load_clusters: Loading cluster information

In MDplot: Visualising Molecular Dynamics Analyses

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 trajectories 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).

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" )

Example output

Loading required package: MASS
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
1 8539    0  175    0    0  284    0    0    0     0     0     0     0     0
2 3027 5224    0  178   62    3  370    1   65     3    10    23    10    12
3 8926    0    0    0    0   71    0    0    0     0     2     0     0     0
4 7999    0  928    0    0   37    0    0    0    35     0     0     0     0
5 2993 5064   12  390  368    7    0  106    9     0    19     0    11     3
6 8837    0  122    0    0   26    0    0    0     8     6     0     0     0
  [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
1     0     0     0     0     2     0     0     0     0     0     0
2     0     4     4     0     0     3     0     1     0     0     0
3     0     0     0     0     1     0     0     0     0     0     0
4     0     0     0     0     0     0     0     0     1     0     0
5    11     0     0     4     0     0     2     0     0     1     0
6     0     0     0     0     0     0     0     0     0     0     1
  [,1] [,2] [,3] [,4]
1  839   91   29   42
2   75   21  860   45
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
1   20   19   17    7    6    5    4    4    4     4     3     2     2     2
  [,15] [,16]
1     1     1
   [,1]  [,2]  [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
1 12705 10151  9473 7700 5354 3285 1826 1044  896   813   738   601   537   433
2 15269 14668 10968 8363 8602 4835 2162 1716 1452  1439  1161   782   733   596
  [,15] [,16] [,17] [,18] [,19]
1   447   253   320   274   246
2   541   476   386   356   286

MDplot documentation built on May 2, 2019, 7:02 a.m.