Package ‘MDplot’

July 4, 2017
Version 1.0.1
Date 2017-07-04
Title Visualising Molecular Dynamics Analyses
Depends R (>= 3.0.0), methods, MASS, RColorBrewer, gplots, gtools
Suggests R.rsp
VignetteBuilder R.rsp
Description
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.
License GPL-3
URL https://github.com/MDplot/MDplot
LazyLoad yes
Author Christian Margreitter [aut, cre], Chris Oostenbrink [aut]
Maintainer Christian Margreitter <[email protected]>
NeedsCompilation no
Repository CRAN
Date/Publication 2017-07-04 20:26:53 UTC

R topics documented:
clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
clusters_ts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
dssp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
dssp_ts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
hbond . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
hbond_ts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
load_clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

1
2 clusters

load_clusters_ts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
load_dssp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
load_dssp_ts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
load_hbond . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
load_hbond_ts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
load_noe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
load_ramachandran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
load_rmsd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
load_rmsf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
load_TIcurve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
load_timeseries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
load_xrmsd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
MDplot_argument-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
noe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
ramachandran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
rmsd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
rmsd_average . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
rmsf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
TIcurve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
timeseries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
translate_aminoacids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
xrmsd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Index 36

clusters Cluster bar plot

Description
This function plots clusters over a set of trajectories as joint, coloured bar plots. The clusters are
sorted beginning with the most populated one in descending order.

Usage
clusters( clusters,
clustersNumber = NA,
legendTitle = "trajectories",
barePlot = FALSE,
... )

Arguments
clusters Matrix with clusters: trajectories are given in row-wise, clusters in column-wise
fashion as provided by load_clusters(), the associated loading function.
clustersNumber When specified, only these first clusters are shown.
legendTitle The title of the legend.
clusters_ts 3

barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value
Returns a nxm-matrix with n being the number of input trajectories and m the number of different
clusters. Each element in the matrix holds the number of snapshots, the respective cluster occurred
in the respective trajectory.

Author(s)
Christian Margreitter

Examples
# GROMOS (see load_clusters() for other input possibilities)
clusters( load_clusters( system.file( "extdata/clusters_example.txt.gz",
package = "MDplot" ) ) )

clusters_ts Cluster timeseries plot

Description
This function plots distributions between clusters over time. In the top sub-plot, the overall distri-
bution is given, while the timeseries is given at the bottom. The clusters are sorted beginning with
the most populated one and then in descending order. Selections can be made and clusters that are
not selected do also not appear in the timeseries plot (white areas).

Usage
clusters_ts( clustersDataTS,
clustersNumber = NA,
selectTraj = NA,
selectTime = NA,
timeUnit = NA,
snapshotsPerTimeInt = 1000,
... )

Arguments
clustersDataTS List of cluster information as provided by load_clusters_ts(), the associated
loading function.
clustersNumber Integer, specifying the number of clusters that is to be plotted.
selectTraj Vector of indices of trajectories that are to be plotted (as given in the input file).
selectTime Range of time in snapshots, which is to be plotted.
4 dssp

timeUnit Abbreviation of time unit.

snapshotsPerTimeInt
Specifies, how many snapshots make up one time unit.
... Additional arguments (ellipsis).

Value
Returns a summary (n+1)xm-matrix with n being the number of input trajectories and m the number
of different clusters (which have been plotted). Each element in the matrix holds the number of
snapshots, the respective cluster occured in the respective trajectory. In addition, the first line is the
overall summary counted over all trajectories.

Author(s)
Christian Margreitter

Examples
# GROMOS (see load_clusters_ts() for other input possibilities)
clusters_ts( load_clusters_ts( system.file( "extdata/clusters_ts_example.txt.gz",
package = "MDplot" ),
lengths = c( 4000, 4000, 4000, 4000, 4000, 4000 ) ),
clustersNumber = 7 )

dssp DSSP plot for secondary structure elements (proteins)

Description
Plots summary plot for secondary structure motifs based on the output of the widely used classifica-
tion program DSSP, which uses hydrogen bonds for classification. The default order is: "3-Helix",
"4-Helix", "5-Helix", "Bend", "Beta-Bridge", "Beta-Strand", "Turn" (depending on the input, not
all types might be included).

Usage
dssp( dsspData,
printLegend = FALSE,
useOwnLegend = FALSE,
elementNames = NA,
colours = NA,
showValues = NA,
showResidues = NA,
plotType = "dots",
selectedElements = NA,
barePlot = FALSE,
... )
dssp_ts 5

Arguments

dsspData Table containing the information on the secondary structure motifs.

printLegend If TRUE, a legend is printed on the right hand side of the plot.
useOwnLegend If FALSE, the names of the secondary structure elements are considered to be in
default order.
elementNames Vector of names for the secondary structure elements.
colours A vector of colours, that can be specified to replace the default ones.
showValues A vector of boundaries for the values (two elements).
showResidues A vector of boundaries for the residues (two elements).
plotType Either "dots", "curves" or "bars".
selectedElements
A vector of names of the elements selected for plotting.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value

Returns matrix, where the first column is the residue-number and the remaining ones denote sec-
ondary structure classes. Residues are given row-wise and values range from 0 to 100 percent.

