chemruby 0.9.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (241) hide show
  1. data/README +120 -0
  2. data/Rakefile +195 -0
  3. data/ext/extconf.rb +4 -0
  4. data/ext/subcomp.c +416 -0
  5. data/lib/chem.rb +130 -0
  6. data/lib/chem/appl.rb +1 -0
  7. data/lib/chem/appl/chem3dole.rb +36 -0
  8. data/lib/chem/appl/tinker/nucleic.rb +40 -0
  9. data/lib/chem/appl/tinker/tinker_reader.rb +43 -0
  10. data/lib/chem/data.rb +4 -0
  11. data/lib/chem/data/atomic_weight.rb +124 -0
  12. data/lib/chem/data/character.rb +2 -0
  13. data/lib/chem/data/electronegativity.rb +14 -0
  14. data/lib/chem/data/periodic_table.rb +6 -0
  15. data/lib/chem/data/prime_numbers.rb +1 -0
  16. data/lib/chem/data/vdw_radii.rb +1 -0
  17. data/lib/chem/db.rb +64 -0
  18. data/lib/chem/db/cansmi.rb +234 -0
  19. data/lib/chem/db/cdx.rb +1525 -0
  20. data/lib/chem/db/eps.rb +164 -0
  21. data/lib/chem/db/g98.rb +909 -0
  22. data/lib/chem/db/gspan.rb +130 -0
  23. data/lib/chem/db/iupac.rb +5 -0
  24. data/lib/chem/db/iupac/a_1.rb +46 -0
  25. data/lib/chem/db/iupac/iuparser.rb +226 -0
  26. data/lib/chem/db/iupac/iuparser.ry +97 -0
  27. data/lib/chem/db/iupac/postfix.rb +2 -0
  28. data/lib/chem/db/kcf.rb +390 -0
  29. data/lib/chem/db/kcf_glycan.rb +19 -0
  30. data/lib/chem/db/kegg.rb +516 -0
  31. data/lib/chem/db/linucs/linparser.rb +144 -0
  32. data/lib/chem/db/linucs/linucs.ry +53 -0
  33. data/lib/chem/db/mdl.rb +379 -0
  34. data/lib/chem/db/molconnz.rb +12 -0
  35. data/lib/chem/db/mopac.rb +88 -0
  36. data/lib/chem/db/msi.rb +107 -0
  37. data/lib/chem/db/pdb_dic.rb +115 -0
  38. data/lib/chem/db/pdf.rb +131 -0
  39. data/lib/chem/db/pubchem.rb +113 -0
  40. data/lib/chem/db/rmagick.rb +70 -0
  41. data/lib/chem/db/sdf.rb +37 -0
  42. data/lib/chem/db/smbl.rb +88 -0
  43. data/lib/chem/db/smiles.rb +2 -0
  44. data/lib/chem/db/smiles/smiles.ry +203 -0
  45. data/lib/chem/db/smiles/smiparser.rb +375 -0
  46. data/lib/chem/db/swf.rb +74 -0
  47. data/lib/chem/db/sybyl.rb +150 -0
  48. data/lib/chem/db/tinker.rb +77 -0
  49. data/lib/chem/db/types/type_cansmi.rb +9 -0
  50. data/lib/chem/db/types/type_cdx.rb +24 -0
  51. data/lib/chem/db/types/type_gspan.rb +31 -0
  52. data/lib/chem/db/types/type_kcf.rb +28 -0
  53. data/lib/chem/db/types/type_kcf_glycan.rb +26 -0
  54. data/lib/chem/db/types/type_kegg.rb +92 -0
  55. data/lib/chem/db/types/type_mdl.rb +31 -0
  56. data/lib/chem/db/types/type_pdf.rb +33 -0
  57. data/lib/chem/db/types/type_png.rb +31 -0
  58. data/lib/chem/db/types/type_rxn.rb +25 -0
  59. data/lib/chem/db/types/type_sdf.rb +25 -0
  60. data/lib/chem/db/types/type_sybyl.rb +30 -0
  61. data/lib/chem/db/types/type_xyz.rb +26 -0
