/** * Utility - get the IAtomContainers as a list. * * @param frags connected fragments * @return list of fragments */ private List<IAtomContainer> toList(IAtomContainerSet frags) { return new ArrayList<>(FluentIterable.from(frags.atomContainers()).toList()); }
/** * Utility - get the IAtomContainers as a list. * * @param frags connected fragments * @return list of fragments */ private List<IAtomContainer> toList(IAtomContainerSet frags) { return new ArrayList<>(FluentIterable.from(frags.atomContainers()).toList()); }
public static int getBondCount(IAtomContainerSet set) { int count = 0; for (IAtomContainer atomContainer : set.atomContainers()) { count += (atomContainer).getBondCount(); } return count; }
public static int getAtomCount(IAtomContainerSet set) { int count = 0; for (IAtomContainer atomContainer : set.atomContainers()) { count += (atomContainer).getAtomCount(); } return count; }
public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom) { for (IAtomContainer atomContainer : containerSet.atomContainers()) { if (atomContainer.contains(atom)) { return atomContainer; } } return null; }
/** * Writes an {@link IAtomContainerSet}. * * @param som the {@link IAtomContainerSet} to serialize */ private void writeMoleculeSet(IAtomContainerSet som) throws Exception { for (IAtomContainer mol : som.atomContainers()) { writeMolecule(mol); } }
public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet containerSet, IBond bond) { for (IAtomContainer atomContainer : containerSet.atomContainers()) { if (atomContainer.contains(bond)) { return atomContainer; } } return null; }
private int fillIndexMap( Map<IAtom, Integer> indexMap, IAtomContainerSet moleculeSet, int index) { for (IAtomContainer atomContainer : moleculeSet.atomContainers()) { for (IAtom atom : atomContainer.atoms()) { indexMap.put(atom, index); index++; } } return index; }
private double caclModelScale(IReaction rxn) { List<IAtomContainer> mols = new ArrayList<>(); for (IAtomContainer mol : rxn.getReactants().atomContainers()) mols.add(mol); for (IAtomContainer mol : rxn.getProducts().atomContainers()) mols.add(mol); for (IAtomContainer mol : rxn.getAgents().atomContainers()) mols.add(mol); return caclModelScale(mols); }
private double caclModelScale(IReaction rxn) { List<IAtomContainer> mols = new ArrayList<>(); for (IAtomContainer mol : rxn.getReactants().atomContainers()) mols.add(mol); for (IAtomContainer mol : rxn.getProducts().atomContainers()) mols.add(mol); for (IAtomContainer mol : rxn.getAgents().atomContainers()) mols.add(mol); return caclModelScale(mols); }
private synchronized IAtom getContainerAtomByID(IAtomContainerSet products, String mappingID) { for (IAtomContainer ac : products.atomContainers()) { for (IAtom atom : ac.atoms()) { if (atom.getID().equals(mappingID)) { return atom; } } } return null; }
public static double calculateAverageBondLength(IAtomContainerSet moleculeSet) { double averageBondModelLength = 0.0; for (IAtomContainer atomContainer : moleculeSet.atomContainers()) { averageBondModelLength += GeometryTools.getBondLengthAverage(atomContainer); } return averageBondModelLength / moleculeSet.getAtomContainerCount(); }
/** * Calculate the average bond length for the bonds in a molecule set. * * @param moleculeSet the molecule set to use * @return the average bond length */ public static double calculateAverageBondLength(IAtomContainerSet moleculeSet) { double averageBondModelLength = 0.0; for (IAtomContainer atomContainer : moleculeSet.atomContainers()) { averageBondModelLength += GeometryUtil.getBondLengthAverage(atomContainer); } return averageBondModelLength / moleculeSet.getAtomContainerCount(); }
private AtomContainerAtomPair getByID(IAtomContainerSet moleculeSet, String id) { // System.out.println("getting id " + id); for (IAtomContainer ac : moleculeSet.atomContainers()) { for (IAtom atom : ac.atoms()) { String atomID = atom.getID(); if (atomID != null && atomID.equals(id)) { return new AtomContainerAtomPair(ac, atom); } } } return null; }
private void printReaction(IReaction reaction) { for (IAtomContainer atomContainer : reaction.getReactants().atomContainers()) { for (IAtom atom : atomContainer.atoms()) { out.println("PRINTING ATOM " + atom.getID()); } } for (IAtomContainer atomContainer : reaction.getProducts().atomContainers()) { for (IAtom atom : atomContainer.atoms()) { out.println("PRINTING ATOM " + atom.getID()); } } }
/** {@inheritDoc} */ @Override public IRenderingElement generateDiagram(IAtomContainerSet molecules) { ElementGroup diagram = new ElementGroup(); for (IAtomContainer molecule : molecules.atomContainers()) { diagram.add(atomContainerRenderer.generateDiagram(molecule)); } return diagram; }
/** {@inheritDoc} */ @Override public IRenderingElement generateDiagram(IAtomContainerSet molecules) { ElementGroup diagram = new ElementGroup(); for (IAtomContainer molecule : molecules.atomContainers()) { diagram.add(atomContainerRenderer.generateDiagram(molecule)); } return diagram; }
public void undo() { if (chemModelRelay != null) { for (IAtomContainer ac : oldsom.atomContainers()) { chemModelRelay.updateAtoms(ac, ac.atoms()); } } chemModel.setMoleculeSet(oldsom); chemModel.setReactionSet(oldsor); }
@Test public void testExampleFile_MolReading() throws Exception { String filename = "data/moss/TKO.mossoutput"; InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); MoSSOutputReader reader = new MoSSOutputReader(ins); IAtomContainerSet moleculeSet = new AtomContainerSet(); moleculeSet = reader.read(moleculeSet); Assert.assertEquals(19, moleculeSet.getAtomContainerCount()); for (IAtomContainer mol : moleculeSet.atomContainers()) { Assert.assertEquals(Integer.valueOf(mol.getProperty("atomCount").toString()).intValue(), mol.getAtomCount()); Assert.assertEquals(Integer.valueOf(mol.getProperty("bondCount").toString()).intValue(), mol.getBondCount()); } }
protected static String cansmi(IReaction rxn) throws CDKException { IReaction copy = rxn.getBuilder().newInstance(IReaction.class); for (IAtomContainer mol : rxn.getReactants().atomContainers()) copy.addReactant(AtomContainerManipulator.copyAndSuppressedHydrogens(mol)); for (IAtomContainer mol : rxn.getProducts().atomContainers()) copy.addProduct(AtomContainerManipulator.copyAndSuppressedHydrogens(mol)); for (IAtomContainer mol : rxn.getAgents().atomContainers()) copy.addAgent(AtomContainerManipulator.copyAndSuppressedHydrogens(mol)); return smigen.create(copy); }