GromacsWrapper

GromacsWrapper copied to clipboard

use gromologist?

6

https://gitlab.com/KomBioMol/gromologist is a Python package for handling top and itp files.

orbeckst

AttributeDict does not support hasattr() but it should: ```python import gromacs ad = gromacs.utilities.AttributeDict(a=1, b=2) assert hasattr(ad, "a") assert not hasattr(ad, "x") # raises AttributeError from KeyError ``` Using ``in``...

orbeckst

Solvate function doesn't support nn and np input

4

Related to https://github.com/Becksteinlab/MDPOW/pull/174 In gromacs, one can add a specific number of ions by using keywords nn and np. But in gromacs wrapper `solvate` function, ions only can be added...

VOD555

problem with pickle

4

The problem: `.names` doubles after interacting with `pickle`, `cPickle` and `dill`. How to reproduce ([test.txt](https://github.com/Becksteinlab/GromacsWrapper/files/6217259/test.txt)): ```python import gromacs.formats as gmx import os import pickle def load_xvg(filepath, failsafe=2): xvg_file = gmx.XVG()...

PolyachenkoYA

JOSS paper

20

Write a short software paper on GromacsWrapper for [JOSS](http://joss.theoj.org/). - [Author instructions](https://joss.readthedocs.io/en/latest/submitting.html) – create a repo and then submit, ~1000 words, see examples - authors? - any contributor (name on...

orbeckst

edit_mdp() should use the MDP parser

1

As pointed out in PR #164 , the `edit_mdp()` function should use the MDP parser. This would also reduce extremely cryptic errors such as `gmx grompp: -include is not an...

orbeckst

JOSS paper

5

Short software paper for submission to the [Journal of Open Source Software](http://joss.theoj.org/). The paper will be part of the GromacsWrapper repository; this appears to be the common pattern with other...

orbeckst

list of software that uses GromacsWrapper

7

For the paper #147 it would be very beneficial to demonstrate that GromacsWrapper has been used elsewhere, especially in software or work that can be cited. Please add to this...

orbeckst

mini tutorial for docs

16

The docs should start with a small tutorial that shows how to use GromacsWrapper. This is also important for the paper #147 because they will review docs together with installability...

orbeckst

XPM reader does not handle multiple frames

2

In attempting to read an .xpm file generated by `g_mdmat` with the `-frames` flag, the xpm reader fails with the error: ``` python 216 s = self.unquote(line) --> 217 data[:,...

synapticarbors