Example #1
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);
  }
Example #2
0
 @Test
 public void testBug70() throws FileNotFoundException, CDKException {
   JPanelFixture jcppanel = applet.panel("appletframe");
   JChemPaintPanel panel = (JChemPaintPanel) jcppanel.target;
   applet.button("hexagon").click();
   applet.click();
   Point2d point = getAtomPoint(panel, 0);
   applet
       .panel("renderpanel")
       .robot
       .click(
           applet.panel("renderpanel").component(),
           new Point((int) point.x, (int) point.y),
           MouseButton.RIGHT_BUTTON,
           1);
   applet
       .panel("renderpanel")
       .robot
       .click(
           applet.panel("renderpanel").component(),
           new Point((int) point.x, (int) point.y),
           MouseButton.RIGHT_BUTTON,
           1);
   applet.menuItem("showACProperties").click();
   DialogFixture dialog = applet.dialog();
   JTextComponent textfield = dialog.robot.finder().find(JTextComponentMatcher.withName("Title"));
   textfield.setText("aaa");
   JButtonFixture okbutton =
       new JButtonFixture(
           dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("OK")));
   okbutton.click();
   applet.menuItem("save").click();
   dialog = applet.dialog();
   File file = new File(System.getProperty("java.io.tmpdir") + File.separator + "test.mol");
   if (file.exists()) file.delete();
   JComboBox combobox =
       dialog
           .robot
           .finder()
           .find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
   combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
   JTextComponentFixture text = dialog.textBox();
   text.setText(file.toString());
   JButtonFixture savebutton =
       new JButtonFixture(
           dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
   savebutton.click();
   MDLReader reader = new MDLReader(new FileInputStream(file));
   IAtomContainer mol =
       (IAtomContainer)
           reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
   Assert.assertEquals("aaa", (String) mol.getProperty(CDKConstants.TITLE));
 }
Example #3
0
  private IRenderingElement generate(IAtomContainer molecule, RendererModel model, int atomNum)
      throws CDKException {

    // tag the atom and bond ids
    String molId = molecule.getProperty(MarkedElement.ID_KEY);
    if (molId != null) {
      int atomId = 0, bondid = 0;
      for (IAtom atom : molecule.atoms())
        setIfMissing(atom, MarkedElement.ID_KEY, molId + "atm" + ++atomId);
      for (IBond bond : molecule.bonds())
        setIfMissing(bond, MarkedElement.ID_KEY, molId + "bnd" + ++bondid);
    }

    if (annotateAtomNum) {
      for (IAtom atom : molecule.atoms()) {
        if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
          throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
        atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(atomNum++));
      }
    } else if (annotateAtomVal) {
      for (IAtom atom : molecule.atoms()) {
        if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
          throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
        atom.setProperty(
            StandardGenerator.ANNOTATION_LABEL, atom.getProperty(CDKConstants.COMMENT));
      }
    } else if (annotateAtomMap) {
      for (IAtom atom : molecule.atoms()) {
        if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
          throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
        int mapidx = accessAtomMap(atom);
        if (mapidx > 0) {
          atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(mapidx));
        }
      }
    }

    ElementGroup grp = new ElementGroup();
    for (IGenerator<IAtomContainer> gen : gens) grp.add(gen.generate(molecule, model));

    // cleanup
    if (annotateAtomNum || annotateAtomMap) {
      for (IAtom atom : molecule.atoms()) {
        atom.removeProperty(StandardGenerator.ANNOTATION_LABEL);
      }
    }

    return grp;
  }
  /**
   * If the molecule has display shortcuts (abbreviations or multiple group sgroups) certain parts
   * of the structure are hidden from display. This method marks the parts to hide and in the case
   * of abbreviations, remaps atom symbols. Appart from additional property flags, the molecule is
   * unchanged by this method.
   *
   * @param container molecule input
   * @param symbolRemap a map that will hold symbol remapping
   */
  static void prepareDisplayShortcuts(IAtomContainer container, Map<IAtom, String> symbolRemap) {

    List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);
    if (sgroups == null || sgroups.isEmpty()) return;

    // select abbreviations that should be contracted
    for (Sgroup sgroup : sgroups) {
      if (sgroup.getType() == SgroupType.CtabAbbreviation) {
        Boolean expansion = sgroup.getValue(SgroupKey.CtabExpansion);
        // abbreviation is displayed as expanded
        if (expansion != null && expansion == Boolean.TRUE) continue;
        // no or empty label, skip it
        if (sgroup.getSubscript() == null || sgroup.getSubscript().isEmpty()) continue;
        contractAbbreviation(container, symbolRemap, sgroup);
      } else if (sgroup.getType() == SgroupType.CtabMultipleGroup) {
        hideMultipleParts(container, sgroup);
      }
    }
  }
Example #5
0
  @Test
  public void checkUniqueMolecularDescriptorNames() throws Exception {
    DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
    List<DescriptorSpecification> specs = engine.getDescriptorSpecifications();