  62. data/lib/chem/db/vector.rb +128 -0
  63. data/lib/chem/db/xyz.rb +39 -0
  64. data/lib/chem/model.rb +119 -0
  65. data/lib/chem/model/skeleton.rb +37 -0
  66. data/lib/chem/utils.rb +11 -0
  67. data/lib/chem/utils/geometry.rb +27 -0
  68. data/lib/chem/utils/graph_db.rb +146 -0
  69. data/lib/chem/utils/math.rb +17 -0
  70. data/lib/chem/utils/prop.rb +123 -0
  71. data/lib/chem/utils/sssr.rb +101 -0
  72. data/lib/chem/utils/sub.rb +78 -0
  73. data/lib/chem/utils/transform.rb +110 -0
  74. data/lib/chem/utils/traverse.rb +37 -0
  75. data/lib/chem/utils/ullmann.rb +134 -0
  76. data/lib/graph.rb +41 -0
  77. data/lib/graph/cluster.rb +20 -0
  78. data/lib/graph/morgan.rb +38 -0
  79. data/sample/frequent_subgraph.rb +46 -0
  80. data/sample/images/ex1.rb +11 -0
  81. data/sample/images/ex2.rb +4 -0
  82. data/sample/images/ex3.rb +5 -0
  83. data/sample/images/ex4.rb +17 -0
  84. data/sample/images/ex5.rb +10 -0
  85. data/sample/images/mol/adenine.mol +26 -0
  86. data/sample/images/mol/atp.mol +69 -0
  87. data/sample/images/temp/ex5.mol +344 -0
  88. data/sample/kegg_db.rb +116 -0
  89. data/setup.rb +1551 -0
  90. data/test/all.rb +6 -0
  91. data/test/coord_test.rb +17 -0
  92. data/test/ctab_test.rb +31 -0
  93. data/test/data/A_21.tar.gz +0 -0
  94. data/test/data/A_21/aceanthrylene.cdx +0 -0
  95. data/test/data/A_21/aceanthrylene.mol +40 -0
  96. data/test/data/A_21/acenaphthylene.cdx +0 -0
  97. data/test/data/A_21/acenaphthylene.mol +31 -0
  98. data/test/data/A_21/acephenanthrylene.cdx +0 -0
  99. data/test/data/A_21/acephenanthrylene.mol +40 -0
  100. data/test/data/A_21/anthracene.cdx +0 -0
  101. data/test/data/A_21/anthracene.mol +35 -0
  102. data/test/data/A_21/as-indacene.cdx +0 -0
  103. data/test/data/A_21/as-indacene.mol +31 -0
  104. data/test/data/A_21/azulene.cdx +0 -0
  105. data/test/data/A_21/azulene.mol +26 -0
  106. data/test/data/A_21/biphenylene.cdx +0 -0
  107. data/test/data/A_21/biphenylene.mol +31 -0
  108. data/test/data/A_21/chrysene.cdx +0 -0
  109. data/test/data/A_21/chrysene.mol +44 -0
  110. data/test/data/A_21/coronen.cdx +0 -0
  111. data/test/data/A_21/coronen.mol +59 -0
  112. data/test/data/A_21/fluoranthene.cdx +0 -0
  113. data/test/data/A_21/fluoranthene.mol +40 -0
  114. data/test/data/A_21/fluorene.cdx +0 -0
  115. data/test/data/A_21/fluorene.mol +33 -0
  116. data/test/data/A_21/heptacene.cdx +0 -0
  117. data/test/data/A_21/heptacene.mol +71 -0
  118. data/test/data/A_21/heptalene.cdx +0 -0
  119. data/test/data/A_21/heptalene.mol +30 -0
  120. data/test/data/A_21/heptaphene.cdx +0 -0
  121. data/test/data/A_21/heptaphene.mol +71 -0
