v0.11.0

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 #572
• Make sure that edge attributes get propagated.
  • Fix #580 by @fgrunewald in #581
• Updates to the documentation
  • Doc new by @fgrunewald in #582
  • Added documentation of file formats by @Tsjerk in #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 #583
• @csbrasnett fixed (or at least improved) when the -modify and -mutate raise a warning about not applying
  • Multiple mutate fixes by @csbrasnett in #565
  • fix error raising for mod not found by @csbrasnett in #602
• More work by @csbrasnett, this time to make martinize2 better with IDPs and the Go model.
  • Idp go by @csbrasnett in #593
  • Idp bugfix by @csbrasnett in #591
• Addition of the -merge all option to the CLI
  • Lazy merge by @csbrasnett in #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 #610
• Fix the deploy pipeline.
  • Rework the deploy pipeline by @pckroon in #611

Full Changelog: v0.10.0...v0.11.0

v0.10.0

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 #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 #546
• Make sure DATA_PATH is always a pathlib.Path by @pckroon in #549
• Cleanup to Go implementation by @Lp0lp in #555
• add warning when mod not found by @csbrasnett in #556
• -el fix by @csbrasnett in #559
• Documentation by @pckroon in #545
• Use MDTraj dssp by @pckroon in #547
• Implementation of the Martini3 Go-model by @fgrunewald in #550
• Issue 560 by @pckroon in #561
• Log a helpful message when an element is not present in the ATOM_MASS dict by @pckroon in #571

Full Changelog: v0.9.6...v0.10.0

v0.9.6

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 #544

v0.9.5

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 #542
• Networkx 3 by @pckroon in #543

Full Changelog: v0.9.4...v0.9.5

v0.9.4

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

v0.9.3

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

v0.9.2

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: v0.9.1...v0.9.2

v0.9.1

What's Changed

• Undo premature optimization in ff loglevel parser by @pckroon in #493

v0.9.0

What's Changed

• Add option to generate log entries from .ff files by @pckroon in #474
• Update README with arXiv badge

v0.8.1

Dependency Updates

• DSSP version 3.0.0 becomes the only supported version. The DSSP processor now raises an error in case any other version is used.
• CI checks are run on Ubuntu20.04 due to DSSP 3 being unavailable for the newer ubuntu versions