    // we work with a simple molecule with 3D coordinates
    String filename = "data/mdl/lobtest2.sdf";
    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
    ChemFile content = (ChemFile) reader.read(new ChemFile());
    List cList = ChemFileManipulator.getAllAtomContainers(content);
    IAtomContainer ac = (IAtomContainer) cList.get(0);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);

    engine.process(ac);

    int ncalc = 0;
    List<String> descNames = new ArrayList<String>();
    for (DescriptorSpecification spec : specs) {
      DescriptorValue value = (DescriptorValue) ac.getProperty(spec);
      if (value == null) continue;
      ncalc++;
      String[] names = value.getNames();
      descNames.addAll(Arrays.asList(names));
    }

    List<String> dups = new ArrayList<String>();
    Set<String> uniqueNames = new HashSet<String>();
    for (String name : descNames) {
      if (!uniqueNames.add(name)) dups.add(name);
    }
    Assert.assertEquals(specs.size(), ncalc);
    Assert.assertEquals(descNames.size(), uniqueNames.size());
    if (dups.size() != 0) {
      System.out.println("Following names were duplicated");
      for (String dup : dups) {
        System.out.println("dup = " + dup);
      }
    }
  }
  /**
   * Generate the Sgroup elements for the provided atom contains.
   *
   * @param container molecule
   * @return Sgroup rendering elements
   */
  IRenderingElement generateSgroups(IAtomContainer container) {

    ElementGroup result = new ElementGroup();
    List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);

    if (sgroups == null || sgroups.isEmpty()) return result;

    for (Sgroup sgroup : sgroups) {

      switch (sgroup.getType()) {
        case CtabAbbreviation:
          result.add(generateAbbreviationSgroup(sgroup));
          break;
        case CtabMultipleGroup:
          result.add(generateMultipleSgroup(sgroup));
          break;
        case CtabAnyPolymer:
        case CtabMonomer:
        case CtabCrossLink:
        case CtabCopolymer:
        case CtabStructureRepeatUnit:
        case CtabMer:
        case CtabGraft:
        case CtabModified:
          result.add(generatePolymerSgroup(sgroup));
          break;
        case CtabComponent:
        case CtabMixture:
        case CtabFormulation:
          result.add(generateMixtureSgroup(sgroup));
          break;
        case CtabGeneric:
          // not strictly a polymer but okay to draw as one
          result.add(generatePolymerSgroup(sgroup));
          break;
      }
    }

    return result;
  }
Example #7
0
 /**
  * Create a predicate to match components for the provided query and target. The target is
  * pre-converted to an adjacency list ({@link GraphUtil#toAdjList(IAtomContainer)}) and the query
  * components extracted from the property {@link #KEY} in the query.
  *
  * @param query query structure
  * @param target target structure
  */
 public ComponentGrouping(IAtomContainer query, int[][] target) {
   this(
       query.getProperty(KEY, int[].class),
       query.getProperty(KEY) != null ? new ConnectedComponents(target) : null);
 }
Example #8
0
  /**
   * Convert the input into a pcore molecule.
   *
   * @param input the compound being converted from
   * @return pcore molecule
   * @throws CDKException match failed
   */
  private IAtomContainer getPharmacophoreMolecule(IAtomContainer input) throws CDKException {

    // XXX: prepare query, to be moved
    prepareInput(input);

    IAtomContainer pharmacophoreMolecule =
        input.getBuilder().newInstance(IAtomContainer.class, 0, 0, 0, 0);

    final Set<String> matched = new HashSet<>();
    final Set<PharmacophoreAtom> uniqueAtoms = new LinkedHashSet<>();

    logger.debug("Converting [" + input.getProperty(CDKConstants.TITLE) + "] to a pcore molecule");

    // lets loop over each pcore query atom
    for (IAtom atom : pharmacophoreQuery.atoms()) {
      final PharmacophoreQueryAtom qatom = (PharmacophoreQueryAtom) atom;
      final String smarts = qatom.getSmarts();

      // a pcore query might have multiple instances of a given pcore atom (say
      // 2 hydrophobic groups separated by X unit). In such a case we want to find
      // the atoms matching the pgroup SMARTS just once, rather than redoing the
      // matching for each instance of the pcore query atom.
      if (!matched.add(qatom.getSymbol())) continue;

