static variables in gromos_system

rinikerlab / PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

https://rinikerlab.github.io/PyGromosTools/

MIT License

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static variables in gromos_system #208

Closed pultar closed 2 years ago

pultar commented 2 years ago

These variables should be member variables and not static class variables:

    _single_multibath:bool  = False
    _single_energy_group:bool = False

    _gromosPP_bin_dir : Union[None, str] = None
    _gromosXX_bin_dir : Union[None, str] = None

MTLehner commented 2 years ago

i second this

MTLehner commented 2 years ago

@SchroederB what do you think? I think they should all be instance members

RiesBen commented 2 years ago

good catch! They should be members for the future. I just thought about some additional functionality checks:

maybe we should add functionality like:

check_presence_gromos_bin_dir (path_to_bin_dir)-> bool
check_presence_gromos_bin (binary_name) -> bool #this function add the bin_dir or PATH var content to see if binary is accessible.

results could be stored in gromosPP_accissble:bool same for gromosXX

additionally see: https://github.com/rinikerlab/PyGromosTools/pull/176

pultar commented 2 years ago

https://github.com/pultar/ppqm/blob/9433bfade69087c1b0f1775d118e658235500854/ppqm/env.py#L10

Something along those lines? I can do that, I suggest the methods be called in the setter function.

pultar commented 2 years ago

I added the PR accordingly. What do you think @SchroederB and @MTLehner ?

RiesBen commented 2 years ago

I think it looks great! :) I will check if we can integrate shutils even a bit more into bash functions.

pultar commented 2 years ago

Fixed with PR #209