ChEMBL_Structure_Pipeline
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chembl
ChEMBL database structure pipelines
This PR fixes some circular import that is encountered during setup/installation, where the version of the structure pipeline is imported from module code. Now it is hard-coded into `setup.py` together...
The assertion in the following statement fails when running `unittest` in Python 3.9.8, using `rdkit` version 2022.3.1: https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/8d599ad389a458c002be9fd8353a91ebaf370743/chembl_structure_pipeline/test/test_standardizer.py#L1655 Which raises: ``` FAIL: testDoubleBondStereoProblem1 (test.test_standardizer.TestCase) a problem found in testing ----------------------------------------------------------------------...
Hi, I have been using the following function for standardizing structures, and since it involves converting SMILES to RDKit_mol, and back to SMILES, I assumed that the output SMILES would...
Thank you for this pipeline; very helpful! I am writing a python command line wrapper to some of this functionality and it appears to me that some of the "runtime"...
Hi everyone, as mentioned in #14 , I've added a command line interface to standartization from SMILES strings (namely, from input files containing SMILES as their first column). Also, I...
For example: ``` std -i input.smi -o output_std.smi [-np NPROCS] ``` The option to process molecules in parallel on a given number of CPUs is also for people working with...
Hi, I noticed the standardizer adds a charge to suphur, which doesn't look correct to me. For instance  is standardised to  and  is standardised to 
Would then take care of dependencies and be immediately executable
Hi, Thanks for developing this pipeline and making it available, it is really useful! I noticed that the standardizer fixes covalent bonds to ionic in alkaline oxides, and it might...
Hi, thanks for implementing this useful pipeline! We come up with one issue related to salt remove: We found that: For these two molecules, the 'standardize_mol' function followed by the...
