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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
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The tools use:
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Please note that the project is under active development.
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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
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Once you have installed RDKit, as described above then install pdbeccdutils using pip:
pip install pdbeccdutils
- gemmi CCD read/write.
- Generation of 2D depictions (
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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.
- Add more unit/regression tests to get higher code coverage.
- Further improvements of the 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