JOSS manuscript

.pre-commit-config.yaml

@@ -33,8 +33,8 @@ repos:
         args: [ --fix ]
       # Run the formatter.
       - id: ruff-format
-  - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.22
-    hooks:
-    - id: mdformat
-      args: ["--wrap=80"]
+  # - repo: https://github.com/executablebooks/mdformat
+  #   rev: 0.7.22
+  #   hooks:
+  #   - id: mdformat
+  #     args: ["--wrap=80"]

paper/.gitignore

@@ -0,0 +1,5 @@
+jats/
+*.xyz
+*.pdf
+*.ipynb
+*.png

paper/bibliography.bib

@@ -0,0 +1,212 @@
+@misc{landrumRdkitRdkit2023_03_22023,
+  title        = {Rdkit/Rdkit: 2023\_03\_2 ({{Q1}} 2023) {{Release}}},
+  shorttitle   = {Rdkit/Rdkit},
+  author       = {Landrum, Greg and Tosco, Paolo and Kelley, Brian and Ric and Cosgrove, David and {sriniker} and {gedeck} and Vianello, Riccardo and NadineSchneider and Kawashima, Eisuke and N, Dan and Jones, Gareth and Dalke, Andrew and Cole, Brian and Swain, Matt and Turk, Samo and AlexanderSavelyev and Vaucher, Alain and W{\'o}jcikowski, Maciej and Take, Ichiru and Probst, Daniel and Ujihara, Kazuya and Scalfani, Vincent F. and {godin}, guillaume and Lehtivarjo, Juuso and Pahl, Axel and Walker, Rachel and Berenger, Francois and {jasondbiggs} and {strets123}},
+  year         = {2023},
+  month        = jun,
+  doi          = {10.5281/zenodo.8053810},
+  urldate      = {2023-08-13},
+  howpublished = {Zenodo}
+}
+@article{abrahamGROMACSHighPerformance2015,
+  title      = {{{GROMACS}}: {{High}} Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers},
+  shorttitle = {{{GROMACS}}},
+  author     = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{\'a}ll, Szil{\'a}rd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
+  year       = {2015},
+  month      = sep,
+  journal    = {SoftwareX},
+  volume     = {1--2},
+  pages      = {19--25},
+  issn       = {2352-7110},
+  doi        = {10.1016/j.softx.2015.06.001},
+  urldate    = {2025-02-11},
+  keywords   = {Free energy,GPU,Molecular dynamics,SIMD}
+}
+
+@article{larsenAtomicSimulationEnvironment2017,
+  title     = {The Atomic Simulation Environment---a {{Python}} Library for Working with Atoms},
+  author    = {Larsen, Ask Hjorth and Mortensen, Jens J{\o}rgen and Blomqvist, Jakob and Castelli, Ivano E. and Christensen, Rune and Du{\l}ak, Marcin and Friis, Jesper and Groves, Michael N. and Hammer, Bj{\o}rk and Hargus, Cory and Hermes, Eric D. and Jennings, Paul C. and Jensen, Peter Bjerre and Kermode, James and Kitchin, John R. and Kolsbjerg, Esben Leonhard and Kubal, Joseph and Kaasbjerg, Kristen and Lysgaard, Steen and Maronsson, J{\'o}n Bergmann and Maxson, Tristan and Olsen, Thomas and Pastewka, Lars and Peterson, Andrew and Rostgaard, Carsten and Schi{\o}tz, Jakob and Sch{\"u}tt, Ole and Strange, Mikkel and Thygesen, Kristian S. and Vegge, Tejs and Vilhelmsen, Lasse and Walter, Michael and Zeng, Zhenhua and Jacobsen, Karsten W.},
+  year      = {2017},
+  month     = jun,
+  journal   = {Journal of Physics: Condensed Matter},
+  volume    = {29},
+  number    = {27},
+  pages     = {273002},
+  publisher = {IOP Publishing},
+  issn      = {0953-8984},
+  doi       = {10.1088/1361-648X/aa680e},
+  urldate   = {2023-07-10},
+  langid    = {english}
+}
+@article{martinezPACKMOLPackageBuilding2009,
+  title      = {{{PACKMOL}}: A Package for Building Initial Configurations for Molecular Dynamics Simulations},
+  shorttitle = {{{PACKMOL}}},
+  author     = {Mart{\'i}nez, L. and Andrade, R. and Birgin, E. G. and Mart{\'i}nez, J. M.},
+  year       = {2009},
+  month      = oct,
+  journal    = {Journal of Computational Chemistry},
+  volume     = {30},
+  number     = {13},
+  pages      = {2157--2164},
+  issn       = {1096-987X},
+  doi        = {10.1002/jcc.21224},
+  langid     = {english},
+  pmid       = {19229944}
+}
+@article{zillsCollaborationMachineLearnedPotentials2024,
+  title      = {Collaboration on {{Machine-Learned Potentials}} with {{IPSuite}}: {{A Modular Framework}} for {{Learning-on-the-Fly}}},
+  shorttitle = {Collaboration on {{Machine-Learned Potentials}} with {{IPSuite}}},
