Merge pull request #181 from marrink-lab/update/README

Updated README.md and citations
marrink-lab · Jan 10, 2022 · 0f66279 · 0f66279
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diff --git a/README.md b/README.md
@@ -1,47 +1,58 @@
 # polyply
 
 [![codecov](https://codecov.io/gh/marrink-lab/polyply_1.0/branch/master/graph/badge.svg)](https://codecov.io/gh/marrink-lab/polyply_1.0)
+[![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)
 [![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)
 
 ## Functionality
-Polyply is a python suite designed to facilitate the generation of input files and coordinates for simulating
+Polyply is a python suite designed to facilitate the generation of input files and system coordinates for simulating
 (bio)macromolecules such as synthetic polymers or polysaccharides. Input files can be generated either from user
 specified building blocks or by using the polymers available in the library. The library currently includes polymer
-definitions for the GROMOS and Martini force-fields. The [quick start](https://github.com/marrink-lab/polyply_1.0/wiki/Quick-Start)
-section in the wiki gives an overview of the most important commands. In addition some [tutorials][wiki] are provided for more
-in-depth information on how to use the program. Tutorials for example include, how to generate
-[Martini polymer systems](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts) or
+definitions for the GROMOS (2016H66 & 54A6), OPLS, Parmbsc1, and Martini (2 & 3) force-fields. Coordinates are generated
+by a multiscale random-walk protocol that is able to generate condensed phase systems at target density, as well as
+more heterogeneous systems such as aqueous two phase systems. In addition, polyply allows to tailor initial chain
+conformations by providing a build file. For example, the persistence length can be used to control the initial chain
+dimensions. The [quick start](https://github.com/marrink-lab/polyply_1.0/wiki/Quick-Start) section in the wiki gives
+an overview of the most important commands. In addition, [tutorials][wiki] are provided for more in-depth information
+on how to use the program. Tutorials include how to generate
+[Martini polymer systems](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts) and
 [write input files](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-writing-.ff-input-files).
-More details on the algorithm and verification can be found in the [publication](https://arxiv.org/abs/2105.05890).
+More details on the algorithm and verification can be found in the [publication](https://doi.org/10.1038/s41467-021-27627-4).
 
 Make sure to always verify the results and give appropriate credit to the developers of the
-force-field, molecule parameters and this program. 
+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)\
 [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: 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)
 
-## Contributions
-We are happy to accept submissions of polymer parameters (mostly for the Martini force-field). After a small quality control
-procedure, parameters are distributed via the Martini library including appropiate citations. To submit parameters simply 
+## Contributions & Support
+We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply 
 open an [issue][bug reports]. More details on submitting parameters can be found 
 [here](https://github.com/marrink-lab/polyply_1.0/wiki/Submit-polymer-parameters). The code development of polyply is done 
-on [github]. Contributions are welcome as [bug reports] and [pull requests] from everyone.
+on [github]. Contributions are welcome as [bug reports] and [pull requests] from everyone. We are also happy to discuss
+any of your projects or hear about how you used polyply in your research project. Let us know on the 
+[discussions board](https://github.com/marrink-lab/polyply_1.0/discussions) or by tweeting with #CG_MARTINI or #polyply.
 
 ## Citation
 ```
-@article{grunewald2021polyply,
-  title={Polyply: a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+@article{Grunewald2022Polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
   author={Gr{\"u}newald, Fabian and Alessandri, Riccardo and Kroon, Peter C and 
   	  Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
-  journal={arXiv preprint arXiv:2105.05890},
-  year={2021}
+  journal={Nature Communications},
+  volume={13},
+  pages={68},
+  doi={https://doi.org/10.1038/s41467-021-27627-4},
+  year={2022}
 }
 ```
 

diff --git a/bin/polyply b/bin/polyply
@@ -201,11 +201,11 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
                                 "using the connects flag.")
     seq_group.add_argument('-connects', dest='connects', nargs='+', type=str,
                            help="Provide connect records for sequence. "
-                                "The format is <seq-index,seq-index-res_id,res_id>. "
+                                "The format is <seq-index:seq-index:res_id-res_id>. "
                                 "For example if we want to connect the first and third "
                                 "block in a sequence, using a connection between the second "
                                 "and third residue in these blocks respectively the input "
-                                "would be <1,3-2,3>.", default=[])
+                                "would be <1:3:2-3>.", default=[])
     seq_group.add_argument('-modf_ter', dest='modifications', nargs='+', type=str,
                            help="change the resname of terminii of a specific block "
                                 "in the sequence. The format is <SeqID:new_resname>.",