Author(s)

Christian Margreitter

Examples
# GROMOS (see load_dssp() for other input possibilities)
dssp( load_dssp( system.file( "extdata/dssp_example.txt.gz",
package = "MDplot" ) ) )

dssp_ts DSSP timeseries plot for secondary structure elements (proteins)

Description

Plots time-series for secondary structure motifs in the context of the widely used DSSP algo-
rithm. The default order is: "3-Helix", "4-Helix", "5-Helix", "Bend", "Beta-Bridge", "Beta-Strand",
"Turn".
6 dssp_ts

Usage

dssp_ts( tsData,
printLegend = TRUE,
timeBoundaries = NA,
residueBoundaries = NA,
timeUnit = NA,
snapshotsPerTimeInt = 1000,
barScaleFactor = 0.25,
barePlot = FALSE,
... )

Arguments

tsData List consisting of lists, which are composed of a name (string) and a values
table (x ... snapshots, y ... residues). Can be generated by load_dssp_ts().
printLegend If TRUE, a legend is printed on the right hand side of the plot.
timeBoundaries A vector of boundaries for the time in snapshots.
residueBoundaries
A vector of boundaries for the residues.
timeUnit If set, the snapshots are transformed into the respective time (depending on pa-
rameter snapshotsPerTime).
snapshotsPerTimeInt
Number of snapshots per respective timeUnit (only used when timeUnit is
set).
barScaleFactor Allows to manually overwrite the height of the bars.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value

This function does not return data.

Author(s)

Christian Margreitter

Examples
# GROMOS (see load_dssp_ts() for other input possibilities)
dssp_ts( load_dssp_ts( system.file( "extdata/dssp_ts_example",
package = "MDplot" ) ) )
hbond 7

hbond Plot hydrogen bond summary

Description
This function plots the summary output of hydrogen bond calculations and allows selection of donor
and acceptor residues and atoms. Occurrence over the whole trajectory is indicated by a colour
scale. A legend indicating the colour scale can be printed. Note, that in case multiple hydrogen
bond interactions between two particular residues take place, the one with prevalence will be used
for colour-coding (and by default, this interaction is marked with a black circle, see below).

Usage
hbond( hbonds,
plotMethod = "residue-wise",
acceptorRange = NA,
donorRange = NA,
printLegend = TRUE,
showMultipleInteractions = TRUE,
barePlot = FALSE,
... )

Arguments
hbonds Table containing the hydrogen bond information in its columns hbondID, resDonor,
resDonorName, resAcceptor, resAcceptorName, atomDonor, atomDonorName,
atomH, atomAcceptor, AtomAcceptorName, percentage. This kind of table is
automatically generated by function load_hbond().
plotMethod Allows to set the detail of hbond information displayed. Options are currently:
• residue-wise
acceptorRange Vector, specifying which range of acceptor residues is used.
donorRange Vector, specifying which range of donor residues is used.
printLegend Boolean, used to print or hide the legend for the occurences.
showMultipleInteractions
If TRUE, this option causes multiple interactions between the same residues as
being represented by a black circle around the coloured dot.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value
Returns a table containing the information used for the plot:

• resDonor Residue number (donor).

8 hbond_ts

• resAcceptor Residue number (acceptor).

• percentage Percentage, that has been used for colour-coding.
• numberInteractions Number of hydrogen bond interactions taking place between the spec-
ified donor and acceptor residues.

Author(s)

Christian Margreitter

Examples

# GROMOS (see load_hbond() for other input possibilities)

hbond( load_hbond( system.file( "extdata/hbond_example.txt.gz",
package = "MDplot" ) ) )

hbond_ts Plot hydrogen bond timeseries

Description

Timeseries plot of hydrogen bonds (various selections possible). In addition to the timeseries file,
depending on the MD engine format used, an additional summary file might also be necessary (see
below for examples).

Usage

hbond_ts( timeseries,
summary,
acceptorRange = NA,
donorRange = NA,
plotOccurences = FALSE,
scalingFactorPlot = NA,
printNames = FALSE,
namesToSingle = FALSE,
printAtoms = FALSE,
timeUnit = NA,
snapshotsPerTimeInt = 1000,
timeRange = NA,
hbondIndices = NA,
barePlot = FALSE,
... )
hbond_ts 9

Arguments
timeseries Table, containing the timeseries information (e.g. produced by load_hbond_ts()).
summary Table, containing the summary information (e.g. produced by load_hbond()).
acceptorRange Vector of acceptor resdiues, which are to be plotted.
donorRange Vector of donor residues, which are to be plotted.
plotOccurences Specifies, whether the overall summary should also be plotted in a subplot on
the right hand side.
scalingFactorPlot
To manually set the scaling factor (if necessary).
printNames Enables human readable names rather than the hbond identifiers.
namesToSingle If printNames is TRUE, this flags enables one letter codes.
printAtoms If printNames is TRUE, this flag adds the atom names in the hydrogen bond
identification on the y-axis.
timeUnit Specifies the time unit on the x-axis.
snapshotsPerTimeInt
Specifies, how many snapshots make up one time unit (see above).
timeRange Selects a certain time range specified by a vector.
hbondIndices List, containing vectors to select hbonds by their identifiers.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value
Returns a nx2 matrix, with the first column being the list of hydrogen bond identifiers plotted and
the second one the occurrence (in percent) over the selected time range.

