molecule.cpp

ncbi源码

        GetAtom(atom, parentSet->showHideManager->OverlayConfEnsembles(), true);
    if (!atomCoord) return gray;

    AtomStyle style;
    if (!parentSet->styleManager->GetAtomStyle(residue, atom, atomCoord, &style)) return gray;
    return style.color;
}

int Molecule::GetAlphaCoords(int nResidues, const int *seqIndexes, const Vector * *coords) const
{
    const StructureObject *object;
    if (!GetParentOfType(&object)) return false;
    if (object->coordSets.size() != 1) {
        ERRORMSG("Can't align structures with multiple CoordSets");
        return -1;
    }

    int nCoords = 0;
    for (int i=0; i<nResidues; ++i) {

        int rID = seqIndexes[i] + 1;    // residueIDs start at 1
        ResidueMap::const_iterator r = residues.find(rID);
        if (r == residues.end()) {
            ERRORMSG("Can't find residueID " << rID
                << " in " << identifier->pdbID << " chain '"
                << (char) identifier->pdbChain << "'");
            return -1;
        }

        int aID = (r->second->alphaID);
        if (aID == Residue::NO_ALPHA_ID) {
            WARNINGMSG("No alpha atom in residueID " << rID
                << " from " << identifier->pdbID << " chain '"
                << (char) identifier->pdbChain << "'");
            coords[i] = NULL;
            continue;
        }

        AtomPntr atom(id, rID, aID);
        const AtomCoord* atomCoord = object->coordSets.front()->atomSet->GetAtom(atom);
        if (!atomCoord) {
            WARNINGMSG("Can't get AtomCoord for (m"
                << id << ",r" << rID << ",a" << aID << ")");
            coords[i] = NULL;
            continue;
        }

        coords[i] = &(atomCoord->site);
        ++nCoords;
    }

    return nCoords;
}

bool Molecule::DrawAllWithTerminiLabels(const AtomSet *atomSet) const
{
    // draw regular objects
    if (!DrawAll(atomSet)) return false;

    // add termini labels
    if ((IsProtein() || IsNucleotide()) && NResidues() >= 2 && parentSet->showHideManager->IsVisible(this)) {

        const StyleSettings& settings = parentSet->styleManager->GetGlobalStyle();
        if ((IsProtein() && settings.proteinLabels.terminiOn) ||
            (IsNucleotide() && settings.nucleotideLabels.terminiOn)) {

            // try to color labels to contrast with background
            static const Vector white(1,1,1), black(0,0,0);
            const Vector& labelColor =
                Colors::IsLightColor(settings.backgroundColor) ? black : white;

            // do start (N or 5') and end (C or 3') labels
            for (int startTerminus=1; startTerminus>=0; --startTerminus) {

                // determine color and location - assumes sequential residue id's (from 1)
                const Vector *alphaPos = NULL, *prevPos = NULL;
                int res = startTerminus ? 1 : residues.size(),
                    resEnd = startTerminus ? residues.size() : 1,
                    resInc = startTerminus ? 1 : -1;

                // find coordinates of two terminal alpha atoms
                const Residue *termRes = NULL;
                for (; res!=resEnd; res+=resInc) {
                    const Residue *residue = residues.find(res)->second;
                    if (residue->alphaID != Residue::NO_ALPHA_ID) {
                        AtomPntr ap(id, res, residue->alphaID);
                        const AtomCoord *atom =
                            atomSet->GetAtom(ap, parentSet->showHideManager->OverlayConfEnsembles(), true);
                        if (atom) {
                            if (!alphaPos) {
                                alphaPos = &(atom->site);
                                termRes = residue;
                            } else if (!prevPos) {
                                prevPos = &(atom->site);
                                break;
                            }
                        }
                    }
                }
                if (!(alphaPos && prevPos)) {
                    WARNINGMSG("Molecule::DrawAllWithTerminiLabels() - "
                        << "can't get two terminal alpha coords");
                    continue;
                }
                if (!parentSet->showHideManager->IsVisible(termRes)) continue;
                Vector labelPosition = *alphaPos + 0.5 * (*alphaPos - *prevPos);

                // determine label text
                CNcbiOstrstream oss;
                if (IsProtein()) {
                    if (startTerminus)
                        oss << "N";
                    else
                        oss << "C";
                } else {
                    if (startTerminus)
                        oss << "5'";
                    else
                        oss << "3'";
                }
                if (identifier->pdbChain != MoleculeIdentifier::VALUE_NOT_SET && identifier->pdbChain != ' ')
                    oss << " (" << (char) identifier->pdbChain << ')';
                oss << '\0';

