We've recently published a Chemistry of Materials perspective "Development of a Cambridge Structural Database Subset: A Collection of Metal–Organic Frameworks for Past, Present, and Future". http://dx.doi.org/10.1021/acs.chemmater.7b00441

The Supporting information for the paper includes two scripts using the CSD Python API as part of the MOF analysis. The scripts aim is to ‘clean up’ metal-organic frameworks i.e. removing solvent molecules and labile ligands from the framework to allow pore-size and surface area analysis to be carried out; I'll add the scripts to this thread where I can include a bit more information.

This first script "SI_MOF_solvent_remover_Hg_version.py" is intended to be used via CSD Python API menu in Mercury. Navigating to CSD Python API > Options... shows the location of built-in scripts in Mercury and also allows you to include additional locations to host your own scripts and specify where output files are to be written. By adding this script to either the built-in scripts or your own file location will allow you to use it from the Mercury menu.

The script will run on whatever structure is currently displayed in the main Mercury visualiser. The script will identify any monodentate solvent molecules (based on a smiles comparison with a list of solvents present within Mercury), remove these from the MOF framework and output a CIF with only this solvent-stripped main residue present for use in third-party analysis tools.

The second script “SI_MOF_solvent_remover.py” works in a similar way via the command line. This command line script has a couple of extra features – mainly the ability to be run over multiple structures from a CSD refcode list. A refcode list can be generated from ConQuest; once a search has been run the results can be exported via File > Export Entries as… and selecting the option “Refcode: CSD entry identifier list. This file is simply a list of the CSD refcodes and is stored as a .gcd format.

A second option is the ability to choose a list of solvents to remove from a framework (the default is the CCDC list that comes with the standard CSD installation). This solvent list should be in mol2 format. There is also an option to simply remove any monodentate entity from a framework. It should be stressed that the analysis carried out as part of the above paper only used these scripts on selected subsets of MOF entries where solvent removal would be chemically reasonable – although the scripts will in theory work on any metal-containing structure.

Hopefully the scripts may be of wider interest too – the ability to manipulate a structure and output a modified cif could potentially be useful in other projects.    

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