chemical_graph.cpp

ncbi源码

        if ((f->GetObject().GetType() == CBiostruc_feature::eType_helix ||
                f->GetObject().GetType() == CBiostruc_feature::eType_strand) &&
            f->GetObject().IsSetLocation() &&
            f->GetObject().GetLocation().IsSubgraph() &&
            f->GetObject().GetLocation().GetSubgraph().IsResidues() &&
            f->GetObject().GetLocation().GetSubgraph().GetResidues().IsInterval()) {

            // find molecule and set region, warning about overlaps
            if (f->GetObject().GetLocation().GetSubgraph().GetResidues().GetInterval().size() > 1) {
                WARNINGMSG("Can't deal with multi-interval sec. struc. regions");
                continue;
            }
            const CResidue_interval_pntr& interval =
                f->GetObject().GetLocation().GetSubgraph().GetResidues().GetInterval().front().GetObject();
            MoleculeMap::const_iterator m = molecules.find(interval.GetMolecule_id().Get());
            if (m == molecules.end()) {
                WARNINGMSG("Bad moleculeID in sec. struc. interval");
                continue;
            }
            Molecule *molecule = const_cast<Molecule*>(m->second);
            for (int r=interval.GetFrom().Get()-1; r<=interval.GetTo().Get()-1; ++r) {
                if (r < 0 || r >= molecule->residues.size()) {
                    ERRORMSG("Bad residue range in sec. struc. feature for moleculeID "
                        << molecule->id << " residueID " << r+1);
                    break;
                } if (molecule->residueSecondaryStructures[r] != Molecule::eCoil) {
                    WARNINGMSG("Overlapping sec. struc. feature at moleculeID "
                        << molecule->id << " residueID " << r+1);
                } else {
                    molecule->residueSecondaryStructures[r] =
                        (f->GetObject().GetType() == CBiostruc_feature::eType_helix) ?
                            Molecule::eHelix : Molecule::eStrand;
                }
            }
        }
    }
}

static int moleculeToRedraw = -1;

void ChemicalGraph::RedrawMolecule(int moleculeID) const
{
    moleculeToRedraw = moleculeID;
    DrawAll(NULL);
    moleculeToRedraw = -1;
}

// This is where the work of breaking objects up into display lists gets done.
bool ChemicalGraph::DrawAll(const AtomSet *ignored) const
{
    const StructureObject *object;
    if (!GetParentOfType(&object)) return false;

    if (moleculeToRedraw != -1)
        TRACEMSG("drawing molecule " << moleculeToRedraw
            << " of ChemicalGraph of object " << object->pdbID);
    else
        TRACEMSG("drawing ChemicalGraph of object " << object->pdbID);

    // put each protein (with its 3d-objects) or nucleotide chain in its own display list
    bool continueDraw;
    AtomSetList::const_iterator a, ae=atomSetList.end();
    MoleculeMap::const_iterator m, me=molecules.end();
    for (m=molecules.begin(); m!=me; ++m) {
        if (!m->second->IsProtein() && !m->second->IsNucleotide()) continue;
        if (moleculeToRedraw >= 0 && m->second->id != moleculeToRedraw) continue;

        Molecule::DisplayListList::const_iterator md=m->second->displayLists.begin();
        for (a=atomSetList.begin(); a!=ae; ++a, ++md) {

            // start new display list
            //TESTMSG("drawing molecule #" << m->second->id << " + its objects in display list " << *md
            //        << " of " << atomSetList.size());
            parentSet->renderer->StartDisplayList(*md);

            // draw this molecule with all alternative AtomSets (e.g., NMR's or altConfs)
            a->first->SetActiveEnsemble(a->second);
            continueDraw = m->second->DrawAllWithTerminiLabels(a->first);

            if (continueDraw) {
                // find 3D objects for this molecule/CoordSet
                const CoordSet *coordSet;
                if (a->first->GetParentOfType(&coordSet)) {
                    CoordSet::Object3DMap::const_iterator objList = coordSet->objectMap.find(m->second->id);
                    if (objList != coordSet->objectMap.end()) {
                        CoordSet::Object3DList::const_iterator o, oe=objList->second.end();
                        for (o=objList->second.begin(); o!=oe; ++o) {
                            if (!(continueDraw = (*o)->Draw(a->first))) break;
                        }
                    }
                }
            }

