Supercell Constructor

Tool for setting up molecular crystal supercells from CIF files

Authors

• Pradip Si, University of North Texas

Requirments

• ASE
• Pymatgen
• Rdkit
• Open babel
• NumPy
• COD Tools cod-tools

Instructions

Generate a PBC supercell from a CIF file collected from the CCDC database

1. Save the CIF files for all polymorphs as PDB and add missing Hs if required ( obabel file.pdb -O file.pdb -h) using openbabel and delete CONECT lines (sed -i '/^CONECT/d' input.pdb)
2. Select one as a template and give unique atom name using unique_atom_name.py (that will be used to match the atom sequence for other PDBs).
3. Use ASE_cif_to_pymatgen_supercell_cif.py to generate the supercell cif file for the template. (Change the space group to "P1" in the cif file if it shows error due to space group)
4. Convert the supercell.cif to sdf (codcif2sdf supercell.cif > supercell.sdf)
5. Split all the molecules (obabel supercell.sdf -O mol.pdb -m --separate) and delete CONECT for all PDB files (sed -i '/^CONECT/d' mol*.pdb)
6. Reorder all the PDBs with a template.pdb (./batch_reorder.sh (There should be a file template.pdb in the path))
7. Merge all the reordered PDBs (obabel mol*_reordered.pdb -O supercell.pdb --join) and delete those files (rm mol*.pdb)
8. Use mapping_sequence.py to match the atom sequence to the template PDB( ./mapping_sequence_new.py --input supercell.pdb --output supercell_reordered.pdb --template template.pdb --matrix 6,5,4.

If the molecule is not selected as the template file, before proceeding to the step3

• First, reorder the PDB file to match the atom sequence with the template PDB file using reorder-atoms.py. (Follow step 4,5 and 6 for unit cell having more than one molecule to split and reorder.)
• It should pass the validation ( might visualize to ensure that the connectivity is similar to the template).
• Return to the step3.

Check the new file after each step to ensure that the code is doing the correct task

Acknowledgements

The development of this tool was supported by a DOE Early Career Award (BES Condensed Phase and Interfacial Molecular Science (CPIMS) / DE-SC0024283)