Vermouth

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

Bug Fixes
* molecule now exposes a box attribute which stores box coordinates read from PDB or GRO files 537
* the PDB parser now correctly propagates the box coordinates to the molecule objects

New Features & Updates
* All modifications for all protonation states in Martini3 were added. Automatic detection of protonation states should work. Limited support for selected M2 force-fields has been added. Protonation state modifications are supported when mapping from AMBER or CHARMM 529

Bug Fixes
* small lint of bin/martinize2 executable 532
* a typo in pdb.py which caused DSSP to fail was fixed. Thank you juminlee! 524

New Features & Updates
* The citation bib text was added to the README 494
* Nodes are sorted to group residues unless the Go model is requested 469 & 520
* A parser to read [ meta ] information on molecules was added to the ff parsers 517
* Box vectors for coordinates files (.gro/.pdb) are now parsed and exposed 516

Bug Fixes
* Code coverage reporting is updated to the latest standard 515
* A DSSP version check was implemented and the DSSP exe can be deleted from CLI again 506

**Full Changelog**: https://github.com/marrink-lab/vermouth-martinize/compare/v0.9.1...v0.9.2