v1.7.0

New Features

• Using a [ bending ] directive in the build_file, polyply now allows sampling from an angle-dependent potential when doing the random walk. This allows tuning the rigidity of the polymer chain. #344
• Martini 3 IDPs are now officially implemented thanks to @csbrasnett #331

v1.6.1

Library Updates

• Add PTMA CGM3 IBI model to polyply library [10.1021/acs.macromol.3c00141] #279
• Add PTMA GBNO2 IBI model to polyply library [10.1021/acs.macromol.3c00141] #343
• Update citation of Martini 3 PTMA #348

Bug Fixes

• Checking of box coordinates caused an error when the box is supplied only via CLI. This is fixed now.

v1.6.0

Library Updates:

• Switch to default OPLS atomtype names #317; OPLS itps can now be used with regular gromacs interaction table

Improvements

• Take box from starting coordinate if supplied or give warning or error #321
• Give a warning if meta-molecule coordinates exceed box #310
• -name flag becomes optional when generating coordinates (default is polymer) #312
• -o flag becomes optional when generating coordinates (default is coords.gro)
• Raise warning when no sequence is given in gen_seq #312

Dependency Updates

• Fix issue 305 when gen_params fails due to sequence resids not starting at 1 #306
• Update CI; Codevoerage is now reported by GHA function #314
• Add scipy 1.11 patch #333
• Replace deprecated pkg_resources by importlib #347
• Change all paths in tests to proper Path objects #347

New Features

• Implement reading of the #error directive #337
• Allow generation of double-stranded DNA itp files. #313

Other Changes

• Only parse files with known extensions in the force-field directory #253
• Ignore tests with coverage by @fgrunewald in #316

v1.5.0

Library Updates:

• Martini3 PPE now prints warnings when termini are not applied
• Martini3 PDMS has been added to the library 10.1039/D2SM00939K

Improvements

• Log entries for force-field data files are now available (#292). This feature allows to print specific messages when specific blocks or links are applied
• Amino acid parsing via fasta files is now possible (#303)

Dependency Updates

• vermouth dependency has been increased to version >= v0.9.1

Other Changes

• python 3.6 is dropped from CI

v1.4.1

Library Updates:

• PTMA CG M3 model was added to the polyply library parameters are taken from [arXiv:2209.02072]
• A library table, i.e., list of models available in the polyply library was added to the README and LIBRARY.md file
• Carbohydrate parameters for Dextran were updated to the final released version, which for the time being disables branched Dextran.
• Cellulose parameters were added to polyply according to the latest parameter definitions https://pubs.acs.org/doi/10.1021/acs.jctc.2c00757

Bug Fixes:

• when reading the topology dihedral directives, where a single dihedral type in the itp file is matched to multiple definitions in the force-field file is now done correctly (i.e. all matches are generated).

Improvements

• Defining a name and output path for gen_params are now optional. By default the name polymer is given with the file called polymer.itp in the current working directory

Full Changelog: v1.4.0...v1.4.1

v1.4.0

Library Updates:

• None

Bug Fixes:

• edges for constraints and angles were not created correctly in gen_coords; now only constraints create edges #243 #242
• previously two itp files could not be directly connected with gen_params even if the residue graph was correctly supplied; this has been fixed allowing stitching together itp files arbitrarily #247
• links that affect bonded interactions within a residue were ignored; now they are taken into account #250

Improvements

• volumes used in the one-bead per residue random-walk can now be defined through an entry in the build_file #237 #241
• templates for back mapping the one-bead per residue random-walk can now be defined through an entry in the build_file #235 #236
• input argument of the top-level programs gen_coords, gen_params, gen_seq are exposed which makes them callable from within python scripts #42 #229

Other Changes

• Create CONTRIBUTING.md #262
• Create issue templates #263 #268

v1.3.1

Library Updates:

• Fix PMMA residue name for atom 6 of block PMMA #215
• Force Field parameters for Martini3 Poly (para-phenylene ethynylene)s by @mbrosz #227

Bug Fixes

• change argument type for grid spacing from int to float by #230 fixes #228

Improvements

• Improve error message top_parser by #219
• Raise more detailed warning about disconnected molecule #210

v1.3.0

This release implements some small bug fixes, API updates, library updates, and new sequence file parsers.

Library Updates:

• polyply now features Martini2 ssDNA #154
• parmbsc1 charges for DT3 were updated see below
• the 2016H66 now features polymer parameters for PMAM (Polymethacrylamide) and PEGylated acrylates
• 2016H66 PS pairs and exclusions were updated to be more consistent with the GROMOS variant

Bug Fixes:

• the from block method in MetaMolecule is working again; fixes #178
• the DT3 residue in parmbsc1 DNA now has correct charges; fixes #199
• the persistence length module now raises a warning only on the sub-sampled end-to-end distances; fixes #203
• the persistence length module now correctly computes the end-to-end distance restraint also for branched molecules within the usual limitations; fixes #202
• missing pair interactions were added to PMMA between CH3 and the ester carbonyl oxygen

API Updates:

• polyply now features additional input parsers for sequence files namely plain, fasta, and ig files

Dependency Updates:

• Polyply requires martinize v0.7.3
• Polyply now runs with the latest version of pytest (#188)

v1.2.1

This release updates citations in the data-files, and fixes the gen_seq help text with the correct syntax. In addition the README has been updated with more links, and a better functionality description. It also includes a future fix for the deferred file-writer syntax change. In addition the PSS martini2 and GROMOS polyvinyl data files have been updated to fix style issues and one bug. This is the official release to go along with the publication of the polyply paper.

v1.2.0

This release implements a new distance restraint code, which allows to set distance restraints in the build file and generate simple cyclic molecule coordinates. In addition it allows to specify the persistence length and specifically generate coordinates with end-to-end distances, which match the worm-like-chain model. Furthermore it implements parmbsc1 DNA parameters. Finally it fixes a bug in the coordinate generator related to the phase of the dihedral. Now dihedral angles have the "correct" phase by GROMACS convention. Last but not least a number of bug related to itp-file manipulation have been solved and new warnings and error messages have been added.