hydrogen_bondifier 0.0.2

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  1. data/.gitignore +3 -0
  2. data/History +9 -0
  3. data/LICENSE +23 -0
  4. data/README.rdoc +67 -0
  5. data/Rakefile +54 -0
  6. data/VERSION +1 -0
  7. data/bin/hydrogen_bondifier.rb +159 -0
  8. data/lib/hydrogen_bondifier/utils.rb +39 -0
  9. data/lib/pymol/connections.rb +55 -0
  10. data/lib/pymol/hydrogen_bonds.rb +157 -0
  11. data/lib/pymol/orientation.rb +23 -0
  12. data/lib/pymol/surface.rb +35 -0
  13. data/lib/pymol.rb +93 -0
  14. data/reference/all_connections.py +24 -0
  15. data/reference/campbell_find_hb.py +18 -0
  16. data/reference/list_hbonds.py +47 -0
  17. data/reference/test_pymol.rb +125 -0
  18. data/spec/pymol/connections_spec.rb +25 -0
  19. data/spec/pymol/hydrogen_bonds_spec.rb +38 -0
  20. data/spec/pymol/surface_spec.rb +47 -0
  21. data/spec/pymol_spec.rb +41 -0
  22. data/spec/scripts/confirm_angle_and_h_dist.rb +126 -0
  23. data/spec/scripts/confirm_distances.rb +83 -0
  24. data/spec/scripts/mins.rb +9 -0
  25. data/spec/scripts/obj_ranges.rb +22 -0
  26. data/spec/scripts/pdb_ranges.rb +30 -0
  27. data/spec/spec_helper.rb +6 -0
  28. data/spec/testfiles/1YQS.pdb +6655 -0
  29. data/spec/testfiles/1YQS_h_added.pdb +7924 -0
  30. data/spec/testfiles/2ERK_Hbond.out +302 -0
  31. data/spec/testfiles/2pERK2_HBOND.out +303 -0
  32. data/spec/testfiles/2pERK2_Hadded.pdb +5767 -0
  33. data/spec/testfiles/2pERK2_dis-surf.txt +330 -0
  34. data/spec/testfiles/little.pdb +210 -0
  35. data/validation/jtp_vs_insight_angles.png +0 -0
  36. data/validation/jtp_vs_insight_distances.png +0 -0
  37. data/validation/jtp_vs_insight_surface_distances.png +0 -0
  38. data/validation/jtp_vs_insight_surface_distances_aa_geometric.png +0 -0
  39. data/validation/jtp_vs_insight_surface_distances_center_of_grav.png +0 -0
  40. data/validation/jtp_vs_insight_surface_distances_closest_atom.png +0 -0
  41. metadata +113 -0
data/spec/testfiles/2pERK2_dis-surf.txt ADDED
@@ -0,0 +1,330 @@
1
+ ALA7 minimum_distance_to_surface 1.19982278465
2
+ GLY8 minimum_distance_to_surface 1.20006688621
3
+ GLU10 minimum_distance_to_surface 2.07145898991
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+ MET11 minimum_distance_to_surface 1.20020203623
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+ VAL12 minimum_distance_to_surface 2.75232828294
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+ ARG13 minimum_distance_to_surface 1.19972429325
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+ GLY14 minimum_distance_to_surface 1.19955152323
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+ GLN15 minimum_distance_to_surface 3.01423948442
