11# Packing Similarity Dendrogram
22
3- ## Summary:
3+ ## Summary
44
55This command-line script is designed to compare the packing of a set of input structures of a molecule (polymorphs,
66co-crystals, solvates, and hydrates). An all-to-all comparison of the structures is performed, considering _ only the
77heaviest components_ in each structure, and a packing-similarity dendrogram or tree is constructed using hierarchical
88clustering. This dendrogram shows the similarity between groups of structures and how these groups relate to one
99another.
1010
11- ## Requirements:
11+ ## Requirements
1212
1313CSD Python API (v. 1.0 or later), ` matplotlib ` and standard python packages.
1414
@@ -18,7 +18,7 @@ CSD Python API (v. 1.0 or later), `matplotlib` and standard python packages.
1818
1919- CSD-Materials or CSD-Enterprise
2020
21- ## Usage and Output:
21+ ## Usage and Output
2222
2323` python Packing_Similarity_Dendrogram.py -h ` will show the help text:
2424
@@ -110,7 +110,7 @@ than an RMSD tolerance). The `-ct` option can therefore be used to specific an R
110110conformations are matched and in, turn, whether two clusters that have only one molecule in common should be merged at
111111that level.
112112
113- ## Understanding the Dendrogram:
113+ ## Understanding the Dendrogram
114114
115115An example dendrogram (produced using CBZdataset.ind and related files; see supporting material
116116of [ Cryst. Growth Des., 2009, 9, 1869 _ –_ 1888] ( https://pubs.acs.org/doi/10.1021/cg801056c ) ) is shown below in Figure 1.
@@ -160,13 +160,14 @@ that could also be implemented.
160160** Figure 3** : Example dendrogram based on a database of carbamazepine solid forms linking clusters based on their
161161average packing similarity.
162162
163- ## Caveats:
163+ ## Caveats
164164
165165The tool considers only the heaviest component in each crystal structure to enable comparison of multi-component forms
166166with pure forms. Results for _ Z_ ’ > 1 systems may not fully reflect differences between structures as the best match is
167167retained by default in the packing-similarity analysis.
168168
169- ## Authors:
169+ ## Authors
170+
170171_ Anthony Reilly_ (2016)
171172
172173> For feedback or to report any issues please contact [ support@ccdc.cam.ac.uk ] ( mailto:support@ccdc.cam.ac.uk )
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