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patch: | ||
default: | ||
target: 90 | ||
ignore: | ||
- polyply/tests | ||
comment: off |
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## Contributing to polyply | ||
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Thanks for contributing to polyply! | ||
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Everyone is welcome to contribute to the polyply package as described below. | ||
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#### Reporting issues | ||
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If you've found something going wrong with polyply let us know by opening an [issue](https://github.com/marrink-lab/polyply_1.0/issues). This way we can fix it as fast as possible. | ||
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If your issue isn't a problem with the code and instead you would like some help using polyply for your project, let us know on the [discussion forum](https://github.com/marrink-lab/polyply_1.0/discussions). | ||
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As a rule of thumb, give a quick look to the [FAQs]( https://github.com/marrink-lab/polyply_1.0/wiki/FAQs) and [discussion forum]( https://github.com/marrink-lab/polyply_1.0/discussions), | ||
if you are in doubt as to whether you are experiencing an actual bug or if the usage of polyply is unclear. In any case we’d love to know, so we can improve the situation. | ||
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#### Contributing parameters | ||
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Polyply curates a library of polymer parameters for different force-fields, especially the Martini force-field. We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply open an [issue](https://github.com/marrink-lab/polyply_1.0/issues). More details on submitting parameters can be found | ||
[here](https://github.com/marrink-lab/polyply_1.0/wiki/Submit-polymer-parameters). | ||
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#### Contributing code | ||
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To contribute code simply open a pull request. The dev-tream will try its best to assist with tips, tricks, and guidance to make a PR as successful as possible. If you are in doubt as to whether your code addition/project would be accepted simply open an issue and let us help you. |
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--- | ||
name: Bug report | ||
about: Create a report to help us improve polyply | ||
title: '' | ||
labels: '' | ||
assignees: '' | ||
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--- | ||
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**Describe the bug** | ||
A clear and concise description of what the bug is and mention the polyply version. | ||
To find the version run `polyply --version` | ||
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**Command line arguments** | ||
Provide all polyply calls and arguments needed to reproduce the issue: | ||
``` | ||
polyply gen_seq ... | ||
polyply gen_itp ... | ||
``` | ||
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**Expected behavior** | ||
A clear and concise description of what you expected to happen. | ||
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**Additional Files** | ||
If applicable, add all files needed in the reproduction. |
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--- | ||
name: Parameter Submission | ||
about: Submit parameters to polyply library. | ||
title: "[PARAMETERS]" | ||
labels: parameter submission | ||
assignees: '' | ||
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--- | ||
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**Parameter Description** | ||
A brief description of the parameters you want to add to the library providing the following information: | ||
- residue/monomer name | ||
- citation if available | ||
- force-field | ||
- simulation program (currently only GROMACS is supported) | ||
- are the termini different? | ||
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** Additional Files & Resources** | ||
If you want us to implement the parameters please provide the following files. However, we encourage users to try implementing files themselves by opening a PR. | ||
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- reference itp file | ||
- link to force-field definition if it is a new force-field not part of the library |
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**.pyc | ||
**.bak | ||
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*.idea | ||
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**.lprof | ||
polyply.egg-info | ||
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| Polymer name | Abbreviation | All-atom model(s) | Coarse-grained model(s) | | ||
|-------------------------------|-------------------------|-----------------------------------------------------------------------|------------------------------------------------------| | ||
|Polyethylene oxide |PEO |[gromos2016H66](polyply/data/2016H66/polyether_blocks.ff) |[martini2](polyply/data/martini2/PEO.martini.2.itp) | | ||
| | |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff)|[martini3](polyply/data/martini3/PEO.martini3.ff) | | ||
|Polystyrene |PS |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) |[martini2](polyply/data/martini2/PS.martini.2.itp) | | ||
| | | |[martini3](polyply/data/martini3/PS.martini3.ff) | | ||
|Polystyrene-b-poly(ethylene oxide)|PS-PEO | |[martini3](polyply/data/martini3/PS_PEO_link.ff) | | ||
|Polymethyl acrylate |PMA |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) |[martini3](polyply/data/martini3/PMA.martini3.ff) | | ||
|Polymethyl methacrylate |PMMA |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) |[martini3](polyply/data/martini3/PMMA.martini3.ff) | | ||
|Polyethylene |PE |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) |[martini3](polyply/data/martini3/PE.martini3.ff) | | ||
| | | |[martini2](polyply/data/martini2/PE.martini.2.itp) | | ||
|Polypropylene |PP |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) |[martini2](polyply/data/martini2/PP.martini.2.itp) | | ||
|Poly(3-hexylthiophene) |P3HT |[gromos53A6](polyply/data/gromos53A6/P3HT.gromos.53A6.ff) |[martini2](polyply/data/martini2/P3HT.martini.2.itp) | | ||
| | | |[martini3](polyply/data/martini3/P3HT.martini3.ff) | | ||
|Polyvinyl alcohol |PVA |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) |[martini3](polyply/data/martini3/PVA.martini3.ff) | | ||
|Poly(2-hydroxyethyl acrylate) |HEA |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) | | | ||
|Polyacrylamide |PAM |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) | | | ||
|Poly(methacrylamide) |PMAM |[gromos2016H66](polyply/data/2016H66/polyvinyl_blocks.ff) | | | ||
|Poly(diallyldimethylammonium) |PDADMA | |[martini2](polyply/data/martini2/PDADMA.martini.2.itp)| | ||
|Polystyrene sulfonate |PSS | |[martini2](polyply/data/martini2/PSS.martini.2.itp) | | ||
| | | |[martini3](polyply/data/martini3/PSS.martini3.ff) | | ||
|Poly(para-phenylene ethynylene)|PPE | |[martini3](polyply/data/martini3/PPE.martini3.ff) | | ||
|Poly(TEMPO methacrylate) |PTMA | |[martini3](polyply/data/martini3/PTMA.martini3.ff) | | ||
|Dextran |DEX | |[martini3](polyply/data/martini3/dextran.martini3.ff) | | ||
|DNA nucleobases |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff) |[martini2](polyply/data/martini2/DNA_M2.ff) | | ||
|Aminoacids |3 letter code | |[martini3](polyply/data/martini3/aminoacids.ff) | | ||
|Polydimethylsiloxane |PDMS | |[martini3](polyply/data/martini3/PDMS.martini3.ff) |
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