Crystal packing similarity

Note

The crystal packing similarity features are available only to CSD-Materials and CSD-Enterprise users.

Introduction

A crystal packing similarity metric may be calculated for very similar crystals. This metric is described in “COMPACK: a program for identifying crystal structure similarity using distances”, J.A. Chisholm and S. Motherwell, J. Appl. Cryst. 38, 228–231, 2005. DOI: 10.1107/S0021889804027074.

This is a method to identify similarity in molecular packing environments within crystal structures. The method can be used to determine whether two crystal structures are the same to within specified tolerances and also provides a measure of similarity for structures that do not match exactly, but have common structural features. The relative position and orientation of molecules is captured using interatomic distances. This is a representation of structure that avoids use of space-group and cell information.

Using the Packing Similarity API

Firstly we shall import the ccdc.crystal.PackingSimilarity class and instantiate it:

>>> from ccdc.crystal import PackingSimilarity
>>> similarity_engine = PackingSimilarity()

The similarity engine currently has just one significant method, to compare to packing shells.

We shall need a couple of crystals to compare:

>>> from ccdc.io import CrystalReader
>>> csd = CrystalReader('csd')
>>> fetsec = csd.crystal('FETSEC')
>>> zerlud = csd.crystal('ZERLUD')

By default the packing similarity engine prohibits the comparison of different molecular structures. This restriction can be disabled:

>>> similarity_engine.settings.allow_molecular_differences = True

Then the structures can be compared:

>>> h = similarity_engine.compare(fetsec, zerlud)

The returned value is an instance of ccdc.crystal.PackingSimilarity.Comparison. It supports properties to extract the number of molecules of the packing shell which are matched, the number of molecules in the packing shell and the RMSD of the matched structures:

>>> print(h.nmatched_molecules)
9
>>> print(h.packing_shell_size)
15
>>> print(round(h.rmsd, 3))
0.183

The ccdc.crystal.PackingSimilarity contains a nested class, ccdc.crystal.PackingSimilarity.Settings allowing aspects of the similarity measure to be inspected or modified. For example, the distance tolerance which is measured in percent. Relaxing this tolerance will allow more molecules to match with a concomitant raising of the RMSD:

>>> print(similarity_engine.settings.distance_tolerance)
0.2
>>> similarity_engine.settings.distance_tolerance = 0.4
>>> similarity_engine.settings.angle_tolerance = 40.
>>> h = similarity_engine.compare(fetsec, zerlud)
>>> print('Number of molecules matched: %d, RMSD: %.3f' % (h.nmatched_molecules, h.rmsd))
Number of molecules matched: 11, RMSD: 1.959