cspy-templating command

The cspy-templating command is used to create a set of unoptimized analogues, albeit being comprised of a new molecule, of a given set of molecular crystal structures. The primary use of this command is in the generation of trial structures in templating CSP

Note

Currently the cspy-templating command and corresponding templating CSP approach is only applicable to Z’=1, G=1 systems. That is, all template crystal structures must be single component and the structure files used must provide Z’=1 representations of the crystal structures. The ‘new molecule’ for analogue formation must also be a single molecule. We hope that future versions of mol-cspy will expand upon this functionality

Note

Use of this command requires access to the ccdc python module and, if beginning from xyz files, openbabel software.

Example Command Line Usage

The analogue creation can be run using a single line of code:

cspy-templating --template_structures  template_structures.zip --targ_mol  target_molecule_file --temp_mol template_molecule_file --end_db_name database_name

Note

Currently, this command runs in serial and so if being run on worker nodes only a single core is needed.

This will produce a database named <database_name.db> containing unoptimized analogues of each template crystal structure – with those analogues being comprised of the target molecule. Each of these will be recorded as having an energy and density of 0. The value 0 here is serving as a stand in for n/a or unknown, within a database structure and code that requires these values to be numerical.

Continuing Templating CSP

To complete the templating CSP process, the resulting database should be clustered using the cspy-db cluster command and then all unique structures should be lattice energy minimised using the cspy-reoptimize command.