Package: vermouth
Martinize2 and vermouth: The ultimate resolution transformation toolsMartinize2 is a rewrite ofMartinize. It is aimed at producing
coarse-grained structures and topologies from an atomistic structure. Martinize
is primarily developed for theMartinicoarse-grained force field and theGromacssimulation engine. However the architecture of the program will
allow us to support a broader range of force fields and simulation engines in
the future.Vermouth (for VERsatile, MOdular,  and Universal Tranformation Helper) is the
python library that powers Martinize2. It allows to describe and apply
transformation on molecular structures and topologies using graph algorithms.DisclaimerMartinize2 and Vermouth are under development. So far they have mostly been
tested on Martini 2 and Martini 3. If you use Martinize 2 and Vermouth for any
other force field be sure to carefully check the resulting topologies!Bugs can occur. If you encounter an issue, please report it onhttps://github.com/marrink-lab/vermouth-martinize/issues. Carefully check your
input and output files before using them; read the messages displayed by the
program.InstallationMartinize2 and vermouth require python 3.6 or greater. They are distributed viaPyPi, and can be
installed using thepipcommand:pip install vermouthThis installs the last released version. You can update an existing installation by runningpip install -U vermouth.
In some cases you may want to experiment with running the latest development version. You can install this version with
the following command:pip install git+https://github.com/marrink-lab/vermouth-martinize.git#vermouthNote that vermouth and Martinize2, in particular development versions, may contain bugs that cause it to produce
incorrect topologies. Check the produced output carefully!Martinize2 and vermouth havemdtrajas optional dependency as an
alternative to dssp.The behavior of thepipcommand can vary depending of the specificity of your
python installation. See thedocumentation on installing a python
packageto learn more.Basic usageInstalling Martinize2 and vermouth withpipadds themartinize2program to
the research PATH. You can see the available option of the program by running:martinize2 -hAt the moment, martinize2 tries to reproduce the interface of the original
Martinize. You can find explanations on how to use Martinize on theMartini
tutorials; in most cases, replacing calls tomartinize.pyby calls tomartinize2should produce similar results.The documentation of the vermouth python library will come soon.Citation@article{kroon2022martinize2,
  title={Martinize2 and Vermouth: Unified Framework for Topology Generation},
  author={Kroon, Peter C and Gr{\"u}newald, Fabian and Barnoud, Jonathan and van Tilburg, Marco 
          and Souza, Paulo CT and Wassenaar, Tsjerk A and Marrink, Siewert-Jan},
  journal={arXiv preprint arXiv:2212.01191},
  year={2022}}DocumentationMore complete documentation, including API documentation can be found athttps://vermouth-martinize.readthedocs.io/LicenseMartinize2 and vermouth are distributed under the Apache 2.0 license.Copyright 2018 University of Groningen

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

	http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.Thefull text of the licenseis available in the source repository.ContributionsThe development of Martinize2 and vermouth is done ongithub. Contributions
are welcome asbug reportsandpull requests. Note however that the
decision of whether or not contributions can give authorship on the resulting
academic paper is left to our sole discretion.