Add normalization and grounding scripts for each entity class

data/normalization/SOFTNAME/amber/codemeta.json

@@ -0,0 +1,115 @@
+{
+    "@context": "https://w3id.org/codemeta/3.0",
+    "type": "SoftwareSourceCode",
+    "applicationCategory": "molecular dynamics",
+    "author": [
+        {
+            "id": "https://orcid.org/0000-0002-2574-6066",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Vertex Pharmaceuticals, 40 Allston Street, Cambridge, MA 02138, USA"
+            },
+            "familyName": "Pearlman",
+            "givenName": "David A.  "
+        },
+        {
+            "id": "_:author_2",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Molecular Biology and Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA"
+            },
+            "familyName": "Case",
+            "givenName": "David A.  "
+        },
+        {
+            "id": "_:author_3",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA"
+            },
+            "familyName": "Caldwell",
+            "givenName": "James W.  "
+        },
+        {
+            "id": "_:author_4",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA"
+            },
+            "familyName": "Ross",
+            "givenName": "Wilson S. "
+        },
+        {
+            "id": "https://orcid.org/0000-0003-0298-3904",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA"
+            },
+            "familyName": "Cheatham III",
+            "givenName": "Thomas E. "
+        },
+        {
+            "id": "_:author_6",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Molecular Biology and Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA"
+            },
+            "familyName": "DeBolt",
+            "givenName": " Steve "
+        },
+        {
+            "id": "https://orcid.org/0000-0001-6294-8057",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "    Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 9055455, USA"
+            },
+            "familyName": "Ferguson",
+            "givenName": "David "
+        },
+        {
+            "id": "_:author_8",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Smith Kline Beecham Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA"
+            },
+            "familyName": "Seibel",
+            "givenName": "George "
+        },
+        {
+            "id": "_:author_9",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA"
+            },
+            "familyName": "Kollman",
+            "givenName": " Peter  "
+        }
+    ],
+    "codeRepository": "https://github.com/Amber-MD/AmberClassic.git",
+    "dateModified": "2024-12-21",
+    "description": "Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community; see our history page and our contributors page for more information.\nThe term \"Amber\" refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules; these force fields are in the public domain, and are used in a variety of simulation programs. Second, it is a package of molecular simulation programs which includes source code and demos.\nAmber is distributed in two parts: AmberTools25 and Amber24. ",
+    "downloadUrl": "https://github.com/Amber-MD/AmberClassic/archive/refs/tags/v1.0.tar.gz",
+    "keywords": "molecular-dynamics",
+    "license": "https://spdx.org/licenses/GPL-2.0",
+    "name": "  amber",
+    "programmingLanguage": [
+        "C++",
+        "C",
+        "Fortran",
+        "Makefile",
+        "HTML",
+        "Shell"
+    ],
+    "relatedLink": "https://ambermd.org/",
+    "version": "1.0",
+    "referencePublication": "https://doi.org/10.1016/0010-4655(95)00041-D"
+}

data/normalization/SOFTNAME/charmm-gui/codemeta.json

@@ -0,0 +1,54 @@
+{
+    "@context": "https://w3id.org/codemeta/3.0",
+    "type": "SoftwareSourceCode",
+    "applicationCategory": "molecular dynamics",
+    "author": [
+        {
+            "id": "https://orcid.org/0000-0002-4104-6473",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Chemistry, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047"
+            },
+            "familyName": "Jo",
+            "givenName": "Sunhwan "
+        },
+        {
+            "id": "_:author_2",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047"
+            },
+            "familyName": "Kim",
+            "givenName": "Taehoon "
+        },
+        {
+            "id": "_:author_3",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Chemistry, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047"
+            },
+            "familyName": "Iyer",
+            "givenName": "Vidyashankara G. "
+        },
+        {
+            "id": "_:author_4",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047"
+            },
+            "familyName": "Im",
+            "givenName": "Wonpil "
+        }
+    ],
+    "codeRepository": "https://github.com/charmm-gui",
+    "dateModified": "2022-07-00",
+    "description": "Since its original development in 2006, CHARMM-GUI has proven to be an ideal web-based platform to interactively build complex systems and prepare their inputs with well-established and reproducible simulation protocols for state-of-the-art molecular simulations using widely used simulation packages such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, Tinker, LAMMPS, Desmond, and OpenMM. The CHARMM-GUI development project has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of molecular simulation systems in Input Generator. Many original modules were developed as an in-house effort, but we have established close collaborations with the developers of CHARMM and other MD simulation packages for addition of newer modules.",
+    "name": "charmm-gui",
+    "relatedLink": "https://www.charmm-gui.org/",
+    "version": "Version 3.8",
+    "referencePublication": "https://doi.org/10.1002/jcc.20945"
+}

