/** *{@inheritDoc} */ @Override public boolean isEmpty() { if (setOfMolecules != null && !setOfMolecules.isEmpty()) return false; if (setOfReactions != null && !setOfReactions.isEmpty()) return false; if (ringSet != null && !ringSet.isEmpty()) return false; if (crystal != null && !crystal.isEmpty()) return false; return true; } }
/** * clean the flags CDKConstants.REACTIVE_CENTER from the molecule. * * @param ac */ private void cleanFlagReactiveCenter(IAtomContainer ac) { for (int j = 0; j < ac.getAtomCount(); j++) ac.getAtom(j).setFlag(CDKConstants.REACTIVE_CENTER, false); for (int j = 0; j < ac.getBondCount(); j++) ac.getBond(j).setFlag(CDKConstants.REACTIVE_CENTER, false); } }
void reset() { final int numAtoms = mol.getAtomCount(); final int numBonds = mol.getBondCount(); for (int i = 0; i < numAtoms; i++) mol.getAtom(i).setPoint2d(coords[i]); for (int i = 0; i < numBonds; i++) mol.getBond(i).setStereo(btypes[i]); } }
public IAtomContainer resetFlags(IAtomContainer ac) { for (int f = 0; f < ac.getAtomCount(); f++) { ac.getAtom(f).setFlag(CDKConstants.VISITED, false); } for (int f = 0; f < ac.getElectronContainerCount(); f++) { ac.getElectronContainer(f).setFlag(CDKConstants.VISITED, false); } return ac; }
public static IAtomContainerSet getAllAgents(IReaction reaction) { IAtomContainerSet moleculeSet = reaction.getBuilder().newInstance(IAtomContainerSet.class); IAtomContainerSet agents = reaction.getAgents(); for (int i = 0; i < agents.getAtomContainerCount(); i++) { moleculeSet.addAtomContainer(agents.getAtomContainer(i)); } return moleculeSet; }
public void select(IAtomContainer atomContainer) { this.chemModel = atomContainer.getBuilder().newInstance(IChemModel.class); IAtomContainerSet molSet = atomContainer.getBuilder().newInstance(IAtomContainerSet.class); molSet.addAtomContainer(atomContainer); this.chemModel.setMoleculeSet(molSet); }
private void addHydrogens(IAtomContainer container, IAtom atom, int numberOfHydrogens) { for (int i = 0; i < numberOfHydrogens; i++) container.addBond(atom.getBuilder().newInstance(IBond.class, atom, atom.getBuilder().newInstance(IAtom.class, "H"))); }
/** * Count the number of double bonds in a container. * * @param container structure representation * @return number of double bonds */ static int nDoubleBonds(IAtomContainer container) { int count = 0; for (IBond bond : container.bonds()) if (IBond.Order.DOUBLE.equals(bond.getOrder())) count++; return count; }
/** * Helper method determines if a bond is defined (not null) and whether it * is a sigma (single) bond with no stereo attribute (wedge/hatch). * * @param bond the bond to test * @return the bond is a planar sigma bond */ private static boolean isPlanarSigmaBond(IBond bond) { return bond != null && IBond.Order.SINGLE.equals(bond.getOrder()) && IBond.Stereo.NONE.equals(bond.getStereo()); }
protected static void resetFlags(IAtomContainer atomContainer) { for (int f = 0; f < atomContainer.getAtomCount(); f++) { atomContainer.getAtom(f).setFlag(CDKConstants.VISITED, false); } for (int f = 0; f < atomContainer.getBondCount(); f++) { atomContainer.getBond(f).setFlag(CDKConstants.VISITED, false); } }
void reset() { final int numAtoms = mol.getAtomCount(); final int numBonds = mol.getBondCount(); for (int i = 0; i < numAtoms; i++) mol.getAtom(i).setPoint2d(coords[i]); for (int i = 0; i < numBonds; i++) mol.getBond(i).setStereo(btypes[i]); } }
/** *{@inheritDoc} */ @Override public boolean isEmpty() { if (setOfMolecules != null && !setOfMolecules.isEmpty()) return false; if (setOfReactions != null && !setOfReactions.isEmpty()) return false; if (ringSet != null && !ringSet.isEmpty()) return false; if (crystal != null && !crystal.isEmpty()) return false; return true; } }
protected static void resetFlags(IAtomContainer atomContainer) { for (int f = 0; f < atomContainer.getAtomCount(); f++) { atomContainer.getAtom(f).setFlag(CDKConstants.VISITED, false); } for (int f = 0; f < atomContainer.getBondCount(); f++) { atomContainer.getBond(f).setFlag(CDKConstants.VISITED, false); } }
/** *{@inheritDoc} */ @Override public boolean isEmpty() { if (setOfMolecules != null && !setOfMolecules.isEmpty()) return false; if (setOfReactions != null && !setOfReactions.isEmpty()) return false; if (ringSet != null && !ringSet.isEmpty()) return false; if (crystal != null && !crystal.isEmpty()) return false; return true; } }
private static void resetFlags(IAtomContainer atomContainer) { for (int f = 0; f < atomContainer.getAtomCount(); f++) { atomContainer.getAtom(f).setFlag(CDKConstants.VISITED, false); } for (int f = 0; f < atomContainer.getBondCount(); f++) { atomContainer.getBond(f).setFlag(CDKConstants.VISITED, false); } }
/** *{@inheritDoc} */ @Override public boolean isEmpty() { if (setOfMolecules != null && !setOfMolecules.isEmpty()) return false; if (setOfReactions != null && !setOfReactions.isEmpty()) return false; if (ringSet != null && !ringSet.isEmpty()) return false; if (crystal != null && !crystal.isEmpty()) return false; return true; } }