PDB to mmCIF conversion

[sofyalaski]

Descriotion:

For a case where user already has a model for PDB deposition, but it's in the PDB format and not mmCIF, the conversion tool wouldn't create a valid output probably.
Add a possibility to use a PDB file instead of mmCIF.

Possible Solution:

There is a conversion tool available at PDB services. Maybe use this or check the specs for both formats and write a custom one.

Workflow changes

In the last bit where a function is called to create an mmCIF, a function parseMmCIF is called. Before it I need to have converted a PDB file already, the rest is the same.

[sofyalaski]

As of now, when coordinates file is deposited in PDB format, OneDep will automatically produce a PDBx/mmCIF file from it and continue with it.
User can convert prior to deposition with pdb-extract

[sofyalaski]

This tool requires Python.
Need to read on the difference between PDB and mmCIF formats for cryoEM