data/normalization/SOFTNAME/espresso++/codemeta.json

@@ -0,0 +1,124 @@
+{
+    "@context": "https://w3id.org/codemeta/3.0",
+    "type": "SoftwareSourceCode",
+    "applicationCategory": "molecular dynamics",
+    "author": [
+        {
+            "id": "_:author_1",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany"
+            },
+            "familyName": "Halverson",
+            "givenName": "Jonathan D."
+        },
+        {
+            "id": "_:author_2",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany"
+            },
+            "familyName": "Brandes",
+            "givenName": "Thomas"
+        },
+        {
+            "id": "https://orcid.org/0000-0002-0189-7935",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany"
+            },
+            "familyName": "Lenz",
+            "givenName": "Olaf"
+        },
+        {
+            "id": "_:author_4",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany"
+            },
+            "familyName": "Arnold",
+            "givenName": "Axel "
+        },
+        {
+            "id": "https://orcid.org/0000-0003-2313-7379",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany"
+            },
+            "familyName": "Starchenko",
+            "givenName": " Vitaliy  "
+        },
+        {
+            "id": "_:author_6",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany"
+            },
+            "familyName": "Kremer",
+            "givenName": "Kurt"
+        },
+        {
+            "id": "_:author_7",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia"
+            },
+            "familyName": "Bevc",
+            "givenName": "Staš  "
+        },
+        {
+            "id": "_:author_8",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany"
+            },
+            "familyName": "Stuehn",
+            "givenName": "Torsten"
+        },
+        {
+            "id": "https://orcid.org/0000-0003-1480-6745",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany"
+            },
+            "familyName": "Reith",
+            "givenName": "Dirk  "
+        }
+    ],
+    "codeRepository": "https://github.com/espressopp/espressopp.git",
+    "dateModified": "2024-01-25",
+    "description": "codecov\n\nESPResSo++ is an extensible, flexible, fast and parallel simulation software for soft matter research. It is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research. ESPResSo and ESPResSo++ have common roots and share parts of the developer/user community. However their development is independent and they are different software packages. ",
+    "downloadUrl": "https://github.com/espressopp/espressopp/archive/refs/tags/v3.1.0.tar.gz",
+    "keywords": [
+        "python",
+        "c-plus-plus",
+        "analysis",
+        "devtools",
+        "espresso",
+        "method",
+        "algorithm-challenges",
+        "adress",
+        "hpc-applications",
+        "lattice-boltzmann",
+        "algorithmic"
+    ],
+    "license": "https://spdx.org/licenses/GPL-3.0",
+    "name": " espressopp ",
+    "programmingLanguage": [
+        "C++",
+        "Python"
+    ],
+    "relatedLink": "http://www.espresso-pp.de/",
+    "version": "v3.1.0",
+    "issueTracker": "https://github.com/espressopp/espressopp/issues",
+    "referencePublication": "https://doi.org/10.1016/j.cpc.2012.12.004"
+}

data/normalization/SOFTNAME/gromacs/codemeta.json

@@ -0,0 +1,57 @@
+{
+    "@context": "https://w3id.org/codemeta/3.0",
+    "type": "SoftwareSourceCode",
+    "applicationCategory": "molecular dynamics",
+    "author": [
+        {
+            "id": "_:author_1",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Bioson Research Institute and Laboratory of Biophysical Chemistry, The University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands"
+            },
+            "familyName": "Berendsen",
+            "givenName": "Herman J.C. "
+        },
+        {
+            "id": "_:author_2",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Bioson Research Institute and Laboratory of Biophysical Chemistry, The University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands"
+            },
+            "familyName": "van der Spoel",
+            "givenName": "David "
+        },
+        {
+            "id": "_:author_3",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Bioson Research Institute and Laboratory of Biophysical Chemistry, The University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands"
+            },
+            "familyName": "van Drunen",
+            "givenName": "Rudi"
+        }
+    ],
+    "codeRepository": "https://github.com/gromacs/gromacs.git",
+    "dateModified": "2026-03-26",
+    "datePublished": "1995-09-02",
+    "description": "GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles and is a community-driven project.",
+    "downloadUrl": "https://ftp.gromacs.org/gromacs/gromacs-2026.1.tar.gz",
+    "license": "https://spdx.org/licenses/LGPL-2.1",
+    "name": "gromacs",
+    "operatingSystem": "Unix",
+    "programmingLanguage": [
+        "C++",
+        "Cmake",
+        "Python",
+        "Cuda",
+        "C",
+        "Shell"
+    ],
+    "relatedLink": "https://www.gromacs.org/",
+    "version": "2026.1",
+    "issueTracker": "https://gitlab.com/gromacs/gromacs/-/issues",
+    "referencePublication": "DOI:10.1016/0010-4655(95)00042-E"
+}

data/normalization/SOFTNAME/lammps/codemeta.json

@@ -0,0 +1,45 @@
+{
+    "@context": "https://w3id.org/codemeta/3.0",
+    "type": "SoftwareSourceCode",
+    "applicationCategory": "molecular dynamics",
+    "author": [
+        {
+            "id": "https://orcid.org/0000-0003-2446-8209",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Parallel Computational Sciences Department 1421, MS 1111, Sandia National Laboratories, Albuquerque, New Mexico 87185-1111"
+            },
+            "familyName": "Plimpton",
+            "givenName": "Steven J. "
+        }
+    ],
+    "codeRepository": "https://github.com/lammps/lammps.git",
+    "dateModified": "2026-03-30",
+    "datePublished": "2002-05-25",
+    "description": "LAMMPS is a classical molecular dynamics simulation code designed to\nrun efficiently on parallel computers. ",
+    "downloadUrl": "https://download.lammps.org/tars/lammps.tar.gz",
+    "funder": {
+        "type": "Organization",
+        "name": " US Department of Energy"
+    },
+    "keywords": [
+        "simulation",
+        "molecular-dynamics",
+        "lammps",
+        "kokkos"
+    ],
+    "license": "https://spdx.org/licenses/GPL-2.0",
+    "name": "lammps",
+    "programmingLanguage": [
+        "C++",
+        "Tcl",
+        "C",
+        "Cuda",
+        "Python",
+        "CMake"
+    ],
+    "relatedLink": "http://www.lammps.org/",
+    "issueTracker": "https://github.com/lammps/lammps/issues",
+    "referencePublication": "https://doi.org/10.1557/JMR.1995.1589"
+}