rubabel 0.1.0

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 (34) hide show
  1. data/.document +5 -0
  2. data/.rspec +1 -0
  3. data/LICENSE +21 -0
  4. data/README.rdoc +52 -0
  5. data/Rakefile +43 -0
  6. data/VERSION +1 -0
  7. data/lib/rubabel.rb +116 -0
  8. data/lib/rubabel/atom.rb +143 -0
  9. data/lib/rubabel/bond.rb +47 -0
  10. data/lib/rubabel/fingerprint.rb +0 -0
  11. data/lib/rubabel/fragmentation.rb +23 -0
  12. data/lib/rubabel/molecule.rb +305 -0
  13. data/lib/rubabel/molecule_data.rb +0 -0
  14. data/lib/rubabel/pm.rb +38 -0
  15. data/lib/rubabel/smarts.rb +27 -0
  16. data/reference/OBConversion_methods.txt +47 -0
  17. data/reference/arity_method_list.txt +3553 -0
  18. data/reference/arity_method_list_CLASS.txt +337 -0
  19. data/reference/atom_methods.txt +145 -0
  20. data/reference/bond_methods.txt +79 -0
  21. data/reference/get_methods.rb +52 -0
  22. data/reference/mol_methods.txt +183 -0
  23. data/spec/rubabel/atom_spec.rb +49 -0
  24. data/spec/rubabel/bond_spec.rb +19 -0
  25. data/spec/rubabel/molecule_spec.rb +91 -0
  26. data/spec/rubabel_spec.rb +67 -0
  27. data/spec/spec_helper.rb +12 -0
  28. data/spec/testfiles/7-oxocholesterol-d7.mol +97 -0
  29. data/spec/testfiles/7-oxocholesterol-d7.sdf +155 -0
  30. data/spec/testfiles/Samples.sdf +2441 -0
  31. data/spec/testfiles/cholesterol.mol +74 -0
  32. data/spec/testfiles/cholesterol.sdf +132 -0
  33. data/spec/testfiles/two.sdf +287 -0
  34. metadata +130 -0
data/spec/testfiles/cholesterol.mol ADDED
@@ -0,0 +1,74 @@
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+ LMST01010001
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+ LIPDMAPS04301221562D
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+
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+ 33 36 0 0 0 0 0 0 0 0999 V2000
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+ 9.0635 6.4671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.0590 8.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.3505 7.6906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.3577 6.8727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7751 7.6987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7722 6.8801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.1892 6.8751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.1921 7.6938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.4850 8.1081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.0612 7.2698 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7492 8.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.4762 8.9040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.1812 9.3042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.4861 9.7068 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.8717 8.9023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 12.5651 9.2993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 13.2556 8.8975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 13.9489 9.2945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7713 6.0846 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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+ 13.2556 8.0895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.6535 6.4671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.6535 5.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.3577 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.8525 9.2963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 5 11 1 1 0 0 0
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+ 9 12 1 0 0 0 0
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+ 12 13 1 0 0 0 0
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+ 12 14 1 1 0 0 0
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+ 13 15 1 0 0 0 0
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+ 15 16 1 0 0 0 0
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+ 16 17 1 0 0 0 0
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+ 17 18 1 0 0 0 0
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+ 6 19 1 6 0 0 0
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+ 17 20 1 0 0 0 0
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+ 4 21 1 0 0 0 0
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+ 21 22 1 0 0 0 0
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+ 27 30 1 1 0 0 0
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+ 9 31 1 6 0 0 0
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+ 12 32 1 6 0 0 0
