public static void removeElectronContainer(IChemModel chemModel, IElectronContainer electrons) { ICrystal crystal = chemModel.Crystal; if (crystal != null) { if (crystal.contains(electrons)) { crystal.removeElectronContainer(electrons); } return; } ISetOfMolecules moleculeSet = chemModel.SetOfMolecules; if (moleculeSet != null) { SetOfMoleculesManipulator.removeElectronContainer(moleculeSet, electrons); } ISetOfReactions reactionSet = chemModel.SetOfReactions; if (reactionSet != null) { SetOfReactionsManipulator.removeElectronContainer(reactionSet, electrons); } }
public static void removeAtomAndConnectedElectronContainers(IChemModel chemModel, IAtom atom) { ICrystal crystal = chemModel.Crystal; if (crystal != null) { if (crystal.contains(atom)) { crystal.removeAtomAndConnectedElectronContainers(atom); } return; } ISetOfMolecules moleculeSet = chemModel.SetOfMolecules; if (moleculeSet != null) { SetOfMoleculesManipulator.removeAtomAndConnectedElectronContainers(moleculeSet, atom); } ISetOfReactions reactionSet = chemModel.SetOfReactions; if (reactionSet != null) { SetOfReactionsManipulator.removeAtomAndConnectedElectronContainers(reactionSet, atom); } }
public static IAtomContainer getRelevantAtomContainer(IReaction reaction, IBond bond) { IAtomContainer result = SetOfMoleculesManipulator.getRelevantAtomContainer(reaction.Reactants, bond); if (result != null) { return(result); } return(SetOfMoleculesManipulator.getRelevantAtomContainer(reaction.Products, bond)); }
/// <summary> Returns all the AtomContainer's of a ChemModel.</summary> public static IAtomContainer[] getAllAtomContainers(IChemModel chemModel) { ISetOfMolecules moleculeSet = chemModel.Builder.newSetOfMolecules(); if (chemModel.SetOfMolecules != null) { moleculeSet.add(chemModel.SetOfMolecules); } if (chemModel.SetOfReactions != null) { moleculeSet.add(SetOfReactionsManipulator.getAllMolecules(chemModel.SetOfReactions)); } return(SetOfMoleculesManipulator.getAllAtomContainers(moleculeSet)); }
public static void setAtomProperties(IChemModel chemModel, System.Object propKey, System.Object propVal) { if (chemModel.SetOfMolecules != null) { SetOfMoleculesManipulator.setAtomProperties(chemModel.SetOfMolecules, propKey, propVal); } if (chemModel.SetOfReactions != null) { SetOfReactionsManipulator.setAtomProperties(chemModel.SetOfReactions, propKey, propVal); } if (chemModel.Crystal != null) { AtomContainerManipulator.setAtomProperties(chemModel.Crystal, propKey, propVal); } }
public static IAtomContainer getRelevantAtomContainer(IChemModel chemModel, IBond bond) { IAtomContainer result = null; if (chemModel.SetOfMolecules != null) { ISetOfMolecules moleculeSet = chemModel.SetOfMolecules; result = SetOfMoleculesManipulator.getRelevantAtomContainer(moleculeSet, bond); if (result != null) { return(result); } } if (chemModel.SetOfReactions != null) { ISetOfReactions reactionSet = chemModel.SetOfReactions; return(SetOfReactionsManipulator.getRelevantAtomContainer(reactionSet, bond)); } // This should never happen. return(null); }
public static int getBondCount(IChemModel chemModel) { int count = 0; ICrystal crystal = chemModel.Crystal; if (crystal != null) { count += crystal.getBondCount(); } ISetOfMolecules moleculeSet = chemModel.SetOfMolecules; if (moleculeSet != null) { count += SetOfMoleculesManipulator.getBondCount(moleculeSet); } ISetOfReactions reactionSet = chemModel.SetOfReactions; if (reactionSet != null) { count += SetOfReactionsManipulator.getBondCount(reactionSet); } return(count); }
/// <summary> Puts all the Molecules of this container together in one /// AtomContainer. /// /// </summary> /// <returns> The AtomContainer with all the Molecules of this container /// /// </returns> /// <deprecated> This method has a serious performace impact. Try to use /// other methods. /// </deprecated> public static IAtomContainer getAllInOneContainer(IChemModel chemModel) { IAtomContainer container = chemModel.Builder.newAtomContainer(); ICrystal crystal = chemModel.Crystal; if (crystal != null) { container.add(crystal); } ISetOfMolecules moleculeSet = chemModel.SetOfMolecules; if (moleculeSet != null) { container.add(SetOfMoleculesManipulator.getAllInOneContainer(moleculeSet)); } ISetOfReactions reactionSet = chemModel.SetOfReactions; if (reactionSet != null) { container.add(SetOfReactionsManipulator.getAllInOneContainer(reactionSet)); } return(container); }
public static System.Collections.IList getAllChemObjects(IChemModel chemModel) { System.Collections.ArrayList list = new System.Collections.ArrayList(); list.Add(chemModel); ICrystal crystal = chemModel.Crystal; if (crystal != null) { list.Add(crystal); } ISetOfMolecules moleculeSet = chemModel.SetOfMolecules; if (moleculeSet != null) { list.AddRange(SetOfMoleculesManipulator.getAllChemObjects(moleculeSet)); } ISetOfReactions reactionSet = chemModel.SetOfReactions; if (reactionSet != null) { list.AddRange(SetOfReactionsManipulator.getAllChemObjects(reactionSet)); } return(list); }
/// <summary> Returns all the AtomContainer's of a Reaction.</summary> public static IAtomContainer[] getAllAtomContainers(ISetOfReactions set_Renamed) { return(SetOfMoleculesManipulator.getAllAtomContainers(getAllMolecules(set_Renamed))); }
/// <summary> Returns all the AtomContainer's of a Reaction.</summary> public static IAtomContainer[] getAllAtomContainers(IReaction reaction) { return(SetOfMoleculesManipulator.getAllAtomContainers(getAllMolecules(reaction))); }