MDplot: Visualising Molecular Dynamics Analyses
Version 1.0.0

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.

AuthorChristian Margreitter [aut, cre]
Date of publication2017-02-23 17:30:56
MaintainerChristian Margreitter <christian.margreitter@gmail.com>
LicenseGPL-3
Version1.0.0
URL https://github.com/MDplot/MDplot
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MDplot")

Popular man pages

dssp: DSSP summary plot for secondary structure elements (proteins)
hbond_ts: Plot hydrogen bond timeseries
load_hbond: Loading hydrogen bond data
noe: Plot NOE violations
ramachandran: Ramachandran plot for two dihedral angles
rmsd_average: Root-mean-square-deviation (RMSD) average plot
xrmsd: XRMSD plot in heatmap style
See all...

All man pages Function index File listing

Man pages

clusters: Cluster bar plot
clusters_ts: Cluster timeseries plot
dssp: DSSP summary plot for secondary structure elements (proteins)
dssp_ts: DSSP timeseries plot for secondary structure elements...
hbond: Plot hydrogen bond summary
hbond_ts: Plot hydrogen bond timeseries
load_clusters: Loading cluster information
load_clusters_ts: Loading timeseries cluster information
load_dssp: Load DSSP information
load_dssp_ts: Load DSSP timeseries
load_hbond: Loading hydrogen bond data
load_hbond_ts: Loading hydrogen bonds timeseries
load_noe: Loading NOE violations
load_ramchandran: Load dihedral information (Ramachandran plot input)
load_rmsd: Loading function for 'rmsd()'
load_rmsf: Loading function for 'rmsf()'
load_TIcurve: Loading function for thermodynamic integration function...
load_timeseries: Loading function for 'timeseries()'
load_xrmsd: Loading function for 'xrmsd()'
MDplot_argument-class: Arguments for bash script interface
MDplot-internal: Internal functions for 'MDplot'
noe: Plot NOE violations
ramachandran: Ramachandran plot for two dihedral angles
rmsd: Root-mean-square-deviation (RMSD) plot
rmsd_average: Root-mean-square-deviation (RMSD) average plot
rmsf: Root-mean-square-fluctuation (RMSF) plot
TIcurve: Thermodynamic integration plot
timeseries: General timeseries plotting function
translate_aminoacids: Function to translate between canonical and GROMOS amino acid...
xrmsd: XRMSD plot in heatmap style

Functions

MDplot_argument Man page
MDplot_argument-class Man page
TIcurve Man page Source code
averaging_dssp_summary Source code
calculate_mid Source code
clusters Man page Source code
clusters_ts Man page Source code
dssp Man page Source code
dssp_summary_multi Source code
dssp_ts Man page Source code
fill_bins Man page Source code
find_Nth_occurrence Man page Source code
getFiles Man page Source code
getListOfKeys Man page Source code
getValue Man page Source code
get_sign_digits Man page Source code
hbond Man page Source code
hbond_ts Man page Source code
integrate_curve Man page Source code
isKeySet Man page Source code
load_TIcurve Man page Source code
load_XPM Man page Source code
load_clusters Man page Source code
load_clusters_GROMACS Man page Man page Source code
load_clusters_ts Man page Source code
load_dssp Man page Source code
load_dssp_GROMACS Man page Source code
load_dssp_ts Man page Source code
load_hbond Man page Source code
load_hbond_ts Man page Source code
load_noe Man page Source code
load_ramachandran Man page Source code
load_rmsd Man page Source code
load_rmsf Man page Source code
load_timeseries Man page Source code
load_xrmsd Man page Source code
noe Man page Source code
parse_arguments Man page Source code
plot_segments Man page Source code
print_help Man page Source code
ramachandran Man page Source code
rmsd Man page Source code
rmsd_average Man page Source code
rmsf Man page Source code
setNumberDigits Man page Source code
split_AMBER_atomnames Man page Source code
split_GROMACS_atomnames Man page Source code
split_equidistant Man page Source code
testAllowed Man page Source code
testRequired Man page Source code
timeseries Man page Source code
translate_aminoacids Man page Source code
xrmsd Man page Source code

