hbond: Plot hydrogen bond summary
In MDplot: Visualising Molecular Dynamics Analyses
Description
Usage
Arguments
Value
Author(s)
Examples
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
1
2
3
4
5
6
7
8
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 information.
...
Additional arguments (ellipsis).
Value
Returns a table containing the information used for the plot:
resDonor Residue number (donor).
resAcceptor Residue number (acceptor).
percentage Percentage, that has been used for colour-coding.
numberInteractions Number of hydrogen bond interactions taking place between the specified donor and acceptor residues.
Author(s)
Christian Margreitter
Examples
1
2
3
# GROMOS (see load_hbond() for other input possibilities)
hbond( load_hbond( system.file( "extdata/hbond_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
resDonor resAcceptor percentage numberInteractions
1 50 46 71.45 3
2 50 47 10.10 2
6 50 67 0.05 1
4 50 70 71.60 5
14 51 47 36.50 1
15 51 48 34.95 1
16 51 49 0.60 1
12 51 51 0.25 2
19 52 48 6.40 1
20 52 49 55.25 1
17 52 50 0.10 1
18 52 51 0.90 1
23 53 10 1.70 6
21 53 51 1.35 6
33 54 52 0.05 1
34 55 53 0.15 1
35 55 75 90.05 1
41 56 11 25.60 1
37 56 12 4.20 3
36 56 54 10.20 5
40 56 78 22.20 2
47 57 78 85.70 1
49 58 14 29.20 1
48 58 116 27.10 1
50 59 79 67.20 2
52 60 57 6.00 1
53 60 79 8.85 2
55 61 62 40.35 6
57 61 152 70.95 6
59 61 271 9.70 3
70 62 59 1.00 1
71 62 62 20.80 1
72 63 59 96.45 1
73 63 60 0.05 1
74 64 60 85.90 2
75 64 61 57.05 2
78 64 73 0.05 1
79 64 74 33.75 1
80 65 61 73.80 1
81 65 62 12.15 1
82 66 62 38.25 1
83 66 63 11.35 1
84 67 63 38.55 1
85 67 64 9.50 1
86 68 64 95.65 1
87 68 65 0.70 1
97 69 23 0.40 2
93 69 24 55.95 3
94 69 26 43.55 5
99 69 27 2.10 5
101 69 46 40.35 4
88 69 65 90.95 1
89 69 66 2.85 2
102 69 69 0.20 1
91 69 70 22.55 6
117 70 66 46.55 1
118 70 67 19.15 1
119 71 67 0.15 1
120 71 68 5.25 1
121 71 69 7.55 1
122 71 70 0.15 1
123 71 71 0.15 1
124 72 67 9.80 1
125 72 70 7.45 1
126 72 71 0.45 1
127 72 72 0.10 1
128 73 71 0.05 1
129 74 72 31.70 1
130 77 55 83.80 1
131 78 54 2.00 1
132 78 78 1.45 1
133 79 137 76.60 1
134 81 79 70.10 2
136 82 79 54.10 3
139 83 79 57.95 1
140 83 80 1.90 1
141 84 80 97.65 1
142 84 81 0.35 1
143 85 81 99.15 1
144 85 82 0.10 1
148 85 89 0.75 1
145 85 91 21.30 1
146 85 141 1.10 1
153 85 273 6.75 1
149 85 276 5.20 2
151 85 279 3.95 2
152 85 280 71.20 2
147 85 433 0.55 1
156 86 82 67.90 1
157 86 83 8.85 1
158 87 83 78.40 1
159 87 84 3.00 1
160 88 84 98.45 1
161 88 85 0.05 1
162 90 88 97.55 3
169 91 84 32.15 1
165 91 88 83.40 2
166 91 89 0.05 1
167 91 91 0.25 1
168 91 101 91.90 1
171 92 90 11.10 2
173 95 95 53.95 2
175 96 93 78.25 2
177 97 93 94.95 1
178 97 94 1.75 1
179 98 94 93.80 1
180 98 95 0.20 1
181 99 95 97.55 1
182 99 96 0.35 1
183 99 104 1.85 5
190 100 90 2.75 4
192 100 91 72.45 1
188 100 96 93.55 2
189 100 97 4.00 1
204 101 91 20.40 2
196 101 97 82.10 2
197 101 98 12.95 1
198 101 122 2.75 1
199 101 126 1.65 4
206 102 98 69.55 1
207 102 99 2.20 1
208 102 100 0.20 1
209 103 98 0.60 1
210 103 101 0.10 1
211 103 103 0.15 1
213 105 95 9.00 2
