This function plots the summary output of hydrogen bond calculations and allows selection of donor and acceptor residues and atoms. Occurence over the whole trajectory is indicated by a colour scale. A legend indicating the colour scale can be printed.
Table containing the hydrogen bond information in the columns hbondID, resDonor, resDonorName, resAcceptor, resAcceptorName, atomDonor, atomDonorName, atomH, atomAcceptor, AtomAcceptorName, percentage (automatically generated by function load_hbond()).
plotMethod
Allows to set the detail of hbond information displayed. Options are:
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.
barePlot
Boolean, indicating whether the plot is to be made without any additional information.
...
Additional arguments (ellipsis).
Author(s)
Christian Margreitter
Examples
# see "extdata/hbond_example.txt.gz" for format information
hbond( load_hbond( system.file( "extdata/hbond_example.txt.gz",
package = "MDplot" ) ) )
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MDplot)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MDplot/hbond.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hbond
> ### Title: Plot hydrogen bond summary
> ### Aliases: hbond
> ### Keywords: hbond hydrogen bond
>
> ### ** Examples
>
> # see "extdata/hbond_example.txt.gz" for format information
> hbond( load_hbond( system.file( "extdata/hbond_example.txt.gz",
+ package = "MDplot" ) ) )
hbondID resDonor resDonorName resAcceptor resAcceptorName atomDonor
1 1 50 ARG 46 TYR 480
2 2 50 ARG 47 LYSH 480
3 3 50 ARG 46 TYR 486
4 4 50 ARG 70 GLU 489
5 5 50 ARG 70 GLU 489
6 6 50 ARG 67 ALA 489
7 7 50 ARG 70 GLU 489
8 8 50 ARG 70 GLU 489
9 9 50 ARG 70 GLU 492
10 10 50 ARG 46 TYR 492
11 11 50 ARG 47 LYSH 492
12 12 51 ASP 51 ASP 497
13 13 51 ASP 51 ASP 497
14 14 51 ASP 47 LYSH 497
15 15 51 ASP 48 ALA 497
16 16 51 ASP 49 LEU 497
17 17 52 LEU 50 ARG 506
18 18 52 LEU 51 ASP 506
19 19 52 LEU 48 ALA 506
20 20 52 LEU 49 LEU 506
21 21 53 LYSH 51 ASP 515
22 22 53 LYSH 51 ASP 522
23 23 53 LYSH 10 GLU 522
24 24 53 LYSH 10 GLU 522
25 25 53 LYSH 51 ASP 522
26 26 53 LYSH 10 GLU 522
27 27 53 LYSH 10 GLU 522
28 28 53 LYSH 51 ASP 522
29 29 53 LYSH 51 ASP 522
30 30 53 LYSH 51 ASP 522
31 31 53 LYSH 10 GLU 522
32 32 53 LYSH 10 GLU 522
33 33 54 GLU 52 LEU 528
34 34 55 ALA 53 LYSH 538
35 35 55 ALA 75 PRO 538
36 36 56 ARG 54 GLU 544
37 37 56 ARG 12 ALA 544
38 38 56 ARG 54 GLU 550
39 39 56 ARG 54 GLU 550
40 40 56 ARG 78 ASP 550
