Metadata-Version: 2.1
Name: chemosanitizer
Version: 0.0.1
Summary: A python script to parallelize basic MolVS functions
Home-page: https://gitlab.unige.ch/Pierre-Marie.Allard/chemo_sanitizer.git
Author: Pierre-Marie Allard
Author-email: pierre-marie.allard@unige.ch
License: MIT
Download-URL: https://gitlab.unige.ch/Pierre-Marie.Allard/chemo_sanitizer/-/archive/version='0.0.1'/chemo_sanitizer-version='0.0.1'.tar.gz
Description: # chemo_sanitizer
        
        A set of script using RDKit and MolVS to proceed to the standardization , sanitization and different format conversion. Parallelized.
        
        In this state it take only InChI as inputs and returns sanitized SMILES, InChI, InChIKeys, Short InChIkeys, MolecularFormula, ExactMass and XLogP.
        
        ## Requirements 
        
        Install the conda environment by
        
        `conda env create -f environment.yml`
        
        ### Specific requirement
        
        Note that some modules of MolVS are not loaded by default. 
        You will need to edit the MolVS  __init__.py in ~/opt/anaconda3/lib/python3.7/site-packages/molvs/ accordingly.
        Add these lines to the __init__.py
        
        ```
        from .fragment import LargestFragmentChooser, FragmentRemover
        from .charge import Uncharger
        ```
        
        
        
        ## Usage
        
        Go to the src folder 
        Then add input and output file path as first and second argument, InChI column header as third argument and finally the number of cpus you want to use.
        
        Example :
                
        ```
        cd src
        python chemosanitizer.py ~/translatedStructureRdkit.tsv ./test.tsv structureTranslated 6
        ```
        
        
        
Keywords: chemoinformatics,MolVS
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
Provides-Extra: sdf_query
