vermouth-martinize

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First version of coordinate generatign processor

8

The coordinate generating processor. Unfortunately, the chirality is not always consistent, even for backbone, which needs to be fixed, and the side chains with rings are not well constructed. Otherwise,...

Tsjerk

GitHub Actions not running devs

1

@pckroon I think that also here in martinize2 github actions is not installing the dev packages but rather running on the latest python version. If you could quickly check then...

fgrunewald

Add "how to contribute" to the README

1

Instruction on how to contribute would make contributors welcome.

jbarnoud

Repair graph can take prohibitively long to identify atoms, especially when the underlying structure is off. This is because the largest common subgraph algorithm is very exponential. For most use...

pckroon

Some workloads are done per residue, such as repair graph. This would result in an appealing target for multiprocessing (separate molecules will have very different sizes, but residues will be...

pckroon

non-edge directive

4

Doesn't this code assume that in the non-edge directive the first node is always in link? If it is not the non-edge would just be ignored or am I missing...

fgrunewald

martinize2 always writes the itp files in the working directory

1

The command line lets you choose where the output PDB and TOP will be written, though the ITP files are always written in the working directory. This causes 2 issues:...

jbarnoud

(re-)Implement GMX RTP parser using lark-parser

2

This PR (re) implements the RTP parser using the lark-parser parsing framework, where the file grammar is separated from the interpretation. If we like this style we'll use this to...

pckroon

Problem with white-spaces when parsing citations in bibtex format

3

As brought up in https://github.com/marrink-lab/polyply_1.0/pull/123#issuecomment-804225680, I've encountered the following issue which @fgrunewald agreed is probably a bug. Namely, Spaces _after_ the `=` at least in the `author` field (didn't test...

ricalessandri

For the 4th biounit of 1zmx, the top file contains ``` #include "martini.itp" #include "molecule_0.itp" #include "molecule_1.itp" #include "molecule_0.itp" #include "molecule_2.itp" #include "molecule_3.itp" ``` This leads to grompp complaining: ```...

jbarnoud