Metadata-Version: 2.1
Name: rdktools
Version: 0.0.9
Summary: Tools and helpers for RDKit.
Home-page: https://github.com/jeremyjyang/rdkit-tools
Author: Jeremy Yang
Author-email: jeremyjyang@gmail.com
License: UNKNOWN
Description: # `RDKIT-TOOLS`
        
        Tools for use with RDKit.
        
        * <https://rdkit.org>
        * <https://www.rdkit.org/docs/Install.html>
        
        ## Dependencies
        
        * RDKit Python package (possibly via conda).
        
        ```
        $ conda create -n rdkit -c conda-forge rdkit ipykernel
        $ conda activate rdkit
        (rdkit) $ conda install -c conda-forge pyvis 
        (rdkit) $ conda install -c conda-forge networkx=2.5 
        ```
        
        ## Execution
        
        Scaffold analysis:
        
        ```
        $ conda activate rdkit
        (rdkit) $ python3 -m rdktools.scaffold.App -h
        usage: App.py [-h] [--i IFILE] [--o OFILE] [--o_html OFILE_HTML]
                      [--scratchdir SCRATCHDIR] [--smicol SMICOL] [--namcol NAMCOL]
                      [--idelim IDELIM] [--odelim ODELIM] [--iheader] [--oheader]
                      [--brics] [-v]
                      {bmscaf,scafnet,demobm,demonet,demonetvis}
        
        RDKit scaffold analysis
        
        positional arguments:
          {bmscaf,scafnet,demobm,demonet,demonetvis}
                                OPERATION
        
        optional arguments:
          -h, --help            show this help message and exit
          --i IFILE             input file, TSV or SDF
          --o OFILE             output file, TSV|SDF
          --o_html OFILE_HTML   output file, HTML
          --scratchdir SCRATCHDIR
          --smicol SMICOL       SMILES column from TSV (counting from 0)
          --namcol NAMCOL       name column from TSV (counting from 0)
          --idelim IDELIM       delim for input TSV
          --odelim ODELIM       delim for output TSV
          --iheader             input TSV has header
          --oheader             output TSV has header
          --brics               BRICS fragmentation rules (Degen, 2008)
          -v, --verbose
        ```
        
        Standardization:
        
        ```
        (rdkit) $ python3 -m rdktools.standard.App
        usage: App.py [-h] [--i IFILE] [--o OFILE] [--norms {default,unm}]
                      [--i_norms IFILE_NORMS] [--remove_isomerism] [-v]
                      {standardize,list_norms,show_params,demo}
        App.py: error: the following arguments are required: op
        lengua$ python3 -m rdktools.standard.App -h
        usage: App.py [-h] [--i IFILE] [--o OFILE] [--norms {default,unm}]
                      [--i_norms IFILE_NORMS] [--remove_isomerism] [-v]
                      {standardize,list_norms,show_params,demo}
        
        RDKit chemical standardizer
        
        positional arguments:
          {standardize,list_norms,show_params,demo}
                                operation
        
        optional arguments:
          -h, --help            show this help message and exit
          --i IFILE             input file, SMI or SDF
          --o OFILE             output file, SMI or SDF
          --norms {default,unm}
                                normalizations
          --i_norms IFILE_NORMS
                                input normalizations file, format: SMIRKS<space>NAME
          --remove_isomerism    if true, output SMILES isomerism removed
          -v, --verbose
        ```
        
        Conformation generation:
        
        ```
        (rdkit) $ python3 -m rdktools.conform.App -h
        usage: App.py [-h] [--i IFILE] [--o OFILE] [--ff {UFF,MMFF}] [--optiters OPTITERS]
                      [--nconf NCONF] [--etol ETOL] [--title_in_header] [-v]
        
        RDKit Conformer Generation
        
        optional arguments:
          -h, --help           show this help message and exit
          --i IFILE            input file, SMI or SDF
          --o OFILE            output SDF with 3D
          --ff {UFF,MMFF}      force-field
          --optiters OPTITERS  optimizer iterations per conf
          --nconf NCONF        # confs per mol
          --etol ETOL          energy tolerance
          --title_in_header    title line in header
          -v, --verbose
        
        Based on distance geometry method by Blaney et al.
        ```
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