Author(s)
Christian Margreitter

Examples
# the examples are valid and wrapped in the "dontrun{}" environment for efficiency purposes only
# GROMOS
## Not run:
hbond_ts( load_hbond_ts( system.file( "extdata/hbond_ts_example.txt.gz",
package = "MDplot" ) ),
load_hbond( system.file( "extdata/hbond_example.txt.gz",
package = "MDplot" ) ) )
## End(Not run)

# GROMACS
## Not run:
hbond_ts( load_hbond_ts( system.file( "extdata/hbond_ts_example_GROMACS.xpm.gz",
package = "MDplot" ),
10 load_clusters

mdEngine = "GROMACS" ),
load_hbond( system.file( "extdata/hbond_ts_example_GROMACS.xpm.gz",
package = "MDplot" ),
system.file( "extdata/hbond_example_GROMACS.txt.gz",
package = "MDplot" ),
mdEngine = "GROMACS" ),
plotOccurences = TRUE, namesToSingle = FALSE, printNames = TRUE,
printAtoms = TRUE, hbondIndices = list( c( 1, 12 ) ),
timeUnit = "ns", snapshotsPerTimeInt = 100 )
## End(Not run)

# AMBER
hbond_ts( load_hbond_ts( system.file( "extdata/hbond_ts_example_AMBER.txt.gz",
package = "MDplot" ),
mdEngine = "AMBER" ),
load_hbond( system.file( "extdata/hbond_ts_example_AMBER.txt.gz",
package = "MDplot" ),
mdEngine = "AMBER" ),
plotOccurences = TRUE, timeRange = c( 20, 60 ) )

load_clusters Loading cluster information

Description
This function loads clusters from a plain text file and stores them in a matrix. The trajectories can
be named by the user. The output of this function can be used as input of function clusters().

Usage
load_clusters( path,
names = NA,
lengths = NA,
mdEngine = "GROMOS" )

Arguments
path Specifies the path of the text input file.
names Optional vector of trajectory names. If provided, needs to be of the same length
as the number of clusters to be plotted.
lengths When GROMACS input needs to be parsed, the lengths of the respective trajec-
tories have to be given. This holds also in the case, that only one is used.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER". Note,
that two different kinds of AMBER output may be loaded (see example input files).
load_clusters_ts 11

Value
Returns a nxm-matrix with n being the number of input trajectories and m the number of different
clusters. Each element in the matrix holds the number of snapshots, the respective cluster occured
in the respective trajectory.

Author(s)
Christian Margreitter

Examples
# GROMOS
load_clusters( system.file( "extdata/clusters_example.txt.gz", package = "MDplot" ) )

# GROMACS
load_clusters( system.file( "extdata/clusters_example_GROMACS.txt.gz", package = "MDplot" ),
mdEngine = "GROMACS", lengths = c( 1001, 1001 ) )

# AMBER (first)
load_clusters( system.file( "extdata/clusters_example_1_AMBER.txt.gz", package = "MDplot" ),
mdEngine = "AMBER" )

# AMBER (second)
load_clusters( system.file( "extdata/clusters_example_2_AMBER.txt.gz", package = "MDplot" ),
mdEngine = "AMBER" )

load_clusters_ts Loading timeseries cluster information

Description
This function loads the timeseries information for clusters from a plain text file and stores them in
a list. The trajectories can be named by the user.

Usage
load_clusters_ts( path,
lengths,
names = NA,
mdEngine = "GROMOS" )

Arguments
path Specifies the path of the text input file.
lengths Mandatory vector holding the number of snapshots for the respective trajecto-
ries (e.g. when three trajectories of 3000 snapshots each have been analysed
together: lengths = c(3000,3000,300)).
12 load_dssp

names Optional vector of trajectory names. If provided, needs to be of the same length
as the number of clusters to be plotted.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value
Returns a list of name-cluster lists, which consist of:
[1] Trajectory name.
[2] Vector of cluster numbers, where 0 indicates a structure not belonging to a clus-
ter specified.

Author(s)
Christian Margreitter

Examples
# GROMOS
load_clusters_ts( system.file( "extdata/clusters_ts_example.txt.gz", package = "MDplot" ),
lengths = c( 4000, 4000, 4000, 4000, 4000, 4000 ) )

# GROMACS
load_clusters_ts( system.file( "extdata/clusters_example_GROMACS.txt.gz", package = "MDplot" ),
mdEngine = "GROMACS", lengths = c( 1001, 1001 ) )

# AMBER
load_clusters_ts( system.file( "extdata/clusters_ts_example_AMBER.txt.gz", package = "MDplot" ),
mdEngine = "AMBER", lengths = c( 50, 50 ) )

load_dssp Load DSSP information

Description
Loads DSSP summary output files from a specified file and combines it into a table. This table may
be used as input for function dssp()

Usage
load_dssp( path,
mdEngine = "GROMOS" )

Arguments
path Path to the input file.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".
load_dssp_ts 13

Value
Returns matrix, where the first column is the residue-number and the remaining ones denote sec-
ondary structure classes. Residues are given row-wise and values range from 0 to 100 percent.

Author(s)
Christian Margreitter

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

# GROMACS
load_dssp( system.file( "extdata/dssp_example_GROMACS.txt.gz",
package = "MDplot" ), mdEngine = "GROMACS" )

# AMBER (same input as for load_dssp_ts())

load_dssp( system.file( "extdata/dssp_ts_example_AMBER.txt.gz",
package = "MDplot" ), mdEngine = "AMBER" )

load_dssp_ts Load DSSP timeseries

Description
Loads DSSP output files from a specified directory (GROMOS) or a specified file (GROMACS,
AMBER) and combines it into a list suited as input for dssp_ts().

