Re: Explicit Valence Error when Calculating PLEC

[Maciek Wójcikowski]

Hi,

In general it is really bad idea to skip the sanitization, as RDKit PDB parser is picky. Which version are you using?

I would strongly recommend reviewing a suite of tools in ODDT for preparing PDB complexes, read more here: https://oddt.readthedocs.io/en/latest/rst/oddt.toolkits.extras.rdkit.html#oddt.toolkits.extras.rdkit.fixer.PreparePDBMol

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Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

pt., 5 lip 2019 o 01:34 <mate...@gmail.com> napisał(a):

Hello,

I encountered an explicit valence error when calculating PLECs for both plk1 and jak2 systems from the DUD-E set.

The protein pdbs passed into the ODDT reader are the ones directly downloaded from DUD-E. The error is caused by the following line in the PLEC function:

    # removing h

    protein_mask = protein_no_h = (protein.atom_dict['atomicnum'] != 1)

I know that this valence error is often caused by a sanitization of the molecule through RDkit. Is a sanitization implicitly called in ODDT's rdk.py file?

If not, where is this error occurring and why?

Thank you in advance,

Mateo Vacacela

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