  122. data/test/data/A_21/hexacene.cdx +0 -0
  123. data/test/data/A_21/hexacene.mol +62 -0
  124. data/test/data/A_21/hexaphene.cdx +0 -0
  125. data/test/data/A_21/hexaphene.mol +62 -0
  126. data/test/data/A_21/indene.cdx +0 -0
  127. data/test/data/A_21/indene.mol +24 -0
  128. data/test/data/A_21/iupac.txt +41 -0
  129. data/test/data/A_21/naphthacene.cdx +0 -0
  130. data/test/data/A_21/naphthacene.mol +44 -0
  131. data/test/data/A_21/naphthalene.cdx +0 -0
  132. data/test/data/A_21/naphthalene.mol +26 -0
  133. data/test/data/A_21/ovalene.cdx +0 -0
  134. data/test/data/A_21/ovalene.mol +78 -0
  135. data/test/data/A_21/pentacene.cdx +0 -0
  136. data/test/data/A_21/pentacene.mol +53 -0
  137. data/test/data/A_21/pentalene.cdx +0 -0
  138. data/test/data/A_21/pentalene.mol +22 -0
  139. data/test/data/A_21/pentaphene.cdx +0 -0
  140. data/test/data/A_21/pentaphene.mol +53 -0
  141. data/test/data/A_21/perylene.cdx +0 -0
  142. data/test/data/A_21/perylene.mol +49 -0
  143. data/test/data/A_21/phenalene.cdx +0 -0
  144. data/test/data/A_21/phenalene.mol +33 -0
  145. data/test/data/A_21/phenanthrene.cdx +0 -0
  146. data/test/data/A_21/phenanthrene.mol +35 -0
  147. data/test/data/A_21/picene.cdx +0 -0
  148. data/test/data/A_21/picene.mol +53 -0
  149. data/test/data/A_21/pleiadene.cdx +0 -0
  150. data/test/data/A_21/pleiadene.mol +44 -0
  151. data/test/data/A_21/pyranthrene.cdx +0 -0
  152. data/test/data/A_21/pyranthrene.mol +72 -0
  153. data/test/data/A_21/pyrene.cdx +0 -0
  154. data/test/data/A_21/pyrene.mol +40 -0
  155. data/test/data/A_21/rubicene.cdx +0 -0
  156. data/test/data/A_21/rubicene.mol +63 -0
  157. data/test/data/A_21/s-indacene.cdx +0 -0
  158. data/test/data/A_21/s-indacene.mol +31 -0
  159. data/test/data/A_21/tetraphenylene.cdx +0 -0
  160. data/test/data/A_21/tetraphenylene.mol +57 -0
  161. data/test/data/A_21/trinaphthylene.cdx +0 -0
  162. data/test/data/A_21/trinaphthylene.mol +71 -0
  163. data/test/data/A_21/triphenylene.cdx +0 -0
  164. data/test/data/A_21/triphenylene.mol +44 -0
  165. data/test/data/C00147.kcf +25 -0
  166. data/test/data/G00147.kcf +13 -0
  167. data/test/data/atp.mol +69 -0
  168. data/test/data/cyclohexane.mol +17 -0
  169. data/test/data/cyclohexane.ps +485 -0
  170. data/test/data/fullerene.mol +155 -0
  171. data/test/data/glycan +33 -0
  172. data/test/data/hypericin.cdx +0 -0
  173. data/test/data/hypericin.cdxml +596 -0
  174. data/test/data/hypericin.chm +0 -0
  175. data/test/data/hypericin.ct +85 -0
  176. data/test/data/hypericin.f1d +0 -0
  177. data/test/data/hypericin.f1q +0 -0
  178. data/test/data/hypericin.gif +0 -0
  179. data/test/data/hypericin.mol +88 -0
