residue.cpp

ncbi源码

    if (!atomSet) {
        ERRORMSG("Residue::Draw(data) - NULL AtomSet*");
        return false;
    }

    // verify presense of OpenGLRenderer
    if (!parentSet->renderer) {
        WARNINGMSG("Residue::Draw() - no renderer");
        return false;
    }

    // get Molecule parent
    const Molecule *molecule;
    if (!GetParentOfType(&molecule)) return false;

    // get object parent
    const StructureObject *object;
    if (!GetParentOfType(&object)) return false;

    // is this residue labeled?
    const StyleSettings& settings = parentSet->styleManager->GetStyleForResidue(object, molecule->id, id);
    bool proteinLabel = (IsAminoAcid() && settings.proteinLabels.spacing > 0 &&
        (id-1)%settings.proteinLabels.spacing == 0);
    bool nucleotideLabel = (IsNucleotide() && settings.nucleotideLabels.spacing > 0 &&
        (id-1)%settings.nucleotideLabels.spacing == 0);

    bool overlayEnsembles = parentSet->showHideManager->OverlayConfEnsembles();
    AtomStyle atomStyle;
    const AtomCoord *atom, *l1 = NULL, *l2 = NULL, *l3 = NULL;
    Vector labelColor;
    bool alphaVisible = false, alphaOnly = false;

    // iterate atoms; key is atomID
    AtomInfoMap::const_iterator a, ae = atomInfos.end();
    for (a=atomInfos.begin(); a!=ae; ++a) {

        // get AtomCoord* for appropriate altConf
        AtomPntr ap(molecule->id, id, a->first);
        atom = atomSet->GetAtom(ap, overlayEnsembles, true);
        if (!atom) continue;

        // get Style
        if (!parentSet->styleManager->GetAtomStyle(this, ap, atom, &atomStyle))
            return false;

        // highlight atom if necessary
        if (atomStyle.isHighlighted)
            atomStyle.color = GlobalColors()->Get(Colors::eHighlight);

        // draw the atom
        if (atomStyle.style != StyleManager::eNotDisplayed && atomStyle.radius > 0.0)
            parentSet->renderer->DrawAtom(atom->site, atomStyle);

        // store coords for positioning label, based on backbone coordinates
        if ((proteinLabel || nucleotideLabel) && a->second->classification != eSideChainAtom) {
            if (IsAminoAcid()) {
                if (a->second->name == " CA ") {
                    l1 = atom;
                    labelColor = atomStyle.color;
                    alphaVisible = (atomStyle.style != StyleManager::eNotDisplayed);
                }
                else if (a->second->name == " C  ") l2 = atom;
                else if (a->second->name == " N  ") l3 = atom;
            } else if (IsNucleotide()) {
                if (a->second->name == " P  ") {
                    l1 = atom;
                    labelColor = atomStyle.color;
                    alphaVisible = (atomStyle.style != StyleManager::eNotDisplayed);
                }
                // labeling by alphas seems to work better for nucleotides
//                else if (a->second->name == " C4*") l2 = atom;
//                else if (a->second->name == " C5*") l3 = atom;
            }
        }
    }

    // if not all backbone atoms present (e.g. alpha only), use alpha coords of neighboring residues
    if (l1 && (!l2 || !l3)) {
        Molecule::ResidueMap::const_iterator prevRes, nextRes;
        const AtomCoord *prevAlpha, *nextAlpha;
        if ((prevRes=molecule->residues.find(id - 1)) != molecule->residues.end() &&
            prevRes->second->alphaID != NO_ALPHA_ID &&
            (prevAlpha=atomSet->GetAtom(AtomPntr(molecule->id, id - 1, prevRes->second->alphaID))) != NULL &&
            (nextRes=molecule->residues.find(id + 1)) != molecule->residues.end() &&
            nextRes->second->alphaID != NO_ALPHA_ID &&
            (nextAlpha=atomSet->GetAtom(AtomPntr(molecule->id, id + 1, nextRes->second->alphaID))) != NULL)
        {
            l2 = prevAlpha;
            l3 = nextAlpha;
            alphaOnly = true;
        }
    }

    // draw residue (but not terminus) labels, assuming we have the necessary coordinates and
    // that alpha atoms are visible
    if (alphaVisible && (proteinLabel|| nucleotideLabel)) {
        Vector labelPosition;
        CNcbiOstrstream oss;

        double contrast = Colors::IsLightColor(settings.backgroundColor) ? 0 : 1;

        // protein label
        if (IsAminoAcid() && l1 && l2 && l3) {
            // position
            if (alphaOnly) {
                Vector forward = - ((l2->site - l1->site) + (l3->site - l1->site));
                forward.normalize();
                labelPosition = l1->site + 1.5 * forward;
            } else {
                Vector up = vector_cross(l2->site - l1->site, l3->site - l1->site);
                up.normalize();
                Vector forward = (-((l2->site - l1->site) + (l3->site - l1->site)) / 2);
                forward.normalize();
                labelPosition = l1->site + 1.5 * forward + 1.5 * up;
            }
            // text
            if (settings.proteinLabels.type == StyleSettings::eOneLetter) {
                oss << code;
            } else if (settings.proteinLabels.type == StyleSettings::eThreeLetter) {
                for (int i=0; i<nameGraph.size() && i<3; ++i)
                    oss << ((i == 0) ? (char) toupper(nameGraph[0]) : (char) tolower(nameGraph[i]));
            }
            // add number if necessary
            if (settings.proteinLabels.numbering == StyleSettings::eSequentialNumbering)
                oss << ' ' << id;
            else if (settings.proteinLabels.numbering == StyleSettings::ePDBNumbering)
                oss << namePDB;
            // contrasting color? (default to CA's color)
            if (settings.proteinLabels.white) labelColor.Set(contrast, contrast, contrast);
        }

