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Fix typos and formatting in README.md (#27)
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amorehead authored Oct 28, 2024
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# pdbeccdutils

* A set of python tools to deal with PDB chemical components definitions.
* 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.
* [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.
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* `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:
For Linux/macOS 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:
* Once you have installed RDKit, as described above then install `pdbeccdutils` using `pip`:

```console
pip install pdbeccdutils
```

## Features

* gemmi CCD read/write.
* `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).
* 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.
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