Update, the explicit or not charge is not relevant. that just determines
the behaviour of the AssignBondOrderstoTemplate. The behaviour is that
GetBestRMS does not consider a carboxylate as symmetric. Can anyone
suggest a workaround to treat as symmetric?
*Kind Regards*
Dr. Martin Watson
VP Structural Analysis
C4X Discovery Ltd
martin.wat...@c4xdiscovery.com
+44 (0)7753 434535
+44 (0)161 235 5085
*www.c4xdiscovery.com <http://www.c4xdiscovery.com>*
On 17 April 2018 at 14:21, Martin Watson <martin.wat...@c4xdiscovery.com>
wrote:
> Hi
>
> I'm using GetBestRMS to score conformers in an sdf relative to a pdb
> extracted sdf ligand using the snippet below. I get odd behaviour when the
> molecule includes a carboxylic acid. depending on whether the charge is
> explicitly defined in the sdf or not I get a different RMS which seems to
> be that the symmetry of the carboxyl is not considered by GetBestRMS is
> that so? And if not can anyone suggest a workaround. (FWIW I have
> examples which "work" when the charge is supplied and "fail" if not as well
> as vice versa)
>
> import sys
> from rdkit import Chem
> from rdkit.Chem import AllChem, rdMolAlign
>
> # The ensemble sdf conformations with hydrogens
> suppl = Chem.SDMolSupplier(sys.argv[2],sanitize=False)
> count=0
>
> #compare them to ref pdb extract no hydrogens
> for molh in suppl:
> count=count+1
> mol1 = Chem.MolFromMolFile(sys.argv[1])
> mol = Chem.RemoveHs(molh)
> mol = AllChem.AssignBondOrdersFromTemplate(mol1, mol)
> rms = AllChem.GetBestRMS(mol1, mol)
> print(rms)
>
>
> *Thanks*
>
> Dr. Martin Watson
>
>
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