CRAN
MDplot 1.0.1
Visualising Molecular Dynamics Analyses
Released Jul 4, 2017 by Christian Margreitter
Dependencies
RColorBrewer 1.1-2 MASS 7.3-50 gplots 3.0.1 gtools 3.5.0
Provides automatization for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis. Currently able to load GROMOS, GROMACS and AMBER formats, respectively.
Installation
Maven
This package can be included as a dependency from a Java or Scala project by including
the following your project's pom.xml file.
Read more
about embedding Renjin in JVM-based projects.
<dependencies>
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>MDplot</artifactId>
<version>1.0.1-b14</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>bedatadriven</id>
<name>bedatadriven public repo</name>
<url>https://nexus.bedatadriven.com/content/groups/public/</url>
</repository>
</repositories>
Renjin CLI
If you're using Renjin from the command line, you load this library by invoking:
library('org.renjin.cran:MDplot')
Test Results
This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.
- TIcurve-examples
- clusters-examples
- clusters_ts-examples
- dssp-examples
- dssp_ts-examples
- hbond-examples
- hbond_ts-examples
- load_TIcurve-examples
- load_clusters-examples
- load_clusters_ts-examples
- load_dssp-examples
- load_dssp_ts-examples
- load_hbond-examples
- load_hbond_ts-examples
- load_noe-examples
- load_ramchandran-examples
- load_rmsd-examples
- load_rmsf-examples
- load_timeseries-examples
- load_xrmsd-examples
- noe-examples
- ramachandran-examples
- rmsd-examples
- rmsd_average-examples
- rmsf-examples
- timeseries-examples
- translate_aminoacids-examples
- xrmsd-examples