diff --git a/README.md b/README.md index 203a876..f5c2059 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,12 @@ # 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. @@ -18,14 +18,14 @@ * `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 @@ -33,10 +33,10 @@ ## 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.