Usage
load_dssp_ts( folder,
filenames = NA,
stride = 1,
mdEngine = "GROMOS" )

Arguments
folder Folder, in which the DSSP output files are located.
filenames Vector with filenames. GROMOS: default file names are "3-Helix.out", "4-
Helix.out", "5-Helix.out", "Bend.out", "Beta-Bridge.out", "Beta-Strand.out" and
"Turn.out". Files not present are ignored. GROMACS and AMBER: just give
the appropriate filename (see examples below).
stride Allows to use only every xth snapshot.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".
14 load_hbond

Value

Returns a list, where every element represents a secondary structure motif holding the following
information:

name The name of the secondary structure motif.

values Holds one vector each for the x and y axis:
• x Snapshots, at which the respective motif has been identified.
• y Residues, for which the respective motif has been identified.

Author(s)

Christian Margreitter

Examples

# GROMOS
load_dssp_ts( system.file( "extdata/dssp_ts_example", package = "MDplot" ) )

# GROMACS
load_dssp_ts( folder = system.file( "extdata", package = "MDplot" ),
filenames = "dssp_example_GROMACS.txt.gz",
mdEngine = "GROMACS" )

# AMBER
load_dssp_ts( folder = system.file( "extdata", package = "MDplot" ),
filenames = "dssp_ts_example_AMBER.txt.gz",
mdEngine = "AMBER" )

load_hbond Loading hydrogen bond data

Description

This function loads hydrogen bond information from a text file and stores it in a table. See functions
hbond() and hbond_ts() for usage of the return value.

Usage

load_hbond( path,
GROMACShbondlogfile = NA,
mdEngine = "GROMOS" )
load_hbond 15

Arguments
path Specifies the path of the text input file.
GROMACShbondlogfile
Additional file path required in case GROMACS format is specified.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER". Note,
that load_hbond() is able to load both summary and time-series data for the
AMBER simulation package.

Value
Returns a table, where the hydrogen bonds are stored in a row-wise fashion and the columns hold
the following information (note, that information not available e.g. because the MD analysis tool
output does not provide it, is represented by NA values):

• hbondID The identifier number of the hydrogen bonds (if not given by the input, they are
numbered ascendingly).
• resDonor Number of the donor residue.
• resDonorName Name of the donor residue.
• resAcceptor Number of the acceptor residue.
• resAcceptorName Name of the acceptor residue.
• atomDonor Number of atom, that is the hydrogen bond donor.
• atomDonorName Name of atom, that is the hydrogen bond donor.
• atomH Number of atom (proton) that is forming the hydrogen bond.
• atomAcceptor Number of atom, that is the hydrogen bond acceptor.
• atomAcceptorName Name of atom, that is the hydrogen bond acceptor.
• percentage Number between 0 and 100 in percent representing the occurence rate of a par-
ticular hydrogen bond over the trajectory.

Author(s)
Christian Margreitter

Examples
# GROMOS
load_hbond( system.file( "extdata/hbond_example.txt.gz", package = "MDplot" ) )

# GROMACS
load_hbond( system.file( "extdata/hbond_ts_example_GROMACS.xpm.gz",
package = "MDplot" ),
system.file( "extdata/hbond_example_GROMACS.txt.gz",
package = "MDplot" ),
mdEngine = "GROMACS" )

# AMBER (summary)
16 load_hbond_ts

load_hbond( system.file( "extdata/hbond_example_AMBER.txt.gz",

package = "MDplot" ), mdEngine = "AMBER" )

# AMBER (time-series)
load_hbond( system.file( "extdata/hbond_ts_example_AMBER.txt.gz",
package = "MDplot" ), mdEngine = "AMBER" )

load_hbond_ts Loading hydrogen bonds timeseries

Description
This function loads hydrogen bond timeseries information from a text file and stores it in a table.
See function hbond_ts() for usage of the return value. In case, AMBER format is used as input,
this functions’ return value might also be used for function hbond().

Usage
load_hbond_ts( path,
mdEngine = "GROMOS" )

Arguments
path Specifies the path of the input file.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value
Returns a nx2-matrix, where the first column holds the time in snapshots and the second one the
respective hydrogen bond identifier. Note, that function hbond_ts() requires additional input pro-
vided by function load_hbond() and that hydrogen bond identifiers have to match.

Author(s)
Christian Margreitter

Examples
# the examples are valid and wrapped in the "dontrun{}" environment for efficiency purposes only
# GROMOS
## Not run:
load_hbond_ts( system.file( "extdata/hbond_ts_example.txt.gz", package = "MDplot" ) )
## End(Not run)

# GROMACS
## Not run:
load_hbond_ts( system.file( "extdata/hbond_ts_example_GROMACS.xpm.gz",
package = "MDplot" ),
load_noe 17

mdEngine = "GROMACS" )
## End(Not run)

# AMBER
## Not run:
load_hbond_ts( system.file( "extdata/hbond_ts_example_AMBER.txt.gz",
package = "MDplot" ),
mdEngine = "AMBER" )
## End(Not run)

load_noe Loading NOE violations

Description
This function load one or more Nuclear-Overhauser-Effect (NOE) violation files. Its output can be
feeded into function noe(). Note, that in case the number of used bins differ between files, the
resulting matrix is automatically expanded to cover all bins.

Usage
load_noe( files,
mdEngine = "GROMOS" )

Arguments
files Vector of file paths to be loaded.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS".

Value
Returns a matrix, in which the first column holds the bin boundaries and the following columns
represent the data from the respective input files, i.e. the number of violations in the respective bin.

