private CMLMoleculeList CDKAtomContainerSetToCMLList(IEnumerableChemObject <IAtomContainer> moleculeSet, bool setIDs)
{
CMLMoleculeList cmlList = new CMLMoleculeList
{
Convention = "cdk:moleculeSet"
};
if (useCMLIDs && setIDs)
{
IDCreator.CreateIDs(moleculeSet);
}
if (!string.IsNullOrEmpty(moleculeSet.Id))
{
cmlList.Id = moleculeSet.Id;
}
foreach (var container in moleculeSet)
{
cmlList.Add(CDKAtomContainerToCMLMolecule(container, false, false));
}
return(cmlList);
}
/// <summary>
/// writes all the molecules supplied in a MoleculeSet class to
/// a single HIN file. You can also supply a single Molecule object
/// as well
/// </summary>
/// <param name="som">the set of molecules to write</param>
/// <exception cref="IOException">if there is a problem writing the molecule</exception>
private void WriteAtomContainer(IEnumerableChemObject <IAtomContainer> som)
{
string sym;
double chrg;
int molnumber = 0;
foreach (var mol in som)
{
molnumber++;
try
{
string molname = "mol " + molnumber + " " + mol.Title;
writer.Write(molname, 0, molname.Length);
writer.Write('\n');
// Loop through the atoms and write them out:
int i = 0;
foreach (var atom in mol.Atoms)
{
string line = "atom ";
sym = atom.Symbol;
chrg = atom.Charge.Value;
Vector3 point = atom.Point3D.Value;
line = line + (i + 1).ToString(NumberFormatInfo.InvariantInfo) + " - " + sym + " ** - " + chrg.ToString(NumberFormatInfo.InvariantInfo) + " "
+ point.X.ToString(NumberFormatInfo.InvariantInfo) + " " + point.Y.ToString(NumberFormatInfo.InvariantInfo) + " "
+ point.Z.ToString(NumberFormatInfo.InvariantInfo) + " ";
string abuf = "";
int ncon = 0;
foreach (var bond in mol.Bonds)
{
if (bond.Contains(atom))
{
// current atom is in the bond so lets get the connected atom
IAtom connectedAtom = bond.GetOther(atom);
BondOrder bondOrder = bond.Order;
int serial;
string bondType = "";
// get the serial no for this atom
serial = mol.Atoms.IndexOf(connectedAtom);
if (bondOrder == BondOrder.Single)
{
bondType = "s";
}
else if (bondOrder == BondOrder.Double)
{
bondType = "d";
}
else if (bondOrder == BondOrder.Triple)
{
bondType = "t";
}
else if (bond.IsAromatic)
{
bondType = "a";
}
abuf = abuf + (serial + 1).ToString(NumberFormatInfo.InvariantInfo) + " " + bondType + " ";
ncon++;
}
}
line = line + " " + ncon.ToString(NumberFormatInfo.InvariantInfo) + " " + abuf;
writer.Write(line, 0, line.Length);
writer.Write('\n');
i++;
}
string buf = "endmol " + molnumber;
writer.Write(buf, 0, buf.Length);
writer.Write('\n');
}
catch (IOException)
{
throw;
}
}
}
public CMLMoleculeList CDKAtomContainerSetToCMLList(IEnumerableChemObject <IAtomContainer> moleculeSet)
{
return(CDKAtomContainerSetToCMLList(moleculeSet, true));
}
