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

v0.8.0

New Features

• add zenodo authors file by @fgrunewald in #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 #477
• Proline termini mappings by @pckroon in #476
• Update aminoacids.ff by @fgrunewald in #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 #456
• Add citation of M3 small molecules (address issue #468)

API Updates

• Fix write_pdb to always define open by @pckroon in #434
• Fix/432 by making sure modifications are connected components by @pckroon in #436
• Update gh actions by @pckroon in #475

Dependency Updates

• Remove redistributed KDTree, and make scipy a hard requirement by @pckroon in #438

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 deffered_open
• the PDB writer gets a new flag ‘defer_writing’ 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

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.

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.

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

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.

Test release

Second mock release to test the new deploy mechanism

Test release

This is a mock release to test deployment using GH actions