Vermouth

New year, new release!

What's Changed
* Martinize2 can now generate Go contact maps internally, rather than requiring users to rely on external webservers. For this, the semantic around the `-go` command line flags changed. Be sure to read the documentation and help!
* internal go contact map by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/643
* It's now possible to specify molecule names using the `-name` flag. This is particularly useful when coarse-graining a system consisting of multiple proteins one protein at-the-time.
* Custom molname by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/634
* The documentation now contains much better tutorials.
* Martinize2 tutorials by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/635
* Fix the generation of spurious `include` statements in the top file when using the go model.
* Go topol header fix by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/637
* Add parameters for lipidated amino acids, developed by P. I. Koukos et al ([10.1021/acs.jctc.3c00604](https://doi.org/10.1021/acs.jctc.3c00604)). Be sure to always cite the papers martinize2 asks you to!
* Lipidations by fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/651

**Full Changelog**: https://github.com/marrink-lab/vermouth-martinize/compare/v0.12.0...v0.13.0

While working on documentation and tutorials csbrasnett spotted some suboptimal default values for some CLI options, and promptly fixed them. Thanks Chris!

What's Changed
* CLI defaults were changed to more sensible values:
* `-scfix` is now on by default, and can be switched off by using `-noscfix`. This means adding `-scfix` is now a no-op, and this CLI flag will be removed in a future release.
* `-ef` now has a default value of 700 kJ/mol/nm^2, which is appropriate for martini3, but not martini2, which uses 500.
* `-cys` now has default value `'auto'`, which makes it harder to accidentally forget your cysteine bridges. The old behaviour can be restored using `-cys none`, which simply removes all cysteine bridges.
* Disulfide bridges nog log a friendly message.

**Full Changelog**: https://github.com/marrink-lab/vermouth-martinize/compare/v0.11.0...v0.12.0

What's Changed
* scfix behaviour change by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/621
* Log disulfide bridges by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/625
* Pylint update by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/629


**Full Changelog**: https://github.com/marrink-lab/vermouth-martinize/compare/v0.11.0...v0.12.0

What's Changed
* Fix for 566 and 560, which caused martini22 protein terminals to have an incorrect beadtype, if they are helices.
* Flank the wildcard SecStruct sequence with dots by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/572
* Make sure that edge attributes get propagated.
* Fix 580 by fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/581
* Updates to the documentation
* Doc new by fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/582
* Added documentation of file formats by Tsjerk in https://github.com/marrink-lab/vermouth-martinize/pull/401
* Fix the exclusions for charged termini in martini22p and elnedyn22p
* Fix 558 by inverting the link logic generating charged backbone charge dummy exclusions for polarizable forcefields by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/583
* csbrasnett fixed (or at least improved) when the `-modify` and `-mutate` raise a warning about not applying
* Multiple mutate fixes by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/565
* fix error raising for mod not found by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/602
* More work by csbrasnett, this time to make martinize2 better with IDPs and the Go model.
* Idp go by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/593
* Idp bugfix by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/591
* Addition of the `-merge all` option to the CLI
* Lazy merge by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/589
* The martini22 forcefield lost its HIS residue at some point, which caused a lot of issues with unmapped residues.
* Add HIS(charmm)->HSE(martini22) mapping to fix 567 by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/610
* Fix the deploy pipeline.
* Rework the deploy pipeline by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/611

**Full Changelog**: https://github.com/marrink-lab/vermouth-martinize/compare/v0.10.0...v0.11.0

New year, new release!

Changes
-------------
- Updated and polished the documentation
- By default (and if installed) martinize2 will use the mdtraj module to determine protein secondary structures, instead of requiring users to install the exact right version of dssp
- Revamp how martinize2 deals with the Go model. Martinize2 can now parse and process the rCSU contact maps which means users no longer need to run another script to produce a functional topology! Thanks Lp0lp fgrunewald !
- Users can specify desired modifications via the command line, but mistakes are easily made. Thanks to csbrasnett we now produce a friendly warning in these cases.
csbrasnett found and fixed an issue with produced elastic networks in some rare cases. See https://github.com/marrink-lab/vermouth-martinize/pull/559 for more details,
- Ladme found an issue with Martini 2.2 topolgies where links override parameters from modifications. In particular, the result was that terminal residues with secondary structure T, E, F, H, 1, 2, or 3; or terminal ALA, PRO, or HYP residues with secondary structure S would end up with a charged BB bead with beadtype N0 rather than the appropriate Q type. This is now fixed by filtering when and where Links get applied based on the modifications present.
- Small maintenance

What's Changed
* Replace deprecated pkg_resources with new importlib by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/546
* Make sure DATA_PATH is always a pathlib.Path by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/549
* Cleanup to Go implementation by Lp0lp in https://github.com/marrink-lab/vermouth-martinize/pull/555
* add warning when mod not found by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/556
* -el fix by csbrasnett in https://github.com/marrink-lab/vermouth-martinize/pull/559
* Documentation by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/545
* Use MDTraj dssp by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/547
* Implementation of the Martini3 Go-model by fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/550
* Issue 560 by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/561
* Log a helpful message when an element is not present in the ATOM_MASS dict by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/571

**Full Changelog**: https://github.com/marrink-lab/vermouth-martinize/compare/v0.9.6...v0.10.0

Minor bug fix. The pdb box dimensions were incorrectly propagated as x, y, y instead of x, y,z. This has been fixed.

What's Changed
* fix pdb box by fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/544

Minor changes which do not affect functionality. The networkx version requirement has been relaxed to allow the use of networkx 3 and higher.

What's Changed
* quick fix doc by fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/542
* Networkx 3 by pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/543


**Full Changelog**: https://github.com/marrink-lab/vermouth-martinize/compare/v0.9.4...v0.9.5