ChEMBL protocols used to standardise and salt strip molecules. First used in ChEMBL 26.
Check the wiki and paper[1] for a detailed description of the different processes.
From source:
git clone https://github.com/chembl/ChEMBL_Structure_Pipeline.git
pip install ./ChEMBL_Structure_Pipeline
with pip:
pip install chembl_structure_pipelinewith conda:
conda install -c conda-forge chembl_structure_pipelineStandardise a compound (info)
from chembl_structure_pipeline import standardizer
o_molblock = """
Mrv1810 07121910172D
4 3 0 0 0 0 999 V2000
-2.5038 0.4060 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
-2.5038 1.2310 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-3.2182 -0.0065 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
-1.7893 -0.0065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 4 0 0 0
M CHG 2 2 -1 3 1
M END
"""
std_molblock = standardizer.standardize_molblock(o_molblock)Get the parent compound (info)
from chembl_structure_pipeline import standardizer
o_molblock = """
Mrv1810 07121910262D
3 1 0 0 0 0 999 V2000
-5.2331 1.1053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.5186 1.5178 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
-2.8647 1.5789 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M CHG 2 2 1 3 -1
M END
"""
parent_molblock, _ = standardizer.get_parent_molblock(o_molblock)Check a compound (info)
The checker assesses the quality of a structure. It highlights specific features or issues in the structure that may need to be revised. Together with the description of the issue, the checker process returns a penalty score (between 0-9) which reflects the seriousness of the issue (the higher the score, the more critical is the issue)
from chembl_structure_pipeline import checker
o_molblock = """
Mrv1810 02151908462D
4 3 0 0 0 0 999 V2000
2.2321 4.4196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0023 4.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4117 4.5059 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9568 3.6420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 1 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
M END
"""
issues = checker.check_molblock(o_molblock)[1] Bento, A.P., Hersey, A., Félix, E. et al. An open source chemical structure curation pipeline using RDKit. J Cheminform 12, 51 (2020). https://doi.org/10.1186/s13321-020-00456-1