  180. data/test/data/hypericin.mol2 +159 -0
  181. data/test/data/hypericin.msm +123 -0
  182. data/test/data/hypericin.pdf +359 -0
  183. data/test/data/hypericin.png +0 -0
  184. data/test/data/hypericin.ps +0 -0
  185. data/test/data/hypericin.skc +0 -0
  186. data/test/data/hypericin2.gif +0 -0
  187. data/test/data/hypericin2.ps +0 -0
  188. data/test/data/kegg/genomes/hsa/hsa_enzyme.list +4 -0
  189. data/test/data/kegg/genomes/hsa/hsa_pfam.list +4 -0
  190. data/test/data/kegg/ligand/mol/C00147.mol +26 -0
  191. data/test/data/kegg/ligand/reaction +14 -0
  192. data/test/data/kegg/ligand/reaction.lst +1 -0
  193. data/test/data/kegg/ligand/reaction_mapformula.lst +3 -0
  194. data/test/data/reaction +14 -0
  195. data/test/data/reaction.lst +1 -0
  196. data/test/data/reaction_mapformula.lst +3 -0
  197. data/test/data/rxn/C00001.mol +6 -0
  198. data/test/data/rxn/C00011.mol +10 -0
  199. data/test/data/rxn/C00014.mol +6 -0
  200. data/test/data/rxn/C01010.mol +18 -0
  201. data/test/data/rxn/sample.rxn +50 -0
  202. data/test/data/rxn/substitution.rxn +45 -0
  203. data/test/data/test.eps +0 -0
  204. data/test/data/test.mol +28 -0
  205. data/test/data/test.sdf +143 -0
  206. data/test/data/test.skc +0 -0
  207. data/test/data/test.xyz +4 -0
  208. data/test/data/test_lf.sdf +143 -0
  209. data/test/heavy_test_pubchem.rb +16 -0
  210. data/test/multiple_test.rb +22 -0
  211. data/test/test_adj.rb +54 -0
  212. data/test/test_canonical_smiles.rb +46 -0
  213. data/test/test_cdx.rb +32 -0
  214. data/test/test_chem.rb +18 -0
  215. data/test/test_cluster.rb +19 -0
  216. data/test/test_db.rb +11 -0
  217. data/test/test_eps.rb +24 -0
  218. data/test/test_geometry.rb +11 -0
  219. data/test/test_gspan.rb +28 -0
  220. data/test/test_iupac.rb +36 -0
  221. data/test/test_kcf.rb +24 -0
  222. data/test/test_kcf_glycan.rb +10 -0
  223. data/test/test_kegg.rb +118 -0
  224. data/test/test_linucs.rb +21 -0
  225. data/test/test_mdl.rb +45 -0
  226. data/test/test_mol2.rb +62 -0
  227. data/test/test_morgan.rb +21 -0
  228. data/test/test_pdf.rb +12 -0
  229. data/test/test_prop.rb +86 -0
  230. data/test/test_rmagick.rb +15 -0
  231. data/test/test_sbdb.rb +23 -0
  232. data/test/test_sdf.rb +30 -0
  233. data/test/test_smiles.rb +84 -0
  234. data/test/test_sssr.rb +18 -0
  235. data/test/test_sub.rb +47 -0
  236. data/test/test_subcomp.rb +37 -0
  237. data/test/test_traverse.rb +29 -0
  238. data/test/test_writer.rb +13 -0
  239. data/test/test_xyz.rb +15 -0
  240. data/test/type_test.rb +25 -0
  241. metadata +290 -0
data/test/data/hypericin.pdf ADDED
@@ -0,0 +1,359 @@
1
+ %PDF-1.3
2
+ 1 0 obj
3
+ << /Type /Catalog
