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Fix typos and formatting in README.md (#27)
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# pdbeccdutils
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* A set of python tools to deal with PDB chemical components definitions.
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* A set of python tools to deal with PDB chemical components definitions
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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)
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* The tools use:
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* [RDKit](http://www.rdkit.org/) for chemistry. Presently tested with `2022.09.4`
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* [GEMMI](https://gemmi.readthedocs.io/en/latest/index.html) for parsing cif files.
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* [GEMMI](https://gemmi.readthedocs.io/en/latest/index.html) for parsing mmCIF files.
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* [scipy](https://www.scipy.org/) for depiction quality check.
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* [numpy](https://www.numpy.org/) for molecular scaling.
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* [networkx](https://networkx.org/) for bound-molecules.
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* `pdbeccdutils` requires RDKit to be installed.
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The official RDKit documentation has [installation instructions for a variety of platforms](http://www.rdkit.org/docs/Install.html).
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For linux/mac OS this is most easily done using the anaconda python with commands similar to:
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For Linux/macOS this is most easily done using the Anaconda Python with commands similar to:
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```console
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conda create -n rdkit-env rdkit python=3.9
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conda activate rdkit-env
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```
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* Once you have installed RDKit, as described above then install pdbeccdutils using pip:
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* Once you have installed RDKit, as described above then install `pdbeccdutils` using `pip`:
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```console
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pip install pdbeccdutils
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```
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## Features
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* gemmi CCD read/write.
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* `gemmi` CCD read/write.
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* Generation of 2D depictions (`No image available` generated if the flattening cannot be done) along with the quality check.
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* Generation of 3D conformations.
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* Fragment library search (PDBe hand currated library, ENAMINE, DSI).
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* Fragment library search (PDBe hand-curated library, ENAMINE, DSI).
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* Chemical scaffolds (Murcko scaffold, Murcko general, BRICS).
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* Lightweight implementation of [parity method](https://doi.org/10.1016/j.str.2018.02.009) by Jon Tyzack.
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* RDKit molecular properties per component.

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