44  2001/05/02 13:46:15  thiessen
* major revision of stuff relating to saving of updates; allow stored null-alignments
*
* Revision 1.43  2001/04/17 20:15:24  thiessen
* load 'pending' Cdd alignments into update window
*
* Revision 1.42  2001/03/23 15:13:46  thiessen
* load sidechains in CDD's
*
* Revision 1.41  2001/03/22 00:32:36  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.40  2001/02/16 00:36:48  thiessen
* remove unused sequences from asn data
*
* Revision 1.39  2001/02/13 01:03:04  thiessen
* backward-compatible domain ID's in output; add ability to delete rows
*
* Revision 1.38  2001/02/02 20:17:42  thiessen
* can read in CDD with multi-structure but no struct. alignments
*
* Revision 1.37  2001/01/18 19:37:01  thiessen
* save structure (re)alignments to asn output
*
* Revision 1.36  2000/12/29 19:23:50  thiessen
* save row order
*
* Revision 1.35  2000/12/22 19:25:47  thiessen
* write cdd output files
*
* Revision 1.34  2000/12/21 23:42:25  thiessen
* load structures from cdd's
*
* Revision 1.33  2000/12/20 23:47:53  thiessen
* load CDD's
*
* Revision 1.32  2000/12/01 19:34:43  thiessen
* better domain assignment
*
* Revision 1.31  2000/11/30 15:49:09  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
* Revision 1.30  2000/11/13 18:05:58  thiessen
* working structure re-superpositioning
*
* Revision 1.29  2000/11/12 04:02:22  thiessen
* working file save including alignment edits
*
* Revision 1.28  2000/11/11 21:12:08  thiessen
* create Seq-annot from BlockMultipleAlignment
*
* Revision 1.27  2000/11/02 16:48:24  thiessen
* working editor undo; dynamic slave transforms
*
* Revision 1.26  2000/10/04 17:40:47  thiessen
* rearrange STL #includes
*
* Revision 1.25  2000/09/15 19:24:33  thiessen
* allow repeated structures w/o different local id
*
* Revision 1.24  2000/09/11 22:57:56  thiessen
* working highlighting
*
* Revision 1.23  2000/09/11 01:45:54  thiessen
* working messenger for sequence<->structure window communication
*
* Revision 1.22  2000/08/30 19:49:05  thiessen
* working sequence window
*
* Revision 1.21  2000/08/29 04:34:15  thiessen
* working alignment manager, IBM
*
* Revision 1.20  2000/08/28 18:52:18  thiessen
* start unpacking alignments
*
* Revision 1.19  2000/08/27 18:50:56  thiessen
* extract sequence information
*
* Revision 1.18  2000/08/21 19:31:17  thiessen
* add style consistency checking
*
* Revision 1.17  2000/08/07 14:12:48  thiessen
* added animation frames
*
* Revision 1.16  2000/08/07 00:20:18  thiessen
* add display list mechanism
*
* Revision 1.15  2000/08/04 22:49:11  thiessen
* add backbone atom classification and selection feedback mechanism
*
* Revision 1.14  2000/08/03 15:12:29  thiessen
* add skeleton of style and show/hide managers
*
* Revision 1.13  2000/07/27 13:30:10  thiessen
* remove 'using namespace ...' from all headers
*
* Revision 1.12  2000/07/18 16:49:44  thiessen
* more friendly rotation center setting
*
* Revision 1.11  2000/07/18 00:05:45  thiessen
* allow arbitrary rotation center
*
* Revision 1.10  2000/07/17 22:36:46  thiessen
* fix vector_math typo; correctly set initial view
*
* Revision 1.9  2000/07/17 04:21:10  thiessen
* now does correct structure alignment transformation
*
* Revision 1.8  2000/07/16 23:18:35  thiessen
* redo of drawing system
*
* Revision 1.7  2000/07/12 02:00:39  thiessen
* add basic wxWindows GUI
*
* Revision 1.6  2000/07/11 13:49:30  thiessen
* add modules to parse chemical graph; many improvements
*
* Revision 1.5  2000/07/01 15:44:23  thiessen
* major improvements to StructureBase functionality
*
* Revision 1.4  2000/06/29 19:18:19  thiessen
* improved atom map
*
* Revision 1.3  2000/06/29 14:35:20  thiessen
* new atom_set files
*
* Revision 1.2  2000/06/28 13:08:13  thiessen
* store alt conf ensembles
*
* Revision 1.1  2000/06/27 20:08:14  thiessen
* initial checkin
*
*/