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+ VAL16 minimum_distance_to_surface 1.20030655653
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+ PHE17 minimum_distance_to_surface 4.90262242589
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+ VAL19 minimum_distance_to_surface 3.32327597868
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+ ARG22 minimum_distance_to_surface 1.20006637589
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+ ARG351 minimum_distance_to_surface 1.43616094216
325
+ PHE352 minimum_distance_to_surface 3.90293584619
326
+ GLN353 minimum_distance_to_surface 3.12791628963
327
+ GLY355 minimum_distance_to_surface 1.19954043576
328
+ TYR356 minimum_distance_to_surface 1.42227125404
329
+ ARG357 minimum_distance_to_surface 1.19934533846
330
+ SER358 minimum_distance_to_surface 1.19987533948
data/spec/testfiles/little.pdb ADDED
@@ -0,0 +1,210 @@
1
+ ATOM 1 N ALA 6 2.707 58.805 3.476 1.00 56.35 N
2
+ ATOM 2 CA ALA 6 2.467 59.882 2.471 1.00 66.74 C
3
+ ATOM 3 C ALA 6 1.909 59.290 1.169 1.00 72.70 C
4
+ ATOM 4 O ALA 6 1.374 58.170 1.170 1.00 71.26 O
5
+ ATOM 5 CB ALA 6 3.768 60.640 2.205 1.00 55.70 C
6
+ ATOM 6 1H ALA 6 2.062 58.925 4.270 1.00 0.00 H
7
+ ATOM 7 2H ALA 6 2.546 57.886 3.040 1.00 0.00 H
8
+ ATOM 8 HA ALA 6 1.750 60.609 2.853 1.00 0.00 H
9
+ ATOM 9 1HB ALA 6 4.567 60.216 2.813 1.00 0.00 H
10
+ ATOM 10 2HB ALA 6 4.030 60.555 1.150 1.00 0.00 H
11
+ ATOM 11 3HB ALA 6 3.636 61.691 2.462 1.00 0.00 H
12
+ ATOM 12 N ALA 7 2.005 60.060 0.078 1.00 73.38 N
13
+ ATOM 13 CA ALA 7 1.535 59.631 -1.249 1.00 72.93 C
14
+ ATOM 14 C ALA 7 2.351 58.414 -1.701 1.00 70.28 C
15
+ ATOM 15 O ALA 7 1.794 57.382 -2.099 1.00 64.46 O
16
+ ATOM 16 CB ALA 7 1.678 60.772 -2.253 1.00 66.37 C
17
+ ATOM 17 H ALA 7 2.427 60.995 0.172 1.00 0.00 H
18
+ ATOM 18 HA ALA 7 0.480 59.366 -1.185 1.00 0.00 H
19
+ ATOM 19 1HB ALA 7 2.097 61.646 -1.754 1.00 0.00 H
20
+ ATOM 20 2HB ALA 7 2.340 60.464 -3.062 1.00 0.00 H
21
+ ATOM 21 3HB ALA 7 0.699 61.022 -2.661 1.00 0.00 H
22
+ ATOM 22 N GLY 8 3.674 58.564 -1.656 1.00 64.54 N
23
+ ATOM 23 CA GLY 8 4.569 57.475 -1.991 1.00 45.92 C
24
+ ATOM 24 C GLY 8 4.860 56.757 -0.681 1.00 41.36 C
25
+ ATOM 25 O GLY 8 3.936 56.476 0.091 1.00 31.25 O
26
+ ATOM 26 H GLY 8 4.069 59.473 -1.377 1.00 0.00 H
27
+ ATOM 27 1HA GLY 8 5.455 57.939 -2.424 1.00 0.00 H
28
+ ATOM 28 2HA GLY 8 4.028 56.852 -2.703 1.00 0.00 H
29
+ ATOM 29 N PRO 9 6.135 56.477 -0.375 1.00 36.57 N
30
+ ATOM 30 CA PRO 9 6.463 55.787 0.876 1.00 31.06 C
31
+ ATOM 31 C PRO 9 6.243 56.656 2.108 1.00 32.22 C
32
+ ATOM 32 O PRO 9 6.319 57.885 2.035 1.00 34.92 O
33
+ ATOM 33 CB PRO 9 7.940 55.454 0.695 1.00 21.74 C
