{ "_id": "6a1f15a5b401979e7341e5f9", "Package": "metadynminer", "Type": "Package", "Title": "Tools to Read, Analyze and Visualize Metadynamics HILLS Files\nfrom 'Plumed'", "Version": "0.1.7", "Date": "2022-04-12", "Authors@R": "person(\"Vojtech\", \"Spiwok\", email = \"spiwokv@vscht.cz\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8108-2033\"))", "Description": "Metadynamics is a state of the art biomolecular simulation\ntechnique. 'Plumed' Tribello, G.A. et al. (2014)\n program makes it possible to\nperform metadynamics using various simulation codes. The\nresults of metadynamics done in 'Plumed' can be analyzed by\n'metadynminer'. The package 'metadynminer' reads 1D and 2D\nmetadynamics hills files from 'Plumed' package. It uses a fast\nalgorithm by Hosek, P. and Spiwok, V. (2016)\n to calculate a free energy\nsurface from hills. Minima can be located and plotted on the\nfree energy surface. Transition states can be analyzed by\nNudged Elastic Band method by Henkelman, G. and Jonsson, H.\n(2000) . Free energy surfaces, minima\nand transition paths can be plotted to produce publication\nquality images.", "LazyData": "true", "License": "GPL-3", "RoxygenNote": "6.1.0", "URL": "https://metadynamics.cz/metadynminer/", "Repository": "https://spiwokv.r-universe.dev", "Date/Publication": "2023-11-28 20:40:21 UTC", "RemoteUrl": "https://github.com/spiwokv/metadynminer", "RemoteRef": "HEAD", "RemoteSha": "026be749a773c8e31c156b8a5d89db2b01839d75", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-17 06:32:30 UTC", "User": "root" }, "Author": "Vojtech Spiwok [aut, cre] (ORCID:\n)", "Maintainer": "Vojtech Spiwok ", "MD5sum": "cb2a7f4e23a5a67adf8bc5926e4918a1", "_user": "spiwokv", "_type": "src", "_file": "metadynminer_0.1.7.tar.gz", "_fileid": "a7b7065032f782071ab043a4f93f1de9898ad25afaf0fa5a6ea8280396104352", "_filesize": 1399865, "_sha256": "a7b7065032f782071ab043a4f93f1de9898ad25afaf0fa5a6ea8280396104352", "_created": "2026-05-17T06:32:30.000Z", "_published": "2026-06-02T17:40:53.399Z", "_distro": "noble", "_jobs": [ { "job": 79134348732, "time": 162, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7040043693" }, { "job": 79134348410, "time": 162, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7040043665" }, { "job": 79134349126, "time": 144, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7040041644" }, { "job": 79134349047, "time": 165, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7040043963" }, { "job": 79134349257, "time": 170, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7040042299" }, { "job": 79134349228, "time": 457, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7040069478" }, { "job": 79134348451, "time": 162, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7040040066" }, { "job": 79134348685, "time": 318, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7040057539" }, { "job": 79134348005, "time": 145, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7040026867" }, { "job": 79134347847, "time": 92, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7365384699" }, { "job": 79134349035, "time": 155, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7040042918" }, { "job": 79134349006, "time": 151, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7040042517" }, { "job": 79134348768, "time": 166, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7040044164" } ], "_buildurl": "https://github.com/r-universe/spiwokv/actions/runs/25983537720", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/spiwokv/metadynminer", "_commit": { "id": "026be749a773c8e31c156b8a5d89db2b01839d75", "author": "Vojtech Spiwok ", "committer": "GitHub ", "message": "Update minimaandpaths.R\n\nBased on https://github.com/spiwokv/metadynminer/issues/11", "time": 1701204021 }, "_maintainer": { "name": "Vojtech Spiwok", "email": "spiwokv@vscht.cz", "login": "spiwokv", "description": "", "uuid": 8507616, "orcid": "0000-0001-8108-2033" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "spiwokv", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_stars": 40, "_contributors": [ { "user": "spiwokv", "count": 598, "uuid": 8507616 } ], "_userbio": { "uuid": 8507616, "type": "user", "name": "Vojtech Spiwok" }, "_downloads": { "count": 211, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/metadynminer" }, "_devurl": "https://github.com/spiwokv/metadynminer", "_searchresults": 50, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/metadynminer.