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Updated Licence requirement NO_JIRA
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scripts/packing_similarity_dendrogram/ReadMe.md

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CSD Python API (v. 1.0 or later), `matplotlib` and standard python packages.
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> Instructions on running example scripts through the CSD-Python API miniconda installation can be found in [the repository ReadMe.md](https://github.com/ccdc-opensource/csd-python-api-scripts#readme)
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> Instructions on running example scripts through the CSD Python API miniconda installation can be found in [the repository ReadMe.md](https://github.com/ccdc-opensource/csd-python-api-scripts#readme)
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## Licensing Requirements
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\#TODO [LIST]
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- CSD-Materials or CSD-Enterprise
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## Usage and Output:
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packing similarity.
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```
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Basic usage (in a command prompt) is:
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## Basic usage (in a command prompt):
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```cmd
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python Packing_Similarity_Dendrogram.py input_file
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packing similarity between the structures. The file names are prefixed with the stem of the input file ( _i.e._ if
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roy.gcd is the input, then the similarity dendrogram will be called `roy_packing_similarity_tree.png`).
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If a large set of structures are inputted, the top _N_ structures can be selected using the -nm options.
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If a large set of structures are inputted, the top _N_ structures can be selected using the `-nm` options.
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Using the `-o` option will result in overlays being saved for each comparison (as .mol2 files). The matrix of
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similarities is also saved as a raw numpy matrix ( _i.e._ as
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`roy_similarity_matrix.txt`), and can be read back in (with `-m`) to skip the packing-similarity analysis, if, for
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example, a different clustering algorithm is desired or part of the script has been changed.
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The `--allow_molecular_differences` option can be used when comparing crystal structures of closely related molecules _
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e.g._ salts and free forms.
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The `--allow_molecular_differences` option can be used when comparing crystal structures of closely related moleculese.g. salts and free forms.
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The `-s` option will strip all terminal atoms and carbon atom chains up to hetero atoms ( _e.g._
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The `-s` option will strip all terminal atoms and carbon atom chains up to hetero atoms (e.g.
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the methyl of a methoxy will be removed), which may be useful for identifying more coarse- grained similarity that
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ignores small changes in the periphery of the molecule. A new cif is created containing the stripped molecule and
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analysis is performed using this file. Note that disordered experimental structures present in the input database will

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