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+ 4 33 1 6 0 0 0
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+ M END
data/spec/testfiles/cholesterol.sdf ADDED
@@ -0,0 +1,132 @@
1
+ LMST01010001
2
+ LIPDMAPS04301223002D
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+
4
+ 33 36 0 0 0 0 0 0 0 0999 V2000
5
+ 9.0635 6.4671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.0590 8.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.3505 7.6906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.3577 6.8727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7751 7.6987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7722 6.8801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.1892 6.8751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.1921 7.6938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.4850 8.1081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.0612 7.2698 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7492 8.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.4762 8.9040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.1812 9.3042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.4861 9.7068 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.8717 8.9023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 12.5651 9.2993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 13.2556 8.8975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 13.9489 9.2945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7713 6.0846 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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+ 13.2556 8.0895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.6535 6.4671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.6535 5.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 8.3577 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.0635 5.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 6.9538 6.8711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 6.2541 6.4671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 6.2541 5.6592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 6.9538 5.2553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 7.6535 7.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 5.5544 5.2553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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+ 11.1832 8.4172 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.8525 9.2963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 1 4 1 0 0 0 0
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+ 15 16 1 0 0 0 0
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+ 16 17 1 0 0 0 0
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+ 17 18 1 0 0 0 0
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+ 6 19 1 6 0 0 0
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+ 17 20 1 0 0 0 0
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+ 4 21 1 0 0 0 0
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+ 21 22 1 0 0 0 0
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+ 22 23 2 0 0 0 0
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+ 23 24 1 0 0 0 0
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+ 24 1 1 0 0 0 0
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+ 21 25 1 0 0 0 0
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+ 25 26 1 0 0 0 0
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+ 26 27 1 0 0 0 0
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+ 27 28 1 0 0 0 0
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+ 28 22 1 0 0 0 0
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+ 21 29 1 1 0 0 0
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+ 27 30 1 1 0 0 0
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+ 9 31 1 6 0 0 0
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+ 12 32 1 6 0 0 0
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+ 4 33 1 6 0 0 0
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+ M END
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+ > <LM_ID>
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+ LMST01010001
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+
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+ > <COMMON_NAME>
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+ Cholesterol
80
+
81
+ > <SYSTEMATIC_NAME>
82
+ cholest-5-en-3beta-ol
83
+
84
+ > <FORMULA>
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+ C27H46O
