Polyply

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

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)

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.

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.

This release is the version that was used for the preprint as published on the ArXiv. This version fixes a number of bugs from the old version, introduces a faster random-walk strategy, a faster backmapping routine, and new default values. Furthermore the library was extended by a number of Martini3 polymers, and GROMOS polymers. Finally it also includes a repository with files needed for Tutorials.