4
+ /Outlines 2 0 R
5
+ /Pages 3 0 R
6
+ >>
7
+ endobj
8
+ 2 0 obj
9
+ << /Type /Outlines
10
+ /Count 0
11
+ >>
12
+ endobj
13
+ 3 0 obj
14
+ << /Type /Pages
15
+ /Kids [ 4 0 R]
16
+ /Count 1
17
+ >>
18
+ endobj
19
+ 4 0 obj
20
+ << /Type /Page
21
+ /Parent 3 0 R
22
+ /MediaBox [ 0 0 612 792]
23
+ /Contents 5 0 R
24
+ /Resources << /ProcSet 6 0 R
25
+ /Font << /F1 7 0 R >>
26
+ >>
27
+ >>
28
+ endobj
29
+ 5 0 obj
30
+ << /Length 5366 >> stream
31
+ q
32
+ 1 0 0 1 10 30 cm
33
+ 0 0 0 RG
34
+ 190 230 m
35
+ 190 30 l
36
+ S
37
+ 0 0 0 RG
38
+ 190 230 m
39
+ 10 230 l
40
+ S
41
+ 0 0 0 RG
42
+ 190 30 m
43
+ 10 30 l
44
+ S
45
+ 0 0 0 RG
46
+ 10 230 m
47
+ 10 30 l
48
+ S
49
+ 0 0 0 RG
50
+ 40.0006998145491 167.016340669723 m
51
+ 40.0006998145491 143.922460547955 l
52
+ S
53
+ 0 0 0 RG
54
+ 40.0006998145491 143.922460547955 m
55
+ 60.0013996290983 132.375520487071 l
56
+ S
57
+ 0 0 0 RG
58
+ 43.7328108051366 145.767871514049 m
59
+ 59.733370656776 136.530319465342 l
60
+ S
61
+ 0 0 0 RG
62
+ 60.0013996290983 132.375520487071 m
63
+ 79.9993001854508 143.922460547955 l
64
+ S
65
+ 0 0 0 RG
66
+ 79.9993001854508 143.922460547955 m
67
+ 79.9993001854508 167.016340669723 l
68
+ S
69
+ 0 0 0 RG
70
+ 76.5352181671857 146.231848560132 m
71
+ 76.5352181671857 164.706952657546 l
72
+ S
73
+ 0 0 0 RG
74
+ 79.9993001854508 167.016340669723 m
75
+ 60.0013996290983 178.563280730606 l
76
+ S
77
+ 0 0 0 RG
78
+ 60.0013996290983 178.563280730606 m
79
+ 40.0006998145491 167.016340669723 l
80
+ S
81
+ 0 0 0 RG
82
+ 59.733370656776 174.408481752336 m
83
+ 43.7328108051366 165.170929703629 l
84
+ S
85
+ 0 0 0 RG
86
+ 79.9993001854508 143.922460547955 m
87
+ 100.0 132.375520487071 l
88
+ S
89
+ 0 0 0 RG
90
+ 100.0 132.375520487071 m
91
+ 120.000699814549 143.922460547955 l
92
+ S
93
+ 0 0 0 RG
94
+ 120.000699814549 143.922460547955 m
95
+ 120.000699814549 167.016340669723 l
96
+ S
97
+ 0 0 0 RG
98
+ 116.536617796284 146.231848560132 m
99
+ 116.536617796284 164.706952657546 l
100
+ S
101
+ 0 0 0 RG
102
+ 120.000699814549 167.016340669723 m
103
+ 100.0 178.563280730606 l
104
+ S
105
+ 0 0 0 RG
106
+ 100.0 178.563280730606 m
107
+ 79.9993001854508 167.016340669723 l
108
+ S
109
+ 0 0 0 RG
110
+ 120.000699814549 143.922460547955 m
111
+ 139.998600370902 132.375520487071 l
112
+ S
113
+ 0 0 0 RG
114
+ 139.998600370902 132.375520487071 m
115
+ 159.999300185451 143.922460547955 l
116
+ S
117
+ 0 0 0 RG
118
+ 140.266629343224 136.530319465342 m
119
+ 156.267189194863 145.767871514049 l
120
+ S
121
+ 0 0 0 RG
122
+ 159.999300185451 143.922460547955 m
123
+ 159.999300185451 167.016340669723 l
124
+ S
125
+ 0 0 0 RG
126
+ 159.999300185451 167.016340669723 m
127