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+
87
+ > <MASS>
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+ 386.35
89
+
90
+ > <CATEGORY>
91
+ Sterol Lipids [ST]
92
+
93
+ > <MAIN_CLASS>
94
+ Sterols [ST01]
95
+
96
+ > <SUB_CLASS>
97
+ Cholesterol and derivatives [ST0101]
98
+
99
+ > <SYNONYMS>
100
+ Cholesterol; Cholest-5-en-3-ol; (3beta)-Cholest-5-en-3-ol; Cholesteryl alcohol
101
+
102
+ > <KEGG_ID>
103
+ C00187
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+
105
+ > <HMDB_ID>
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+ HMDB00067
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+
108
+ > <CHEBI_ID>
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+ 16113
110
+
111
+ > <METABOLOMICS_ID>
112
+ -
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+
114
+ > <PUBCHEM_SUBSTANCE_ID>
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+ 4266362
116
+
117
+ > <LIPIDBANK_ID>
118
+ SST9061
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+
120
+ > <LIPIDAT_ID>
121
+ -
122
+
123
+ > <STATUS>
124
+ Active
125
+
126
+ > <REFS>
127
+ -
128
+
129
+ > <LIPID_MAPS_URL>
130
+ http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMST01010001
131
+
132
+ $$$$
data/spec/testfiles/two.sdf ADDED
@@ -0,0 +1,287 @@
1
+ LMST01010005
2
+ LIPDMAPS04301223002D
3
+
4
+ 41 44 0 0 0 0 0 0 0 0999 V2000
5
+ 9.1152 6.1944 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 17 38 1 0 0 0 0
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+ 38 39 1 0 0 0 0
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+ 38 40 1 0 0 0 0
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+ 38 41 1 0 0 0 0
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+ M STY 2 1 SUP 2 SUP
91
+ M SAL 1 4 34 35 36 37
92
+ M SBL 1 1 37
93
+ M SMT 1 CD3
94
+ M SAL 2 4 38 39 40 41
95
+ M SBL 2 1 41
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+ M SMT 2 CD3
97
+ M END
98
+ > <LM_ID>
99
+ LMST01010005
100
+
101
+ > <COMMON_NAME>
102
+ 7-oxocholesterol(d7)
103
+
104
+ > <SYSTEMATIC_NAME>
105
+ 7-oxo-cholest-5-en-3beta-ol(d7)
106
+
107
+ > <FORMULA>
108
+ C27H37D7O2
109
+
110
+ > <MASS>
111
+ 407.38
112
+
113
+ > <CATEGORY>
114
+ Sterol Lipids [ST]
115
+
116
+ > <MAIN_CLASS>
117
+ Sterols [ST01]
118
+
119
+ > <SUB_CLASS>
120
+ Cholesterol and derivatives [ST0101]
121
+
122
+ > <SYNONYMS>
123
+ -
124
+
125
+ > <KEGG_ID>
126
+ -
127
+
128
+ > <HMDB_ID>
129
+ HMDB00501
130
+
131
+ > <CHEBI_ID>
132
+ -
133
+
134
+ > <METABOLOMICS_ID>
135
+ -
136
+
137
+ > <PUBCHEM_SUBSTANCE_ID>
138
+ 4266366
139
+
140
+ > <LIPIDBANK_ID>
141
+ -
142
+
143
+ > <LIPIDAT_ID>
144
+ -
145
+
146
+ > <STATUS>
147
+ Active
148
+
149
+ > <REFS>
150
+ -
151
+
152
+ > <LIPID_MAPS_URL>
153
+ http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMST01010005
154
+ $$$$
155
+
156
+ LMST01010001
157
+ LIPDMAPS04301223002D
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+
159
+ 33 36 0 0 0 0 0 0 0 0999 V2000
160
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204
+ 5 11 1 1 0 0 0
205
+ 9 12 1 0 0 0 0
206
+ 12 13 1 0 0 0 0
207
+ 12 14 1 1 0 0 0
208
+ 13 15 1 0 0 0 0
209
+ 15 16 1 0 0 0 0
210
+ 16 17 1 0 0 0 0
211
+ 17 18 1 0 0 0 0
212
+ 6 19 1 6 0 0 0
213
+ 17 20 1 0 0 0 0
214
+ 4 21 1 0 0 0 0
215
+ 21 22 1 0 0 0 0
216
+ 22 23 2 0 0 0 0
217
+ 23 24 1 0 0 0 0
218
+ 24 1 1 0 0 0 0
219
+ 21 25 1 0 0 0 0
220
+ 25 26 1 0 0 0 0
221
+ 26 27 1 0 0 0 0
222
+ 27 28 1 0 0 0 0
223
+ 28 22 1 0 0 0 0
224
+ 21 29 1 1 0 0 0
225
+ 27 30 1 1 0 0 0
226
+ 9 31 1 6 0 0 0
227
+ 12 32 1 6 0 0 0
228
+ 4 33 1 6 0 0 0
229
+ M END
230
+ > <LM_ID>
231
+ LMST01010001
232
+
233
+ > <COMMON_NAME>
234
+ Cholesterol
235
+
236
+ > <SYSTEMATIC_NAME>
237
+ cholest-5-en-3beta-ol
238
+
239
+ > <FORMULA>
240
+ C27H46O
241
+
242
+ > <MASS>
243
+ 386.35
244
+
245
+ > <CATEGORY>
246
+ Sterol Lipids [ST]
247
+
248
+ > <MAIN_CLASS>
249
+ Sterols [ST01]
250
+
251
+ > <SUB_CLASS>
252
+ Cholesterol and derivatives [ST0101]
253
+
254
+ > <SYNONYMS>
255
+ Cholesterol; Cholest-5-en-3-ol; (3beta)-Cholest-5-en-3-ol; Cholesteryl alcohol
256
+
257
+ > <KEGG_ID>
258
+ C00187
259
+
260
+ > <HMDB_ID>
261
+ HMDB00067
262
+
263
+ > <CHEBI_ID>
264
+ 16113
265
+
266
+ > <METABOLOMICS_ID>
267
+ -
268
+
269
+ > <PUBCHEM_SUBSTANCE_ID>
270
+ 4266362
271
+
272
+ > <LIPIDBANK_ID>
273
+ SST9061
274
+
275
+ > <LIPIDAT_ID>
276
+ -
277
+
278
+ > <STATUS>
279
+ Active
280
+
281
+ > <REFS>
282
+ -
283
+
284
+ > <LIPID_MAPS_URL>
285
+ http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMST01010001
286
+
287
+ $$$$