34
+ ATOM 34 CG PRO 9 8.437 56.599 -0.115 1.00 37.03 C
35
+ ATOM 35 CD PRO 9 7.351 56.756 -1.155 1.00 32.73 C
36
+ ATOM 36 HA PRO 9 5.865 54.889 1.035 1.00 0.00 H
37
+ ATOM 37 1HB PRO 9 8.069 54.502 0.180 1.00 0.00 H
38
+ ATOM 38 2HB PRO 9 8.448 55.382 1.656 1.00 0.00 H
39
+ ATOM 39 1HG PRO 9 9.406 56.376 -0.562 1.00 0.00 H
40
+ ATOM 40 2HG PRO 9 8.554 57.494 0.496 1.00 0.00 H
41
+ ATOM 41 1HD PRO 9 7.328 57.759 -1.580 1.00 0.00 H
42
+ ATOM 42 2HD PRO 9 7.464 56.052 -1.980 1.00 0.00 H
43
+ ATOM 43 N GLU 10 5.933 56.007 3.230 1.00 36.73 N
44
+ ATOM 44 CA GLU 10 5.730 56.696 4.506 1.00 34.17 C
45
+ ATOM 45 C GLU 10 7.111 57.117 4.995 1.00 25.87 C
46
+ ATOM 46 O GLU 10 8.080 56.382 4.814 1.00 30.32 O
47
+ ATOM 47 CB GLU 10 5.113 55.747 5.530 1.00 30.48 C
48
+ ATOM 48 CG GLU 10 3.999 54.887 4.977 1.00 38.89 C
49
+ ATOM 49 CD GLU 10 3.310 54.075 6.045 1.00 38.81 C
50
+ ATOM 50 OE1 GLU 10 2.831 54.679 7.022 1.00 44.65 O
51
+ ATOM 51 OE2 GLU 10 3.239 52.838 5.907 1.00 37.17 O1-
52
+ ATOM 52 H GLU 10 5.832 54.982 3.198 1.00 0.00 H
53
+ ATOM 53 HA GLU 10 5.087 57.551 4.297 1.00 0.00 H
54
+ ATOM 54 1HB GLU 10 4.701 56.342 6.345 1.00 0.00 H
55
+ ATOM 55 2HB GLU 10 5.895 55.083 5.898 1.00 0.00 H
56
+ ATOM 56 1HG GLU 10 4.352 54.173 4.232 1.00 0.00 H
57
+ ATOM 57 2HG GLU 10 3.220 55.474 4.491 1.00 0.00 H
58
+ ATOM 58 N MET 11 7.202 58.300 5.592 1.00 28.07 N
59
+ ATOM 59 CA MET 11 8.472 58.808 6.100 1.00 20.43 C
60
+ ATOM 60 C MET 11 8.471 58.791 7.615 1.00 16.11 C
61
+ ATOM 61 O MET 11 7.419 58.777 8.243 1.00 27.75 O
62
+ ATOM 62 CB MET 11 8.681 60.253 5.655 1.00 19.24 C
63
+ ATOM 63 CG MET 11 8.363 60.519 4.205 1.00 29.41 C
64
+ ATOM 64 SD MET 11 9.466 59.631 3.127 1.00 37.22 S
65
+ ATOM 65 CE MET 11 10.986 60.594 3.341 1.00 15.35 C
66
+ ATOM 66 H MET 11 6.354 58.874 5.699 1.00 0.00 H
67
+ ATOM 67 HA MET 11 9.294 58.188 5.742 1.00 0.00 H
68
+ ATOM 68 1HB MET 11 9.728 60.510 5.813 1.00 0.00 H
69
+ ATOM 69 2HB MET 11 8.032 60.891 6.255 1.00 0.00 H
70
+ ATOM 70 1HG MET 11 8.454 61.579 3.967 1.00 0.00 H
71
+ ATOM 71 2HG MET 11 7.346 60.213 3.960 1.00 0.00 H
72
+ ATOM 72 1HE MET 11 10.804 61.411 4.040 1.00 0.00 H
73
+ ATOM 73 2HE MET 11 11.773 59.950 3.733 1.00 0.00 H
74
+ ATOM 74 3HE MET 11 11.297 61.002 2.379 1.00 0.00 H
75
+ ATOM 75 N VAL 12 9.662 58.771 8.194 1.00 14.82 N
76
+ ATOM 76 CA VAL 12 9.845 58.810 9.643 1.00 19.53 C
77
+ ATOM 77 C VAL 12 11.212 59.455 9.824 1.00 20.79 C
78
+ ATOM 78 O VAL 12 12.208 58.940 9.315 1.00 21.16 O
79
+ ATOM 79 CB VAL 12 9.881 57.403 10.300 1.00 24.28 C
80
+ ATOM 80 CG1 VAL 12 9.925 57.540 11.817 1.00 12.93 C
81
+ ATOM 81 CG2 VAL 12 8.671 56.575 9.893 1.00 28.89 C
82
