PDBeurope/ccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

pdbeccdutils

• A set of python tools to deal with PDB chemical components definitions. for small molecules, taken from the wwPDB Chemical Component Dictionary and wwPDB The Biologically Interesting Molecule Reference Dictionary

• The tools use:

  • RDKit for chemistry. Presently tested with 2022.09.4
  • GEMMI for parsing cif files.
  • scipy for depiction quality check.
  • numpy for molecular scaling.
  • networkx for bound-molecules.

• 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. For linux/mac OS this is most easily done using the anaconda python with commands similar to:

  conda create -n rdkit-env rdkit python=3.9
  conda activate rdkit-env

• Once you have installed RDKit, as described above then install pdbeccdutils using pip:

  pip install pdbeccdutils

Features

• gemmi 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 (PDBe hand currated library, ENAMINE, DSI).
• Chemical scaffolds (Murcko scaffold, Murcko general, BRICS).
• Lightweight implementation of parity method by Jon Tyzack.
• RDKit molecular properties per component.
• UniChem mapping.

TODO list

• Add more unit/regression tests to get higher code coverage.
• Further improvements of the documentation.

Documentation

The documentation depends on the following packages:

• sphinx
• sphinx_rtd_theme
• myst-parser
• 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 myst-parser package 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.

sphinx-apidoc -f -o /path/to/output/dir ../pdbeccdutils/

Use this to re-generate the documentation from the doc/ directory:

make html