212 105 103 0.10 1
215 105 112 3.25 2
217 105 116 2.20 3
220 106 104 7.70 1
221 106 106 0.05 1
222 106 111 50.65 2
224 107 106 0.05 1
225 107 111 0.05 1
226 108 106 1.45 2
228 108 107 0.55 1
229 108 111 0.15 1
230 109 108 5.60 1
231 110 108 74.10 2
233 111 108 64.40 2
240 112 16 63.50 1
237 112 105 0.15 2
238 112 106 62.45 3
239 112 107 2.50 3
235 112 108 98.30 1
236 112 109 0.05 1
246 113 109 95.70 1
247 113 110 1.50 1
248 114 110 92.40 1
249 114 111 0.65 1
250 115 111 96.45 1
251 115 112 0.55 1
257 116 13 0.40 1
258 116 14 51.85 2
260 116 15 0.10 1
252 116 112 90.60 2
253 116 113 4.50 2
256 116 116 1.35 1
261 117 113 55.25 1
262 117 114 2.05 1
263 117 116 0.15 2
267 118 102 1.50 3
265 118 114 68.60 1
266 118 115 1.10 1
270 119 115 99.20 1
271 119 116 0.25 1
275 120 78 2.05 3
276 120 79 0.15 2
274 120 80 0.15 1
272 120 116 89.30 1
273 120 117 1.85 1
278 120 137 4.30 2
282 121 117 85.05 1
283 121 118 1.65 1
286 122 101 2.20 2
284 122 118 79.95 1
285 122 119 2.35 1
288 122 122 0.10 1
289 123 119 97.85 1
290 123 120 0.40 1
300 124 78 0.60 1
291 124 120 98.95 1
292 124 121 0.15 1
293 124 128 21.30 6
301 124 137 0.35 1
299 124 138 1.35 2
303 125 121 74.80 1
304 125 122 1.55 1
309 126 100 0.10 2
311 126 101 0.35 2
305 126 122 64.50 5
306 126 123 7.35 1
315 126 436 2.60 1
316 127 123 85.65 1
317 127 124 4.55 1
318 128 124 93.95 1
319 128 125 1.45 1
320 128 127 0.10 1
321 129 127 1.00 1
322 129 128 4.45 2
324 130 127 33.00 1
325 130 128 1.50 1
326 130 129 0.30 1
327 131 129 0.25 1
328 131 130 6.30 2
330 131 131 1.50 2
332 132 130 84.10 6
336 132 131 0.05 1
338 132 428 10.05 6
340 132 429 0.40 3
341 132 430 13.40 4
337 132 431 0.10 4
343 132 518 0.50 2
358 133 130 93.00 2
360 134 130 71.45 1
361 134 131 0.55 1
362 135 131 92.15 1
363 135 132 1.55 2
369 135 136 0.05 1
364 135 139 11.00 5
370 135 431 3.85 2
373 136 132 98.50 1
374 136 133 0.30 1
378 137 78 99.95 2
377 137 79 0.35 1
375 137 133 86.90 1
376 137 134 1.70 1
382 138 128 0.05 1
380 138 134 92.55 1
381 138 135 0.70 1
383 139 135 94.95 1
384 139 136 0.05 1
385 140 135 0.35 1
386 140 136 42.50 1
387 140 137 0.65 1
388 140 139 5.85 1
389 140 141 0.15 1
390 141 136 85.80 1
391 141 137 0.10 1
393 142 78 0.65 1
392 142 137 94.45 1
MDplot documentation built on May 2, 2019, 7:02 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) Examples
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
1 2 3 4 5 6 7 8 |
Arguments
hbonds |
Table containing the hydrogen bond information in its columns |
plotMethod |
Allows to set the detail of hbond information displayed. Options are currently:
|
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 |
barePlot |
Boolean, indicating whether the plot is to be made without any additional information. |
... |
Additional arguments (ellipsis). |
Value
Returns a table containing the information used for the plot:
resDonorResidue number (donor).resAcceptorResidue number (acceptor).percentagePercentage, that has been used for colour-coding.numberInteractionsNumber of hydrogen bond interactions taking place between the specified donor and acceptor residues.
