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;
}
}
}
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;
}
/// <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 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;
}