            // end display list
            parentSet->renderer->EndDisplayList();

            if (!continueDraw) return false;
        }

        // we're done if this was the single molecule meant to be redrawn
        if (moleculeToRedraw >= 0) break;
    }

    // then put everything else (solvents, hets, and intermolecule bonds) in a single display list
    if (displayListOtherStart == OpenGLRenderer::NO_LIST) return true;
    //TESTMSG("drawing hets/solvents/i-m bonds");

    // always redraw all these even if only a single molecule is to be redrawn -
    // that way connections can show/hide in cases where a particular residue
    // changes its display
    int n = 0;
    for (a=atomSetList.begin(); a!=ae; ++a, ++n) {

        a->first->SetActiveEnsemble(a->second);
        parentSet->renderer->StartDisplayList(displayListOtherStart + n);

        for (m=molecules.begin(); m!=me; ++m) {
            if (m->second->IsProtein() || m->second->IsNucleotide()) continue;
            if (!(continueDraw = m->second->DrawAll(a->first))) break;
        }

        if (continueDraw) {
            BondList::const_iterator b, be=interMoleculeBonds.end();
            for (b=interMoleculeBonds.begin(); b!=be; ++b) {
                if (!(continueDraw = (*b)->Draw(a->first))) break;
            }
        }

        parentSet->renderer->EndDisplayList();

        if (!continueDraw) return false;
    }

    return true;
}

bool ChemicalGraph::CheckForDisulfide(const Molecule *molecule,
    const CAtom_pntr& atomPtr1, const CAtom_pntr& atomPtr2,
    list < const Bond * > *bondList, Bond *bond, StructureBase *parent)
{
    if (atomPtr1.GetMolecule_id().Get() == atomPtr2.GetMolecule_id().Get() &&
        atomPtr1.GetResidue_id().Get() == atomPtr2.GetResidue_id().Get()) return false;

    const Molecule *mol1, *mol2;
    if (molecule) { // when called from Molecule::Molecule() on interresidue (intramolecular) bond
        mol1 = mol2 = molecule;
    } else {        // when called from ChemicalGraph::ChemicalGraph() on intermolecule bond
        MoleculeMap::const_iterator
            m1 = molecules.find(atomPtr1.GetMolecule_id().Get()),
            m2 = molecules.find(atomPtr2.GetMolecule_id().Get());
        if (m1 == molecules.end() || m2 == molecules.end()) {
            ERRORMSG("ChemicalGraph::CheckForDisulfide() - bad molecule ID");
            return false;
        }
        mol1 = m1->second;
        mol2 = m2->second;
    }

    Molecule::ResidueMap::const_iterator
        res1 = mol1->residues.find(atomPtr1.GetResidue_id().Get()),
        res2 = mol2->residues.find(atomPtr2.GetResidue_id().Get());
    if (res1 == mol1->residues.end() || res2 == mol2->residues.end()) {
        ERRORMSG("ChemicalGraph::CheckForDisulfide() - bad residue ID");
        return false;
    }

    // check to make sure both residues are cysteine
    if (res1->second->type != Residue::eAminoAcid || res1->second->code != 'C' ||
        res2->second->type != Residue::eAminoAcid || res2->second->code != 'C') return false;

    const Residue::AtomInfo
        *atom1 = res1->second->GetAtomInfo(atomPtr1.GetAtom_id().Get()),
        *atom2 = res2->second->GetAtomInfo(atomPtr2.GetAtom_id().Get());
    if (!atom1 || !atom2) {
        ERRORMSG("ChemicalGraph::CheckForDisulfide() - bad atom ID");
        return false;
    }

    // check to make sure both atoms are sulfur, and that residue has an alpha
    if (atom1->atomicNumber != 16 || res1->second->alphaID == Residue::NO_ALPHA_ID ||
        atom2->atomicNumber != 16 || res2->second->alphaID == Residue::NO_ALPHA_ID) return false;

    TRACEMSG("found disulfide between molecule " << atomPtr1.GetMolecule_id().Get()
        << " residue " << atomPtr1.GetResidue_id().Get()
        << " and molecule " << atomPtr2.GetMolecule_id().Get()
        << " residue " << atomPtr2.GetResidue_id().Get());