      // see if the smarts for this pcore query atom gets any matches
      // in our query molecule. If so, then collect each set of
      // matching atoms and for each set make a new pcore atom and
      // add it to the pcore atom container object
      int count = 0;
      for (final IQueryAtomContainer query : qatom.getCompiledSmarts()) {

        // create the lazy mappings iterator
        final Mappings mappings = Pattern.findSubstructure(query).matchAll(input).uniqueAtoms();

        for (final int[] mapping : mappings) {
          uniqueAtoms.add(newPCoreAtom(input, qatom, smarts, mapping));
          count++;
        }
      }
      logger.debug("\tFound " + count + " unique matches for " + smarts);
    }

    pharmacophoreMolecule.setAtoms(uniqueAtoms.toArray(new IAtom[uniqueAtoms.size()]));

    // now that we have added all the pcore atoms to the container
    // we need to join all atoms with pcore bonds   (i.e. distance constraints)
    if (hasDistanceConstraints(pharmacophoreQuery)) {
      int npatom = pharmacophoreMolecule.getAtomCount();
      for (int i = 0; i < npatom - 1; i++) {
        for (int j = i + 1; j < npatom; j++) {
          PharmacophoreAtom atom1 = (PharmacophoreAtom) pharmacophoreMolecule.getAtom(i);
          PharmacophoreAtom atom2 = (PharmacophoreAtom) pharmacophoreMolecule.getAtom(j);
          PharmacophoreBond bond = new PharmacophoreBond(atom1, atom2);
          pharmacophoreMolecule.addBond(bond);
        }
      }
    }

    // if we have angle constraints, generate only the valid
    // possible angle relationships, rather than all possible
    if (hasAngleConstraints(pharmacophoreQuery)) {
      int nangleDefs = 0;

      for (IBond bond : pharmacophoreQuery.bonds()) {
        if (!(bond instanceof PharmacophoreQueryAngleBond)) continue;

        IAtom startQAtom = bond.getAtom(0);
        IAtom middleQAtom = bond.getAtom(1);
        IAtom endQAtom = bond.getAtom(2);

        // make a list of the patoms in the target that match
        // each type of angle atom
        List<IAtom> startl = new ArrayList<IAtom>();
        List<IAtom> middlel = new ArrayList<IAtom>();
        List<IAtom> endl = new ArrayList<IAtom>();

        for (IAtom tatom : pharmacophoreMolecule.atoms()) {
          if (tatom.getSymbol().equals(startQAtom.getSymbol())) startl.add(tatom);
          if (tatom.getSymbol().equals(middleQAtom.getSymbol())) middlel.add(tatom);
          if (tatom.getSymbol().equals(endQAtom.getSymbol())) endl.add(tatom);
        }

        // now we form the relevant angles, but we will
        // have reversed repeats
        List<IAtom[]> tmpl = new ArrayList<IAtom[]>();
        for (IAtom middle : middlel) {
          for (IAtom start : startl) {
            if (middle.equals(start)) continue;
            for (IAtom end : endl) {
              if (start.equals(end) || middle.equals(end)) continue;
              tmpl.add(new IAtom[] {start, middle, end});
            }
          }
        }

        // now clean up reversed repeats
        List<IAtom[]> unique = new ArrayList<IAtom[]>();
        for (int i = 0; i < tmpl.size(); i++) {
          IAtom[] seq1 = tmpl.get(i);
          boolean isRepeat = false;
          for (int j = 0; j < unique.size(); j++) {
            if (i == j) continue;
            IAtom[] seq2 = unique.get(j);
            if (seq1[1] == seq2[1] && seq1[0] == seq2[2] && seq1[2] == seq2[0]) {
              isRepeat = true;
            }
          }
          if (!isRepeat) unique.add(seq1);
        }

        // finally we can add the unique angle to the target
        for (IAtom[] seq : unique) {
          PharmacophoreAngleBond pbond =
              new PharmacophoreAngleBond(
                  (PharmacophoreAtom) seq[0],
                  (PharmacophoreAtom) seq[1],
                  (PharmacophoreAtom) seq[2]);
          pharmacophoreMolecule.addBond(pbond);
          nangleDefs++;
        }
      }
      logger.debug("Added " + nangleDefs + " defs to the target pcore molecule");
    }

    return pharmacophoreMolecule;
  }
Example #9
0
File: Misc.java Project: egonw/cdkr
 public static Object getProperty(IAtomContainer molecule, String key) {
   return molecule.getProperty(key);
 }