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/spiwokv/metadynminer", "_realowner": "spiwokv", "_cranurl": true, "_releases": [ { "version": "0.1.2", "date": "2018-09-20" }, { "version": "0.1.3", "date": "2018-11-05" }, { "version": "0.1.4", "date": "2019-03-13" }, { "version": "0.1.5", "date": "2019-07-18" }, { "version": "0.1.6", "date": "2019-08-20" }, { "version": "0.1.7", "date": "2022-04-14" } ], "_exports": [ "emptyhills", "feprof", "fes", "fes2", "fes2d21d", "fesminima", "fespoint", "linesonfes", "neb", "oneminimum", "plotheights", "pointsonfes", "prob", "read.hills", "read.plumed" ], "_datasets": [ { "name": "acealanme", "title": "Hills from 30 ns metadynamics of AceAlaNme in water with two collective variables", "object": "acealanme", "class": [ "hillsfile" ], "fields": [], "table": false, "tojson": false }, { "name": "acealanme1d", "title": "Hills from 30 ns metadynamics of AceAlaNme in water with one collective variable", "object": "acealanme1d", "class": [ "hillsfile" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "acealanme", "title": "Hills from 30 ns metadynamics of AceAlaNme in water with two collective variables", "topics": [ "acealanme" ] }, { "page": "acealanme1d", "title": "Hills from 30 ns metadynamics of AceAlaNme in water with one collective variable", "topics": [ "acealanme1d" ] }, { "page": "emptyhills", "title": "Generate empty HILLS from Plumed", "topics": [ "emptyhills" ] }, { "page": "feprof", "title": "Calculate free energy profile for minima object (generic function for 'metadynminer' and 'metadynminer3d')", "topics": [ "feprof" ] }, { "page": "feprof.minima", "title": "Calculate free energy profile for minima object", "topics": [ "feprof.minima" ] }, { "page": "fes", "title": "Calculate free energy surface by Bias Sum algorithm (generic function for 'metadynminer' and 'metadynminer3d')", "topics": [ "fes" ] }, { "page": "fes.hillsfile", "title": "Calculate free energy surface by Bias Sum algorithm", "topics": [ "fes.hillsfile" ] }, { "page": "fes2", "title": "Calculate free energy surface by conventional algorithm (generic function for 'metadynminer' and 'metadynminer3d')", "topics": [ "fes2" ] }, { "page": "fes2.hillsfile", "title": "Calculate free energy surface by conventional algorithm", "topics": [ "fes2.hillsfile" ] }, { "page": "fes2d21d", "title": "Calculate 1D free energy surface from hillsfile object", "topics": [ "fes2d21d" ] }, { "page": "fesminima", "title": "Find free energy minima in the fes object (generic function for 'metadynminer' and 'metadynminer3d')", "topics": [ "fesminima" ] }, { "page": "fesminima.fes", "title": "Find free energy minima in the fes object", "topics": [ "fesminima.fes" ] }, { "page": "fespoint", "title": "Calculate free energy at given point in the CV space (generic function for 'metadynminer' and 'metadynminer3d')", "topics": [ "fespoint" ] }, { "page": "fespoint.hillsfile", "title": "Calculate free energy at given point in the CV space", "topics": [ "fespoint.hillsfile" ] }, { "page": "head.hillsfile", "title": "Print first n lines of hillsfile", "topics": [ "head.hillsfile" ] }, { "page": "lines.fes", "title": "Plots 1D free energy surface object as lines", "topics": [ "lines.fes" ] }, { "page": "lines.hillsfile", "title": "Plot lines for hillsfile object", "topics": [ "lines.hillsfile" ] }, { "page": "lines.nebpath", "title": "Plot lines for Nudged Elastic Band", "topics": [ "lines.nebpath" ] }, { "page": "linesonfes", "title": "Plot lines for Nudged Elastic Band projected onto free energy surface", "topics": [ "linesonfes" ] }, { "page": "max.fes", "title": "Calculate