+  author     = {Zills, Fabian and Sch{\"a}fer, Moritz Ren{\'e} and Segreto, Nico and K{\"a}stner, Johannes and Holm, Christian and Tovey, Samuel},
+  year       = {2024},
+  month      = apr,
+  journal    = {The Journal of Physical Chemistry B},
+  volume     = {128},
+  number     = {15},
+  pages      = {3662--3676},
+  publisher  = {American Chemical Society},
+  issn       = {1520-6106},
+  doi        = {10.1021/acs.jpcb.3c07187},
+  urldate    = {2024-07-17},
+  copyright  = {All rights reserved}
+}
+@misc{elijosiusZeroShotMolecular2024,
+  title         = {Zero {{Shot Molecular Generation}} via {{Similarity Kernels}}},
+  author        = {Elijo{\v s}ius, Rokas and Zills, Fabian and Batatia, Ilyes and Norwood, Sam Walton and Kov{\'a}cs, D{\'a}vid P{\'e}ter and Holm, Christian and Cs{\'a}nyi, G{\'a}bor},
+  year          = {2024},
+  month         = feb,
+  number        = {arXiv:2402.08708},
+  eprint        = {2402.08708},
+  primaryclass  = {physics},
+  publisher     = {arXiv},
+  doi           = {10.48550/arXiv.2402.08708},
+  urldate       = {2024-02-15},
+  archiveprefix = {arXiv},
+  copyright     = {All rights reserved},
+  keywords      = {Computer Science - Machine Learning,Physics - Chemical Physics}
+}
+@article{LAMMPS,
+  title  = {{{LAMMPS}} - a Flexible Simulation Tool for Particle-Based Materials Modeling at the Atomic, Meso, and Continuum Scales},
+  author = {Thompson, A. P. and Aktulga, H. M. and Berger, R. and Bolintineanu, D. S. and Brown, W. M. and Crozier, P. S. and in 't Veld, P. J. and Kohlmeyer, A. and Moore, S. G. and Nguyen, T. D. and Shan, R. and Stevens, M. J. and Tranchida, J. and Trott, C. and Plimpton, S. J.},
+  year   = {2022},
+  volume = {271},
+  pages  = {108171},
+  doi    = {10.1016/j.cpc.2021.108171}
+}
+@article{weikESPResSo40Extensible2019,
+  title   = {{{ESPResSo}} 4.0 -- an Extensible Software Package for Simulating Soft Matter Systems},
+  author  = {Weik, Florian and Weeber, Rudolf and Szuttor, Kai and Breitsprecher, Konrad and {de Graaf}, Joost and Kuron, Michael and Landsgesell, Jonas and Menke, Henri and Sean, David and Holm, Christian},
+  year    = {2019},
+  month   = mar,
+  journal = {The European Physical Journal Special Topics},
+  volume  = {227},
+  number  = {14},
+  pages   = {1789--1816},
+  issn    = {1951-6401},
+  doi     = {10.1140/epjst/e2019-800186-9},
+  urldate = {2025-05-23},
+  langid  = {english}
+}
+@article{eastmanOpenMM8Molecular2024,
+  title      = {{{OpenMM}} 8: {{Molecular Dynamics Simulation}} with {{Machine Learning Potentials}}},
+  shorttitle = {{{OpenMM}} 8},
+  author     = {Eastman, Peter and Galvelis, Raimondas and Pel{\'a}ez, Ra{\'u}l P. and Abreu, Charlles R. A. and Farr, Stephen E. and Gallicchio, Emilio and Gorenko, Anton and Henry, Michael M. and Hu, Frank and Huang, Jing and Kr{\"a}mer, Andreas and Michel, Julien and Mitchell, Joshua A. and Pande, Vijay S. and Rodrigues, Jo{\~a}o PGLM and {Rodriguez-Guerra}, Jaime and Simmonett, Andrew C. and Singh, Sukrit and Swails, Jason and Turner, Philip and Wang, Yuanqing and Zhang, Ivy and Chodera, John D. and De Fabritiis, Gianni and Markland, Thomas E.},
+  year       = {2024},
+  month      = jan,
+  journal    = {The Journal of Physical Chemistry B},
+  volume     = {128},
+  number     = {1},
+  pages      = {109--116},
+  publisher  = {American Chemical Society},
+  issn       = {1520-6106},
+  doi        = {10.1021/acs.jpcb.3c06662},
+  urldate    = {2025-05-23}
+}
+@article{phillipsScalableMolecularDynamics2020,
+  title   = {Scalable Molecular Dynamics on {{CPU}} and {{GPU}} Architectures with {{NAMD}}},
+  author  = {Phillips, James C. and Hardy, David J. and Maia, Julio D. C. and Stone, John E. and Ribeiro, Jo{\~a}o V. and Bernardi, Rafael C. and Buch, Ronak and Fiorin, Giacomo and H{\'e}nin, J{\'e}r{\^o}me and Jiang, Wei and McGreevy, Ryan and Melo, Marcelo C. R. and Radak, Brian K. and Skeel, Robert D. and Singharoy, Abhishek and Wang, Yi and Roux, Beno{\^i}t and Aksimentiev, Aleksei and {Luthey-Schulten}, Zaida and Kal{\'e}, Laxmikant V. and Schulten, Klaus and Chipot, Christophe and Tajkhorshid, Emad},
+  year    = {2020},