41 41 56 ARG 11 GLY 553
42 42 56 ARG 12 ALA 553
43 43 56 ARG 12 ALA 553
44 44 56 ARG 54 GLU 556
45 45 56 ARG 54 GLU 556
46 46 56 ARG 78 ASP 556
47 47 57 GLY 78 ASP 561
48 48 58 LEU 116 SER 566
49 49 58 LEU 14 VAL 566
50 50 59 LEU 79 ASP 575
51 51 59 LEU 79 ASP 575
52 52 60 ALA 57 GLY 584
53 53 60 ALA 79 ASP 584
54 54 60 ALA 79 ASP 584
55 55 61 LYSH 62 ASP 597
56 56 61 LYSH 62 ASP 597
57 57 61 LYSH 152 GLU 597
58 58 61 LYSH 152 GLU 597
59 59 61 LYSH 271 PHE 597
60 60 61 LYSH 62 ASP 597
61 61 61 LYSH 62 ASP 597
62 62 61 LYSH 152 GLU 597
63 63 61 LYSH 152 GLU 597
64 64 61 LYSH 271 PHE 597
65 65 61 LYSH 62 ASP 597
66 66 61 LYSH 62 ASP 597
67 67 61 LYSH 152 GLU 597
68 68 61 LYSH 152 GLU 597
69 69 61 LYSH 271 PHE 597
70 70 62 ASP 59 LEU 603
71 71 62 ASP 62 ASP 603
72 72 63 LEU 59 LEU 612
73 73 63 LEU 60 ALA 612
74 74 64 SER 60 ALA 621
75 75 64 SER 61 LYSH 621
76 76 64 SER 60 ALA 625
77 77 64 SER 61 LYSH 625
78 78 64 SER 73 GLY 625
79 79 64 SER 74 LEU 625
80 80 65 VAL 61 LYSH 629
81 81 65 VAL 62 ASP 629
82 82 66 LEU 62 ASP 637
83 83 66 LEU 63 LEU 637
84 84 67 ALA 63 LEU 646
85 85 67 ALA 64 SER 646
86 86 68 LEU 64 SER 652
87 87 68 LEU 65 VAL 652
88 88 69 ARG 65 VAL 661
89 89 69 ARG 66 LEU 661
90 90 69 ARG 66 LEU 667
91 91 69 ARG 70 GLU 667
92 92 69 ARG 70 GLU 667
93 93 69 ARG 24 MET 667
94 94 69 ARG 26 ALA 667
95 95 69 ARG 70 GLU 670
96 96 69 ARG 70 GLU 670
97 97 69 ARG 23 PRO 670
98 98 69 ARG 26 ALA 670
99 99 69 ARG 27 ASP 670
100 100 69 ARG 27 ASP 670
101 101 69 ARG 46 TYR 670
102 102 69 ARG 69 ARG 670
103 103 69 ARG 23 PRO 670
104 104 69 ARG 24 MET 670
105 105 69 ARG 26 ALA 670
106 106 69 ARG 46 TYR 670
107 107 69 ARG 26 ALA 673
108 108 69 ARG 27 ASP 673
109 109 69 ARG 27 ASP 673
110 110 69 ARG 46 TYR 673
111 111 69 ARG 70 GLU 673
112 112 69 ARG 70 GLU 673
113 113 69 ARG 24 MET 673
114 114 69 ARG 26 ALA 673
115 115 69 ARG 27 ASP 673
116 116 69 ARG 46 TYR 673
117 117 70 GLU 66 LEU 678
118 118 70 GLU 67 ALA 678
119 119 71 GLY 67 ALA 688
120 120 71 GLY 68 LEU 688
121 121 71 GLY 69 ARG 688
122 122 71 GLY 70 GLU 688
123 123 71 GLY 71 GLY 688
124 124 72 LEU 67 ALA 693
125 125 72 LEU 70 GLU 693
126 126 72 LEU 71 GLY 693
127 127 72 LEU 72 LEU 693
128 128 73 GLY 71 GLY 702
129 129 74 LEU 72 LEU 707
130 130 77 GLY 55 ALA 730
131 131 78 ASP 54 GLU 735
132 132 78 ASP 78 ASP 735
133 133 79 ASP 137 TYR 744
134 134 81 MET 79 ASP 760
135 135 81 MET 79 ASP 760
136 136 82 LEU 79 ASP 769
137 137 82 LEU 79 ASP 769
138 138 82 LEU 79 ASP 769