Author(s)
Christian Margreitter
Examples
1 2 3 | # GROMOS (see load_hbond() for other input possibilities)
hbond( load_hbond( system.file( "extdata/hbond_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
resDonor resAcceptor percentage numberInteractions
1 50 46 71.45 3
2 50 47 10.10 2
6 50 67 0.05 1
4 50 70 71.60 5
14 51 47 36.50 1
15 51 48 34.95 1
16 51 49 0.60 1
12 51 51 0.25 2
19 52 48 6.40 1
20 52 49 55.25 1
17 52 50 0.10 1
18 52 51 0.90 1
23 53 10 1.70 6
21 53 51 1.35 6
33 54 52 0.05 1
34 55 53 0.15 1
35 55 75 90.05 1
41 56 11 25.60 1
37 56 12 4.20 3
36 56 54 10.20 5
40 56 78 22.20 2
47 57 78 85.70 1
49 58 14 29.20 1
48 58 116 27.10 1
50 59 79 67.20 2
52 60 57 6.00 1
53 60 79 8.85 2
55 61 62 40.35 6
57 61 152 70.95 6
59 61 271 9.70 3
70 62 59 1.00 1
71 62 62 20.80 1
72 63 59 96.45 1
73 63 60 0.05 1
74 64 60 85.90 2
75 64 61 57.05 2
78 64 73 0.05 1
79 64 74 33.75 1
80 65 61 73.80 1
81 65 62 12.15 1
82 66 62 38.25 1
83 66 63 11.35 1
84 67 63 38.55 1
85 67 64 9.50 1
86 68 64 95.65 1
87 68 65 0.70 1
97 69 23 0.40 2
93 69 24 55.95 3
94 69 26 43.55 5
99 69 27 2.10 5
101 69 46 40.35 4
88 69 65 90.95 1
89 69 66 2.85 2
102 69 69 0.20 1
91 69 70 22.55 6
117 70 66 46.55 1
118 70 67 19.15 1
119 71 67 0.15 1
120 71 68 5.25 1
121 71 69 7.55 1
122 71 70 0.15 1
123 71 71 0.15 1
124 72 67 9.80 1
125 72 70 7.45 1
126 72 71 0.45 1
127 72 72 0.10 1
128 73 71 0.05 1
129 74 72 31.70 1
130 77 55 83.80 1
131 78 54 2.00 1
132 78 78 1.45 1
133 79 137 76.60 1
134 81 79 70.10 2
136 82 79 54.10 3
139 83 79 57.95 1
140 83 80 1.90 1
141 84 80 97.65 1
142 84 81 0.35 1
143 85 81 99.15 1
144 85 82 0.10 1
148 85 89 0.75 1
145 85 91 21.30 1
146 85 141 1.10 1
153 85 273 6.75 1
149 85 276 5.20 2
151 85 279 3.95 2
152 85 280 71.20 2
147 85 433 0.55 1
156 86 82 67.90 1
157 86 83 8.85 1
158 87 83 78.40 1
159 87 84 3.00 1
160 88 84 98.45 1
161 88 85 0.05 1
162 90 88 97.55 3
169 91 84 32.15 1
165 91 88 83.40 2
166 91 89 0.05 1
167 91 91 0.25 1
168 91 101 91.90 1
171 92 90 11.10 2
173 95 95 53.95 2
175 96 93 78.25 2
177 97 93 94.95 1
178 97 94 1.75 1
179 98 94 93.80 1
180 98 95 0.20 1
181 99 95 97.55 1
182 99 96 0.35 1
183 99 104 1.85 5
190 100 90 2.75 4
192 100 91 72.45 1
188 100 96 93.55 2
189 100 97 4.00 1
204 101 91 20.40 2
196 101 97 82.10 2
197 101 98 12.95 1
198 101 122 2.75 1
199 101 126 1.65 4
206 102 98 69.55 1
207 102 99 2.20 1