+  month   = jul,
+  journal = {The Journal of Chemical Physics},
+  volume  = {153},
+  number  = {4},
+  pages   = {044130},
+  issn    = {0021-9606},
+  doi     = {10.1063/5.0014475},
+  urldate = {2025-05-23}
+}
+@article{jainCommentaryMaterialsProject2013,
+  title      = {Commentary: {{The Materials Project}}: {{A}} Materials Genome Approach to Accelerating Materials Innovation},
+  shorttitle = {Commentary},
+  author     = {Jain, Anubhav and Ong, Shyue Ping and Hautier, Geoffroy and Chen, Wei and Richards, William Davidson and Dacek, Stephen and Cholia, Shreyas and Gunter, Dan and Skinner, David and Ceder, Gerbrand and Persson, Kristin A.},
+  year       = {2013},
+  month      = jul,
+  journal    = {APL Materials},
+  volume     = {1},
+  number     = {1},
+  pages      = {011002},
+  issn       = {2166-532X},
+  doi        = {10.1063/1.4812323},
+  urldate    = {2024-08-27}
+}
+@article{weiningerSMILESChemicalLanguage1988,
+  title     = {{{SMILES}}, a Chemical Language and Information System. 1. {{Introduction}} to Methodology and Encoding Rules},
+  author    = {Weininger, David},
+  year      = {1988},
+  month     = feb,
+  journal   = {Journal of Chemical Information and Computer Sciences},
+  volume    = {28},
+  number    = {1},
+  pages     = {31--36},
+  publisher = {American Chemical Society},
+  issn      = {0095-2338},
+  doi       = {10.1021/ci00057a005},
+  urldate   = {2023-07-10}
+}
+@article{kimUniversalStructureConversion2015,
+  title      = {Universal {{Structure Conversion Method}} for {{Organic Molecules}}: {{From Atomic Connectivity}} to {{Three-Dimensional Geometry}}},
+  shorttitle = {Universal {{Structure Conversion Method}} for {{Organic Molecules}}},
+  author     = {Kim, Yeonjoon and Kim, Woo Youn},
+  year       = {2015},
+  journal    = {Bulletin of the Korean Chemical Society},
+  volume     = {36},
+  number     = {7},
+  pages      = {1769--1777},
+  issn       = {1229-5949},
+  doi        = {10.1002/bkcs.10334},
+  urldate    = {2025-05-23},
+  copyright  = {{\copyright} 2015 Korean Chemical Society, Seoul \& Wiley-VCH Verlag GmbH \& Co. KGaA, Weinheim},
+  langid     = {english}
+}
+@article{gowersMDAnalysisPythonPackage2016,
+  title      = {{{MDAnalysis}}: {{A Python Package}} for the {{Rapid Analysis}} of {{Molecular Dynamics Simulations}}},
+  shorttitle = {{{MDAnalysis}}},
+  author     = {Gowers, Richard J. and Linke, Max and Barnoud, Jonathan and Reddy, Tyler J. E. and Melo, Manuel N. and Seyler, Sean L. and Doma{\'n}ski, Jan and Dotson, David L. and Buchoux, S{\'e}bastien and Kenney, Ian M. and Beckstein, Oliver},
+  year       = {2016},
+  journal    = {Proceedings of the 15th Python in Science Conference},
+  pages      = {98--105},
+  doi        = {10.25080/Majora-629e541a-00e},
+  urldate    = {2024-02-10}
+}
+@article{tingleZINC22AFreeMultiBillionScale2023,
+  title     = {{{ZINC-22}}-{{A Free Multi-Billion-Scale Database}} of {{Tangible Compounds}} for {{Ligand Discovery}}},
+  author    = {Tingle, Benjamin I. and Tang, Khanh G. and Castanon, Mar and Gutierrez, John J. and Khurelbaatar, Munkhzul and Dandarchuluun, Chinzorig and Moroz, Yurii S. and Irwin, John J.},
+  year      = {2023},
+  month     = feb,
+  journal   = {Journal of Chemical Information and Modeling},
+  volume    = {63},
+  number    = {4},
+  pages     = {1166--1176},
+  publisher = {American Chemical Society},
+  issn      = {1549-9596},
+  doi       = {10.1021/acs.jcim.2c01253},
+  urldate   = {2025-05-24}
+}
+@inproceedings{hagbergExploringNetworkStructure2008,
+  author    = {Aric A. Hagberg and Daniel A. Schult and Pieter J. Swart},
+  title     = {Exploring Network Structure, Dynamics, and Function using NetworkX},
+  booktitle = {Proceedings of the 7th Python in Science Conference},
+  pages     = {11 - 15},
+  address   = {Pasadena, CA USA},
+  year      = {2008},
+  editor    = {Ga\"el Varoquaux and Travis Vaught and Jarrod Millman}
+}

paper/build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker run --rm  --volume $PWD:/data --user $(id -u):$(id -g) --platform=linux/amd64 --env JOURNAL=joss openjournals/inara