chemruby 0.9.3

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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
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+ 12 33 1 0
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+ 28 34 1 0
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+ 26 35 1 0
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+ 24 36 2 0
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+ 22 37 1 0
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+ 20 38 1 0
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+ M END
data/test/data/hypericin.mol2 ADDED
@@ -0,0 +1,159 @@
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+ # Name: Unnamed
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+ # Creating user name: miki
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+ # Creation time: Wed Sep 21 16:19:09 2005
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+
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+ # Modifying user name: miki
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+ # Modification time: Wed Sep 21 16:19:09 2005
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+
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+ @<TRIPOS>MOLECULE
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+ Unnamed
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+ 67 70 1 1 0
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+ SMALL
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+ GAST_HUCK
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+
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+
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+ @<TRIPOS>ATOM
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+ 7 C7 0.746489 1.629048 1.684431 C.3 1 <1> -0.049323
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+ 9 C9 2.204639 1.558281 2.204247 C.3 1 <1> -0.047008
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+ 38 H38 2.246632 1.059648 3.183891 H 1 <1> 0.026901
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+ 39 H39 2.556935 2.593046 2.349477 H 1 <1> 0.026901
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+ 40 H40 3.376532 -0.722093 -1.135023 H 1 <1> 0.027150
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+ 53 H53 5.780854 2.561980 1.940968 H 1 <1> 0.209900
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+ 60 H60 -4.920329 -2.301872 1.618476 H 1 <1> 0.024481
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+ 62 H62 -6.206665 0.073542 -2.726510 H 1 <1> 0.039061
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+ 63 H63 -5.868660 0.480866 -1.036373 H 1 <1> 0.039061
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+ 64 H64 -7.043130 -0.810931 -1.418049 H 1 <1> 0.039061
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+ 65 H65 -5.672092 -2.159679 -3.594598 H 1 <1> 0.039061
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+ 67 H67 -5.981755 -3.200901 -2.176024 H 1 <1> 0.039061
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+ @<TRIPOS>BOND
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+ 1 10 13 1
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+ 2 14 11 1
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+ 3 13 15 1
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+ 70 31 67 1
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+ @<TRIPOS>SUBSTRUCTURE
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+ 1 **** 1 TEMP 0 **** **** 0 ROOT
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+ @<TRIPOS>NORMAL
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+ @<TRIPOS>FF_PBC
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+ FORCE_FIELD_SETUP_FEATURE Force Field Setup information
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+ v1.0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 NONE 0 0 0 0 1 0 0 0 0 0 0 0 0
data/test/data/hypericin.msm ADDED
@@ -0,0 +1,123 @@
1
+ ! Polygen 133
2
+ ChemNote molecule file created by CS ChemDraw�
3
+ * File format version number
4
+ 90.0928
5
+ * File update version number
6
+ 92.0319
7
+ *
8
+ * molecule name
9
+ Undefined Name
10
+ * empirical formula
11
+ Undefined Empirical Formula
12
+ * need 3D conversion?
13
+ 1
14
+ * 3D displacement vector
15
+ 0.000 0.000 0.000
16
+ * 3D rotation matrix
17
+ 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000
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+ * 3D scale factor
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+ 0.000000
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+ * 2D scale factor
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+ 1.000000
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+ * 2D attributes
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+ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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+ * 3D attributes
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+ 0 0 0 0 0 0 0 0 0 0 0
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+ * Global display attributes