diff --git a/polyply/data/2016H66/citation.bib b/polyply/data/2016H66/citation.bib
@@ -0,0 +1,20 @@
+@article{2016H66,
+  title={A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set},
+  author={Horta, Bruno AC and Merz, Pascal T and Fuchs, Patrick FJ and Dolenc, Jozica and Riniker, Sereina and Hünenberger, Philippe H},
+  journal={Journal of chemical theory and computation},
+  volume={12},
+  number={8},
+  pages={3825--3850},
+  year={2016},
+  publisher={ACS Publications}
+}
+
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  volume={18},
+  pages={382--388},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022}
+}
diff --git a/polyply/data/2016H66/polyether_blocks.ff b/polyply/data/2016H66/polyether_blocks.ff
@@ -1,3 +1,7 @@
+[ citations ]
+2016H66
+polyply
+
 [ moleculetype ]
 PEO 3
 [ atoms ]

diff --git a/polyply/data/2016H66/polyvinyl_blocks.ff b/polyply/data/2016H66/polyvinyl_blocks.ff
@@ -1,3 +1,6 @@
+[ citations ]
+2016H66
+polyply
 [ moleculetype ]
 PE 3
 [ atoms ]

diff --git a/polyply/data/gromos53A6/P3HT.gromos.53A6.ff b/polyply/data/gromos53A6/P3HT.gromos.53A6.ff
@@ -185,3 +185,4 @@ P3HT     3
 [ citations ]
 P3HT_GROMOS
 GROMOS53A5and53A6
+polyply
diff --git a/polyply/data/gromos53A6/citations.bib b/polyply/data/gromos53A6/citations.bib
@@ -23,3 +23,14 @@ @article{P3HT_GROMOS
   doi      ={10.1021/jacs.6b11717},
   url      ={https://doi.org/10.1021/jacs.6b11717}
 }
+
+
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}
diff --git a/polyply/data/martini2/P3HT.martini.2.itp b/polyply/data/martini2/P3HT.martini.2.itp
@@ -66,3 +66,4 @@ P3HT               1
 [ citation ]
 Martini2
 P3HT_M2
+polyply
diff --git a/polyply/data/martini2/PDADMA.martini.2.itp b/polyply/data/martini2/PDADMA.martini.2.itp
@@ -39,3 +39,4 @@ PDADMA         2
 [ citation ]
 Martini2
 PSS_M2
+polyply
diff --git a/polyply/data/martini2/PE.martini.2.itp b/polyply/data/martini2/PE.martini.2.itp
@@ -23,3 +23,4 @@ PE         1
 [ citation ]
 Martini2
 PP_PE_M2
+polyply
diff --git a/polyply/data/martini2/PEO.martini.2.itp b/polyply/data/martini2/PEO.martini.2.itp
@@ -17,6 +17,7 @@ PEO         1
 [ citation ]
 Martini2
 PEO_M2
+polyply
 [ dihedrals ]
 1  2  3  4     1    180.00    1.96   1
 1  2  3  4     1     0        0.18   2  

diff --git a/polyply/data/martini2/PP.martini.2.itp b/polyply/data/martini2/PP.martini.2.itp
@@ -23,3 +23,4 @@ PP         1
 [ citation ]
 Martini2
 PP_PE_M2
+polyply
diff --git a/polyply/data/martini2/PS.martini.2.itp b/polyply/data/martini2/PS.martini.2.itp
@@ -62,3 +62,4 @@ PS 3
 [ citation ]
 Martini2
 PS_M2
+polyply
diff --git a/polyply/data/martini2/PSS.martini.2.itp b/polyply/data/martini2/PSS.martini.2.itp
@@ -51,3 +51,4 @@ PSS       3
 [ citation ]
 Martini2
 PSS_M2
+polyply
diff --git a/polyply/data/martini2/citations.bib b/polyply/data/martini2/citations.bib
@@ -70,3 +70,12 @@ @article{P3HT_M2
   doi={10.1021/jacs.6b11717}
 }
 
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}
diff --git a/polyply/data/martini2/links.ff b/polyply/data/martini2/links.ff
@@ -1,5 +1,6 @@
 [ citations ]
 Martini2
+polyply
 
 [ moleculetype ]
 OHter 1

diff --git a/polyply/data/martini3/P3HT.martini3.ff b/polyply/data/martini3/P3HT.martini3.ff
@@ -1,3 +1,6 @@
+[ citations ]
+Martini3
+polyply
 ; ;;;;; poly(3-hexyl-thiophene) (P3HT)
 ;
 [ moleculetype ]

diff --git a/polyply/data/martini3/PE.martini3.ff b/polyply/data/martini3/PE.martini3.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 [ moleculetype ]
 PE  1
 

diff --git a/polyply/data/martini3/PEL_link.ff b/polyply/data/martini3/PEL_link.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 [ link ]
 resname "DPPE|POPE|DOPE|PEO"
 [ atoms ]

diff --git a/polyply/data/martini3/PEO.martini3.ff b/polyply/data/martini3/PEO.martini3.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 [ moleculetype ]
 ; name nexcl.
 PEO         1

diff --git a/polyply/data/martini3/PMA.martini3.ff b/polyply/data/martini3/PMA.martini3.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 [ moleculetype ]
 PMA 1
 ;

diff --git a/polyply/data/martini3/PMMA.martini3.ff b/polyply/data/martini3/PMMA.martini3.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 [ moleculetype ]
 PMMA 1
 ;

