dssp: DSSP plot for secondary structure elements (proteins)
In MDplot: Visualising Molecular Dynamics Analyses
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Plots summary plot for secondary structure motifs based on the output of the widely used classification 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
1
2
3
4
5
6
7
8
9
10
11
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 information.
...
Additional arguments (ellipsis).
Value
Returns matrix, where the first column is the residue-number and the remaining ones denote secondary structure classes. Residues are given row-wise and values range from 0 to 100 percent.
Author(s)
Christian Margreitter
Examples
1
2
3
# GROMOS (see load_dssp() for other input possibilities)
dssp( load_dssp( system.file( "extdata/dssp_example.txt.gz",
package = "MDplot" ) ) )
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
3-Helix 4-Helix 5-Helix Turn B-Strand B-Bridge Bend
[1,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[2,] 0.0 0.0 0.0 0.0 0.0 0.3 0.0
[3,] 0.0 0.0 0.0 0.0 0.0 0.0 1.7
[4,] 0.0 0.0 0.0 0.0 0.0 37.1 4.5
[5,] 0.0 0.0 0.0 0.0 0.0 0.0 4.3
[6,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[7,] 0.0 0.0 0.0 0.0 97.6 0.0 0.0
[8,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[9,] 0.0 0.0 0.0 0.0 99.9 0.0 0.0
[10,] 0.0 0.0 0.0 0.0 92.3 0.0 0.0
[11,] 0.0 0.0 0.0 0.0 69.5 0.0 0.0
[12,] 0.0 0.0 0.0 0.0 0.0 0.0 0.1
[13,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[14,] 0.0 0.0 0.0 98.8 0.0 0.0 0.0
[15,] 2.4 79.6 0.0 2.3 0.0 0.0 15.8
[16,] 4.3 79.8 0.0 14.8 0.0 0.0 1.1
[17,] 16.1 79.8 0.0 1.0 0.0 0.0 3.1
[18,] 15.6 79.8 0.0 0.0 0.0 0.0 4.5
[19,] 20.7 43.5 0.0 0.0 0.0 0.0 35.6
[20,] 0.0 0.0 0.0 0.5 0.0 0.0 99.1
[21,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[22,] 0.0 0.0 0.0 0.0 87.8 4.1 6.7
[23,] 0.0 0.0 0.0 0.0 95.0 0.0 0.0
[24,] 0.0 0.0 0.0 0.0 95.4 0.0 0.0
[25,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[26,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[27,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[28,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[29,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[30,] 0.0 0.0 0.0 0.0 99.3 0.0 0.0
[31,] 0.0 0.0 0.0 0.0 0.0 0.0 71.5
[32,] 0.0 0.0 0.0 0.0 9.9 48.6 0.0
[33,] 0.0 0.0 0.0 0.0 9.9 0.6 84.9
[34,] 0.0 0.0 0.0 4.5 0.0 0.0 94.7
[35,] 0.0 0.0 0.0 0.0 0.0 0.0 95.9
[36,] 0.0 0.0 0.0 0.0 0.0 0.0 0.6
[37,] 0.0 0.0 0.0 0.0 0.5 0.0 0.0
[38,] 0.0 0.0 0.0 0.0 96.8 3.0 0.0
[39,] 0.0 0.0 0.0 0.0 96.9 0.0 0.0
[40,] 0.0 0.0 0.0 0.0 85.5 0.0 0.0
[41,] 0.0 0.0 0.0 0.0 88.1 0.0 0.0
[42,] 0.0 0.0 0.0 0.0 97.2 2.6 0.0
[43,] 0.0 0.0 0.0 5.4 51.9 0.1 2.5
