{ "_id": "6a1eeb01b401979e734121be", "Package": "metadynminer3d", "Type": "Package", "Title": "Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files\nfrom 'Plumed'", "Version": "0.0.2", "Date": "2022-04-14", "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. As an addendum,\n'metadynaminer3d' is used to visualize 3D hills. 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. Free energy surfaces and minima can be\nplotted to produce publication quality images.", "LazyData": "true", "License": "GPL-3", "RoxygenNote": "6.1.0", "URL": "https://metadynamics.cz/metadynminer3d/", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-19 09:55:39 UTC", "User": "root" }, "Author": "Vojtech Spiwok [aut, cre]\n()", "Maintainer": "Vojtech Spiwok ", "Config/pak/sysreqs": "cmake libfreetype6-dev libglu1-mesa-dev make\ntexlive libpng-dev libuv1-dev libgl1-mesa-dev zlib1g-dev", "Repository": "https://spiwokv.r-universe.dev", "Date/Publication": "2022-04-14 13:32:34 UTC", "RemoteUrl": "https://github.com/cran/metadynminer3d", "RemoteRef": "HEAD", "RemoteSha": "f99f72b05a6806e54862535cb807a42490a038fe", "MD5sum": "977df10c8e8968d688df8b163ff23f8a", "_user": "spiwokv", "_type": "src", "_file": "metadynminer3d_0.0.2.tar.gz", "_fileid": "59d8d8b3e32ff1bd43914dcb95682e26cddc23a09502efadd971a7d8291031eb", "_filesize": 1075432, "_sha256": 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"f99f72b05a6806e54862535cb807a42490a038fe", "author": "Vojtech Spiwok ", "committer": "cran-robot ", "message": "version 0.0.2\n", "time": 1649943154 }, "_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": "metadynminer", "role": "Depends" }, { "package": "rgl", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "misc3d", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "spiwokv", "count": 2, "uuid": 8507616 } ], "_userbio": { "uuid": 8507616, "type": "user", "name": "Vojtech Spiwok" }, "_downloads": { "count": 236, "source": 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free energy profile for minima3d object", "topics": [ "feprof.minima3d" ] }, { "page": "fes.hillsfile3d", "title": "Calculate 3D free energy surface by Bias Sum algorithm", "topics": [ "fes.hillsfile3d" ] }, { "page": "fes2.hillsfile3d", "title": "Calculate 3D free energy surface by conventional algorithm", "topics": [ "fes2.hillsfile3d" ] }, { "page": "fesminima.fes3d", "title": "Find free energy minima in the fes3d object", "topics": [ "fesminima.fes3d" ] }, { "page": "fespoint.hillsfile3d", "title": "Calculate free energy at given point in the CV space", "topics": [ "fespoint.hillsfile3d" ] }, { "page": "head.hillsfile3d", "title": "Print first n lines of hillsfile3d", "topics": [ "head.hillsfile3d" ] }, { "page": "max.fes3d", "title": "Calculate maximum of 3D free energy surface", "topics": [ "max.fes3d" ] }, { "page": "min.fes3d", "title": "Calculate minimum of 3D free energy surface", "topics": [ "min.fes3d" ] }, { "page": "oneminimum.fes3d", "title": "Creates one ad hoc 3D free energy minimum for a fes object", "topics": [ "oneminimum.fes3d" ] }, { "page": "plot.fes3d", "title": "Plot 3D free energy surface object", "topics": [ "plot.fes3d" ] }, { "page": "plot.hillsfile3d", "title": "Plot hillsfile3d object", "topics": [ "plot.hillsfile3d" ] }, { "page": "plot.minima3d", "title": "Plot minima3d object", "topics": [ "plot.minima3d" ] }, { "page": "plotheights.hillsfile3d", "title": "Plot evolution of heights of hills in hillsfile3d object", "topics": [ "plotheights.hillsfile3d" ] }, { "page": "print.fes3d", "title": "Print minimum and maximum of 3D free energy surface", "topics": [ "print.fes3d" ] }, { "page": "print.hillsfile3d", "title": "Print hillsfile3d", "topics": [ "print.hillsfile3d" ] }, { "page": "print.minima3d", "title": "Print minima3d object", "topics": [ "print.minima3d" ] }, { "page": "read.hills3d", "title": "Read 3D HILLS from Plumed", "topics": [ "read.hills3d" ] }, { "page": "read.plumed3d", "title": "Read 3D free energy surface from PLUMED sum_hills", "topics": [ "read.plumed3d" ] }, { "page": "summary.fes3d", "title": "Print summary of 3D free energy surface", "topics": [ "summary.fes3d" ] }, { "page": "summary.hillsfile3d", "title": "Print summary for hillsfile3d", "topics": [ "summary.hillsfile3d" ] }, { "page": "summary.minima3d", "title": "Print minima3d object summary", "topics": [ "summary.minima3d" ] }, { "page": "tail.hillsfile3d", "title": "Print last n lines of hillsfile3d", "topics": [ "tail.hillsfile3d" ] } ], "_readme": "https://github.com/cran/metadynminer3d/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cli", "digest", "evaluate", "fastmap", "fontawesome", "fs", "highr", "htmltools", "htmlwidgets", "jquerylib", "jsonlite", "knitr", "lifecycle", "magrittr", "memoise", "metadynminer", "mime", "misc3d", "R6", "rappdirs", "Rcpp", "rgl", "rlang", "rmarkdown", "sass", "tinytex", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", 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