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scripts/packing_similarity_dendrogram/ReadMe.md

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# Packing Similarity Dendrogram
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## Summary:
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## Summary
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This command-line script is designed to compare the packing of a set of input structures of a molecule (polymorphs,
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co-crystals, solvates, and hydrates). An all-to-all comparison of the structures is performed, considering _only the
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heaviest components_ in each structure, and a packing-similarity dendrogram or tree is constructed using hierarchical
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clustering. This dendrogram shows the similarity between groups of structures and how these groups relate to one
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another.
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## Requirements:
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## Requirements
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CSD Python API (v. 1.0 or later), `matplotlib` and standard python packages.
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- CSD-Materials or CSD-Enterprise
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## Usage and Output:
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## Usage and Output
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`python Packing_Similarity_Dendrogram.py -h` will show the help text:
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conformations are matched and in, turn, whether two clusters that have only one molecule in common should be merged at
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that level.
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## Understanding the Dendrogram:
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## Understanding the Dendrogram
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An example dendrogram (produced using CBZdataset.ind and related files; see supporting material
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of [Cryst. Growth Des., 2009, 9, 1869 __ 1888](https://pubs.acs.org/doi/10.1021/cg801056c) ) is shown below in Figure 1.
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**Figure 3** : Example dendrogram based on a database of carbamazepine solid forms linking clusters based on their
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average packing similarity.
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## Caveats:
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## Caveats
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The tool considers only the heaviest component in each crystal structure to enable comparison of multi-component forms
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with pure forms. Results for _Z_ ’ > 1 systems may not fully reflect differences between structures as the best match is
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retained by default in the packing-similarity analysis.
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## Authors:
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## Authors
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_Anthony Reilly_(2016)
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> For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](mailto:support@ccdc.cam.ac.uk)

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