/// <summary>
/// Tries to parses text as SMILES, InChI, or MolBlock and returns RDKit ROMol.
/// </summary>
/// <param name="molIdent">Text expression of molecule like SMILES, InChI, or MolBlock.</param>
/// <returns>RDKit ROMol.</returns>
public static ROMol Parse(string molIdent)
{
if (molIdent == null)
{
throw new ArgumentNullException(nameof(molIdent));
}
var mol = MolecularCache.GetOrAdd(molIdent, a_ident =>
{
string notationType = null;
ROMol a_mol;
a_mol = RWMol.MolFromSmiles(molIdent);
if (a_mol != null)
{
notationType = "SMILES";
goto L_Found;
}
using (var rv = new ExtraInchiReturnValues())
{
a_mol = RDKFuncs.InchiToMol(molIdent, rv);
if (a_mol != null)
{
notationType = "InChI";
goto L_Found;
}
}
a_mol = RWMol.MolFromMolBlock(molIdent);
if (a_mol != null)
{
RDKFuncs.assignStereochemistryFrom3D(a_mol);
notationType = "MolBlock";
goto L_Found;
}
L_Found:
if (a_mol == null)
{
a_mol = nullMol;
}
else
{
if (notationType != null)
{
a_mol.setProp("source", notationType);
}
}
return(a_mol);
});
if (object.ReferenceEquals(mol, nullMol))
{
return(null);
}
return(mol);
}
static void Demo()
{
var toluene = RWMol.MolFromSmiles("Cc1ccccc1");
var mol1 = RWMol.MolFromMolFile(Path.Combine("Data", "input.mol"));
var stringWithMolData = new StreamReader(Path.Combine("Data", "input.mol")).ReadToEnd();
var mol2 = RWMol.MolFromMolBlock(stringWithMolData);
using (var suppl = new SDMolSupplier(Path.Combine("Data", "5ht3ligs.sdf")))
{
while (!suppl.atEnd())
{
var mol = suppl.next();
if (mol == null)
{
continue;
}
Console.WriteLine(mol.getAtoms().Count);
using (var maccs = RDKFuncs.MACCSFingerprintMol(mol))
{
Console.WriteLine(ToString(maccs));
}
}
}
using (var gzsuppl = new ForwardSDMolSupplier(new gzstream("Data/actives_5ht3.sdf.gz")))
{
while (!gzsuppl.atEnd())
{
var mol = gzsuppl.next();
if (mol == null)
{
continue;
}
Console.WriteLine(mol.getAtoms().Count);
using (var maccs = RDKFuncs.MACCSFingerprintMol(mol))
{
Console.WriteLine(ToString(maccs));
}
}
}
}
// TODO: Add strictParsing
public static RWMol MolFromMolBlock(string molBlock, bool sanitize = true, bool removeHs = true)
{
return(RWMol.MolFromMolBlock(molBlock, sanitize, removeHs));
}
