/// <summary>
/// MolfileV3000ToAtomContainer
/// </summary>
/// <param name="molfile"></param>
/// <returns></returns>
public static IAtomContainer MolfileV3000ToAtomContainer(string molfile)
{
// Extract any mass info before conversion to avoid losing our custom info in conversion
Dictionary <int, int> map = new Dictionary <int, int>();
if (molfile.Contains(" MASS="))
{
map = ExtractMassAttributes(ref molfile);
}
cdk.io.DefaultChemObjectReader cor;
java.io.StringReader sr = new java.io.StringReader(molfile);
cor = new MDLV3000Reader(sr);
cor.setReaderMode(IChemObjectReader.Mode.RELAXED);
IAtomContainer mol = (IAtomContainer)cor.read(new AtomContainer());
cor.close();
for (int ai = 0; ai < mol.getAtomCount(); ai++)
{
IAtom a = mol.getAtom(ai);
if (map.ContainsKey(ai + 1))
{
a.setMassNumber(new java.lang.Integer(map[ai + 1]));
}
else
{
a.setMassNumber(null);
}
}
ConfigureAtomContainer(mol);
return(mol);
}
/// <summary>
/// Set integer MassNumber (isotope value) for an atom
/// </summary>
/// <param name="atom"></param>
/// <param name="mass"></param>
public static void SetMassNumber(
IAtom atom,
int mass)
{
atom.setMassNumber(new java.lang.Integer(mass));
return;
}
/// <summary>
/// Convert isotope labels to hilighting.
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public string ConvertIsotopeValuesToHilighting(
IAtomContainer mol)
{
bool hilight;
string molfile2 = "";
bool clearAttachmentPointLabels = true;
bool hilightAttachmentBond = true;
List <int> atomSet = new List <int>();
List <int> bondSet = new List <int>();
for (int bi = 0; bi < mol.getBondCount(); bi++)
{
IBond b = mol.getBond(bi);
if (b.getAtomCount() != 2)
{
continue;
}
IAtom a1 = b.getAtom(0);
IAtom a2 = b.getAtom(1);
if (hilightAttachmentBond)
{
hilight = (GetMassNumber(a1) != 0 && GetMassNumber(a2) != 0);
}
else
{
hilight = (GetMassNumber(a1) < 0 && GetMassNumber(a2) < 0);
}
if (hilight)
{
bondSet.Add(bi);
}
}
//String posMap = ""; // debug (note that hydrogens can get repositioned)
for (int ai = 0; ai < mol.getAtomCount(); ai++) // scan atoms for hilighting and reset isotope values
{
IAtom a = mol.getAtom(ai);
hilight = GetMassNumber(a) < 0;
if (hilight)
{
atomSet.Add(ai);
}
//posMap += ai.ToString() + ", " + a.getSymbol() + ", " + hilight + "\r\n"; // debug
int massNo = GetMassNumber(a);
if (massNo == hilightIsotopeValue)
{
a.setMassNumber(null); // set back to original value
}
else if (massNo < 0)
{
if (clearAttachmentPointLabels)
{
a.setMassNumber(null);
}
else
{
SetMassNumber(a, -massNo); // set back to positive
}
}
}
//mol = GenerateCoordinates(mol); // (should already be done)
try { molfile2 = AtomContainerToMolFileV3000(mol); }
catch (Exception ex) { ex = ex; }
if (Lex.IsUndefined(molfile2)) // couldn't convert to v3000, just return unhilighted v2000 file
{
molfile2 = AtomContainerToMolfile(mol);
return(molfile2);
}
string txt = "MDLV30/HILITE";
if (atomSet.Count > 0)
{
txt += " " + BuildV3000KeywordList("ATOMS", atomSet);
}
if (bondSet.Count > 0)
{
txt += " " + BuildV3000KeywordList("BONDS", bondSet);
}
txt = BuildV3000Lines(txt);
bool hasCollection = Lex.Contains(molfile2, "M V30 END COLLECTION");
if (hasCollection) // already have collection begin and end
{
txt = txt +
"M V30 END COLLECTION";
molfile2 = Lex.Replace(molfile2, "M V30 END COLLECTION", txt);
}
else // add collection begin & end
{
txt =
"M V30 BEGIN COLLECTION\n" +
txt +
"M V30 END COLLECTION\n" +
"M V30 END CTAB";
molfile2 = Lex.Replace(molfile2, "M V30 END CTAB", txt);
}
return(molfile2);
}