diff --git a/polyply/data/martini3/PS.martini3.ff b/polyply/data/martini3/PS.martini3.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 ; POLYSTYRENE (A-mapping, see ref. below)
 ;
 ;

diff --git a/polyply/data/martini3/PSS.martini3.ff b/polyply/data/martini3/PSS.martini3.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 ; POLYSTYRENE (A-mapping, see ref. below)
 ;
 ;

diff --git a/polyply/data/martini3/PS_PEO_link.ff b/polyply/data/martini3/PS_PEO_link.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 [ link ]
 resname "PS|PEO"
 [ bonds ]

diff --git a/polyply/data/martini3/PVA.martini3.ff b/polyply/data/martini3/PVA.martini3.ff
@@ -1,3 +1,6 @@
+[ citations ]
+Martini3
+polyply
 ;
 [ moleculetype ]
 PVA 1

diff --git a/polyply/data/martini3/aminoacids.ff b/polyply/data/martini3/aminoacids.ff
@@ -22,6 +22,10 @@ stiff_fc 1000000
 elastic_network_bond_type 1
 res_min_dist 3
 
+[ citations ]
+Martini3
+polyply
+
 ;;; GLYCINE
 
 [ moleculetype ]

diff --git a/polyply/data/martini3/citations.bib b/polyply/data/martini3/citations.bib
@@ -0,0 +1,21 @@
+@article{Martini3,
+abstract={The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein–protein and protein–lipid interactions and material science applications as ionic liquids and aedamers.},
+author={Souza, Paulo C T and Alessandri, Riccardo and Barnoud, Jonathan and Thallmair, Sebastian and Faustino, Ignacio and Grünewald, Fabian and Patmanidis, Ilias and Abdizadeh, Haleh and Bruininks, Bart M H and Wassenaar, Tsjerk A and Kroon, Peter C and Melcr, Josef and Nieto, Vincent and Corradi, Valentina and Khan, Hanif M and Domański, Jan and Javanainen, Matti and Martinez-Seara, Hector and Reuter, Nathalie and Best, Robert B and Vattulainen, Ilpo and Monticelli, Luca and Periole, Xavier and Tieleman, D Peter and de Vries, Alex H and Marrink, Siewert J},
+doi={10.1038/s41592-021-01098-3},                                             
+issn={1548-7105},                                                             
+journal={Nature Methods},                                                     
+title={{Martini 3: a general purpose force field for coarse-grained molecular dynamics}},
+url={https://doi.org/10.1038/s41592-021-01098-3},                             
+year={2021},
+volume={18},
+pages={382--388}                                                                
+}
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}
diff --git a/polyply/data/martini3/dextran.martini3.ff b/polyply/data/martini3/dextran.martini3.ff
@@ -1,3 +1,7 @@
+[ citations ]
+Martini3
+polyply
+
 [ moleculetype ]
 ; molname    nrexcl
   DEX   3

diff --git a/polyply/data/martini3_beta/PEO.martini.3.itp b/polyply/data/martini3_beta/PEO.martini.3.itp
@@ -1,3 +1,6 @@
+[ citations ]
+PEO_M2
+polyply
 [ moleculetype ]
 ; name nexcl.
 PEO         1

diff --git a/polyply/data/martini3_beta/citations.bib b/polyply/data/martini3_beta/citations.bib
@@ -0,0 +1,21 @@
+@article{PEO_M2,
+  title={Transferable MARTINI model of poly (ethylene oxide)},
+  author={Grunewald, Fabian and Rossi, Giulia and de Vries, Alex H and Marrink, Siewert J and Monticelli, Luca},
+  journal={The Journal of Physical Chemistry B},
+  volume={122},
+  number={29},
+  pages={7436--7449},
+  year={2018},
+  publisher={ACS Publications},
+  doi={10.1021/acs.jpcb.8b04760}
+}
+
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}
diff --git a/polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff b/polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff
@@ -51,3 +51,4 @@ PEO                   3
 OPLSLigParGen1
 OPLSLigParGen2
 OPLSLigParGen3
+polyply
diff --git a/polyply/data/oplsaaLigParGen/citations.bib b/polyply/data/oplsaaLigParGen/citations.bib
@@ -35,3 +35,13 @@ @article{OPLSLigParGen3
   year={2017},
   doi={10.1021/acs.jpcb.7b00272}
 }
+
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}
diff --git a/polyply/data/parmbsc1/citations.bib b/polyply/data/parmbsc1/citations.bib
@@ -8,3 +8,13 @@ @article{parmbsc1
   year={2016},
   publisher={Nature Publishing Group}
 }
+
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}
diff --git a/polyply/data/parmbsc1/dna_final.ff b/polyply/data/parmbsc1/dna_final.ff
@@ -3,6 +3,7 @@ base_pairs "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3"
 
 [ citations ]
 parmbsc1
+polyply
 
 [ moleculetype ]
 DA5 3