Dear JP,
To confuse you even more, you can also have a look at the ChEMBL
open-source molecular standardizer:
https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py
No need to thank me. :D
On 18/06/2021 03:12, JP Ebejer wrote:
Dear all,
I am trying to standardize(/normalize?) some molecules from different
sources, to generate a set of descriptors for them. I have done this
a number of times, and each time I find the process slightly
confusing. I have the following questions please, if you don't mind:
1. What is the relation between molvs and rdkit (I remember there was
an integration project between the two a while back). When I call
rdMolStandardize does rdkit code or molvs code get called? The github
repo for molvs hasn't been updated in a while (2 yrs), but
rdMolStandardize has.
2. What is the difference between standardization and normalization
of a molecule? Does one automatically imply the other or should these
two processes be both run on a molecule?
3. Specifically, what is the difference between
rdMolStandardize.Cleanup(mol), Chem.SanitizeMol(mol),
rdMolStandardize.Normalize(mol). Should I call any of these manually
three after I run "standardization/cleaning operations" such as
uncharging, reionizing, etc?
4. I understand what uncharge does, but what does reionizer do?
5. Is there a way to chain operations together
standardize+ChooseLargestFragment+uncharge+normalize (am not sure the
order makes sense here), other than creating a class instance for each
calling the method, returning a new mol and using this mol in the next
operation?
Apologies for the many questions. Have I missed the documentation
about this? I have found some excellent examples here:
https://github.com/susanhleung/rdkit/blob/dev/GSOC2018_MolVS_Integration/rdkit/Chem/MolStandardize/tutorial/MolStandardize.ipynb
(thanks!). This is not exactly a cleaning pipeline, but still quite
helpful to understand these methods.
Many thanks,
JP
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