Files

inst
inst/CITATION
inst/bash
inst/bash/test.sh
inst/bash/MDplot_install.R
inst/bash/MDplot_bash.R
inst/bash/install.sh
inst/extdata
inst/extdata/TIcurve_fb_forward_example.txt.gz
inst/extdata/clusters_example_2_AMBER.txt.gz
inst/extdata/clusters_ts_example.txt.gz
inst/extdata/dssp_ts_example_AMBER.txt.gz
inst/extdata/noe_example_2.txt.gz
inst/extdata/noe_example_1.txt.gz
inst/extdata/dssp_example.txt.gz
inst/extdata/hbond_ts_example.txt.gz
inst/extdata/clusters_example.txt.gz
inst/extdata/xrmsd_example_GROMACS.xpm.gz
inst/extdata/hbond_example_GROMACS.txt.gz
inst/extdata/TIcurve_example.txt.gz
inst/extdata/dssp_example_GROMACS.txt.gz
inst/extdata/dssp_ts_example
inst/extdata/dssp_ts_example/3-Helix.out
inst/extdata/dssp_ts_example/4-Helix.out
inst/extdata/dssp_ts_example/Bend.out
inst/extdata/dssp_ts_example/Beta-Strand.out
inst/extdata/dssp_ts_example/Beta-Bridge.out
inst/extdata/dssp_ts_example/Turn.out
inst/extdata/dssp_ts_example/5-Helix.out
inst/extdata/clusters_ts_example_AMBER.txt.gz
inst/extdata/timeseries_example_1.txt.gz
inst/extdata/TIcurve_fb_backward_example.txt.gz
inst/extdata/clusters_example_GROMACS.txt.gz
inst/extdata/rmsf_example_GROMACS.txt.gz
inst/extdata/hbond_ts_example_AMBER.txt.gz
inst/extdata/rmsd_example_AMBER.txt.gz
inst/extdata/clusters_example_1_AMBER.txt.gz
inst/extdata/rmsf_example_2.txt.gz
inst/extdata/ramachandran_example.txt.gz
inst/extdata/hbond_ts_example_GROMACS.xpm.gz
inst/extdata/ramachandran_example_GROMACS.txt.gz
inst/extdata/rmsf_example_AMBER.txt.gz
inst/extdata/rmsf_example_1.txt.gz
inst/extdata/rmsd_example_2.txt.gz
inst/extdata/xrmsd_example_AMBER.txt.gz
inst/extdata/xrmsd_example.txt.gz
inst/extdata/hbond_example.txt.gz
inst/extdata/rmsd_example_GROMACS.txt.gz
inst/extdata/timeseries_example_2.txt.gz
inst/extdata/ramachandran_example_AMBER.txt.gz
inst/extdata/rmsd_example_1.txt.gz
inst/extdata/hbond_example_AMBER.txt.gz
NAMESPACE
NEWS
R
R/rmsd.R
R/clusters.R
R/xrmsd.R
R/helperclasses.R
R/hbond.R
R/helperfunctions.R
R/rmsf.R
R/dssp.R
R/ramachandran.R
R/timeseries.R
R/noe.R
R/TIcurve.R
MD5
DESCRIPTION
man
man/hbond_ts.Rd
man/load_rmsd.Rd
man/load_clusters.Rd
man/load_dssp_ts.Rd
man/translate_aminoacids.Rd
man/xrmsd.Rd
man/load_TIcurve.Rd
man/noe.Rd
man/load_dssp.Rd
man/load_rmsf.Rd
man/load_timeseries.Rd
man/load_clusters_ts.Rd
man/MDplot-internal.Rd
man/dssp_ts.Rd
man/clusters.Rd
man/rmsd_average.Rd
man/load_hbond.Rd
man/timeseries.Rd
man/load_hbond_ts.Rd
man/dssp.Rd
man/hbond.Rd
man/clusters_ts.Rd
man/MDplot_argument-class.Rd
man/ramachandran.Rd
man/load_xrmsd.Rd
man/TIcurve.Rd
man/rmsf.Rd
man/load_noe.Rd
man/load_ramchandran.Rd
man/rmsd.Rd
MDplot documentation built on May 20, 2017, 4:39 a.m.

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