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+ 1 0 1 12 256
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+ * Atom List
29
+ * Atom# Lbl Type x y x y z bits chrg ichrg frag istp lp chrl ring frad name seg grp FLAGS sat dfoxid useroxid Sh_type Sh_nr Qstring
30
+ 1 C 255 -389 -299 0 0 0 1 0.0 0 00
31
+ 2 C 255 -389 -149 0 0 0 1 0.0 0 00
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+ 3 C 255 -259 -74 0 0 0 1 0.0 0 00
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+ 4 C 255 -129 -149 0 0 0 1 0.0 0 00
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+ 5 C 255 -129 -299 0 0 0 1 0.0 0 00
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+ 6 C 255 -259 -374 0 0 0 1 0.0 0 00
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+ 7 C 255 0 -74 0 0 0 1 0.0 0 00
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+ 8 C 255 130 -149 0 0 0 1 0.0 0 00
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+ 9 C 255 130 -299 0 0 0 1 0.0 0 00
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+ 10 C 255 0 -374 0 0 0 1 0.0 0 00
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+ 11 C 255 260 -74 0 0 0 1 0.0 0 00
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+ 12 C 255 390 -149 0 0 0 1 0.0 0 00
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+ 13 C 255 390 -299 0 0 0 1 0.0 0 00
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+ 14 C 255 260 -374 0 0 0 1 0.0 0 00
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+ 15 C 255 -259 75 0 0 0 1 0.0 0 00
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+ 16 C 255 -129 150 0 0 0 1 0.0 0 00
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+ 17 C 255 0 75 0 0 0 1 0.0 0 00
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+ 18 C 255 130 150 0 0 0 1 0.0 0 00
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+ 19 C 255 260 75 0 0 0 1 0.0 0 00
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+ 20 C 255 -389 150 0 0 0 1 0.0 0 00
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+ 21 C 255 -389 300 0 0 0 1 0.0 0 00
51
+ 22 C 255 -259 375 0 0 0 1 0.0 0 00
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+ 23 C 255 -129 300 0 0 0 1 0.0 0 00
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+ 24 C 255 0 375 0 0 0 1 0.0 0 00
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+ 25 C 255 130 300 0 0 0 1 0.0 0 00
55
+ 26 C 255 260 375 0 0 0 1 0.0 0 00
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+ 27 C 255 390 300 0 0 0 1 0.0 0 00
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+ 28 C 255 390 150 0 0 0 1 0.0 0 00
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+ 29 O 255 -259 -524 0 0 0 1 0.0 0 00
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+ 30 O 255 -519 -74 0 0 0 1 0.0 0 00
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+ 31 O 255 0 -524 0 0 0 1 0.0 0 00
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+ 32 O 255 260 -524 0 0 0 1 0.0 0 00
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+ 33 C 255 520 -74 0 0 0 1 0.0 0 00
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+ 34 C 255 520 75 0 0 0 1 0.0 0 00
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+ 35 O 255 260 525 0 0 0 1 0.0 0 00
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+ 36 O 255 0 525 0 0 0 1 0.0 0 00
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+ 37 O 255 -259 525 0 0 0 1 0.0 0 00
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+ 38 O 255 -519 75 0 0 0 1 0.0 0 00
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+ * Bond List
69
+ * Bond# bond_type atom1 atom2 cis/trans length locked ring Sh_type Sh_nr Qorder Qtopol Qstereo
70
+ 1 1 1 2
71
+ 2 2 2 3
72
+ 3 1 3 4
73
+ 4 2 4 5
74
+ 5 1 5 6
75
+ 6 2 6 1
76
+ 7 1 4 7
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+ 8 1 7 8
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+ 9 2 8 9
79
+ 10 1 9 10
80
+ 11 1 10 5
81
+ 12 1 8 11
82
+ 13 2 11 12
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+ 14 1 12 13
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+ 15 2 13 14
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+ 16 1 14 9
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+ 17 1 3 15
87
+ 18 1 15 16
88
+ 19 1 16 17
89
+ 20 2 17 7
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+ 21 1 17 18
91
+ 22 1 18 19
92
+ 23 1 19 11
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+ 24 2 15 20
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+ 25 1 20 21
95
+ 26 2 21 22
96
+ 27 1 22 23
97
+ 28 2 23 16
98
+ 29 1 23 24
99
+ 30 1 24 25
100
+ 31 2 25 18
101
+ 32 1 25 26
102
+ 33 2 26 27
103
+ 34 1 27 28
104
+ 35 2 28 19
105
+ 36 1 6 29
106
+ 37 1 2 30
107
+ 38 2 10 31
108
+ 39 1 14 32
109
+ 40 1 12 33
110
+ 41 1 28 34
111
+ 42 1 26 35
112
+ 43 2 24 36
113
+ 44 1 22 37
114
+ 45 1 20 38
115
+ * Fragment List
116
+ * Fgmt# Label Atoms
117
+ * Bond Angles
118
+ * bond1 bond2 angle locked
119
+ * Dihedral Angles
120
+ * at1-cons at1 at2 at2-cons angle locked
121
+ * Planarity data
122
+ * User data area
123
+ * End of File