Hi Greg,
On Sun, Aug 12, 2012 at 10:00 AM, Greg Landrum <[email protected]>wrote:
> Hi Fabian,
>
> On Fri, Aug 10, 2012 at 3:21 PM, Fabian Dey <[email protected]> wrote:
> >
> >
> > I am in the process of a scaffold analysis, printing the scaffolds in
> smiles
> > format, and came across some unexpected behaviour:
> > Whenever I remove hydrogens with RemoveHs() and print out the smiles
> string,
> > some hydrogens remain attached (irrespective
> > if the original input file type is SDF or smiles):
> >
> >
> >
> > from rdkit import Chem
> > from rdkit.Chem.Scaffolds import MurckoScaffold
> >
> > # molecule from zinc:
> > suppl = Chem.SDMolSupplier("zinc_69443014.sdf");
> > for mol in suppl:
> > mol = Chem.RemoveHs(mol)
> > print 'Mol1: %s' %(Chem.MolToSmiles(mol))
> >
> > mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
> > mol = Chem.RemoveHs(mol)
> > print 'Mol2: %s' %(Chem.MolToSmiles(mol))
> >
> >
> > Output:
> > Mol1: Cn1nccc1C[NH2+]CC1CNc2ccnn2C1
> > Mol2: c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1
>
> The function RemoveHs() goes through the molecular graph and removes
> hydrogens that are present as explicit atoms. It doesn't affect the
> hydrogen count on any given atom though. Any other behavior would
> change the chemistry of the molecule, which is definitely not the
> intent.
>
> What are you trying to do? What output would you expect above?
>
I was in the process of doing a scaffold analysis when I ran into the
"persistent" hydrogens that would not be removed and thus
decided to check also what the function does on a complete molecule. I
understand that information on the hydrogen count
should not be deleted, but I was expecting that the hydrogens would not be
part of the Smiles output (print 'Scaffold2: %s'
%(Chem.MolToSmiles(sc2[0])).
Would it make sense to include an argument for "MolToSmiles(...)" which
results in that only the heavy-atom graph is returned
(one could still keep the default as "false") ?
Thanks for the help
Fabian
ps: For the Bemis & Murcko scaffold the output is similar:
>>> from rdkit import Chem
>>> from rdkit.Chem.Scaffolds import MurckoScaffold
>>> mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
>>> sc = [MurckoScaffold.GetScaffoldForMol(mol)]
>>> print '%s ' %(Chem.MolToSmiles(sc[0]))
c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1
>
> > This is also the case when extracting the carbon scaffold of a molecule
> > (even after
> > resetting all formal charges to zero)
> >
> > mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
> > mol = Chem.RemoveHs(mol,implicitOnly=False)
> > sc = [MurckoScaffold.MakeScaffoldGeneric(mol)]
> > print 'Scaffold1: %s' %(Chem.MolToSmiles(sc[0]))
> >
> >
> > mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
> > sc2 = [MurckoScaffold.MakeScaffoldGeneric(mol)]
> > sc2[0] = Chem.RemoveHs(sc2[0],implicitOnly=False)
> > print 'Scaffold2: %s' %(Chem.MolToSmiles(sc2[0]))
> >
> >
> > mol = Chem.MolFromSmiles("c1cc(C[NH2+]CC2CNc3ccnn3C2)[nH]n1")
> > mol = Chem.RemoveHs(mol,implicitOnly=False)
> > for atom in mol.GetAtoms():
> > atom.SetFormalCharge(0)
> > sc3 = [MurckoScaffold.MakeScaffoldGeneric(mol)]
> > sc3[0] = Chem.RemoveHs(sc3[0],implicitOnly=False)
> > print 'Scaffold3: %s' %(Chem.MolToSmiles(sc3[0]))
> >
> > Output:
> > Scaffold1: [CH]1CCCC1C[CH2+]CC1CCC2CCCC2C1
> > Scaffold2: [CH]1CCCC1C[CH2+]CC1CCC2CCCC2C1
> > Scaffold3: [CH]1CCCC1CCCC1CCC2CCCC2C1
>
> That looks like it's a bug in MurckoScaffold.MakeScaffoldGeneric(); it
> should be removing the explict H counts and setting charges to zero.
> Thanks for reporting it.
>
> -greg
>
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