public static int getBondCount(ISetOfAtomContainers set_Renamed) { int count = 0; IAtomContainer[] acs = set_Renamed.AtomContainers; for (int i = 0; i < acs.Length; i++) { count += acs[i].getBondCount(); } return count; }
public static System.Collections.IList getAllChemObjects(ISetOfAtomContainers set_Renamed) { System.Collections.ArrayList list = new System.Collections.ArrayList(); list.Add(set_Renamed); IAtomContainer[] acs = set_Renamed.AtomContainers; for (int i = 0; i < acs.Length; i++) { list.Add(acs[i]); // don't recurse into AC's for now } return(list); }
/// <summary> Puts all the AtomContainers of this set together in one /// AtomCcntainer. /// /// </summary> /// <returns> The AtomContainer with all the AtomContainers of this set /// /// </returns> /// <deprecated> This method has a serious performace impact. Try to use /// other methods. /// </deprecated> public static IAtomContainer getAllInOneContainer(ISetOfAtomContainers set_Renamed) { IAtomContainer container = set_Renamed.Builder.newAtomContainer(); IAtomContainer[] acs = set_Renamed.AtomContainers; for (int i = 0; i < acs.Length; i++) { container.add(acs[i]); } return(container); }
public static IAtomContainer getRelevantAtomContainer(ISetOfAtomContainers containerSet, IBond bond) { IAtomContainer[] containers = containerSet.AtomContainers; for (int i = 0; i < containers.Length; i++) { if (containers[i].contains(bond)) { return(containers[i]); } } return(null); }
/// <returns> The summed formal charges of all atoms in this set. /// </returns> public static double getTotalFormalCharge(ISetOfAtomContainers set_Renamed) { int charge = 0; for (int i = 0; i < set_Renamed.AtomContainerCount; i++) { int thisCharge = AtomContainerManipulator.getTotalFormalCharge(set_Renamed.getAtomContainer(i)); double stoich = set_Renamed.getMultiplier(i); charge = (int)(charge + stoich * thisCharge); } return(charge); }
/// <summary> Adds all atomContainers in the SetOfAtomContainers to this container. /// /// </summary> /// <param name="atomContainerSet"> The SetOfAtomContainers /// </param> public virtual void add(ISetOfAtomContainers atomContainerSet) { IAtomContainer[] mols = atomContainerSet.AtomContainers; for (int i = 0; i < mols.Length; i++) { addAtomContainer(mols[i]); } /* * notifyChanged() is called by addAtomContainer() */ }
public static System.Collections.ArrayList getAllIDs(ISetOfAtomContainers set_Renamed) { System.Collections.ArrayList idList = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10)); if (set_Renamed != null) { if (set_Renamed.ID != null) { idList.Add(set_Renamed.ID); } for (int i = 0; i < set_Renamed.AtomContainerCount; i++) { idList.Add(AtomContainerManipulator.getAllIDs(set_Renamed.getAtomContainer(i))); } } return(idList); }
public static void removeElectronContainer(ISetOfAtomContainers set_Renamed, IElectronContainer electrons) { IAtomContainer[] acs = set_Renamed.AtomContainers; for (int i = 0; i < acs.Length; i++) { IAtomContainer container = acs[i]; if (container.contains(electrons)) { container.removeElectronContainer(electrons); IMolecule[] molecules = ConnectivityChecker.partitionIntoMolecules(container).Molecules; if (molecules.Length > 1) { set_Renamed.removeAtomContainer(container); for (int k = 0; k < molecules.Length; k++) { set_Renamed.addAtomContainer(molecules[k]); } } return; } } }
/// <summary> Returns all the AtomContainer's of a SetOfMolecules.</summary> public static IAtomContainer[] getAllAtomContainers(ISetOfAtomContainers set_Renamed) { return(set_Renamed.AtomContainers); }
/// <summary> Returns all the AtomContainer's of a SetOfMolecules.</summary> public static IAtomContainer[] getAllAtomContainers(ISetOfAtomContainers set_Renamed) { return set_Renamed.AtomContainers; }
