Metadata-Version: 2.1
Name: pdbeccdutils
Version: 0.5.10
Summary: Toolkit to deal with wwPDB chemical components definitions for small molecules.
Home-page: http://pypi.python.org/pypi/pdbeccdutils/
Author: Protein Data Bank in Europe
Author-email: pdbehelp@ebi.ac.uk
License: Apache License 2.0.
Project-URL: Source code, https://github.com/PDBeurope/ccdutils
Project-URL: Documentation, https://pdbeurope.github.io/ccdutils/
Description: [![CodeFactor](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/badge/master)](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/overview/master)  ![PYPi](https://img.shields.io/pypi/v/pdbeccdutils?color=green&style=flat)  ![GitHub](https://img.shields.io/github/license/pdbeurope/ccdutils)   ![ccdutils documentation](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20documentation/badge.svg) ![ccdutils tests](https://github.com/PDBeurope/ccdutils/workflows/ccdutils%20tests/badge.svg)
        
        # pdbeccdutils
        
        * A set of python tools to deal with PDB chemical components definitions
          for small molecules, taken from the [wwPDB Chemical Component Dictionary](https://www.wwpdb.org/data/ccd)
        
        * The tools use:
          * [RDKit](http://www.rdkit.org/) for chemistry
          * [PDBeCIF](https://github.com/PDBeurope/pdbecif) cif parser.
          * [scipy](https://www.scipy.org/) for depiction quality check.
          * [numpy](https://www.numpy.org/) for molecular scaling.
        
        * Please note that the project is under active development.
        
        ## Installation instructions
        
        * `pdbeccdutils` requires RDKit to be installed.
          The official RDKit documentation has [installation instructions for a variety of platforms](http://www.rdkit.org/docs/Install.html).
          For linux/mac OS this is most easily done using the anaconda python with commands similar to:
        
          ```console
          conda create -c conda-forge -n rdkit-env rdkit python=3.7
          conda activate rdkit-env
          ```
        
        * Once you have installed RDKit, as described above then install pdbeccdutils using pip:
        
          ```console
          pip install pdbeccdutils
          ```
        
        ## Features
        
        * mmCIF CCD read/write.
        * Generation of 2D depictions (`No image available` generated if the flattening cannot be done) along with the quality check.
        * Generation of 3D conformations.
        * Fragment library search.
        * Chemical scaffolds (Murcko scaffold, Murcko general, BRICS).
        * Lightweight implementation of [parity method](https://doi.org/10.1016/j.str.2018.02.009) by Jon Tyczak.
        * RDKit molecular properties per component.
        * UniChem mapping.
        
        ## TODO list
        
        * Add more unit/regression tests to get higher code coverage.
        * Further improvements of the documentation.
        
        ## Notes
        
        * Protein-ligand interaction has been extracted [here](https://gitlab.ebi.ac.uk/pdbe/release/interactions). This was because of the fact that at the end of the day it was not using any of the pdbeccdutils functionality and introduced additional dependencies on the package.
        
        ## Documentation
        
        The documentation depends on the following packages:
        
        * `sphinx`
        * `sphinx_rtd_theme`
        * `recommonmark`
        * `sphinx-autodoc-typehints`
        
        Note that `sphinx` needs to be a part of the virtual environment, if you want to generate documentation by yourself.
        Otherwise it cannot pick `rdkit` module. `sphinx_rtd_theme` is a theme providing nice `ReadtheDocs` mobile friendly style.
        
        * Generate *.rst* files to be included as a part of the documentation. Inside the directory `pdbeccdutils/doc` run the following commands to generate documentation.
        * Alternatively, use the `recommonmark` package along with the proper configuration to get the Markdown working.
        
         Use the following to generate initial markup files to be used by sphinx.  This needs to be used when adding another sub-packages.
        
        ```console
        sphinx-apidoc -f -o /path/to/output/dir ../pdbeccdutils/
        ```
        
        Use this to re-generate the documentation from the doc/ directory:
        
        ```console
        make html
        ```
        
Keywords: PDB CCD wwPDB small molecule
Platform: UNKNOWN
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Development Status :: 5 - Production/Stable
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: tests
Provides-Extra: docs