[44,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[45,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[46,] 0.0 0.0 0.0 0.0 35.7 0.9 23.0
[47,] 0.0 0.0 0.0 0.0 36.9 6.2 0.0
[48,] 0.0 0.0 0.0 0.5 11.6 8.8 0.0
[49,] 0.0 0.0 0.0 0.1 0.0 0.0 22.8
[50,] 0.0 0.0 0.0 0.0 0.0 0.0 4.9
[51,] 0.0 0.0 0.0 0.0 72.6 3.7 0.0
[52,] 0.0 0.0 0.0 0.0 87.9 0.3 0.0
[53,] 0.0 0.0 0.0 0.0 85.4 5.6 0.0
[54,] 0.0 0.0 0.0 0.0 6.1 0.1 0.0
[55,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[56,] 0.0 0.0 0.0 0.0 0.1 0.0 0.4
[57,] 0.0 0.0 0.0 0.0 98.1 1.0 0.0
[58,] 0.0 0.0 0.0 0.0 98.2 0.8 0.0
[59,] 0.0 0.0 0.0 83.4 5.0 0.2 0.0
[60,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[61,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[62,] 0.0 0.0 0.0 0.0 0.0 0.4 99.4
[63,] 0.0 0.0 0.0 0.0 4.8 0.0 14.3
[64,] 0.0 0.0 0.0 0.0 99.4 0.3 0.0
[65,] 0.0 0.0 0.0 0.0 99.7 0.0 0.0
[66,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[67,] 0.0 0.0 0.0 0.0 99.9 0.0 0.0
[68,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[69,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[70,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[71,] 0.0 0.0 0.0 0.0 95.4 0.0 0.0
[72,] 0.0 0.0 0.0 0.0 95.0 0.0 0.0
[73,] 0.0 0.0 0.0 6.7 87.8 4.1 0.0
[74,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[75,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[76,] 0.0 0.0 0.0 99.8 0.0 0.0 0.1
[77,] 0.1 99.3 0.0 0.3 0.0 0.0 0.3
[78,] 0.0 99.7 0.0 0.3 0.0 0.0 0.0
[79,] 0.0 99.9 0.0 0.0 0.0 0.0 0.0
[80,] 0.0 100.0 0.0 0.0 0.0 0.0 0.0
[81,] 0.1 99.9 0.0 0.1 0.0 0.0 0.0
[82,] 0.4 99.0 0.0 0.2 0.0 0.0 0.5
[83,] 1.7 95.5 0.0 0.0 0.0 0.0 2.8
[84,] 3.4 52.1 0.1 0.0 0.0 0.0 44.4
[85,] 0.0 0.8 0.5 0.0 0.0 0.0 90.4
[86,] 0.0 0.0 0.0 0.0 0.0 0.0 27.3
[87,] 0.0 0.0 0.0 0.0 0.1 0.0 0.0
[88,] 0.0 0.0 0.0 0.0 25.8 0.0 0.0
[89,] 0.0 0.0 0.0 0.0 96.5 3.5 0.0
[90,] 0.0 0.0 0.0 0.0 96.0 0.0 0.0
[91,] 0.0 0.0 0.0 0.0 96.1 0.0 0.0
[92,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[93,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[94,] 0.0 0.0 0.0 76.9 0.5 0.0 0.0
[95,] 0.0 0.0 0.0 0.2 0.0 0.0 99.8
[96,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[97,] 0.0 0.0 0.0 66.4 0.0 27.0 6.2
[98,] 16.6 0.0 0.0 0.9 0.0 0.0 82.5
[99,] 16.7 0.0 0.0 0.0 0.0 0.0 83.3
[100,] 16.7 0.0 0.0 0.0 0.1 0.0 83.1
[101,] 0.0 0.0 0.0 0.0 92.9 1.1 1.9
[102,] 0.0 0.0 0.0 0.0 98.3 0.5 0.0
[103,] 0.0 0.0 0.0 0.0 80.9 0.0 0.0
[104,] 0.0 0.0 0.0 0.0 81.0 0.0 0.0
[105,] 0.0 0.0 0.0 0.0 80.6 18.6 0.0
[106,] 0.0 0.0 0.0 0.0 10.1 0.0 1.6
[107,] 0.0 0.0 0.0 0.0 0.1 0.0 0.0
[108,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
MDplot documentation built on May 2, 2019, 7:02 a.m.