139 139 83 LEU 79 ASP 778
140 140 83 LEU 80 PRO 778
141 141 84 ALA 80 PRO 787
142 142 84 ALA 81 MET 787
143 143 85 TYR 81 MET 793
144 144 85 TYR 82 LEU 793
145 145 85 TYR 91 ASN 798
146 146 85 TYR 141 GLU 800
147 147 85 TYR 433 ARG 800
148 148 85 TYR 89 PRO 802
149 149 85 TYR 276 THR 802
150 150 85 TYR 276 THR 802
151 151 85 TYR 279 GLY 804
152 152 85 TYR 280 ARG 804
153 153 85 TYR 273 GLN 807
154 154 85 TYR 279 GLY 807
155 155 85 TYR 280 ARG 807
156 156 86 LEU 82 LEU 811
157 157 86 LEU 83 LEU 811
158 158 87 LEU 83 LEU 820
159 159 87 LEU 84 ALA 820
160 160 88 ASP 84 ALA 829
161 161 88 ASP 85 TYR 829
162 162 90 SER 88 ASP 845
163 163 90 SER 88 ASP 849
164 164 90 SER 88 ASP 849
165 165 91 ASN 88 ASP 853
166 166 91 ASN 89 PRO 853
167 167 91 ASN 91 ASN 853
168 168 91 ASN 101 TYR 859
169 169 91 ASN 84 ALA 859
170 170 91 ASN 88 ASP 859
171 171 92 THR 90 SER 864
172 172 92 THR 90 SER 868
173 173 95 GLU 95 GLU 889
174 174 95 GLU 95 GLU 889
175 175 96 GLY 93 THR 899
176 176 96 GLY 93 THR 899
177 177 97 VAL 93 THR 904
178 178 97 VAL 94 PRO 904
179 179 98 ALA 94 PRO 912
180 180 98 ALA 95 GLU 912
181 181 99 ARG 95 GLU 918
182 182 99 ARG 96 GLY 918
183 183 99 ARG 104 GLU 924
184 184 99 ARG 104 GLU 924
185 185 99 ARG 104 GLU 927
186 186 99 ARG 104 GLU 930
187 187 99 ARG 104 GLU 930
188 188 100 ARG 96 GLY 935
189 189 100 ARG 97 VAL 935
190 190 100 ARG 90 SER 941
191 191 100 ARG 90 SER 944
192 192 100 ARG 91 ASN 944
193 193 100 ARG 96 GLY 944
194 194 100 ARG 90 SER 947
195 195 100 ARG 90 SER 947
196 196 101 TYR 97 VAL 952
197 197 101 TYR 98 ALA 952
198 198 101 TYR 122 ASN 957
199 199 101 TYR 126 ARG 957
200 200 101 TYR 126 ARG 957
201 201 101 TYR 126 ARG 957
202 202 101 TYR 97 VAL 959
203 203 101 TYR 126 ARG 961
204 204 101 TYR 91 ASN 963
205 205 101 TYR 91 ASN 963
206 206 102 GLY 98 ALA 970
207 207 102 GLY 99 ARG 970
208 208 102 GLY 100 ARG 970
209 209 103 GLY 98 ALA 975
210 210 103 GLY 101 TYR 975
211 211 103 GLY 103 GLY 975
212 212 105 TRP 103 GLY 990
213 213 105 TRP 95 GLU 995
214 214 105 TRP 95 GLU 995
215 215 105 TRP 112 ARG 998
216 216 105 TRP 112 ARG 1005
217 217 105 TRP 116 SER 1005
218 218 105 TRP 116 SER 1005
219 219 105 TRP 116 SER 1007
220 220 106 THR 104 GLU 1011
221 221 106 THR 106 THR 1011
222 222 106 THR 111 GLU 1015
223 223 106 THR 111 GLU 1015
224 224 107 GLU 106 THR 1020
225 225 107 GLU 111 GLU 1020
226 226 108 GLU 106 THR 1030
227 227 108 GLU 106 THR 1030
228 228 108 GLU 107 GLU 1030
