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ccdutils

(★ 83)

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

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- - documentation.yml
  - publish.yml
  - tests.yml
- - codeine.svg
  - fragment_example.svg
  - HEM_300.svg
  - HEM_300_names.svg
  - pdbe_fragments.svg
  - scaffold_example.svg
- - depictions.md
  - fragments.md
  - intro.md
  - pipelines.md
  - scaffolds.md
  - similarity.md
- api.md
- conf.py
- index.md
- logo.png
- Makefile
- pdbeccdutils.computations.md
- pdbeccdutils.core.md
- pdbeccdutils.helpers.md
- pdbeccdutils.scripts.md
- pdbeccdutils.utils.md
- - __init__.py
  - parity_method.py
- - __init__.py
  - boundmolecule.py
  - ccd_reader.py
  - ccd_writer.py
  - clc_reader.py
  - clc_writer.py
  - component.py
  - depictions.py
  - exceptions.py
  - fragment_library.py
  - models.py
  - prd_reader.py
  - prd_writer.py
- - fragment_library.tsv
- - __init__.py
  - cif_tools.py
  - conversions.py
  - drawing.py
  - helper.py
  - mol_tools.py
- - __init__.py
  - boundmolecule_cli.py
  - process_components_cif_cli.py
  - setup_pubchem_library_cli.py
- - conftest.py
  - test_bound_molecule.py
  - test_boundmolecule_cli.py
  - test_ccd_reader.py
  - test_clc_reader.py
  - test_clc_writer.py
  - test_file_writing.py
  - test_fragment_library.py
  - test_helper_methods.py
  - test_inchi_key_matches.py
  - test_load_eoh_cif.py
  - test_parity.py
  - test_prd_reader.py
  - test_process_components_cif_cli.py
  - test_property_generation.py
  - test_rdkit_fixtures.py
  - test_residue.py
  - test_scaffold_generation.py
  - test_web_services.py
  - test_write_img.py
  - tst_utilities.py
- - __init__.py
  - config.py
  - pubchem_downloader.py
  - web_services.py
.gitignore
.gitlab-ci.yml
.pre-commit-config.yaml
CHANGELOG.md
CITATION.cff
Dockerfile
LICENSE
Makefile
MANIFEST.in
poetry.lock
poetry.toml
pyproject.toml
README.md
setup.py

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# pdbeccdutils

An RDKit-based python toolkit for parsing and processing small molecule definitions in [wwPDB Chemical Component Dictionary](https://www.wwpdb.org/data/ccd) and [wwPDB The Biologically Interesting Molecule Reference Dictionary](https://www.wwpdb.org/data/bird).`pdbeccdutils` provides streamlined access to all metadata of small molecules in the PDB and offers a set of convenient methods to compute various properties of small molecules using RDKIt such as 2D depictions, 3D conformers, physicochemical properties, matching common fragments and scaffolds, mapping to small-molecule databases using UniChem.

## 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-curated 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.
* Generating complete representation of multiple [Covalently Linked Components (CLC)](https://www.ebi.ac.uk/pdbe/news/introducing-covalently-linked-components)

## Dependencies

* [RDKit](http://www.rdkit.org/) for small molecule representation. Presently tested with `2023.9.6`
  * [GEMMI](https://gemmi.readthedocs.io/en/latest/index.html) for parsing mmCIF 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.

## Installation

create a [virtual environment](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/#create-and-use-virtual-environments) and install using pip

```bash
  pip install pdbeccdutils
  ```

## Contribution
We encourage you to contribute to this project. The package uses [poetry](https://python-poetry.org/) for packaging and dependency management. You can develop locally using:

```bash
git clone https://github.com/PDBeurope/ccdutils.git
cd ccdutils
pip install poetry
poetry install --with tests,docs
pre-commit install
```

The pre-commit hook will run linting, formatting and update `poetry.lock`. The `poetry.lock` file will lock all dependencies and ensure that they match pyproject.toml versions.

To add a new dependency

```bash
# Latest resolvable version
poetry add <package>

# Optionally fix a version
poetry add <package>@<version>
```

To change a version of a dependency, either edit pyproject.toml and run:

```bash
poetry sync --with dev
```

or

```bash
poetry add <package>@<version>
```

## Documentation

The documentation is generated using `sphinx` in `sphinx_rtd_theme` and hosted on GitHub Pages. To generate the documentation locally,

```bash
cd doc
poetry run sphinx-build -b html . _build/html

# See the documentation at http://localhost:8080.
python -m http.server 8080 -d _build/html
```