implement topocg module and helper functions

[rversin]

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[amjjbonvin]

To check if we have a CG version of it - or should be adapted

[rversin]

I think this file is in the same situation as build-missing.cns ?

[amjjbonvin]

hmmm... since we don't use the AA topo to define breaks, that part is required (also for the protein part)

[amjjbonvin]

Is this relevant for CG mode? Do we have various HIS states in Martini and do we check for it?

[rversin]

We have multiple states of HIS in Martini, a protonated (charged) and non protonated (neutral) state. We could implement it

[amjjbonvin]

This should then be based on the protonation of HIS from the AA model, looking at which hydrogen exist on the HIS ring. Topo and parameters will have to be added for those histidines which have most likely different names.

[rversin]

Yes, I was just thinking about this !

[amjjbonvin]

Should probably not be gzipped as they will be used later on in the cg-to-aa module

[rvhonorato]

This PR adds a dependency, please also add the installation instructions and proper checks to ensure it's all configured before the workflow is executed

[rvhonorato]

Keep in mind this adds mkdsspas a dependency and it also needs to be installed.

$ python3.9 -m venv dssp-dep
$ source dssp/bin/activate
(dssp-dep) $ pip install biopython==1.79
(dssp-dep) $ wget -q https://files.rcsb.org/view/1CRN.pdb
(dssp-dep) $ python -c 'from Bio.PDB.DSSP import DSSP;DSSP("model", "1CRN.pdb")'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/rodrigo/dbg/.venv/lib/python3.11/site-packages/Bio/PDB/DSSP.py", line 446, in __init__
    dssp_dict, dssp_keys = dssp_dict_from_pdb_file(in_file, dssp)
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/rodrigo/dbg/.venv/lib/python3.11/site-packages/Bio/PDB/DSSP.py", line 233, in dssp_dict_from_pdb_file
    p = subprocess.Popen(
        ^^^^^^^^^^^^^^^^^
  File "/home/rodrigo/.pyenv/versions/3.11.2/lib/python3.11/subprocess.py", line 1024, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/rodrigo/.pyenv/versions/3.11.2/lib/python3.11/subprocess.py", line 1901, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mkdssp'

[rversin]

I think a first step is to install DSSP: 'sudo apt install dssp'
But I'm still running into some issues

[rvhonorato]

This is currently at +5,566 lines and I assume you are not close to being done, please break it down into smaller PRs

[amjjbonvin]

Or - so we make subbranches of the topocg branch and merge every time into the topocg branch, which we should rename to CG-HADDOCK for example