229 229 108 GLU 111 GLU 1030
230 230 109 ALA 108 GLU 1040
231 231 110 GLY 108 GLU 1046
232 232 110 GLY 108 GLU 1046
233 233 111 GLU 108 GLU 1051
234 234 111 GLU 108 GLU 1051
235 235 112 ARG 108 GLU 1061
236 236 112 ARG 109 ALA 1061
237 237 112 ARG 105 TRP 1067
238 238 112 ARG 106 THR 1067
239 239 112 ARG 107 GLU 1067
240 240 112 ARG 16 PHE 1070
241 241 112 ARG 105 TRP 1070
242 242 112 ARG 106 THR 1073
243 243 112 ARG 107 GLU 1073
244 244 112 ARG 106 THR 1073
245 245 112 ARG 107 GLU 1073
246 246 113 ALA 109 ALA 1078
247 247 113 ALA 110 GLY 1078
248 248 114 ALA 110 GLY 1084
249 249 114 ALA 111 GLU 1084
250 250 115 LEU 111 GLU 1090
251 251 115 LEU 112 ARG 1090
252 252 116 SER 112 ARG 1099
253 253 116 SER 113 ALA 1099
254 254 116 SER 112 ARG 1103
255 255 116 SER 113 ALA 1103
256 256 116 SER 116 SER 1103
257 257 116 SER 13 PHE 1103
258 258 116 SER 14 VAL 1103
259 259 116 SER 14 VAL 1103
260 260 116 SER 15 GLY 1103
261 261 117 GLU 113 ALA 1107
262 262 117 GLU 114 ALA 1107
263 263 117 GLU 116 SER 1107
264 264 117 GLU 116 SER 1107
265 265 118 ARG 114 ALA 1117
266 266 118 ARG 115 LEU 1117
267 267 118 ARG 102 GLY 1123
268 268 118 ARG 102 GLY 1126
269 269 118 ARG 102 GLY 1129
270 270 119 LEU 115 LEU 1134
271 271 119 LEU 116 SER 1134
272 272 120 PHE 116 SER 1143
273 273 120 PHE 117 GLU 1143
274 274 120 PHE 80 PRO 1148
275 275 120 PHE 78 ASP 1152
276 276 120 PHE 79 ASP 1152
277 277 120 PHE 79 ASP 1152
278 278 120 PHE 137 TYR 1152
279 279 120 PHE 78 ASP 1156
280 280 120 PHE 78 ASP 1156
281 281 120 PHE 137 TYR 1156
282 282 121 ALA 117 GLU 1160
283 283 121 ALA 118 ARG 1160
284 284 122 ASN 118 ARG 1166
285 285 122 ASN 119 LEU 1166
286 286 122 ASN 101 TYR 1172
287 287 122 ASN 101 TYR 1172
288 288 122 ASN 122 ASN 1172
289 289 123 LEU 119 LEU 1177
290 290 123 LEU 120 PHE 1177
291 291 124 TRP 120 PHE 1186
292 292 124 TRP 121 ALA 1186
293 293 124 TRP 128 GLU 1191
294 294 124 TRP 128 GLU 1191
295 295 124 TRP 128 GLU 1194
296 296 124 TRP 128 GLU 1194
297 297 124 TRP 128 GLU 1199
298 298 124 TRP 128 GLU 1199
299 299 124 TRP 138 ARG 1199
300 300 124 TRP 78 ASP 1201
301 301 124 TRP 137 TYR 1201
302 302 124 TRP 138 ARG 1203
303 303 125 GLY 121 ALA 1207
304 304 125 GLY 122 ASN 1207
305 305 126 ARG 122 ASN 1212
306 306 126 ARG 123 LEU 1212
307 307 126 ARG 122 ASN 1218
308 308 126 ARG 122 ASN 1218
309 309 126 ARG 100 ARG 1221
310 310 126 ARG 100 ARG 1224
311 311 126 ARG 101 TYR 1224
312 312 126 ARG 101 TYR 1224
313 313 126 ARG 122 ASN 1224
