vermouth-martinize - v0.14.0

Quite a few things have changed since the last release, so high time to it's high time for v0.14.0. This will (probably) also be the last release before v1.0.0 :partying_face:

Code fixes and improvements

• Sort atoms before running DSSP and the Go pipeline (#649, #704)
• Provide better user output if DSSP is not installed but requested (#653)
• Allow for citations that are not force field specific (#655)
• Allow for easier tuning of the header written to gromacs files (#658)
• Correct some issues in the documentation (#661, #665)
• Correct logic for writing out the Go contact map to an external file (#667)
• Disable tests for dssp executable since it's no longer supported in ubuntu-latest (#676)
• Some small cleanup (#681)
• Write the correct secondary structure header to GMX files (#691)
• Allow adding chain specifiers to the -id-regions flag (#697)
• Simplify the way atom attributes are preserved throughout martinize2 (#695)
• Change the last stray reference to ubuntu-20.04 to ubuntu-latest (#709)

Data and force field fixes and improvements

• Protect angles in helices when adjacent to prolines (#675) (Thanks @mnmelo!)
• Change posres_fc format so that it gets written to the gromacs files as a variable, meaning it's easier for users to adjust (#659)
• Add a bb_atomname variable to Martini force fields (#671, #686)
• Implement Martini3-IDP (#647)
• Add parser for .cif files (#679)
• Add GoMartini3 citation (#693)
• Remove non-existent HE11 HE12 atoms from GLN mappings (#700)
• Allow reading of cmap interactions (#705)

Full Changelog: https://github.com/marrink-lab/vermouth-martinize/compare/v0.13.0...v0.14.0

- Python
Published by pckroon 8 months ago

vermouth-martinize - v0.13.0

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). 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

- Python
Published by pckroon about 1 year ago

vermouth-martinize - v0.12.0

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

- Python
Published by pckroon over 1 year ago

vermouth-martinize - 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 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

- Python
Published by pckroon over 1 year ago

vermouth-martinize - 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 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

- Python
Published by pckroon about 2 years ago

vermouth-martinize - 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

- Python
Published by pckroon about 2 years ago

vermouth-martinize - 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 https://github.com/marrink-lab/vermouth-martinize/pull/544

- Python
Published by fgrunewald over 2 years ago

vermouth-martinize - 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 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

- Python
Published by pckroon over 2 years ago

vermouth-martinize - 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

- Python
Published by fgrunewald over 2 years ago

vermouth-martinize - 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

- Python
Published by fgrunewald over 2 years ago

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

- Python
Published by fgrunewald almost 3 years ago

vermouth-martinize - v0.9.1

What's Changed

• Undo premature optimization in ff loglevel parser by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/493

- Python
Published by fgrunewald about 3 years ago

vermouth-martinize - v0.9.0

What's Changed

• Add option to generate log entries from .ff files by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/474
• Update README with arXiv badge

- Python
Published by fgrunewald about 3 years ago

vermouth-martinize - 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

- Python
Published by fgrunewald over 3 years ago

vermouth-martinize - v0.8.0

New Features

• add zenodo authors file by @fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/431
• resids from the input structure can now be preserved using the -resid flag; this fixes #421 #153 & #366
• elastic networks can be fine-tuned via the eunit flag which now allows selection of resid ranges
• default mapping force-field universal is removed; mapping now happens by default from CHARMM; users can select AMBER as well. The only difference to universal is that titratable AAs are picked up correctly.

Bug Fixes

• Issue #424 & #439 regarding a bug, which prevented removal of atoms is now fixed.
• Correct the version check in Molecule.remove_interaction by #484

Library Updates

• Issues #425 #426 #426 regarding issues with legacy Martini2 data-files were fixed
• Add charmm data for NCAP and CCAP mappings by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/477
• Proline termini mappings by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/476
• Update aminoacids.ff by @fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/473
• Protonation states are now implemented by resname for AMBER and CHARMM
  
• HSD modification was fixed for AMBER
• implement small molecule DB by @fgrunewald in https://github.com/marrink-lab/vermouth-martinize/pull/456
• Add citation of M3 small molecules (address issue #468)
  ## API Updates
• Fix write_pdb to always define open by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/434
• Fix/432 by making sure modifications are connected components by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/436
• Update gh actions by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/475
• ## Dependency Updates
• Remove redistributed KDTree, and make scipy a hard requirement by @pckroon in https://github.com/marrink-lab/vermouth-martinize/pull/438

- Python
Published by fgrunewald over 3 years ago

vermouth-martinize - v0.7.3

This release implements some performance enhancements, small bug fixes and updated API.

Performance Improvements: - accelerated making of residue graphs related to issue #379 - accelerated parsing of itp files related to issue #377 - accelerated mapping of molecules related to issue #408

Bug Fixes: - itp reader now reads virtual_sites1 and settle directives - itp reader can handle #else statements

API Updates: - the deferred file writer doesn’t overwrite the built-in open anymore instead now we expose defferedopen - the PDB writer gets a new flag ‘deferwriting’ that either uses the deferred file writing or just regular file writing

Dependency Updates: - Martinize2 now supports the latest version of Sphinx - Martinize2 now runs with the latest version of pylint

- Python
Published by fgrunewald almost 4 years ago

vermouth-martinize - v0.7.2

This bugfix release fixes two issues: - Warnings issued by MakeBonds now have a type. - The N-ter modification in the 'universal' force field was modified to also fit on N-terminal prolines. This also affects the mapping weights of N termini.

- Python
Published by pckroon over 4 years ago

vermouth-martinize - v0.7.1

Alanine was missing a bond between BB and SC1 in the force field martini3001 if the FLEXIBLE flag was used. This release fixes that.

- Python
Published by pckroon almost 5 years ago

vermouth-martinize - v0.7.0

With the publication of the Martini 3 paper we can include the relevant data files, and switch the default output force field to Martini 3!

You can find the paper here: https://www.nature.com/articles/s41592-021-01098-3

- Python
Published by pckroon almost 5 years ago

vermouth-martinize - v0.6.0

This release has a few important usability features: - Support for citations from the data files, which make martinize2 print the relevant citations. - Make the -nter and -cter CLI flags only affect protein residues. This does mean that non protein molecules don't get their termini patched automatically.

In addition, there are a number of bug fixes: - Fixed a bug in the ISMAGS symmetry detection. - Fix #311. - Change CI to Github actions. - Fix #317, which sometimes triggered DSSP errors when one of the terminal oxygens is missing. - Fix issues where resids from the PDB file were ignored when itp files are used as input forcefield. - Fix #354 which would trigger if there were multiple unknown modifications in a residue.

- Python
Published by pckroon almost 5 years ago

vermouth-martinize - Test release

Second mock release to test the new deploy mechanism

- Python
Published by pckroon about 5 years ago

vermouth-martinize - Test release

This is a mock release to test deployment using GH actions

- Python
Published by pckroon about 5 years ago