MMTF Parser

[vratins]

Added a basic parser that can read in either an mmtf file or a mmtf structure (decoder) object into an atom group. Includes header retrieval for biomolecule building.

[jamesmkrieger]

Thanks. Can you add a test for this too, please

[dkoes]

Need to add

from . import mmtffile
from .mmtffile import *
__all__.extend(mmtffile.__all__)

to proteins/__init__.py
and

__all__ = ['parseMMTF']

to mmtffile.py

[vratins]

Test and fixes added.

[jamesmkrieger]

ok, it's working now. I would prefer a pip install in main.yml but I guess it's not that heavy a dependency so it's fine.

The last thing then is to give the user-facing function(s) a doc string.

Thanks again for contributing this!

[dkoes]

I think this is ready to be merged. Vratin still needs to add a section to the tutorial on how to use this to parse the entire PDB in a few minutes using pyspark and MMTF, but that is a different repository.

[jamesmkrieger]

No, I think there are still a few last things to fix:

1. The try/except for the import should be inside the function, so users don’t get the warning every time they import prody

2. There are some redundancies between the two parts of the doc string that need to be cleaned up

Besides that, yes, it sounds good

[jamesmkrieger]

Thanks! Very almost there now

[vratins]

Could you let me know what further formatting you'd like to the docstring? I'll make the changes asap.

[jamesmkrieger]

Doc string is fine.

the last thing is for the try/except to raise ImportError

[jamesmkrieger]

Looks good now. Thanks again!

and thanks, David, for other fixes too!

[jamesmkrieger]

optional isn't really part of the type

[jamesmkrieger]

Ideally this should change but it’s ok really