314 314 126 ARG 122 ASN 1224
315 315 126 ARG 436 TYR 1224
316 316 127 LEU 123 LEU 1229
317 317 127 LEU 124 TRP 1229
318 318 128 GLU 124 TRP 1238
319 319 128 GLU 125 GLY 1238
320 320 128 GLU 127 LEU 1238
321 321 129 GLY 127 LEU 1248
322 322 129 GLY 128 GLU 1248
323 323 129 GLY 128 GLU 1248
324 324 130 GLU 127 LEU 1253
325 325 130 GLU 128 GLU 1253
326 326 130 GLU 129 GLY 1253
327 327 131 GLU 129 GLY 1263
328 328 131 GLU 130 GLU 1263
329 329 131 GLU 130 GLU 1263
330 330 131 GLU 131 GLU 1263
331 331 131 GLU 131 GLU 1263
332 332 132 ARG 130 GLU 1273
333 333 132 ARG 130 GLU 1273
334 334 132 ARG 130 GLU 1279
335 335 132 ARG 130 GLU 1279
336 336 132 ARG 131 GLU 1279
337 337 132 ARG 431 PHE 1279
338 338 132 ARG 428 GLU 1282
339 339 132 ARG 428 GLU 1282
340 340 132 ARG 429 THR 1282
341 341 132 ARG 430 LEU 1282
342 342 132 ARG 431 PHE 1282
343 343 132 ARG 518 TYR 1282
344 344 132 ARG 430 LEU 1282
345 345 132 ARG 431 PHE 1282
346 346 132 ARG 428 GLU 1285
347 347 132 ARG 428 GLU 1285
348 348 132 ARG 429 THR 1285
349 349 132 ARG 430 LEU 1285
350 350 132 ARG 518 TYR 1285
351 351 132 ARG 130 GLU 1285
352 352 132 ARG 130 GLU 1285
353 353 132 ARG 428 GLU 1285
354 354 132 ARG 428 GLU 1285
355 355 132 ARG 429 THR 1285
356 356 132 ARG 430 LEU 1285
357 357 132 ARG 431 PHE 1285
358 358 133 LEU 130 GLU 1290
359 359 133 LEU 130 GLU 1290
360 360 134 LEU 130 GLU 1299
361 361 134 LEU 131 GLU 1299
362 362 135 TRP 131 GLU 1308
363 363 135 TRP 132 ARG 1308
364 364 135 TRP 139 GLU 1313
365 365 135 TRP 139 GLU 1313
366 366 135 TRP 139 GLU 1316
367 367 135 TRP 139 GLU 1316
368 368 135 TRP 132 ARG 1319
369 369 135 TRP 136 LEU 1319
370 370 135 TRP 431 PHE 1319
371 371 135 TRP 139 GLU 1321
372 372 135 TRP 431 PHE 1323
373 373 136 LEU 132 ARG 1329
374 374 136 LEU 133 LEU 1329
375 375 137 TYR 133 LEU 1338
376 376 137 TYR 134 LEU 1338
377 377 137 TYR 79 ASP 1347
378 378 137 TYR 78 ASP 1349
379 379 137 TYR 78 ASP 1352
380 380 138 ARG 134 LEU 1356
381 381 138 ARG 135 TRP 1356
382 382 138 ARG 128 GLU 1368
383 383 139 GLU 135 TRP 1373
384 384 139 GLU 136 LEU 1373
385 385 140 VAL 135 TRP 1383
386 386 140 VAL 136 LEU 1383
387 387 140 VAL 137 TYR 1383
388 388 140 VAL 139 GLU 1383
389 389 140 VAL 141 GLU 1383
390 390 141 GLU 136 LEU 1391
391 391 141 GLU 137 TYR 1391
392 392 142 ARG 137 TYR 1401
393 393 142 ARG 78 ASP 1407
atomDonorName atomH atomAcceptor atomAcceptorName percentage
1 N 481 451 O 71.45
2 N 481 464 O 10.10
3 NE 487 451 O 0.70
4 NH1 490 684 OE1