Merge branch 'master' into DNA-exten/itp

.codecov.yml

@@ -10,4 +10,6 @@ coverage:
         patch:
             default:
                 target: 90
+ignore:
+   - polyply/tests
 comment: off

.github/CONTRIBUTING.md

@@ -0,0 +1,23 @@
+## Contributing to polyply
+
+Thanks for contributing to polyply!
+
+Everyone is welcome to contribute to the polyply package as described below. 
+
+#### Reporting issues
+
+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. 
+
+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).
+
+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. 
+
+#### Contributing parameters
+
+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).
+
+#### Contributing code
+
+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. 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,25 @@
+---
+name: Bug report
+about: Create a report to help us improve polyply
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**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`
+
+**Command line arguments**
+Provide all polyply calls and arguments needed to reproduce the issue:
+```
+polyply gen_seq ...
+polyply gen_itp ...
+```
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Additional Files**
+If applicable, add all files needed in the reproduction.

.github/ISSUE_TEMPLATE/parameter-submission.md

@@ -0,0 +1,22 @@
+---
+name: Parameter Submission
+about: Submit parameters to polyply library.
+title: "[PARAMETERS]"
+labels: parameter submission
+assignees: ''
+
+---
+
+**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? 
+
+** 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. 
+
+- reference itp file
+- link to force-field definition if it is a new force-field not part of the library 

.github/workflows/pypi_deploy.yml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-       py_version: ["3.6", "3.7", "3.8", "3.9"] 
+       py_version: ["3.7", "3.8", "3.9", "3.10", "3.11"] 
 
     steps:
     - uses: actions/checkout@v2
@@ -28,11 +28,15 @@ jobs:
         pip install -r requirements-tests.txt
         
     - name: Run pytest with codecoverage
-      run: |
-        coverage run --source=polyply $(which pytest) -vv polyply
-        coverage report --omit='*/bin/pytest'
-        codecov
-  
+      run:  pytest --cov polyply --cov-report=xml
+    - name: Upload coverage codecov   
+      uses: codecov/codecov-action@v3 
+      with:
+            verbose: true
+            token: ${{ secrets.CODECOV_TOKEN }}
+            files: ./coverage.xml
+            fail_ci_if_error: true
+            verbose: true
 
   deploy:
     needs: test

.github/workflows/python-app.yml

@@ -5,9 +5,9 @@ name: test package
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, develop ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, develop ]
 
 jobs:
   build:
@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-       py_version: ["3.6", "3.7", "3.8", "3.9"] 
+       py_version: ["3.7", "3.8", "3.9", "3.10", "3.11"] 
 
     steps:
     - uses: actions/checkout@v2
@@ -31,11 +31,15 @@ jobs:
         pip install -r requirements-tests.txt
         
     - name: Run pytest with codecoverage
-      run: |
-        coverage run --source=polyply $(which pytest) -vv polyply
-        coverage report --omit='*/bin/pytest'
-        codecov
-        
+      run:  pytest --cov polyply --cov-report=xml
+    - name: Upload coverage codecov   
+      uses: codecov/codecov-action@v3 
+      with:
+            token: ${{ secrets.CODECOV_TOKEN }}
+            files: ./coverage.xml
+            fail_ci_if_error: true
+            verbose: true
+
   lint:
     runs-on: ubuntu-latest
 

.gitignore

@@ -3,6 +3,8 @@ est.pdb
 **.pyc
 **.bak
 
+*.idea
+
 **.lprof
 polyply.egg-info
 

LIBRARY.md

@@ -0,0 +1,28 @@
+
+| 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)

README.md

@@ -4,7 +4,7 @@
 [![Build Status](https://github.com/marrink-lab/polyply_1.0/actions/workflows/python-app.yml/badge.svg)](https://github.com/marrink-lab/polyply_1.0/actions)
 [![PyPI version](https://badge.fury.io/py/polyply.svg)](https://badge.fury.io/py/polyply)
 ![license](https://img.shields.io/github/license/marrink-lab/polyply_1.0)
-![GitHub Workflow Status](https://img.shields.io/github/workflow/status/marrink-lab/polyply_1.0/Upload%20Python%20Package)
+![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/marrink-lab/polyply_1.0/pypi_deploy.yml)
 [![arXiv](https://img.shields.io/badge/arXiv-2105.05890-b31b1b.svg)](https://arxiv.org/abs/2105.05890)
 [![DOI:10.1038/s41467-021-27627-4](https://zenodo.org/badge/DOI/10.1038/s41467-021-27627-4.svg)](https://doi.org/10.1038/s41467-021-27627-4)
 
@@ -29,13 +29,16 @@ force-field, molecule parameters and this program.
 ## Quick references
 [Installation Guide](https://github.com/marrink-lab/polyply_1.0/wiki/Installation)\
 [FAQs](https://github.com/marrink-lab/polyply_1.0/wiki/FAQs)\
+[Current Polyply Polymer Library](./LIBRARY.md)\
 [Submissions to Martini Polymer Library](https://github.com/marrink-lab/polyply_1.0/wiki/Submit-polymer-parameters)\
 [Tutorial: Martini Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts)\
 [Tutorial: GROMOS Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-GROMOS-polymer-melts)\
-[Tutorial: PEGylated lipid bilayers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-PEGylated-lipid-bilayers)
-
+[Tutorial: PEGylated lipid bilayers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-PEGylated-lipid-bilayers)\
+[Tutorial: Single-stranded DNA](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-Single-stranded-circular-DNA)
 ## News 
-- (Feb 8) **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor.   
+- (Feb 8, 22') **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor.   
+- (May 23, 22') **Fighting Cancer with polyply.** Dane et al. used polyply to setup simulations of vesicles and lipid nanodiscs (LNDs) containing PEGylated lipids, which are used as nanocarriers for cancer therapeutics. They find that LNDs are more effective in delivery likely due to their higher flexibility.  Check it out in [Nature Materials](https://www.nature.com/articles/s41563-022-01251-z). 
+- (Jan 18, 23') **Towards whole cell simulations with polyply.** In [a perspective on whole-cell simulations](https://www.frontiersin.org/articles/10.3389/fchem.2023.1106495/full) using the Martini force field, Stevens *et al.* utilize polyply to construct the full 0.5 Mio bp chromosome of the Syn3A minimal cell. This impressive task is a good example of the power of the upcoming DNA implementation into polyply and the role of polyply in the Martini Ecosystem.
 
 ## Contributions & Support
 We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply