[](https://www.codefactor.io/repository/github/pdbeurope/ccdutils/overview/master)    
# 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) and [wwPDB The Biologically Interesting Molecule Reference Dictionary](https://www.wwpdb.org/data/bird)
* The tools use:
* [RDKit](http://www.rdkit.org/) for chemistry. Presently tested with `2022.09.4`
* [GEMMI](https://gemmi.readthedocs.io/en/latest/index.html) for parsing cif files.
* [scipy](https://www.scipy.org/) for depiction quality check.
* [numpy](https://www.numpy.org/) for molecular scaling.
* [networkx](https://networkx.org/) 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](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 -n rdkit-env rdkit python=3.9
conda activate rdkit-env
```
* Once you have installed RDKit, as described above then install pdbeccdutils using pip:
```console
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](https://doi.org/10.1016/j.str.2018.02.009) 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.
```console
sphinx-apidoc -f -o /path/to/output/dir ../pdbeccdutils/
```
Use this to re-generate the documentation from the doc/ directory:
```console
make html
```
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