+ ATOM 82 H VAL 12 10.498 58.726 7.595 1.00 0.00 H
83
+ ATOM 83 HA VAL 12 9.059 59.397 10.118 1.00 0.00 H
84
+ ATOM 84 HB VAL 12 10.765 56.860 9.966 1.00 0.00 H
85
+ ATOM 85 1HG1 VAL 12 9.921 58.596 12.087 1.00 0.00 H
86
+ ATOM 86 2HG1 VAL 12 9.053 57.051 12.252 1.00 0.00 H
87
+ ATOM 87 3HG1 VAL 12 10.832 57.071 12.198 1.00 0.00 H
88
+ ATOM 88 1HG2 VAL 12 8.039 57.159 9.223 1.00 0.00 H
89
+ ATOM 89 2HG2 VAL 12 9.004 55.671 9.383 1.00 0.00 H
90
+ ATOM 90 3HG2 VAL 12 8.102 56.301 10.781 1.00 0.00 H
91
+ ATOM 91 N ARG 13 11.249 60.609 10.484 1.00 16.66 N
92
+ ATOM 92 CA ARG 13 12.498 61.329 10.721 1.00 14.04 C
93
+ ATOM 93 C ARG 13 13.208 61.692 9.425 1.00 19.50 C
94
+ ATOM 94 O ARG 13 14.436 61.615 9.339 1.00 25.10 O
95
+ ATOM 95 CB ARG 13 13.429 60.496 11.594 1.00 14.42 C
96
+ ATOM 96 CG ARG 13 12.817 60.069 12.912 1.00 21.47 C
97
+ ATOM 97 CD ARG 13 13.827 59.296 13.742 1.00 28.24 C
98
+ ATOM 98 NE ARG 13 14.039 59.942 15.029 1.00 31.00 N
99
+ ATOM 99 CZ ARG 13 15.223 60.095 15.605 1.00 17.80 C
100
+ ATOM 100 NH1 ARG 13 16.317 59.640 15.014 1.00 19.86 N1+
101
+ ATOM 101 NH2 ARG 13 15.309 60.732 16.760 1.00 26.13 N
102
+ ATOM 102 H ARG 13 10.369 61.008 10.840 1.00 0.00 H
103
+ ATOM 103 HA ARG 13 12.340 62.263 11.261 1.00 0.00 H
104
+ ATOM 104 1HB ARG 13 14.316 61.090 11.815 1.00 0.00 H
105
+ ATOM 105 2HB ARG 13 13.700 59.594 11.045 1.00 0.00 H
106
+ ATOM 106 1HG ARG 13 11.950 59.430 12.741 1.00 0.00 H
107
+ ATOM 107 2HG ARG 13 12.496 60.940 13.484 1.00 0.00 H
108
+ ATOM 108 1HD ARG 13 14.787 59.239 13.228 1.00 0.00 H
109
+ ATOM 109 2HD ARG 13 13.479 58.279 13.925 1.00 0.00 H
110
+ ATOM 110 HE ARG 13 13.213 60.305 15.526 1.00 0.00 H
111
+ ATOM 111 1HH1 ARG 13 16.250 59.165 14.103 1.00 0.00 H
112
+ ATOM 112 2HH1 ARG 13 17.235 59.761 15.466 1.00 0.00 H
113
+ ATOM 113 1HH2 ARG 13 14.459 61.106 17.207 1.00 0.00 H
114
+ ATOM 114 2HH2 ARG 13 16.226 60.855 17.214 1.00 0.00 H
115
+ ATOM 115 N GLY 14 12.423 62.070 8.417 1.00 29.61 N
116
+ ATOM 116 CA GLY 14 12.971 62.442 7.120 1.00 26.78 C
117
+ ATOM 117 C GLY 14 13.479 61.265 6.304 1.00 32.20 C
118
+ ATOM 118 O GLY 14 13.962 61.440 5.182 1.00 37.50 O
119
+ ATOM 119 H GLY 14 11.403 62.100 8.559 1.00 0.00 H
120
+ ATOM 120 1HA GLY 14 13.808 63.121 7.282 1.00 0.00 H
121
+ ATOM 121 2HA GLY 14 12.187 62.933 6.544 1.00 0.00 H
122
+ ATOM 122 N GLN 15 13.361 60.062 6.860 1.00 32.76 N
123
+ ATOM 123 CA GLN 15 13.813 58.842 6.192 1.00 29.54 C
124
+ ATOM 124 C GLN 15 12.648 58.057 5.612 1.00 28.04 C
125
+ ATOM 125 O GLN 15 11.523 58.111 6.118 1.00 19.50 O
126
+ ATOM 126 CB GLN 15 14.550 57.928 7.176 1.00 33.32 C
127
+ ATOM 127 CG GLN 15 15.796 58.517 7.803 1.00 51.07 C
128
+ ATOM 128 CD GLN 15 17.035 58.225 6.998 1.00 59.01 C