    // first flag this bond as "real disulfide", so it's not drawn with connection style
    if (bond) bond->order = Bond::eRealDisulfide;

    // then, make a new virtual disulfide bond between the alphas of these residues
    const Bond *virtualDisulfide = MakeBond(parent,
        atomPtr1.GetMolecule_id().Get(), atomPtr1.GetResidue_id().Get(), res1->second->alphaID,
        atomPtr2.GetMolecule_id().Get(), atomPtr2.GetResidue_id().Get(), res2->second->alphaID,
        Bond::eVirtualDisulfide);
    if (!virtualDisulfide) return false;

    bondList->push_back(virtualDisulfide);
    return true;
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: chemical_graph.cpp,v $
* Revision 1000.2  2004/06/01 18:28:03  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.40
*
* Revision 1.40  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.39  2004/03/15 18:19:23  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.38  2004/02/19 17:04:46  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.37  2003/08/21 17:56:29  thiessen
* change header order for Mac compilation
*
* Revision 1.36  2003/06/21 21:04:41  thiessen
* draw per-model 3D objects
*
* Revision 1.35  2003/03/06 19:23:18  thiessen
* minor tweaks
*
* Revision 1.34  2003/02/03 19:20:02  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.33  2002/05/31 14:51:28  thiessen
* small tweaks
*
* Revision 1.32  2002/03/18 15:17:29  thiessen
* fix minor omission
*
* Revision 1.31  2001/12/12 14:04:13  thiessen
* add missing object headers after object loader change
*
* Revision 1.30  2001/11/27 16:26:07  thiessen
* major update to data management system
*
* Revision 1.29  2001/08/21 01:10:45  thiessen
* add labeling
*
* Revision 1.28  2001/07/27 13:52:47  thiessen
* make sure domains are assigned in order of molecule id; tweak pattern dialog
*
* Revision 1.27  2001/07/12 17:35:15  thiessen
* change domain mapping ; add preliminary cdd annotation GUI
*
* Revision 1.26  2001/06/21 02:02:33  thiessen
* major update to molecule identification and highlighting ; add toggle highlight (via alt)
*
* Revision 1.25  2001/05/31 18:47:07  thiessen
* add preliminary style dialog; remove LIST_TYPE; add thread single and delete all; misc tweaks
*
* Revision 1.24  2001/05/18 22:58:52  thiessen
* fix display list bug with disulfides
*
* Revision 1.23  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 1.22  2001/03/23 04:18:52  thiessen
* parse and display disulfides
*
* Revision 1.21  2001/02/13 01:03:56  thiessen
* backward-compatible domain ID's in output; add ability to delete rows
*
* Revision 1.20  2001/02/08 23:01:48  thiessen
* hook up C-toolkit stuff for threading; working PSSM calculation
*
* Revision 1.19  2000/12/20 23:47:47  thiessen
* load CDD's
*
* Revision 1.18  2000/12/19 16:39:08  thiessen
* tweaks to show/hide
*
* Revision 1.17  2000/12/01 19:35:56  thiessen
* better domain assignment; basic show/hide mechanism
*
* Revision 1.16  2000/11/30 15:49:36  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
* Revision 1.15  2000/11/02 16:56:01  thiessen
* working editor undo; dynamic slave transforms
*
* Revision 1.14  2000/09/14 14:55:34  thiessen
* add row reordering; misc fixes
*
* Revision 1.13  2000/09/11 01:46:14  thiessen
* working messenger for sequence<->structure window communication
*
* Revision 1.12  2000/08/27 18:52:20  thiessen
* extract sequence information
*
* Revision 1.11  2000/08/21 17:22:37  thiessen
* add primitive highlighting for testing
*
* Revision 1.10  2000/08/17 14:24:05  thiessen
* added working StyleManager
*
* Revision 1.9  2000/08/16 14:18:44  thiessen
* map 3-d objects to molecules
*
* Revision 1.8  2000/08/13 02:43:00  thiessen
* added helix and strand objects
*
* Revision 1.7  2000/08/07 14:13:15  thiessen
* added animation frames
*
* 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
*
*/