Add an option to cap termini with missing residues

[jthorton]

Thanks for the great tool!

When prepping structures using PDBfixer I noticed some poor geometries for the added missing residues (see screenshot and attached cif file). I think it might be nice to add an option which instead just adds neutral ACE/NME caps in these cases where having the full structure might not be critical. In my case, these structures are used for binding free energy calculations.

Its not too bad to add the caps manually using something like pymol but it would be great to use a single tool if possible. Also very happy to contribute this feature if you feel it would be generally useful.

4py1.cif.txt

[Rob-Welch]

Hi, good idea! I'd happily accept a pull request with this feature. It's something that had occasionally entered my head, but I wasn't sure about the best way to implement it. Please let me know if you need any extra info as the developer documentation is currently quite spare.