129
+ ATOM 129 NE2 GLN 15 17.406 56.950 6.933 1.00 62.59 N
130
+ ATOM 130 OE1 GLN 15 17.658 59.131 6.440 1.00 64.88 O
131
+ ATOM 131 H GLN 15 12.936 59.987 7.795 1.00 0.00 H
132
+ ATOM 132 HA GLN 15 14.495 59.063 5.371 1.00 0.00 H
133
+ ATOM 133 1HB GLN 15 14.853 57.029 6.639 1.00 0.00 H
134
+ ATOM 134 2HB GLN 15 13.864 57.684 7.987 1.00 0.00 H
135
+ ATOM 135 1HG GLN 15 15.980 58.128 8.804 1.00 0.00 H
136
+ ATOM 136 2HG GLN 15 15.739 59.601 7.899 1.00 0.00 H
137
+ ATOM 137 1HE2 GLN 15 18.246 56.685 6.400 1.00 0.00 H
138
+ ATOM 138 2HE2 GLN 15 16.853 56.228 7.416 1.00 0.00 H
139
+ ATOM 139 N VAL 16 12.937 57.311 4.554 1.00 21.68 N
140
+ ATOM 140 CA VAL 16 11.936 56.474 3.913 1.00 19.90 C
141
+ ATOM 141 C VAL 16 11.767 55.210 4.762 1.00 15.05 C
142
+ ATOM 142 O VAL 16 12.746 54.612 5.204 1.00 14.12 O
143
+ ATOM 143 CB VAL 16 12.388 56.048 2.488 1.00 15.89 C
144
+ ATOM 144 CG1 VAL 16 11.358 55.133 1.859 1.00 16.83 C
145
+ ATOM 145 CG2 VAL 16 12.621 57.268 1.608 1.00 15.12 C
146
+ ATOM 146 H VAL 16 13.895 57.325 4.177 1.00 0.00 H
147
+ ATOM 147 HA VAL 16 11.006 57.041 3.866 1.00 0.00 H
148
+ ATOM 148 HB VAL 16 13.340 55.519 2.534 1.00 0.00 H
149
+ ATOM 149 1HG1 VAL 16 10.532 54.983 2.554 1.00 0.00 H
150
+ ATOM 150 2HG1 VAL 16 10.982 55.585 0.941 1.00 0.00 H
151
+ ATOM 151 3HG1 VAL 16 11.818 54.172 1.628 1.00 0.00 H
152
+ ATOM 152 1HG2 VAL 16 12.417 58.173 2.180 1.00 0.00 H
153
+ ATOM 153 2HG2 VAL 16 13.657 57.279 1.268 1.00 0.00 H
154
+ ATOM 154 3HG2 VAL 16 11.957 57.226 0.745 1.00 0.00 H
155
+ ATOM 155 N PHE 17 10.524 54.856 5.057 1.00 11.99 N
156
+ ATOM 156 CA PHE 17 10.238 53.637 5.806 1.00 16.50 C
157
+ ATOM 157 C PHE 17 9.124 53.001 4.999 1.00 12.30 C
158
+ ATOM 158 O PHE 17 7.964 52.981 5.400 1.00 14.77 O
159
+ ATOM 159 CB PHE 17 9.801 53.937 7.241 1.00 9.95 C
160
+ ATOM 160 CG PHE 17 10.129 52.828 8.205 1.00 10.94 C
161
+ ATOM 161 CD1 PHE 17 11.412 52.725 8.754 1.00 5.99 C
162
+ ATOM 162 CD2 PHE 17 9.185 51.856 8.521 1.00 12.82 C
163
+ ATOM 163 CE1 PHE 17 11.754 51.674 9.598 1.00 5.64 C
164
+ ATOM 164 CE2 PHE 17 9.515 50.793 9.368 1.00 10.17 C
165
+ ATOM 165 CZ PHE 17 10.808 50.703 9.908 1.00 8.45 C
166
+ ATOM 166 H PHE 17 9.743 55.454 4.751 1.00 0.00 H
167
+ ATOM 167 HA PHE 17 11.117 52.996 5.865 1.00 0.00 H
168
+ ATOM 168 1HB PHE 17 8.727 54.099 7.338 1.00 0.00 H
169
+ ATOM 169 2HB PHE 17 10.269 54.830 7.655 1.00 0.00 H
170
+ ATOM 170 HD1 PHE 17 12.158 53.483 8.515 1.00 0.00 H
171
+ ATOM 171 HD2 PHE 17 8.180 51.923 8.105 1.00 0.00 H
172
+ ATOM 172 HE1 PHE 17 12.759 51.612 10.015 1.00 0.00 H
173
+ ATOM 173 HE2 PHE 17 8.769 50.035 9.609 1.00 0.00 H
174
+ ATOM 174 HZ PHE 17 11.069 49.875 10.568 1.00 0.00 H
