metadynminer3d

0.0.2

Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed'

0packages depend

2.7Kdownloads / year

53.6%test coverage

12/13checks pass

Overview

About

Maintained by Vojtech SpiwokFirst published 2019-07-282 releasesCRAN page ↗

Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) doi:10.1016/j.cpc.2013.09.018 program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. As an addendum, 'metadynaminer3d' is used to visualize 3D hills. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) doi:10.1016/j.cpc.2015.08.037 to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Free energy surfaces and minima can be plotted to produce publication quality images.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("metadynminer3d", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-metadynminer3d

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-metadynminer3d

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-metadynminer3d

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.3 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.14

53.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 215 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 71%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #15,612 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

16630 days

67890 days

2.7K1 year

Compare downloads with other packages →

Also on395 r2u1 autocran

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.3.0metadynminer rgl

Imports (2)

Rcpp misc3d

LinkingTo (1)

Rcpp

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Vojtech Spiwok

Author, Maintainer

Authors (1)

Vojtech Spiwok

Author, Maintainer

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.0.2Latest
2022-04-14 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.0.1
2019-07-28
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-07-28
Total releases: 2 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.3.0
Bundled data: 904 KB / 2 files
Download size: 929 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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