+ 139.998600370902 178.563280730606 l
128
+ S
129
+ 0 0 0 RG
130
+ 156.267189194863 165.170929703629 m
131
+ 140.266629343224 174.408481752336 l
132
+ S
133
+ 0 0 0 RG
134
+ 139.998600370902 178.563280730606 m
135
+ 120.000699814549 167.016340669723 l
136
+ S
137
+ 0 0 0 RG
138
+ 60.0013996290983 132.375520487071 m
139
+ 60.0013996290983 109.281640365303 l
140
+ S
141
+ 0 0 0 RG
142
+ 60.0013996290983 109.281640365303 m
143
+ 79.9993001854508 97.7347003044193 l
144
+ S
145
+ 0 0 0 RG
146
+ 79.9993001854508 97.7347003044193 m
147
+ 100.0 109.281640365303 l
148
+ S
149
+ 0 0 0 RG
150
+ 100.0 109.281640365303 m
151
+ 100.0 132.375520487071 l
152
+ S
153
+ 0 0 0 RG
154
+ 96.5359179817348 111.59102837748 m
155
+ 96.5359179817348 130.066132474894 l
156
+ S
157
+ 0 0 0 RG
158
+ 100.0 109.281640365303 m
159
+ 120.000699814549 97.7347003044193 l
160
+ S
161
+ 0 0 0 RG
162
+ 120.000699814549 97.7347003044193 m
163
+ 139.998600370902 109.281640365303 l
164
+ S
165
+ 0 0 0 RG
166
+ 139.998600370902 109.281640365303 m
167
+ 139.998600370902 132.375520487071 l
168
+ S
169
+ 0 0 0 RG
170
+ 60.0013996290983 109.281640365303 m
171
+ 40.0006998145491 97.7347003044193 l
172
+ S
173
+ 0 0 0 RG
174
+ 59.733370656776 105.126841387032 m
175
+ 43.7328108051366 95.8892893383254 l
176
+ S
177
+ 0 0 0 RG
178
+ 40.0006998145491 97.7347003044193 m
179
+ 40.0006998145491 74.6408201826516 l
180
+ S
181
+ 0 0 0 RG
182
+ 40.0006998145491 74.6408201826516 m
183
+ 60.0013996290983 63.0938801217677 l
184
+ S
185
+ 0 0 0 RG
186
+ 43.7328108051366 76.4862311487456 m
187
+ 59.733370656776 67.2486791000385 l
188
+ S
189
+ 0 0 0 RG
190
+ 60.0013996290983 63.0938801217677 m
191
+ 79.9993001854508 74.6408201826516 l
192
+ S
193
+ 0 0 0 RG
194
+ 79.9993001854508 74.6408201826516 m
195
+ 79.9993001854508 97.7347003044193 l
196
+ S
197
+ 0 0 0 RG
198
+ 76.5352181671857 76.9502081948284 m
199
+ 76.5352181671857 95.4253122922426 l
200
+ S
201
+ 0 0 0 RG
202
+ 79.9993001854508 74.6408201826516 m
203
+ 100.0 63.0938801217677 l
204
+ S
205
+ 0 0 0 RG
206
+ 100.0 63.0938801217677 m
207
+ 120.000699814549 74.6408201826516 l
208
+ S
209
+ 0 0 0 RG
210
+ 120.000699814549 74.6408201826516 m
211
+ 120.000699814549 97.7347003044193 l
212
+ S
213
+ 0 0 0 RG
214
+ 116.536617796284 76.9502081948284 m
215
+ 116.536617796284 95.4253122922426 l
216
+ S
217
+ 0 0 0 RG
218
+ 120.000699814549 74.6408201826516 m
219
+ 139.998600370902 63.0938801217677 l
220
+ S
221
+ 0 0 0 RG
222
+ 139.998600370902 63.0938801217677 m
223
+ 159.999300185451 74.6408201826516 l
224
+ S
225
+ 0 0 0 RG
226
+ 140.266629343224 67.2486791000385 m
227
+ 156.267189194863 76.4862311487456 l
228
+ S
229
+ 0 0 0 RG
230
