marrink-lab/vermouth-martinize: v0.8.0

Published November 25, 2022 | Version v0.8.0

Software Open

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

Files

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marrink-lab/vermouth-martinize-v0.8.0.zip md5:a4f60a6dbd63bb55c050071fb5ee265b	2.8 MB	Preview Download

Is supplement to: https://github.com/marrink-lab/vermouth-martinize/tree/v0.8.0 (URL)