/**
* 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;
}
/**
* 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);
}
/**
* 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;
}
/**
* 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);
}
}
}
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);
}