175
+ ATOM 175 N ASP 18 9.509 52.520 3.823 1.00 21.94 N
176
+ ATOM 176 CA ASP 18 8.588 51.942 2.858 1.00 28.59 C
177
+ ATOM 177 C ASP 18 8.029 50.582 3.224 1.00 22.21 C
178
+ ATOM 178 O ASP 18 8.435 49.553 2.685 1.00 27.49 O
179
+ ATOM 179 CB ASP 18 9.252 51.911 1.478 1.00 32.70 C
180
+ ATOM 180 CG ASP 18 8.252 51.775 0.345 1.00 39.60 C
181
+ ATOM 181 OD1 ASP 18 7.030 51.903 0.583 1.00 41.53 O
182
+ ATOM 182 OD2 ASP 18 8.695 51.546 -0.798 1.00 49.77 O1-
183
+ ATOM 183 H ASP 18 10.510 52.558 3.582 1.00 0.00 H
184
+ ATOM 184 HA ASP 18 7.742 52.621 2.751 1.00 0.00 H
185
+ ATOM 185 1HB ASP 18 9.949 51.081 1.361 1.00 0.00 H
186
+ ATOM 186 2HB ASP 18 9.825 52.813 1.263 1.00 0.00 H
187
+ ATOM 187 N VAL 19 7.047 50.597 4.114 1.00 26.24 N
188
+ ATOM 188 CA VAL 19 6.413 49.370 4.563 1.00 27.93 C
189
+ ATOM 189 C VAL 19 4.997 49.223 4.021 1.00 29.01 C
190
+ ATOM 190 O VAL 19 4.062 48.906 4.759 1.00 21.23 O
191
+ ATOM 191 CB VAL 19 6.462 49.245 6.100 1.00 16.65 C
192
+ ATOM 192 CG1 VAL 19 7.886 48.958 6.527 1.00 9.89 C
193
+ ATOM 193 CG2 VAL 19 5.971 50.527 6.765 1.00 16.63 C
194
+ ATOM 194 H VAL 19 6.727 51.498 4.495 1.00 0.00 H
195
+ ATOM 195 HA VAL 19 6.962 48.483 4.246 1.00 0.00 H
196
+ ATOM 196 HB VAL 19 5.810 48.429 6.411 1.00 0.00 H
197
+ ATOM 197 1HG1 VAL 19 8.527 48.910 5.647 1.00 0.00 H
198
+ ATOM 198 2HG1 VAL 19 8.235 49.752 7.187 1.00 0.00 H
199
+ ATOM 199 3HG1 VAL 19 7.923 48.005 7.055 1.00 0.00 H
200
+ ATOM 200 1HG2 VAL 19 5.693 51.251 5.999 1.00 0.00 H
201
+ ATOM 201 2HG2 VAL 19 5.103 50.305 7.387 1.00 0.00 H
202
+ ATOM 202 3HG2 VAL 19 6.765 50.942 7.385 1.00 0.00 H
203
+ ATOM 203 N GLY 20 4.885 49.419 2.701 1.00 43.33 N
204
+ ATOM 204 CA GLY 20 3.627 49.308 1.972 1.00 28.08 C
205
+ ATOM 205 C GLY 20 2.404 49.815 2.702 1.00 29.49 C
206
+ ATOM 206 O GLY 20 2.524 50.633 3.614 1.00 33.59 O
207
+ ATOM 207 H GLY 20 5.734 49.662 2.171 1.00 0.00 H
208
+ ATOM 208 1HA GLY 20 3.457 48.254 1.752 1.00 0.00 H
209
+ ATOM 209 2HA GLY 20 3.718 49.888 1.053 1.00 0.00 H
210
+ END
metadata ADDED
@@ -0,0 +1,113 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: hydrogen_bondifier
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.2
5
+ platform: ruby
6
+ authors:
7
+ - John T. Prince
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+
12
+ date: 2010-02-10 00:00:00 -07:00
13
+ default_executable: hydrogen_bondifier.rb
14
+ dependencies:
15
+ - !ruby/object:Gem::Dependency
16
+ name: spec-more
17
+ type: :development
18
+ version_requirement:
19
+ version_requirements: !ruby/object:Gem::Requirement
20
+ requirements:
21
+ - - ">="
22
+ - !ruby/object:Gem::Version
23
+ version: "0"
24
+ version:
25
+ description: uses pymol
