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2 | 2 |
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3 | 3 | # pdbeccdutils |
4 | 4 |
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5 | | -* A set of python tools to deal with PDB chemical components definitions. |
| 5 | +* A set of python tools to deal with PDB chemical components definitions |
6 | 6 | 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) |
7 | 7 |
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8 | 8 | * The tools use: |
9 | 9 | * [RDKit](http://www.rdkit.org/) for chemistry. Presently tested with `2022.09.4` |
10 | | - * [GEMMI](https://gemmi.readthedocs.io/en/latest/index.html) for parsing cif files. |
| 10 | + * [GEMMI](https://gemmi.readthedocs.io/en/latest/index.html) for parsing mmCIF files. |
11 | 11 | * [scipy](https://www.scipy.org/) for depiction quality check. |
12 | 12 | * [numpy](https://www.numpy.org/) for molecular scaling. |
13 | 13 | * [networkx](https://networkx.org/) for bound-molecules. |
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18 | 18 |
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19 | 19 | * `pdbeccdutils` requires RDKit to be installed. |
20 | 20 | The official RDKit documentation has [installation instructions for a variety of platforms](http://www.rdkit.org/docs/Install.html). |
21 | | - For linux/mac OS this is most easily done using the anaconda python with commands similar to: |
| 21 | + For Linux/macOS this is most easily done using the Anaconda Python with commands similar to: |
22 | 22 |
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23 | 23 | ```console |
24 | 24 | conda create -n rdkit-env rdkit python=3.9 |
25 | 25 | conda activate rdkit-env |
26 | 26 | ``` |
27 | 27 |
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28 | | -* Once you have installed RDKit, as described above then install pdbeccdutils using pip: |
| 28 | +* Once you have installed RDKit, as described above then install `pdbeccdutils` using `pip`: |
29 | 29 |
|
30 | 30 | ```console |
31 | 31 | pip install pdbeccdutils |
32 | 32 | ``` |
33 | 33 |
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34 | 34 | ## Features |
35 | 35 |
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36 | | -* gemmi CCD read/write. |
| 36 | +* `gemmi` CCD read/write. |
37 | 37 | * Generation of 2D depictions (`No image available` generated if the flattening cannot be done) along with the quality check. |
38 | 38 | * Generation of 3D conformations. |
39 | | -* Fragment library search (PDBe hand currated library, ENAMINE, DSI). |
| 39 | +* Fragment library search (PDBe hand-curated library, ENAMINE, DSI). |
40 | 40 | * Chemical scaffolds (Murcko scaffold, Murcko general, BRICS). |
41 | 41 | * Lightweight implementation of [parity method](https://doi.org/10.1016/j.str.2018.02.009) by Jon Tyzack. |
42 | 42 | * RDKit molecular properties per component. |
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