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Description Usage Arguments Value Author(s) Examples
Description
Plots summary plot for secondary structure motifs based on the output of the widely used classification 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
1 2 3 4 5 6 7 8 9 10 11 |
Arguments
dsspData |
Table containing the information on the secondary structure motifs. |
printLegend |
If |
useOwnLegend |
If |
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 " |
selectedElements |
A vector of names of the elements selected for plotting. |
barePlot |
Boolean, indicating whether the plot is to be made without any additional information. |
... |
Additional arguments (ellipsis). |
Value
Returns matrix, where the first column is the residue-number and the remaining ones denote secondary structure classes. Residues are given row-wise and values range from 0 to 100 percent.
Author(s)
Christian Margreitter
Examples
1 2 3 | # GROMOS (see load_dssp() for other input possibilities)
dssp( load_dssp( system.file( "extdata/dssp_example.txt.gz",
package = "MDplot" ) ) )
|
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
3-Helix 4-Helix 5-Helix Turn B-Strand B-Bridge Bend
[1,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[2,] 0.0 0.0 0.0 0.0 0.0 0.3 0.0
[3,] 0.0 0.0 0.0 0.0 0.0 0.0 1.7
[4,] 0.0 0.0 0.0 0.0 0.0 37.1 4.5
[5,] 0.0 0.0 0.0 0.0 0.0 0.0 4.3
[6,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[7,] 0.0 0.0 0.0 0.0 97.6 0.0 0.0
[8,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[9,] 0.0 0.0 0.0 0.0 99.9 0.0 0.0
[10,] 0.0 0.0 0.0 0.0 92.3 0.0 0.0
[11,] 0.0 0.0 0.0 0.0 69.5 0.0 0.0
[12,] 0.0 0.0 0.0 0.0 0.0 0.0 0.1
[13,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[14,] 0.0 0.0 0.0 98.8 0.0 0.0 0.0
[15,] 2.4 79.6 0.0 2.3 0.0 0.0 15.8
[16,] 4.3 79.8 0.0 14.8 0.0 0.0 1.1
[17,] 16.1 79.8 0.0 1.0 0.0 0.0 3.1
[18,] 15.6 79.8 0.0 0.0 0.0 0.0 4.5
[19,] 20.7 43.5 0.0 0.0 0.0 0.0 35.6
[20,] 0.0 0.0 0.0 0.5 0.0 0.0 99.1
[21,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[22,] 0.0 0.0 0.0 0.0 87.8 4.1 6.7
[23,] 0.0 0.0 0.0 0.0 95.0 0.0 0.0
[24,] 0.0 0.0 0.0 0.0 95.4 0.0 0.0
[25,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[26,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[27,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[28,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[29,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[30,] 0.0 0.0 0.0 0.0 99.3 0.0 0.0
[31,] 0.0 0.0 0.0 0.0 0.0 0.0 71.5
[32,] 0.0 0.0 0.0 0.0 9.9 48.6 0.0
[33,] 0.0 0.0 0.0 0.0 9.9 0.6 84.9
[34,] 0.0 0.0 0.0 4.5 0.0 0.0 94.7
[35,] 0.0 0.0 0.0 0.0 0.0 0.0 95.9
[36,] 0.0 0.0 0.0 0.0 0.0 0.0 0.6
[37,] 0.0 0.0 0.0 0.0 0.5 0.0 0.0
[38,] 0.0 0.0 0.0 0.0 96.8 3.0 0.0
[39,] 0.0 0.0 0.0 0.0 96.9 0.0 0.0