Author(s)
Christian Margreitter

Examples
# GROMOS
load_noe( c( system.file( "extdata/noe_example_1.txt.gz",
package = "MDplot" ),
system.file( "extdata/noe_example_2.txt.gz",
package = "MDplot" ) ) )
18 load_ramachandran

load_ramachandran Load dihedral information (Ramachandran plot input)

Description
Loads a textfile with dihedral angles, which are to be stored in a matrix. By default, the first column
is phi and the second psi. Angles can be shifted by a constant value (in order to transform them
from 0 to 360 to the usually used -180 to 180).

Usage
load_ramachandran( path,
angleColumns = c(1,2),
shiftAngles = NA,
mdEngine = "GROMOS" )

Arguments
path Path to input file. At least two columns of the same length are expected.
angleColumns If more columns are present, the angle columns can be chosen by this vector.
shiftAngles In order to shift the values by a constant factor (e.g. -180).
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value
A nx2-matrix with phi and psi angles in the respective columns.

Author(s)
Christian Margreitter

Examples
# GROMOS
load_ramachandran( system.file( "extdata/ramachandran_example.txt.gz", package = "MDplot" ) )

# GROMACS
load_ramachandran( system.file( "extdata/ramachandran_example_GROMACS.txt.gz",
package = "MDplot" ), mdEngine = "GROMACS" )

# AMBER
load_ramachandran( system.file( "extdata/ramachandran_example_AMBER.txt.gz",
package = "MDplot" ), mdEngine = "AMBER" )
load_rmsd 19

load_rmsd Loading function for rmsd()

Description

Returns a list of vector pairs of datapoint indices and RMSD values.

Usage

load_rmsd( files,
mdEngine = "GROMOS" )

Arguments

files Vector of paths to input text files.

mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value

A list of vectors, alternately holding indices and their respective values.

Author(s)

Christian Margreitter

Examples
# GROMOS
load_rmsd( c( system.file( "extdata/rmsd_example_1.txt.gz", package = "MDplot" ),
system.file( "extdata/rmsd_example_2.txt.gz", package = "MDplot" ) ) )

# GROMACS
load_rmsd( c( system.file( "extdata/rmsd_example_GROMACS.txt.gz",
package = "MDplot" ) ),
mdEngine = "GROMACS" )

# AMBER
load_rmsd( c( system.file( "extdata/rmsd_example_AMBER.txt.gz",
package = "MDplot" ) ),
mdEngine = "AMBER" )
20 load_rmsf

load_rmsf Loading function for rmsf()

Description

Returns a list of vector pairs of datapoint indices and RMSF values.

Usage

load_rmsf( files,
mdEngine = "GROMOS" )

Arguments

files Vector of paths to input text files.

mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value

A list of vectors, alternately holding atom indices and their respective values.

Author(s)

Christian Margreitter

Examples
# GROMOS
load_rmsf( c( system.file( "extdata/rmsf_example_1.txt.gz", package = "MDplot" ),
system.file( "extdata/rmsf_example_2.txt.gz", package = "MDplot" ) ) )

# GROMACS
load_rmsf( c( system.file( "extdata/rmsf_example_GROMACS.txt.gz",
package = "MDplot" ) ),
mdEngine = "GROMACS" )

# AMBER
load_rmsf( c( system.file( "extdata/rmsf_example_AMBER.txt.gz",
package = "MDplot" ) ),
mdEngine = "AMBER" )
load_TIcurve 21

load_TIcurve Loading function for thermodynamic integration function TIcurve()

Description

Returns a list of matrices holding three columns (lambda state point, value and error) for every file.

Usage

load_TIcurve( files,
mdEngine = "GROMOS" )

Arguments

files Vector of files (up to two) to be loaded.)

mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS".

Value

Returns a list of (at least) nx3-matrices, each holding three columns:

1 lambda-points
2 partial derivative of the Hamiltonian in respect to lambda at respective lambda
3 error associated with partial derivative at respective lambda

Author(s)

Christian Margreitter

Examples

# GROMOS
load_TIcurve( c( system.file( "extdata/TIcurve_example.txt.gz",
package = "MDplot" ) ) )
22 load_timeseries

load_timeseries Loading function for timeseries()

Description

Returns a list of vector pairs of datapoint indices and values.

Usage

load_timeseries( files,
mdEngine = "GROMOS" )

Arguments

files Vector of paths to input text files.

mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER". Note,
that for GROMACS input, mulit-column data is supported.

Value

List of vectors, holding alternately indices and values.

Author(s)

Christian Margreitter

Examples

# GROMOS
load_timeseries( c( system.file( "extdata/timeseries_example_1.txt.gz",
package = "MDplot" ),
system.file( "extdata/timeseries_example_2.txt.gz",
package = "MDplot" ) ) )

# GROMACS
load_timeseries( c( system.file( "extdata/timeseries_example_GROMACS.txt.gz",
package = "MDplot" ) ),
mdEngine = "GROMACS" )
load_xrmsd 23

load_xrmsd Loading function for xrmsd()

Description
Loads matrix information from the specified file.

Usage
load_xrmsd( path,
factor = 1,
removeLowerHalf = TRUE,
mdEngine = "GROMOS" )

Arguments
path Specifies the input file.
factor In case the RMSD values are given in

nm ∗ f actor

, the factor can be specified. If the unit is already nanometers, 1 is the appropriate
value.
removeLowerHalf
If TRUE, the lower half of the plot will be white.
mdEngine Argument distinguishes between input formats based on the molecular dynamics
engine used. Currently available: "GROMOS", "GROMACS" and "AMBER".

Value
Returns a nx3-matrix, with the first two columns holding the position (x- and y-axis) and the third
the respective RMSD value.