public static System.Collections.IList getAllChemObjects(ISetOfAtomContainers set_Renamed) { System.Collections.ArrayList list = new System.Collections.ArrayList(); list.Add(set_Renamed); IAtomContainer[] acs = set_Renamed.AtomContainers; for (int i = 0; i < acs.Length; i++) { list.Add(acs[i]); // don't recurse into AC's for now } return list; }
public static IAtomContainer getRelevantAtomContainer(ISetOfAtomContainers containerSet, IBond bond) { IAtomContainer[] containers = containerSet.AtomContainers; for (int i = 0; i < containers.Length; i++) { if (containers[i].contains(bond)) { return containers[i]; } } return null; }
public static void setAtomProperties(ISetOfAtomContainers set_Renamed, System.Object propKey, System.Object propVal) { if (set_Renamed != null) { for (int i = 0; i < set_Renamed.AtomContainerCount; i++) { AtomContainerManipulator.setAtomProperties(set_Renamed.getAtomContainer(i), propKey, propVal); } } }
public static System.Collections.ArrayList getAllIDs(ISetOfAtomContainers set_Renamed) { System.Collections.ArrayList idList = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10)); if (set_Renamed != null) { if (set_Renamed.ID != null) idList.Add(set_Renamed.ID); for (int i = 0; i < set_Renamed.AtomContainerCount; i++) { idList.Add(AtomContainerManipulator.getAllIDs(set_Renamed.getAtomContainer(i))); } } return idList; }
/// <returns> The summed implicit hydrogens of all atoms in this set. /// </returns> public static int getTotalHydrogenCount(ISetOfAtomContainers set_Renamed) { int hCount = 0; for (int i = 0; i < set_Renamed.AtomContainerCount; i++) { hCount += AtomContainerManipulator.getTotalHydrogenCount(set_Renamed.getAtomContainer(i)); } return hCount; }
/// <returns> The summed formal charges of all atoms in this set. /// </returns> public static double getTotalFormalCharge(ISetOfAtomContainers set_Renamed) { int charge = 0; for (int i = 0; i < set_Renamed.AtomContainerCount; i++) { int thisCharge = AtomContainerManipulator.getTotalFormalCharge(set_Renamed.getAtomContainer(i)); double stoich = set_Renamed.getMultiplier(i); charge = (int)(charge + stoich * thisCharge); } return charge; }
public static int getBondCount(ISetOfAtomContainers set_Renamed) { return(SetOfAtomContainersManipulator.getBondCount(set_Renamed)); }
/// <summary> Labels the Atom's and Bond's in each AtomContainer using the a1, a2, b1, b2 /// scheme often used in CML. It will also set id's for all AtomContainers, naming /// them m1, m2, etc. /// It will not the SetOfAtomContainers itself. /// </summary> public virtual void createIDs(ISetOfAtomContainers containerSet) { if (tabuList == null) tabuList = SetOfAtomContainersManipulator.getAllIDs(containerSet); if (containerSet.ID == null) { moleculeCount++; while (tabuList.Contains("molSet" + moleculeCount)) moleculeCount++; containerSet.ID = "molSet" + moleculeCount; } IAtomContainer[] containers = containerSet.AtomContainers; for (int i = 0; i < containers.Length; i++) { IAtomContainer container = containers[i]; if (container.ID == null) { createIDs(container); } } }
/// <summary> Puts all the AtomContainers of this set together in one /// AtomCcntainer. /// /// </summary> /// <returns> The AtomContainer with all the AtomContainers of this set /// /// </returns> /// <deprecated> This method has a serious performace impact. Try to use /// other methods. /// </deprecated> public static IAtomContainer getAllInOneContainer(ISetOfAtomContainers set_Renamed) { IAtomContainer container = set_Renamed.Builder.newAtomContainer(); IAtomContainer[] acs = set_Renamed.AtomContainers; for (int i = 0; i < acs.Length; i++) { container.add(acs[i]); } return container; }