208 102 100 0.20 1
209 103 98 0.60 1
210 103 101 0.10 1
211 103 103 0.15 1
213 105 95 9.00 2
212 105 103 0.10 1
215 105 112 3.25 2
217 105 116 2.20 3
220 106 104 7.70 1
221 106 106 0.05 1
222 106 111 50.65 2
224 107 106 0.05 1
225 107 111 0.05 1
226 108 106 1.45 2
228 108 107 0.55 1
229 108 111 0.15 1
230 109 108 5.60 1
231 110 108 74.10 2
233 111 108 64.40 2
240 112 16 63.50 1
237 112 105 0.15 2
238 112 106 62.45 3
239 112 107 2.50 3
235 112 108 98.30 1
236 112 109 0.05 1
246 113 109 95.70 1
247 113 110 1.50 1
248 114 110 92.40 1
249 114 111 0.65 1
250 115 111 96.45 1
251 115 112 0.55 1
257 116 13 0.40 1
258 116 14 51.85 2
260 116 15 0.10 1
252 116 112 90.60 2
253 116 113 4.50 2
256 116 116 1.35 1
261 117 113 55.25 1
262 117 114 2.05 1
263 117 116 0.15 2
267 118 102 1.50 3
265 118 114 68.60 1
266 118 115 1.10 1
270 119 115 99.20 1
271 119 116 0.25 1
275 120 78 2.05 3
276 120 79 0.15 2
274 120 80 0.15 1
272 120 116 89.30 1
273 120 117 1.85 1
278 120 137 4.30 2
282 121 117 85.05 1
283 121 118 1.65 1
286 122 101 2.20 2
284 122 118 79.95 1
285 122 119 2.35 1
288 122 122 0.10 1
289 123 119 97.85 1
290 123 120 0.40 1
300 124 78 0.60 1
291 124 120 98.95 1
292 124 121 0.15 1
293 124 128 21.30 6
301 124 137 0.35 1
299 124 138 1.35 2
303 125 121 74.80 1
304 125 122 1.55 1
309 126 100 0.10 2
311 126 101 0.35 2
305 126 122 64.50 5
306 126 123 7.35 1
315 126 436 2.60 1
316 127 123 85.65 1
317 127 124 4.55 1
318 128 124 93.95 1
319 128 125 1.45 1
320 128 127 0.10 1
321 129 127 1.00 1
322 129 128 4.45 2
324 130 127 33.00 1
325 130 128 1.50 1
326 130 129 0.30 1
327 131 129 0.25 1
328 131 130 6.30 2
330 131 131 1.50 2
332 132 130 84.10 6
336 132 131 0.05 1
338 132 428 10.05 6
340 132 429 0.40 3
341 132 430 13.40 4
337 132 431 0.10 4
343 132 518 0.50 2
358 133 130 93.00 2
360 134 130 71.45 1
361 134 131 0.55 1
362 135 131 92.15 1
363 135 132 1.55 2
369 135 136 0.05 1
364 135 139 11.00 5
370 135 431 3.85 2
373 136 132 98.50 1
374 136 133 0.30 1
378 137 78 99.95 2
377 137 79 0.35 1
375 137 133 86.90 1
376 137 134 1.70 1
382 138 128 0.05 1
380 138 134 92.55 1
381 138 135 0.70 1
383 139 135 94.95 1
384 139 136 0.05 1
385 140 135 0.35 1
386 140 136 42.50 1
387 140 137 0.65 1
388 140 139 5.85 1
389 140 141 0.15 1
390 141 136 85.80 1
391 141 137 0.10 1
393 142 78 0.65 1
392 142 137 94.45 1
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