Author(s)
Christian Margreitter

Examples
# GROMOS
load_xrmsd( system.file( "extdata/xrmsd_example.txt.gz",
package = "MDplot" ),
factor = 10000 )

# GROMACS
load_xrmsd( system.file( "extdata/xrmsd_example_GROMACS.xpm.gz",
package = "MDplot" ),
mdEngine = "GROMACS" )
24 noe

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

MDplot_argument-class Arguments for bash script interface

Description

Container for bash arguments with "key" <> "value" pairs.

Slots

key: Object of class "character".

value: Object of class "character".

Author(s)

Christian Margreitter

noe Plot NOE violations

Description

This function plots Nuclear-Overhauser-Effect (NOE) violations. Note, that negative violations are
not considered, in case they are part of the input.

Usage

noe( noeData,
printPercentages = TRUE,
colours = NA,
lineTypes = NA,
names = NA,
plotSumCurves = TRUE,
maxYAxis = NA,
printLegend = FALSE,
... )
ramachandran 25

Arguments
noeData Input matrix. Can be generated by using function load_noe().
printPercentages
If TRUE, the violations will be reported in a relative manner (percent) instead
absolute numbers.
colours Vector of colours to be used for the bars.
lineTypes If plotSumCurves is TRUE, this vector might be used to specify the types of
curves plotted.
names Vector to name the input columns (legend).
plotSumCurves If TRUE, the violations are summed up from left to right to show the overall
behaviour.
maxYAxis Can be used to manually set the y-axis of the plot.
printLegend Boolean, which triggers plotting of the legend.
... Additional arguments (ellipsis).

Value
Returns a matrix, in which the first column holds the bin boundaries used and the following columns
represent either the percentage or absolute numbers of the violations per bin, depending on the
specification.

Author(s)
Christian Margreitter

Examples
# GROMOS
noe( load_noe( c( system.file( "extdata/noe_example_1.txt.gz",
package = "MDplot" ),
system.file( "extdata/noe_example_2.txt.gz",
package = "MDplot" ) ) ),
names = c( "run1", "run2" ), printLegend = TRUE )

ramachandran Ramachandran plot for two dihedral angles

Description
This plotting function divides a full rotation (360 degrees) into x- and y- bins and colors them
according to the number of angle pairs that are provided in the input, a so-called Ramachandran
plot.
26 ramachandran

Usage
ramachandran( dihedrals,
xBins = 150,
yBins = 150,
heatFun = "norm",
structureAreas = c(),
plotType = "sparse",
printLegend = FALSE,
plotContour = FALSE,
barePlot = FALSE,
... )

Arguments
dihedrals Matrix with angles (two columns).
xBins Number of x-axis bins to be plotted.
yBins Number of y-axis bins to be plotted.
heatFun Function selector for calculation of the colour, possible are either:
• "norm" (default) for linear calculation, or
• "log" for logarithmic calculation.
structureAreas List of areas, which are plotted as black lines.
plotType Type of plot to be used, either "sparse" (default, using function hist2d()),
"comic" (own binning, use for very few datapoints) or "fancy" (3D, using func-
tion persp()).
printLegend Boolean, specifying whether a heat legend is to be plotted or not.
plotContour Boolean, specifying whether a contour should be plotted or no.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value
Returns a list of binned dihedral angle occurrences.

Author(s)
Christian Margreitter

Examples
# GROMOS (see load_rmsd() for other input possibilities)
ramachandran( load_ramachandran( system.file( "extdata/ramachandran_example.txt.gz",
package = "MDplot" ) ) )
rmsd 27

rmsd Root-mean-square-deviation (RMSD) plot

Description
Plot (multiple) RMSD file(s) as produced by molecular dynamics packages.

Usage
rmsd( rmsdData,
printLegend = TRUE,
snapshotsPerTimeInt = 1000,
timeUnit = "ns",
rmsdUnit = "nm",
colours = NA,
names = NA,
legendPosition = "bottomright",
barePlot = FALSE,
... )

Arguments
rmsdData List of (alternating) indices and RMSD values, as produced e.g. by load_rmsd().
printLegend Boolean, which triggers plotting of the legend.
snapshotsPerTimeInt
Number, specifying how many snapshots are comprising one timeUnit.
timeUnit Specifies, which unit the x-axis is given in.
rmsdUnit Specifies, which unit the y-axis is given in.
colours Vector of colours used for plotting.
names Vector of the names of the trajectories.
legendPosition Indicates position of legend: either "bottomright", "bottomleft", "topleft"
or "topright".
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value
Returns a list of lists, where each sub-list represents a RMSD curve and contains:
minValue The minimum value over the whole time range.
maxValue The maximum value over the whole time range.
meanValue The mean value calculated over the whole time range.
sd The standard deviation calculated over the whole time range.
28 rmsd_average

Author(s)
Christian Margreitter

Examples
# GROMOS (see load_rmsd() for other input possibilities)
rmsd( load_rmsd( c( system.file( "extdata/rmsd_example_1.txt.gz", package = "MDplot" ),
system.file( "extdata/rmsd_example_2.txt.gz", package = "MDplot" ) ) ) )

rmsd_average Root-mean-square-deviation (RMSD) average plot

Description
Combines several RMSD index-value pairs and computes and plots the mean value and the spread
(the respective minimum and maximum values) at every timepoint. This function is particularly
useful, when multiple identical simulation runs (replicates) need to be analysed since it shows a
’corridor’ which allows interpretation e.g. of the overall stability.

