MDplot: Visualise Molecular Dynamics Analyses

MDplot is an R package that allows automated plot generation directly from the output produced by Molecular Dynamics (MD) engines. Currently, loading functions for GROMOS, GROMACS and AMBER type of output is provided. See the the MDplot publication for a full description.

Call from within bash script

An Rscript interface is provided, allowing to set most options:

#!/bin/bash
# analysis program (e.g. clustering algorithm)
Rscript MDplot_bash.R clusters \
                 files=clusters_example.txt.gz \
                 title="clust" size=900,900 \
                 outformat=pdf \
                 clustersNumber=7 \
                 ...

A script including many examples is available in the package (path: "MDplot/inst/bash/test.sh").

Additional information and examples

Loading functions parse input and translate it into data structures that can be read by the respective plotting functions.

dssp( load_dssp( system.file( "extdata/dssp_example.txt.gz",
                 package = "MDplot" ) ) )

The type of molecular dynamics engine used can be set by parameter mdEngine for both the bash interface and the call from within R:

xrmsd( load_xrmsd( system.file( "extdata/xrmsd_example_AMBER.txt.gz",
                                package = "MDplot" ),
                   mdEngine = "AMBER" ),
       rmsdUnit = "angstrom" )

Example pictures

New in the latest version

Version: 1.1.3 Date: 2022-03-23

• added interface option for limiting the range of 'xrmsd()'

Version: 1.1.2 Date: 2021-05-18

• added more interface options for 'clusters_ts()'

Version: 1.1.1 Date: 2019-08-25

• changed selection of hydrogen bond IDs for 'hbond_ts()'
• fixed typo in 'hbond_ts()' interface ("plotOccurences")
• fixed bug in 'load_hbond_ts()' when loading AMBER-style input

Version: 1.0.1 Date: 2017-07-04

• fixed some typos in the manual pages
• added vignette (publication)
• added special input support for function "load_timeseries()" to be able to load multi-column timeseries data

Version: 1.0.0 Date: 2017-02-24

• fixed issue with proper residue display when sub-selection was done in function 'dssp()'
• fixed issue with bin-expansion in function 'load_noe()'
• removed unnecessary input parameters from several functions
• added 'stride' to function 'load_dssp_ts()'
• changed parameters of function 'load_rmsf()'
• renamed functions 'load_dssp_summary()' and 'dssp_summary()' into 'load_dssp()' and 'dssp()', respectively
• added additional box lines to function 'ramachandran()' for 'plotType = "comic"'
• changed colour coding to be more consistent in function 'ramachandran()'
• added 'barScaleFactor' to function 'dssp_ts()' to account for the possibility that very small peptides might be plotted
• added GROMACS support for functions: 'load_dssp()', 'load_dssp_ts()', 'load_hbond()', 'load_hbond_ts()', 'load_clusters()', 'load_clusters_ts()', 'load_ramachandran()' and 'load_xrmsd()'
• added AMBER support for functions: 'load_rmsd()', 'load_ramachandran()', 'load_dssp()', 'load_dssp_ts()', 'load_hbond()', 'load_clusters()', 'load_clusters_ts()', 'load_rmsf()' and 'load_xrmsd()'
• added function 'load_XPM()' to load "X PixMap" data as commonly produced by GROMACS
• added functions 'find_Nth_occurrence()', 'split_GROMACS_atomnames()' and 'split_AMBER_atomnames()' to the collection of helper functions
• added parameter 'showMultipleInteractions' to function 'hbond()' to represent multi- or hybrid hydrogen bond donors and acceptors
• fixed time-axis issue in functions 'rmsd()' and 'rmsf()'
• changed all names on example input files according to convention

Version: 0.3.1 Date: 2016-04-28

• added 'printErrors' flag to function 'TIcurve()'
• added 'errorBarThreshold' flag to function 'TIcurve()'
• fixed bug in function 'ramachandran()' for type "fancy"
• added return information to functions where appropriate
• fixed 'xrmsd()' ellipsis
• changed some phrases and the title

Version: 0.3.0 Date: 2016-02-15

• added multiple vector selection by hydrogen bond identifiers to function 'hbond_ts()'
• added argument 'printValues' functionality to function 'TIcurve()'
• removed hard-coding for the filenames of function 'load_dssp_ts()'
• included new functions 'load_timeseries()' and 'timeseries()'
• added argument 'legendPosition' to functions 'rmsd()' and 'rmsf()'
• added labels for axes for function 'xrmsd()'
• renamed title ("Analyses") to comply with the publication title

Outlook (probably)

1. support for other MD engines such as NAMD, CHARMM, ...
2. support DISICL input (both C++ and phyton implementation)
3. provide more plotting
4. support multiple rmsd average curves at the same time