maximum of free energy surface", "topics": [ "max.fes" ] }, { "page": "min.fes", "title": "Calculate minimum of free energy surface", "topics": [ "min.fes" ] }, { "page": "neb", "title": "Find transition path on free energy surface by Nudged Elastic Band method", "topics": [ "neb" ] }, { "page": "oneminimum", "title": "Creates one ad hoc free energy minimum for a fes object (generic function for 'metadynminer' and 'metadynminer3d')", "topics": [ "oneminimum" ] }, { "page": "oneminimum.fes", "title": "Creates one ad hoc free energy minimum for a fes object", "topics": [ "oneminimum.fes" ] }, { "page": "plot.fes", "title": "Plot free energy surface object", "topics": [ "plot.fes" ] }, { "page": "plot.hillsfile", "title": "Plot hillsfile object", "topics": [ "plot.hillsfile" ] }, { "page": "plot.minima", "title": "Plot minima object", "topics": [ "plot.minima" ] }, { "page": "plot.nebpath", "title": "Plot Nudged Elastic Band", "topics": [ "plot.nebpath" ] }, { "page": "plot.profiles", "title": "Plot free energy profile", "topics": [ "plot.profiles" ] }, { "page": "plotheights", "title": "Plot evolution of heights of hills (generic function for 'metadynminer' and 'metadynminer3d')", "topics": [ "plotheights" ] }, { "page": "plotheights.hillsfile", "title": "Plot evolution of heights of hills in hillsfile object", "topics": [ "plotheights.hillsfile" ] }, { "page": "points.fes", "title": "Plots 1D free energy surface object as points", "topics": [ "points.fes" ] }, { "page": "points.hillsfile", "title": "Plot points for hillsfile object", "topics": [ "points.hillsfile" ] }, { "page": "points.nebpath", "title": "Plot points for Nudged Elastic Band", "topics": [ "points.nebpath" ] }, { "page": "pointsonfes", "title": "Plot points for Nudged Elastic Band projected onto free energy surface", "topics": [ "pointsonfes" ] }, { "page": "print.fes", "title": "Print dimensionality, minimum and maximum of free energy surface", "topics": [ "print.fes" ] }, { "page": "print.hillsfile", "title": "Print hillsfile", "topics": [ "print.hillsfile" ] }, { "page": "print.minima", "title": "Print minima object", "topics": [ "print.minima" ] }, { "page": "print.nebpath", "title": "Print Nudged Elastic Band minima", "topics": [ "print.nebpath" ] }, { "page": "print.profiles", "title": "Print profiles object", "topics": [ "print.profiles" ] }, { "page": "prob", "title": "Calculate probability of free energy surface", "topics": [ "prob" ] }, { "page": "read.hills", "title": "Read HILLS from Plumed", "topics": [ "read.hills" ] }, { "page": "read.plumed", "title": "Read 1D or 2D free energy surface from PLUMED sum_hills", "topics": [ "read.plumed" ] }, { "page": "summary.fes", "title": "Print summary of free energy surface", "topics": [ "summary.fes" ] }, { "page": "summary.hillsfile", "title": "Print summary for hillsfile", "topics": [ "summary.hillsfile" ] }, { "page": "summary.minima", "title": "Print minima object summary", "topics": [ "summary.minima" ] }, { "page": "summary.nebpath", "title": "Print summary for Nudged Elastic Band", "topics": [ "summary.nebpath" ] }, { "page": "summary.profiles", "title": "Print summary for free energy profile", "topics": [ "summary.profiles" ] }, { "page": "tail.hillsfile", "title": "Print last n lines of hillsfile", "topics": [ "tail.hillsfile" ] } ], "_readme": "https://github.com/spiwokv/metadynminer/raw/HEAD/README.md", "_rundeps": [ "Rcpp" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 5.477121254719663, "_indexed": true, "_nocasepkg": "metadynminer", "_universes": [ "spiwokv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.7", "date": "2026-05-17T06:34:50.000Z", "distro": "noble", "arch": "aarch64", "commit": "026be749a773c8e31c156b8a5d89db2b01839d75", "fileid": "8752123a36f47c1d1a5f9d23160efa4e574ca2aad9be5508027db56bedd3b2f6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/spiwokv/actions/runs/25983537720" }, { "r": "4.7.0", "os": "linux", 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