Usage
rmsd_average( rmsdInput,
levelFactor = NA,
snapshotsPerTimeInt = 1000,
timeUnit = "ns",
rmsdUnit = "nm",
maxYAxis = NA,
barePlot = FALSE,
... )

Arguments
rmsdInput List of input tables (which are provided by function load_rmsd()).
levelFactor If there are many datapoints, this parameter may be used to use only the levelFactorth
datapoints to obtain a nicer graph.
snapshotsPerTimeInt
Number, specifying how many snapshots are comprising one timeUnit.
timeUnit Specifies, which unit the x-axis is given in.
rmsdUnit Specifies, which unit the y-axis is given in.
maxYAxis Can be used to manually set the y-axis of the plot.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).
rmsf 29

Value

Returns a nx4-matrix, with the rows representing different snapshots and the columns the respective
values as follows:

• snapshot Index of the snapshot.

• minimum The minimum RMSD value over all input sources at a given time.
• mean The mean RMSD value over all input sources at a given time.
• maximum The maximum RMSD value over all input sources at a given time.

Author(s)

Christian Margreitter

Examples
# GROMOS (see load_rmsd() for other input possibilities)
rmsd_average( list( load_rmsd( system.file( "extdata/rmsd_example_1.txt.gz",
package = "MDplot" ) ),
load_rmsd( system.file( "extdata/rmsd_example_2.txt.gz",
package = "MDplot" ) ) ),
snapshotsPerTimeInt = 2000, maxYAxis = 0.445 )

rmsf Root-mean-square-fluctuation (RMSF) plot

Description

Plot (multiple) RMSF file(s) as produced by molecular dynamics packages.

Usage

rmsf( rmsfData,
printLegend = TRUE,
rmsfUnit = "nm",
colours = NA,
residuewise = FALSE,
atomsPerResidue = NA,
names = NA,
rangeAtoms = NA,
legendPosition = "topright",
barePlot = FALSE,
... )
30 TIcurve

Arguments
rmsfData List of (alternating) indices and RMSF values, as produced e.g. by load_rmsf().
printLegend Boolean, which triggers plotting of the legend.
rmsfUnit Specifies, which unit the y-axis is given in.
colours Vector of colours used for plotting.
residuewise Boolean, specifying whether atoms or residues are plotted on the x-axis.
atomsPerResidue
If residuewise is TRUE, this parameter can be used to specify the number of
atoms per residue for plotting.
names Vector of the names of the trajectories.
rangeAtoms Range of atoms to be plotted.
legendPosition Indicate position of legend: either "bottomright", "bottomleft", "topleft"
or "topright".
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value
A list of vectors, alternately holding atom indices and their respective values.

Author(s)
Christian Margreitter

Examples
# GROMOS (see load_rmsf() for other input possibilities)
rmsf( load_rmsf( c( system.file( "extdata/rmsf_example_1.txt.gz", package = "MDplot" ),
system.file( "extdata/rmsf_example_2.txt.gz", package = "MDplot" ) ) ) )

TIcurve Thermodynamic integration plot

Description
Plot the thermodynamic integration(s) (TIs) specified in the input files. Files have to have at least
three columns (lambda point, free energy and error) in order to be valid. In addition, the delta free
energiy (to a precision dependent on the error) are calculated. In case, two data input series are
provided, the hysteresis is calculated.
TIcurve 31

Usage

TIcurve( lambdas,
invertedBackwards = FALSE,
energyUnit = "kJ/mol",
printValues = TRUE,
printErrors = TRUE,
errorBarThreshold = 0,
barePlot = FALSE,
... )

Arguments

lambdas List of matrices (automatically generated by load_TIcurve()) holding the ther-

modynamic integration information.
invertedBackwards
In case a forward and backward TI have been performed and the lambda points
are enumerated reversely (i.e. 0.3 of one TI is equivalent to 0.7 of the other),
this flag can be set to be TRUE in order to automatically mirror the values appro-
priately.
energyUnit Defines the energy unit used for the plot.
printValues Boolean, indicating whether the computed integration and error values are to be
plotted.
printErrors Boolean, indicating whether error bars are to be plotted.
errorBarThreshold
If the error at a given lambda point is below this theshold, it is not plotted.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value

Returns a list with the the following information:

• lambdapoints A list containing a (at least) nx3-matrix for every data input series.
• integrationresults A matrix containing one row of "deltaG" and "error" columns from the
integration for every data input series.
• hysteresis If two (i.e. forward and backward) data input series are provided, the resulting
hysteresis is reported (and set to be NA otherwise).

Author(s)

Christian Margreitter
32 timeseries

Examples
# GROMOS (forward integration)
TIcurve( load_TIcurve( system.file( "extdata/TIcurve_example.txt.gz",
package = "MDplot" ) ) )

# GROMOS (forward and backward integration)

TIcurve( load_TIcurve( c( system.file( "extdata/TIcurve_fb_forward_example.txt.gz",
package = "MDplot" ),
system.file( "extdata/TIcurve_fb_backward_example.txt.gz",
package = "MDplot" ) ) ),
invertedBackwards = TRUE )

timeseries General timeseries plotting function

Description
Plot one (or more) timeseries plots.

Usage
timeseries( tsData,
printLegend = TRUE,
snapshotsPerTimeInt = 1000,
timeUnit = "ns",
valueName = NA,
valueUnit = NA,
colours = NA,
names = NA,
legendPosition = "bottomright",
barePlot = FALSE,
... )

Arguments
tsData List of (alternating) indices and response values, as also produced by load_timeseries()
for example.
printLegend Boolean, which triggers plotting of the legend.
snapshotsPerTimeInt
Number, specifying how many snapshots are within one timeUnit.
timeUnit Specifies, which unit the x-axis is given in.
valueName Name of response variable.
valueUnit Specifies, which unit the y-axis is given in.
colours Vector of colours used for plotting.
names Vector of the names of the trajectories.
translate_aminoacids 33

legendPosition Indicate position of legend: either "bottomright", "bottomleft", "topleft"

or "topright".
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).

