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< 8102 /a> and AMBER type of output is provided. See the the MDplot publication for a full description.
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").
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" )
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
- support for other MD engines such as NAMD, CHARMM, ...
- support DISICL input (both C++ and phyton implementation)
- provide more plotting
- support multiple rmsd average curves at the same time