MDplot: Visualising Molecular Dynamics Analyses

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
https://github.com/MDplot/MDplot

View on CRAN

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.