[40,] 0.0 0.0 0.0 0.0 85.5 0.0 0.0
[41,] 0.0 0.0 0.0 0.0 88.1 0.0 0.0
[42,] 0.0 0.0 0.0 0.0 97.2 2.6 0.0
[43,] 0.0 0.0 0.0 5.4 51.9 0.1 2.5
[44,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[45,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[46,] 0.0 0.0 0.0 0.0 35.7 0.9 23.0
[47,] 0.0 0.0 0.0 0.0 36.9 6.2 0.0
[48,] 0.0 0.0 0.0 0.5 11.6 8.8 0.0
[49,] 0.0 0.0 0.0 0.1 0.0 0.0 22.8
[50,] 0.0 0.0 0.0 0.0 0.0 0.0 4.9
[51,] 0.0 0.0 0.0 0.0 72.6 3.7 0.0
[52,] 0.0 0.0 0.0 0.0 87.9 0.3 0.0
[53,] 0.0 0.0 0.0 0.0 85.4 5.6 0.0
[54,] 0.0 0.0 0.0 0.0 6.1 0.1 0.0
[55,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[56,] 0.0 0.0 0.0 0.0 0.1 0.0 0.4
[57,] 0.0 0.0 0.0 0.0 98.1 1.0 0.0
[58,] 0.0 0.0 0.0 0.0 98.2 0.8 0.0
[59,] 0.0 0.0 0.0 83.4 5.0 0.2 0.0
[60,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[61,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[62,] 0.0 0.0 0.0 0.0 0.0 0.4 99.4
[63,] 0.0 0.0 0.0 0.0 4.8 0.0 14.3
[64,] 0.0 0.0 0.0 0.0 99.4 0.3 0.0
[65,] 0.0 0.0 0.0 0.0 99.7 0.0 0.0
[66,] 0.0 0.0 0.0 0.0 99.8 0.0 0.0
[67,] 0.0 0.0 0.0 0.0 99.9 0.0 0.0
[68,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[69,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[70,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[71,] 0.0 0.0 0.0 0.0 95.4 0.0 0.0
[72,] 0.0 0.0 0.0 0.0 95.0 0.0 0.0
[73,] 0.0 0.0 0.0 6.7 87.8 4.1 0.0
[74,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[75,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[76,] 0.0 0.0 0.0 99.8 0.0 0.0 0.1
[77,] 0.1 99.3 0.0 0.3 0.0 0.0 0.3
[78,] 0.0 99.7 0.0 0.3 0.0 0.0 0.0
[79,] 0.0 99.9 0.0 0.0 0.0 0.0 0.0
[80,] 0.0 100.0 0.0 0.0 0.0 0.0 0.0
[81,] 0.1 99.9 0.0 0.1 0.0 0.0 0.0
[82,] 0.4 99.0 0.0 0.2 0.0 0.0 0.5
[83,] 1.7 95.5 0.0 0.0 0.0 0.0 2.8
[84,] 3.4 52.1 0.1 0.0 0.0 0.0 44.4
[85,] 0.0 0.8 0.5 0.0 0.0 0.0 90.4
[86,] 0.0 0.0 0.0 0.0 0.0 0.0 27.3
[87,] 0.0 0.0 0.0 0.0 0.1 0.0 0.0
[88,] 0.0 0.0 0.0 0.0 25.8 0.0 0.0
[89,] 0.0 0.0 0.0 0.0 96.5 3.5 0.0
[90,] 0.0 0.0 0.0 0.0 96.0 0.0 0.0
[91,] 0.0 0.0 0.0 0.0 96.1 0.0 0.0
[92,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[93,] 0.0 0.0 0.0 0.0 100.0 0.0 0.0
[94,] 0.0 0.0 0.0 76.9 0.5 0.0 0.0
[95,] 0.0 0.0 0.0 0.2 0.0 0.0 99.8
[96,] 0.0 0.0 0.0 0.0 0.0 0.0 100.0
[97,] 0.0 0.0 0.0 66.4 0.0 27.0 6.2
[98,] 16.6 0.0 0.0 0.9 0.0 0.0 82.5
[99,] 16.7 0.0 0.0 0.0 0.0 0.0 83.3
[100,] 16.7 0.0 0.0 0.0 0.1 0.0 83.1
[101,] 0.0 0.0 0.0 0.0 92.9 1.1 1.9
[102,] 0.0 0.0 0.0 0.0 98.3 0.5 0.0
[103,] 0.0 0.0 0.0 0.0 80.9 0.0 0.0
[104,] 0.0 0.0 0.0 0.0 81.0 0.0 0.0
[105,] 0.0 0.0 0.0 0.0 80.6 18.6 0.0
[106,] 0.0 0.0 0.0 0.0 10.1 0.0 1.6
[107,] 0.0 0.0 0.0 0.0 0.1 0.0 0.0
[108,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
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