ChEMBL_Structure_Pipeline
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chembl
ChEMBL database structure pipelines
Despite having a running conda environment with chembl_structure_pipeline installed, every new environnement I create fail to install the package. Issue is: ``` (early_2021) C02XJ285JGH6:~ nbosc$ conda install -c chembl chembl_structure_pipeline...
I was surprised to see this form of an azide in the database:  It's an odd form and I only find it once in ChEMBL26 (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1652082/) in contrast to...
In order to help prevent users from getting themselves into trouble, we should add a `standardize` argument to `standardize_mol()` that defaults to True. One argument against setting the default to...
Hello, In ChEMBL_Structure_Pipeline/chembl_structure_pipeline/exclude_flag.py: METAL_LIST should be a dictionary or a string set, instead of a list. Cool project, thanks a lot for releasing it. Regards, F.
Is `standardize_mol` writing atomic properties to the mol object expected behavior? Here is a situation I came across: ``` import rdkit from chembl_structure_pipeline import standardizer smi = "CC1COCC[S@]1=O |&1:6|" mol...
``` from rdkit import Chem from chembl_structure_pipeline import standardizer # a molecule with enhanced stereochemistry m3bis = Chem.MolFromSmiles('Cl.O[C@@H]1CC[C@H](Cl)C[C@@H]1O |a:5,&1:2,8|') m3bis ```  (the carbon bearing Cl has absolute configuration, the...
Consider alternate handling of chiral centers which have overlapping atoms or atoms on the same line
The standardizer currently assigns a penalty of 5 when there are overlapping atoms or 6 if there are more than six overlapping atoms. This still allows molecules which have overlapping...
After processing to Chembl Standardization functions, a double bond inside a 5-membered ring (which can only be cis) is converted to crossed (unknown cis/trans) type double bond - two examples...