+ 159.999300185451 74.6408201826516 m
231
+ 159.999300185451 97.7347003044193 l
232
+ S
233
+ 0 0 0 RG
234
+ 159.999300185451 97.7347003044193 m
235
+ 139.998600370902 109.281640365303 l
236
+ S
237
+ 0 0 0 RG
238
+ 156.267189194863 95.8892893383253 m
239
+ 140.266629343224 105.126841387032 l
240
+ S
241
+ 0 0 0 RG
242
+ 60.0013996290983 178.563280730606 m
243
+ 60.0013996290983 196.057160852374 l
244
+ S
245
+ 0 0 0 RG
246
+ 40.0006998145491 143.922460547955 m
247
+ 24.8497915421259 135.175435128256 l
248
+ S
249
+ 0 0 0 RG
250
+ 100.0 178.563280730606 m
251
+ 100.0 196.057160852374 l
252
+ S
253
+ 0 0 0 RG
254
+ 96.5359179817348 180.872668742783 m
255
+ 96.5359179817348 193.747772840197 l
256
+ S
257
+ 0 0 0 RG
258
+ 139.998600370902 178.563280730606 m
259
+ 139.998600370902 196.057160852374 l
260
+ S
261
+ 0 0 0 RG
262
+ 159.999300185451 143.922460547955 m
263
+ 180.0 132.375520487071 l
264
+ S
265
+ 0 0 0 RG
266
+ 159.999300185451 97.7347003044193 m
267
+ 180.0 109.281640365303 l
268
+ S
269
+ 0 0 0 RG
270
+ 139.998600370902 63.0938801217677 m
271
+ 139.998600370902 45.6 l
272
+ S
273
+ 0 0 0 RG
274
+ 100.0 63.0938801217677 m
275
+ 100.0 45.6 l
276
+ S
277
+ 0 0 0 RG
278
+ 103.464082018265 60.784492109591 m
279
+ 103.464082018265 47.9093880121768 l
280
+ S
281
+ 0 0 0 RG
282
+ 60.0013996290983 63.0938801217677 m
283
+ 60.0013996290983 45.6 l
284
+ S
285
+ 0 0 0 RG
286
+ 40.0006998145491 97.7347003044193 m
287
+ 24.8497915421259 106.481725724118 l
288
+ S
289
+ BT
290
+ /F1 8.0 Tf
291
+ 1 0 0 1 56.8013996290983 198.457160852374 Tm
292
+ (O) Tj
293
+ ET
294
+ BT
295
+ /F1 8.0 Tf
296
+ 1 0 0 1 16.8 129.175520487071 Tm
297
+ (O) Tj
298
+ ET
299
+ BT
300
+ /F1 8.0 Tf
301
+ 1 0 0 1 96.8 198.457160852374 Tm
302
+ (O) Tj
303
+ ET
304
+ BT
305
+ /F1 8.0 Tf
306
+ 1 0 0 1 136.798600370902 198.457160852374 Tm
307
+ (O) Tj
308
+ ET
309
+ BT
310
+ /F1 8.0 Tf
311
+ 1 0 0 1 136.798600370902 36.8 Tm
312
+ (O) Tj
313
+ ET
314
+ BT
315
+ /F1 8.0 Tf
316
+ 1 0 0 1 96.8 36.8 Tm
317
+ (O) Tj
318
+ ET
319
+ BT
320
+ /F1 8.0 Tf
321
+ 1 0 0 1 56.8013996290983 36.8 Tm
322
+ (O) Tj
323
+ ET
324
+ BT
325
+ /F1 8.0 Tf
326
+ 1 0 0 1 16.8 106.081640365303 Tm
327
+ (O) Tj
328
+ ET
329
+ Q
330
+ endstream
331
+ endobj
332
+ 6 0 obj
333
+ [ /PDF /Text ]
334
+ endobj
335
+ 7 0 obj
336
+ << /Type /Font
337
+ /Subtype /Type1
338
+ /Name /F1
339
+ /BaseFont /Helvetica
340
+ /Encoding /MacRomanEncoding
341
+ >>
342
+ endobj
343
+ xref
344
+ 0 8
345
+ 0000000000 65535 f
346
+ 0000000009 00000 n
347
+ 0000000074 00000 n
348
+ 0000000120 00000 n
349
+ 0000000179 00000 n
350
+ 0000000364 00000 n
351
+ 0000000466 00000 n
352
+ 0000000496 00000 n
353
+ trailer
354
+ << /Size 8