26
+ email: jtprince@gmail.com
27
+ executables:
28
+ - hydrogen_bondifier.rb
29
+ extensions: []
30
+
31
+ extra_rdoc_files:
32
+ - LICENSE
33
+ - README.rdoc
34
+ files:
35
+ - .gitignore
36
+ - History
37
+ - LICENSE
38
+ - README.rdoc
39
+ - Rakefile
40
+ - VERSION
41
+ - bin/hydrogen_bondifier.rb
42
+ - lib/hydrogen_bondifier/utils.rb
43
+ - lib/pymol.rb
44
+ - lib/pymol/connections.rb
45
+ - lib/pymol/hydrogen_bonds.rb
46
+ - lib/pymol/orientation.rb
47
+ - lib/pymol/surface.rb
48
+ - reference/all_connections.py
49
+ - reference/campbell_find_hb.py
50
+ - reference/list_hbonds.py
51
+ - reference/test_pymol.rb
52
+ - spec/pymol/connections_spec.rb
53
+ - spec/pymol/hydrogen_bonds_spec.rb
54
+ - spec/pymol/surface_spec.rb
55
+ - spec/pymol_spec.rb
56
+ - spec/scripts/confirm_angle_and_h_dist.rb
57
+ - spec/scripts/confirm_distances.rb
58
+ - spec/scripts/mins.rb
59
+ - spec/scripts/obj_ranges.rb
60
+ - spec/scripts/pdb_ranges.rb
61
+ - spec/spec_helper.rb
62
+ - spec/testfiles/1YQS.pdb
63
+ - spec/testfiles/1YQS_h_added.pdb
64
+ - spec/testfiles/2ERK_Hbond.out
65
+ - spec/testfiles/2pERK2_HBOND.out
66
+ - spec/testfiles/2pERK2_Hadded.pdb
67
+ - spec/testfiles/2pERK2_dis-surf.txt
68
+ - spec/testfiles/little.pdb
69
+ - validation/jtp_vs_insight_angles.png
70
+ - validation/jtp_vs_insight_distances.png
71
+ - validation/jtp_vs_insight_surface_distances.png
72
+ - validation/jtp_vs_insight_surface_distances_aa_geometric.png
73
+ - validation/jtp_vs_insight_surface_distances_center_of_grav.png
74
+ - validation/jtp_vs_insight_surface_distances_closest_atom.png
75
+ has_rdoc: true
76
+ homepage: http://jtprince.github.com/hydrogen_bondifier
77
+ licenses: []
78
+
79
+ post_install_message:
80
+ rdoc_options:
81
+ - --charset=UTF-8
82
+ require_paths:
83
+ - lib
84
+ required_ruby_version: !ruby/object:Gem::Requirement
85
+ requirements:
86
+ - - ">="
87
+ - !ruby/object:Gem::Version
88
+ version: "0"
89
+ version:
90
+ required_rubygems_version: !ruby/object:Gem::Requirement
91
+ requirements:
92
+ - - ">="
93
+ - !ruby/object:Gem::Version
94
+ version: "0"
95
+ version:
96
+ requirements: []
97
+
98
+ rubyforge_project:
99
+ rubygems_version: 1.3.5
100
+ signing_key:
101
+ specification_version: 3
102
+ summary: finds hydrogen bonds using pymol
103
+ test_files:
104
+ - spec/scripts/obj_ranges.rb
105
+ - spec/scripts/pdb_ranges.rb
106
+ - spec/scripts/mins.rb
107
+ - spec/scripts/confirm_angle_and_h_dist.rb
108
+ - spec/scripts/confirm_distances.rb
109
+ - spec/pymol_spec.rb
110
+ - spec/spec_helper.rb
111
+ - spec/pymol/hydrogen_bonds_spec.rb
112
+ - spec/pymol/connections_spec.rb
113
+ - spec/pymol/surface_spec.rb