        // nucleotide label
        else if (IsNucleotide() && l2 && l3) {
            if (alphaOnly) {
                Vector forward = - ((l2->site - l1->site) + (l3->site - l1->site));
                forward.normalize();
                labelPosition = l1->site + 3 * forward;
            } else {
                labelPosition = l3->site + 3 * (l3->site - l2->site);
            }
            // text
            if (settings.nucleotideLabels.type == StyleSettings::eOneLetter) {
                oss << code;
            } else if (settings.nucleotideLabels.type == StyleSettings::eThreeLetter) {
                for (int i=0; i<3; ++i)
                    if (nameGraph.size() > i && nameGraph[i] != ' ')
                        oss << nameGraph[i];
            }
            // add number if necessary
            if (settings.nucleotideLabels.numbering == StyleSettings::eSequentialNumbering)
                oss << ' ' << id;
            else if (settings.nucleotideLabels.numbering == StyleSettings::ePDBNumbering)
                oss << namePDB;
            // contrasting color? (default to C4*'s color)
            if (settings.nucleotideLabels.white) labelColor.Set(contrast, contrast, contrast);
        }

        // draw label
        if (oss.pcount() > 0) {
            oss << '\0';
            string labelText = oss.str();
            delete oss.str();

            // apply highlight color if necessary
            if (GlobalMessenger()->IsHighlighted(molecule, id))
                labelColor = GlobalColors()->Get(Colors::eHighlight);

            parentSet->renderer->DrawLabel(labelText, labelPosition, labelColor);
        }
    }

    return true;
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: residue.cpp,v $
* Revision 1000.2  2004/06/01 18:29:02  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.34
*
* Revision 1.34  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.33  2004/03/15 18:27:12  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.32  2004/02/19 17:05:05  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.31  2003/06/21 08:18:58  thiessen
* show all atoms with coordinates, even if not in all coord sets
*
* Revision 1.30  2003/02/03 19:20:05  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.29  2002/11/06 00:18:10  thiessen
* fixes for new CRef/const rules in objects
*
* Revision 1.28  2001/12/12 14:04:14  thiessen
* add missing object headers after object loader change
*
* Revision 1.27  2001/10/16 21:49:07  thiessen
* restructure MultiTextDialog; allow virtual bonds for alpha-only PDB's
*
* Revision 1.26  2001/08/24 00:41:36  thiessen
* tweak conservation colors and opengl font handling
*
* Revision 1.25  2001/08/21 01:10:45  thiessen
* add labeling
*
* Revision 1.24  2001/08/09 19:07:13  thiessen
* add temperature and hydrophobicity coloring
*
* Revision 1.23  2001/05/17 18:34:26  thiessen
* spelling fixes; change dialogs to inherit from wxDialog
*
* Revision 1.22  2001/05/15 23:48:37  thiessen
* minor adjustments to compile under Solaris/wxGTK
*
* Revision 1.21  2001/04/18 15:46:53  thiessen
* show description, length, and PDB numbering in status line
*
* Revision 1.20  2001/03/23 23:31:56  thiessen
* keep atom info around even if coords not all present; mainly for disulfide parsing in virtual models
*
* Revision 1.19  2001/03/22 00:33:17  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.18  2000/12/01 19:35:57  thiessen
* better domain assignment; basic show/hide mechanism
*
* Revision 1.17  2000/11/30 15:49:39  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
* Revision 1.16  2000/09/11 22:57:32  thiessen
* working highlighting
*
* Revision 1.15  2000/08/25 14:22:00  thiessen
* minor tweaks
*
* Revision 1.14  2000/08/19 02:59:05  thiessen
* fix transparent sphere bug
*
* Revision 1.13  2000/08/18 18:57:39  thiessen
* added transparent spheres
*
* Revision 1.12  2000/08/17 14:24:06  thiessen
* added working StyleManager
*
* Revision 1.11  2000/08/13 02:43:01  thiessen
* added helix and strand objects
*
* Revision 1.10  2000/08/11 12:58:31  thiessen
* added worm; get 3d-object coords from asn1
*
* Revision 1.9  2000/08/07 00:21:18  thiessen
* add display list mechanism
*
* Revision 1.8  2000/08/04 22:49:03  thiessen
* add backbone atom classification and selection feedback mechanism
*
* Revision 1.7  2000/08/03 15:12:23  thiessen
* add skeleton of style and show/hide managers
*
* Revision 1.6  2000/07/27 13:30:51  thiessen
* remove 'using namespace ...' from all headers
*
* Revision 1.5  2000/07/17 22:37:18  thiessen
* fix vector_math typo; correctly set initial view
*
* Revision 1.4  2000/07/17 11:59:16  thiessen
* fix nucleotide virtual bonds
*
* Revision 1.3  2000/07/17 04:20:50  thiessen
* now does correct structure alignment transformation
*
* Revision 1.2  2000/07/16 23:19:11  thiessen
* redo of drawing system
*
* Revision 1.1  2000/07/11 13:45:31  thiessen
* add modules to parse chemical graph; many improvements
*
*/