コード例 #1
0
ファイル: DepictionGenerator.java プロジェクト: rajarshi/cdk
 /**
  * Prepare a collection of molecules for rendering. If coordinates are not present they are
  * generated, if coordinates exists they are scaled to be consistent (length=1.5).
  *
  * @param mols molecules
  * @return coordinates
  * @throws CDKException
  */
 private List<Double> prepareCoords(Iterable<IAtomContainer> mols) throws CDKException {
   List<Double> scaleFactors = new ArrayList<>();
   for (IAtomContainer mol : mols) {
     if (ensure2dLayout(mol)) {
       scaleFactors.add(Double.NaN);
     } else if (mol.getBondCount() > 0) {
       final double factor = GeometryUtil.getScaleFactor(mol, 1.5);
       GeometryUtil.scaleMolecule(mol, factor);
       scaleFactors.add(factor);
     } else {
       scaleFactors.add(1d); // no bonds
     }
   }
   return scaleFactors;
 }
コード例 #2
0
  /**
   * Performs the pharmacophore matching.
   *
   * @param atomContainer The target molecule. Must have 3D coordinates
   * @param initializeTarget If <i>true</i>, the target molecule specified in the first argument
   *     will be analyzed to identify matching pharmacophore groups. If <i>false</i> this is not
   *     performed. The latter case is only useful when dealing with conformers since for a given
   *     molecule, all conformers will have the same pharmacophore groups and only the constraints
   *     will change from one conformer to another.
   * @return true is the target molecule contains the query pharmacophore
   * @throws org.openscience.cdk.exception.CDKException if the query pharmacophore was not set or
   *     the query is invalid or if the molecule does not have 3D coordinates
   */
  public boolean matches(IAtomContainer atomContainer, boolean initializeTarget)
      throws CDKException {
    if (!GeometryUtil.has3DCoordinates(atomContainer))
      throw new CDKException("Molecule must have 3D coordinates");
    if (pharmacophoreQuery == null)
      throw new CDKException("Must set the query pharmacophore before matching");
    if (!checkQuery(pharmacophoreQuery))
      throw new CDKException(
          "A problem in the query. Make sure all pharmacophore groups of the same symbol have the same same SMARTS");
    String title = (String) atomContainer.getProperty(CDKConstants.TITLE);

    if (initializeTarget) pharmacophoreMolecule = getPharmacophoreMolecule(atomContainer);
    else {
      // even though the atoms comprising the pcore groups are
      // constant, their coords will differ, so we need to make
      // sure we get the latest set of effective coordinates
      for (IAtom iAtom : pharmacophoreMolecule.atoms()) {
        PharmacophoreAtom patom = (PharmacophoreAtom) iAtom;
        List<Integer> tmpList = new ArrayList<Integer>();
        for (int idx : patom.getMatchingAtoms()) tmpList.add(idx);
        Point3d coords = getEffectiveCoordinates(atomContainer, tmpList);
        patom.setPoint3d(coords);
      }
    }

    if (pharmacophoreMolecule.getAtomCount() < pharmacophoreQuery.getAtomCount()) {
      logger.debug("Target [" + title + "] did not match the query SMARTS. Skipping constraints");
      return false;
    }

    mappings = Pattern.findSubstructure(pharmacophoreQuery).matchAll(pharmacophoreMolecule);

    // XXX: doing one search then discarding
    return mappings.atLeast(1);
  }
コード例 #3
0
ファイル: DepictionGenerator.java プロジェクト: rajarshi/cdk
 /**
  * Automatically generate coordinates if a user has provided a molecule without them.
  *
  * @param container a molecule
  * @return if coordinates needed to be generated
  * @throws CDKException coordinates could not be generated
  */
 private boolean ensure2dLayout(IAtomContainer container) throws CDKException {
   if (!GeometryUtil.has2DCoordinates(container)) {
     StructureDiagramGenerator sdg = new StructureDiagramGenerator();
     sdg.generateCoordinates(container);
     return true;
   }
   return false;
 }
コード例 #4
0
ファイル: DepictionGenerator.java プロジェクト: rajarshi/cdk
 /**
  * Reset the coordinates to their position before rendering.
  *
  * @param mols molecules
  * @param scales how molecules were scaled
  */
 private static void resetCoords(Iterable<IAtomContainer> mols, List<Double> scales) {
   Iterator<Double> it = scales.iterator();
   for (IAtomContainer mol : mols) {
     final double factor = it.next();
     if (!Double.isNaN(factor)) {
       GeometryUtil.scaleMolecule(mol, 1 / factor);
     } else {
       for (IAtom atom : mol.atoms()) atom.setPoint2d(null);
     }
   }
 }
コード例 #5
0
 private IRenderingElement generateAbbreviationSgroup(Sgroup sgroup) {
   String label = sgroup.getSubscript();
   // already handled by symbol remapping
   if (sgroup.getBonds().size() > 0 || label == null || label.isEmpty()) {
     return new ElementGroup();
   }
   // we're showing a label where there were no atoms before, we put it in the
   // middle of all of those which were hidden
   final Point2d labelCoords = GeometryUtil.get2DCenter(sgroup.getAtoms());
   ElementGroup group = new ElementGroup();
   for (Shape outline :
       atomGenerator
           .generatePseudoSymbol(label, HydrogenPosition.Right)
           .resize(1 / scale, 1 / -scale)
           .getOutlines()) group.add(GeneralPath.shapeOf(outline, foreground));
   return MarkedElement.markupAtom(group, null);
 }