355
+ /Root 1 0 R
356
+ >>
357
+ startxref
358
+ 625
359
+ %%EOF
data/test/data/hypericin.png ADDED
Binary file
data/test/data/hypericin.ps ADDED
File without changes
data/test/data/hypericin.skc ADDED
Binary file
data/test/data/hypericin2.gif ADDED
Binary file
data/test/data/hypericin2.ps ADDED
File without changes
data/test/data/kegg/genomes/hsa/hsa_enzyme.list ADDED
@@ -0,0 +1,4 @@
1
+ hsa:10 ec:2.3.1.5
2
+ hsa:100 ec:3.5.4.4
3
+ hsa:10000 ec:2.7.1.37
4
+ hsa:10003 ec:3.4.17.21
data/test/data/kegg/genomes/hsa/hsa_pfam.list ADDED
@@ -0,0 +1,4 @@
1
+ hsa:1 pf:DUF427
2
+ hsa:1 pf:ig
3
+ hsa:10 pf:Acetyltransf_2
4
+ hsa:100 pf:A_deaminase
data/test/data/kegg/ligand/mol/C00147.mol ADDED
@@ -0,0 +1,26 @@
1
+
2
+ ISISHOST03240423012D 1 1.00000 0.00000 145
3
+
4
+ 10 11 0 0 0 999 V2000
5
+ -0.2345 0.2862 0.0000 C 0 0 0 0 0 0 0 0 0
6
+ -0.2345 -0.6069 0.0000 C 0 0 0 0 0 0 0 0 0
7
+ 0.4517 0.6897 0.0000 C 0 0 0 0 0 0 0 0 0
8
+ -0.9379 0.5379 0.0000 N 0 0 0 0 0 0 0 0 0
9
+ 0.4724 -1.0310 0.0000 N 0 0 0 0 0 0 0 0 0
10
+ -0.9448 -0.8483 0.0000 N 0 0 0 0 0 0 0 0 0
11
+ 1.2069 0.2517 0.0000 N 0 0 0 0 0 0 0 0 0
12
+ 0.4517 1.4759 0.0000 N 0 0 0 0 0 0 0 0 0
13
+ -1.4345 -0.1379 0.0000 C 0 0 0 0 0 0 0 0 0
14
+ 1.2034 -0.6172 0.0000 C 0 0 0 0 0 0 0 0 0
15
+ 1 2 2 0 0 0
16
+ 1 3 1 0 0 0
17
+ 1 4 1 0 0 0
18
+ 2 5 1 0 0 0
19
+ 2 6 1 0 0 0
20
+ 3 7 2 0 0 0
21
+ 3 8 1 0 0 0
22
+ 4 9 2 0 0 0
23
+ 5 10 2 0 0 0
24
+ 6 9 1 0 0 0
25
+ 7 10 1 0 0 0
26
+ M END
data/test/data/kegg/ligand/reaction ADDED
@@ -0,0 +1,14 @@
1
+ ENTRY R00001 Reaction
2
+ NAME Dummy reaction
3
+ DEFINITION DNA + RNA <=> ATP
4
+ EQUATION C00100 + C00001 <=> C10000
5
+ RPAIR A02000
6
+ ENZYME 1.2.99.1
7
+ ///
8
+ ENTRY R00100 Reaction
9
+ NAME Dummy reaction2
10
+ DEFINITION Undecane + Dodecane <=> Tridecane
11
+ EQUATION C00890 + C00001 <=> C02174 + C12100
12
+ RPAIR A03000
13
+ ENZYME 3.6.1.-
14
+ ///
data/test/data/kegg/ligand/reaction.lst ADDED
@@ -0,0 +1 @@
1
+ R00001: 2 C00890 + C00001 <=> 2 C02174
data/test/data/kegg/ligand/reaction_mapformula.lst ADDED
@@ -0,0 +1,3 @@
1
+ R00001: 00190: C00147 => C00009
2
+ R00005: 00220: C01010 => C00011
3
+ R00005: 00791: C01010 <=> C00011
data/test/data/reaction ADDED
@@ -0,0 +1,14 @@
1
+ ENTRY R00001 Reaction
2
+ NAME Dummy reaction
3
+ DEFINITION DNA + RNA <=> ATP
4
+ EQUATION C00100 + C00001 <=> C10000
5
+ RPAIR A02000
6
+ ENZYME 1.2.99.1
7
+ ///
8
+ ENTRY R00100 Reaction
9
+ NAME Dummy reaction2
10
+ DEFINITION Undecane + Dodecane <=> Tridecane
11
+ EQUATION C00890 + C00001 <=> C02174 + C12100
12
+ RPAIR A03000
13
+ ENZYME 3.6.1.-
14
+ ///
data/test/data/reaction.lst ADDED
@@ -0,0 +1 @@
1
+ R00001: 2 C00890 + C00001 <=> 2 C02174