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.

Author
Christian Margreitter [aut, cre]
Date of publication
2016-04-28 15:55:21
Maintainer
Christian Margreitter <christian.margreitter@gmail.com>
License
GPL-3
Version
0.3.1
URLs

View on CRAN

Man pages

clusters
Cluster bar plot
clusters_ts
Cluster timeseries plot
dssp_summary
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_summary
Load DSSP information
load_dssp_ts
Load DSSP timeseries
load_hbond
Loading hydrogen bonds
load_hbond_ts
Loading hydrogen bonds timeseries
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'
ramachandran
Ramachandran plot for two dihedral angles
rmsd
Root-mean-square-deviation plot
rmsf
Root-mean-square-fluctuation 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

Files in this package

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/3-Helix.out
MDplot/inst/extdata/TIcurve_fb_forward_example.txt.gz
MDplot/inst/extdata/clusters_ts_example.txt.gz
MDplot/inst/extdata/rmsf1_example.txt.gz
MDplot/inst/extdata/4-Helix.out
MDplot/inst/extdata/timeseries_example.txt.gz
MDplot/inst/extdata/Bend.out
MDplot/inst/extdata/hbond_ts_example.txt.gz
MDplot/inst/extdata/clusters_example.txt.gz
MDplot/inst/extdata/TIcurve_example.txt.gz
MDplot/inst/extdata/Beta-Strand.out
MDplot/inst/extdata/TIcurve_fb_backward_example.txt.gz
MDplot/inst/extdata/Beta-Bridge.out
MDplot/inst/extdata/rmsd1_example.txt.gz
MDplot/inst/extdata/ramachandran_example.txt.gz
MDplot/inst/extdata/Turn.out
MDplot/inst/extdata/5-Helix.out
MDplot/inst/extdata/dssp_summary_example.txt.gz
MDplot/inst/extdata/rmsd2_example.txt.gz
MDplot/inst/extdata/rmsf2_example.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/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/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/dssp_summary.Rd
MDplot/man/load_TIcurve.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/load_hbond.Rd
MDplot/man/timeseries.Rd
MDplot/man/load_hbond_ts.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_ramchandran.Rd
MDplot/man/load_dssp_summary.Rd
MDplot/man/rmsd.Rd