                // draw label
                string labelText = oss.str();
                delete oss.str();
                parentSet->renderer->DrawLabel(labelText, labelPosition, labelColor);
            }
        }
    }

    return true;
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: molecule.cpp,v $
* Revision 1000.2  2004/06/01 18:28:41  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.43
*
* Revision 1.43  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.42  2004/05/20 18:49:21  thiessen
* don't do structure realignment if < 3 coords present
*
* Revision 1.41  2004/03/15 17:34:03  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.40  2004/02/19 17:04:57  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.39  2003/06/21 08:18:58  thiessen
* show all atoms with coordinates, even if not in all coord sets
*
* Revision 1.38  2003/02/03 19:20:04  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.37  2002/04/19 17:34:03  thiessen
* fix for alpha-only nucleotides
*
* Revision 1.36  2002/02/01 13:55:31  thiessen
* fix labeling bug when domain hidden
*
* Revision 1.35  2002/02/01 00:41:21  thiessen
* tweaks
*
* Revision 1.34  2002/01/24 20:08:16  thiessen
* fix local id problem
*
* Revision 1.33  2001/12/12 14:04:13  thiessen
* add missing object headers after object loader change
*
* Revision 1.32  2001/10/16 21:49:07  thiessen
* restructure MultiTextDialog; allow virtual bonds for alpha-only PDB's
*
* Revision 1.31  2001/08/24 00:41:35  thiessen
* tweak conservation colors and opengl font handling
*
* Revision 1.30  2001/08/21 01:10:45  thiessen
* add labeling
*
* Revision 1.29  2001/08/09 19:07:13  thiessen
* add temperature and hydrophobicity coloring
*
* Revision 1.28  2001/07/16 15:35:37  thiessen
* fix unaligned chain identifier ommission
*
* Revision 1.27  2001/06/21 02:02:33  thiessen
* major update to molecule identification and highlighting ; add toggle highlight (via alt)
*
* Revision 1.26  2001/04/04 00:27:14  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.25  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 1.24  2001/03/23 04:18:52  thiessen
* parse and display disulfides
*
* Revision 1.23  2001/02/09 20:17:32  thiessen
* ignore atoms w/o alpha when doing structure realignment
*
* Revision 1.22  2001/02/08 23:01:50  thiessen
* hook up C-toolkit stuff for threading; working PSSM calculation
*
* Revision 1.21  2000/12/15 15:51:47  thiessen
* show/hide system installed
*
* Revision 1.20  2000/12/01 19:35:57  thiessen
* better domain assignment; basic show/hide mechanism
*
* Revision 1.19  2000/11/30 15:49:39  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
* Revision 1.18  2000/11/13 18:06:53  thiessen
* working structure re-superpositioning
*
* Revision 1.17  2000/11/11 21:15:54  thiessen
* create Seq-annot from BlockMultipleAlignment
*
* Revision 1.16  2000/09/15 19:24:22  thiessen
* allow repeated structures w/o different local id
*
* Revision 1.15  2000/09/11 22:57:32  thiessen
* working highlighting
*
* Revision 1.14  2000/09/08 20:16:55  thiessen
* working dynamic alignment views
*
* Revision 1.13  2000/09/03 18:46:48  thiessen
* working generalized sequence viewer
*
* Revision 1.12  2000/08/28 23:47:18  thiessen
* functional denseg and dendiag alignment parsing
*
* Revision 1.11  2000/08/28 18:52:42  thiessen
* start unpacking alignments
*
* Revision 1.10  2000/08/27 18:52:21  thiessen
* extract sequence information
*
* Revision 1.9  2000/08/17 14:24:05  thiessen
* added working StyleManager
*
* Revision 1.8  2000/08/11 12:58:31  thiessen
* added worm; get 3d-object coords from asn1
*
* Revision 1.7  2000/08/04 22:49:03  thiessen
* add backbone atom classification and selection feedback mechanism
*
* Revision 1.6  2000/08/03 15:12:23  thiessen
* add skeleton of style and show/hide managers
*
* Revision 1.5  2000/07/27 13:30:51  thiessen
* remove 'using namespace ...' from all headers
*
* Revision 1.4  2000/07/18 02:41:33  thiessen
* fix bug in virtual bonds and altConfs
*
* Revision 1.3  2000/07/17 04:20:49  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 13:45:30  thiessen
* add modules to parse chemical graph; many improvements
*
*/