Value
Returns a list of list, the latter each holding for every data input series:

• minValue The minimum value over the whole set.

• maxValue The maximum value over the whole set.
• meanValue The mean value over the whole set.
• sd The standard deviation over the whole set.

Author(s)
Christian Margreitter

Examples
# GROMOS
timeseries( load_timeseries( c( system.file( "extdata/timeseries_example_1.txt.gz",
package = "MDplot" ),
system.file( "extdata/timeseries_example_2.txt.gz",
package = "MDplot" ) ) ),
snapshotsPerTimeInt = 100 )

# GROMACS
timeseries( load_timeseries( c( system.file( "extdata/timeseries_example_GROMACS.txt.gz",
package = "MDplot" ) ),
mdEngine = "GROMACS" ),
ylim = c( 0.545, 0.7 ), valueName = "Area per lipid", valueUnit = "nm^2" )

translate_aminoacids Function to translate between canonical and GROMOS amino acid

abbreviations

Description
Converts an aminoacid naming scheme in the context of GROMOS (e.g. containing HISH) into
canonical three- or one-letter codes.

Usage
translate_aminoacids( input,
switchMode )
34 xrmsd

Arguments
input Vector of GROMOS abbreviations.
switchMode Type "1" results in single-letter, type "2" in three-letter code.

Author(s)
Christian Margreitter

Examples
translate_aminoacids( c( "ALA", "HISA", "SER" ),
switchMode = 2 )

xrmsd XRMSD plot in heatmap style

Description
Plots an heatmap according to the RMSD values for a 2D snapshot matrix, based on molecular
dynamics trajectories.

Usage
xrmsd( xrmsdValues,
printLegend = TRUE,
xaxisRange = NA,
yaxisRange = NA,
colours = NA,
rmsdUnit = "nm",
barePlot = FALSE,
... )

Arguments
xrmsdValues Input matrix (three rows: x-values, y-values, RMSD-value). Can be generated
by function load_xrmsd().
printLegend If TRUE, a legend is printed on the right hand side of the plot.
xaxisRange A vector of boundaries for the x-snapshots.
yaxisRange A vector of boundaries for the y-snapshots.
colours A vector with colour names for the span palette.
rmsdUnit Specifies, in which unit the RMSD values are given.
barePlot Boolean, indicating whether the plot is to be made without any additional infor-
mation.
... Additional arguments (ellipsis).
xrmsd 35

Value
This function does not return data.

Author(s)
Christian Margreitter

Examples
# GROMOS (see load_xrmsd() for other input possibilities)
xrmsd( load_xrmsd( system.file( "extdata/xrmsd_example.txt.gz",
package = "MDplot" ),
factor = 10000 ) )
Index

∗Topic Clusters noe, 24

clusters, 2 ∗Topic ramachandran
load_clusters, 10 ramachandran, 25
load_clusters_ts, 11 ∗Topic rmsd
∗Topic DSSP load_rmsd, 19
load_dssp_ts, 13 ∗Topic rmsf
∗Topic MDplot_argument load_rmsf, 20
MDplot_argument-class, 24 ∗Topic thermodynamic integration
∗Topic Ramachandran load_TIcurve, 21
load_ramachandran, 18 ∗Topic timeseries
∗Topic Root-mean-square-deviation hbond_ts, 8
rmsd, 27 load_timeseries, 22
rmsd_average, 28 timeseries, 32
∗Topic Root-mean-square-fluctuation ∗Topic xrmsd
rmsf, 29 load_xrmsd, 23
∗Topic Thermodynamic integration xrmsd, 34
TIcurve, 30
∗Topic aminoacids clusters, 2, 10
translate_aminoacids, 33 clusters_ts, 3
∗Topic angles
dssp, 4, 12
ramachandran, 25
dssp_ts, 5, 13
∗Topic clusters_ts
clusters_ts, 3 hbond, 7, 14, 16
∗Topic dihedral hbond_ts, 8, 14, 16
ramachandran, 25 hist2d, 26
∗Topic dssp
dssp, 4 load_clusters, 2, 10
dssp_ts, 5 load_clusters_ts, 3, 11
load_dssp, 12 load_dssp, 12
∗Topic hbond load_dssp_ts, 6, 13
hbond, 7 load_hbond, 7, 9, 14, 16
hbond_ts, 8 load_hbond_ts, 9, 16
load_hbond, 14 load_noe, 17, 25
load_hbond_ts, 16 load_ramachandran, 18
load_noe, 17 load_rmsd, 19, 27, 28
noe, 24 load_rmsf, 20, 30
∗Topic hydrogen bond load_TIcurve, 21, 31
hbond, 7 load_timeseries, 22, 32
hbond_ts, 8 load_xrmsd, 23, 34

36
INDEX 37

MDplot_argument
(MDplot_argument-class), 24
MDplot_argument-class, 24

noe, 17, 24

persp, 26

ramachandran, 25
rmsd, 19, 27
rmsd_average, 28
rmsf, 20, 29

TIcurve, 21, 30
timeseries, 22, 32
translate_aminoacids, 33

xrmsd, 23, 34