Release 3 PR

Content

-All the developments of the recent months

• Solvation
• rework subSys
• Improved Gromos_System
• Bug fixes
• More Gromos++ Wrappers

TODOS

• [x] Gromos-Day
• [x] Solvation
• [x] Project-Release 3
• [x] Final clean-up

This is a slight modification to @pultars nice binary directoy changes. Mainly I changed the location of the test and moved it from the gromos system to the Gromos classes in a way, the test can not be circumvented, except explicitly stated. :)

• [x] Ready to go

Presentation for the PyGromosToolsDay

Content and Discussions

1. Current State and Features
2. Overview over new tools
3. Release 3
   1. Bug fixes
   2. Restructuring
   3. new features
4. Final Discussions

Description

Update of TRC using mdtraj.

Todos

Notable points that this PR has either accomplished or will accomplish.

• [x] Write Tests - in progress
• [x] Include more mdtraj functionality
• [x] Create dummy topology
• [x] Refactoring
• [x] Example notebook visualization
• [x] Change Cnf to also use nglview
• [x] Make future promisable
• [x] Test with gromosSystem
• [x] Write TRC
• [x] Load h5 and hdf5

This branch contains my expirience with Euler and the submission system

This pull request grew a bit beyond! So it's time to merge !

Features:

• minor bug fixes for submission system
• visualization
• doc update
• more testing

• [x] Ready To Go

Description

This merge should help

Todos

Notable points that this PR has either accomplished or will accomplish.

• [x] add PTP - PERTPROPERDIH Block
• [x] add functions for ptp generation

Status

• [ ] Ready to go

Description

Rework of the forcefield structure in PyGromos

Introducing a generic_forcfield and all other forcefield have this class as super. This makes code more readable and unifies the structure.

In the TI example notebook examples/example_TI_gromos_simulation.ipynb, the file /examples/example_files/TI_Calculation/TI_input/M030_6KET.disres is specified, but this file isn't in the repository. This leads to the following error:

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-13-14f2d2d90c97> in <module>
      6 grom_system = Gromos_System(in_cnf_path=cnf_path, in_top_path=top_path,
      7                             in_disres_path=disres_path,
----> 8                             system_name=sys_name, work_folder=input_dir)
      9 
     10 

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py in __init__(self, work_folder, system_name, in_smiles, in_top_path, in_cnf_path, in_imd_path, in_disres_path, in_ptp_path, in_posres_path, in_refpos_path, in_gromosXX_bin_dir, in_gromosPP_bin_dir, rdkitMol, readIn, Forcefield, auto_convert, adapt_imd_automatically, verbose)
    136                         "refpos": in_refpos_path,
    137                         }
--> 138         self.parse_attribute_files(file_mapping, readIn=readIn, verbose=verbose)
    139 
    140         ##System Information:

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py in parse_attribute_files(self, file_mapping, readIn, verbose)
    523         [check_file_paths.append(x) for k, x in file_mapping.items() if (not x is None)]
    524         if (len(check_file_paths) > 0):
--> 525             bash.check_path_dependencies(check_file_paths, verbose=verbose)
    526 
    527         # SET Attribute-FILES

/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/utils/bash.py in check_path_dependencies(check_required_paths, check_warn_paths, verbose)
    123         print("\n==================\nAUTSCH\n==================\n")
    124         missing_str = "\n\t".join(map(str, missing))
--> 125         raise IOError("COULD NOT FIND all DEPENDENCY!\n\t Could not find path to: \n\t" + str(missing_str), "\n\n")
    126     elif verbose:
    127         print("All dependencies are correct!", "\n\n")

OSError: [Errno COULD NOT FIND all DEPENDENCY!
	 Could not find path to: 
	./example_files/TI_Calculation/TI_input/M030_6KET.disres] 

@SchroederB I think you originally wrote this tutorial. Do you still have the file on one of your local branches?

Description

• restructuring forcefield class in pygromos and making a generic-ff class from which others inherit to remove code duplication and make the usage of ffs more clear.
• adding a python version of make_top to the gromosff class to create topologies in python

Todos

a lot

Can we improve the speed of the unit test?

A few points possible points:

• [x] reduce size of trajectories
  • [x] trc
  • [x] tre
  • [x] trg (seem to take the longest)
• [x] remove unnecessary dependencies from conda incubator
• [x] TI submission
• [x] dummy submissions

Description

More gromos++ functions are wrapped (sasa, filter). There was also a minor bug in the way rgyr is wrapped.

In addition, qmmm blocks are now supported in imd files. An example notebook is provided with example files. It is also planned to support qmmm specification files and for that purpose some code has been copy/pasted in place.

Removed duplicate code from a fix a long time ago (RE-EDS block no longer having the ALPHALJ / ALPHAC) parameters. I also tweaked the EDS block so it is compatible with the current up to date gromosXX code. Added a comment in the electrostatics block to account for the recent work from Salomé.

Status

• [ ] Ready to go

Hi rinikerlab/PyGromosTools!

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Questions? Check out the FAQ below!

FAQ

GROMOS starts counting from "1" in topologies (and other places). However, sometimes atom indices are 0 indexed (for example functions that use mdtraj). We should make this more consistent before too many people use functions.

I think we should stick to GROMOS convention and start everywhere from "1".

@MTLehner ideas?

I reimplemented (and re-tested) the changes in #222 (as I didn't want to have trouble with merge conflicts, although they all seemed super minor and would have been easily fixed).

The code in here is essentially the same as in #222 with the exception of some imd related functions, where I simplified a call to str2bool (previously was put in an if, else block based on input given to function, which already happens in the function).

To do

• [ ] Pre-commit passed

Status

• [ ] Ready to go

PS: Please don't delete the pygromos3_for_reeds branch after merge. I would like to keep this branch in parallel at all times (and probably also have a "release" for it so that there is an easily accessible version for RE-EDS users once I have implemented all I need to).

PyMakeTop

Content

With the new addition of the mtb files a python version of make_top should be possible. The resnames are already stored in a dict after the mtb parsing.

TODOs

• [ ] Option to just call the resname and get back a top
  • [ ] parse all mtb blocks to top blocks
  • [ ] add solvent
• [ ] Option to pass a rdkit molecule (matching to a resname) and get a gromos topology
  • [ ] all of the above
  • [ ] mtb -> rdkit mol or smiles parser from atoms and bond blocks
• [ ] Option to pass a rdkit molecule (any) and get a gromos topology
  • [ ] all of the above
  • [ ] fragment based matching