chemruby 0.9.3
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- data/README +120 -0
- data/Rakefile +195 -0
- data/ext/extconf.rb +4 -0
- data/ext/subcomp.c +416 -0
- data/lib/chem.rb +130 -0
- data/lib/chem/appl.rb +1 -0
- data/lib/chem/appl/chem3dole.rb +36 -0
- data/lib/chem/appl/tinker/nucleic.rb +40 -0
- data/lib/chem/appl/tinker/tinker_reader.rb +43 -0
- data/lib/chem/data.rb +4 -0
- data/lib/chem/data/atomic_weight.rb +124 -0
- data/lib/chem/data/character.rb +2 -0
- data/lib/chem/data/electronegativity.rb +14 -0
- data/lib/chem/data/periodic_table.rb +6 -0
- data/lib/chem/data/prime_numbers.rb +1 -0
- data/lib/chem/data/vdw_radii.rb +1 -0
- data/lib/chem/db.rb +64 -0
- data/lib/chem/db/cansmi.rb +234 -0
- data/lib/chem/db/cdx.rb +1525 -0
- data/lib/chem/db/eps.rb +164 -0
- data/lib/chem/db/g98.rb +909 -0
- data/lib/chem/db/gspan.rb +130 -0
- data/lib/chem/db/iupac.rb +5 -0
- data/lib/chem/db/iupac/a_1.rb +46 -0
- data/lib/chem/db/iupac/iuparser.rb +226 -0
- data/lib/chem/db/iupac/iuparser.ry +97 -0
- data/lib/chem/db/iupac/postfix.rb +2 -0
- data/lib/chem/db/kcf.rb +390 -0
- data/lib/chem/db/kcf_glycan.rb +19 -0
- data/lib/chem/db/kegg.rb +516 -0
- data/lib/chem/db/linucs/linparser.rb +144 -0
- data/lib/chem/db/linucs/linucs.ry +53 -0
- data/lib/chem/db/mdl.rb +379 -0
- data/lib/chem/db/molconnz.rb +12 -0
- data/lib/chem/db/mopac.rb +88 -0
- data/lib/chem/db/msi.rb +107 -0
- data/lib/chem/db/pdb_dic.rb +115 -0
- data/lib/chem/db/pdf.rb +131 -0
- data/lib/chem/db/pubchem.rb +113 -0
- data/lib/chem/db/rmagick.rb +70 -0
- data/lib/chem/db/sdf.rb +37 -0
- data/lib/chem/db/smbl.rb +88 -0
- data/lib/chem/db/smiles.rb +2 -0
- data/lib/chem/db/smiles/smiles.ry +203 -0
- data/lib/chem/db/smiles/smiparser.rb +375 -0
- data/lib/chem/db/swf.rb +74 -0
- data/lib/chem/db/sybyl.rb +150 -0
- data/lib/chem/db/tinker.rb +77 -0
- data/lib/chem/db/types/type_cansmi.rb +9 -0
- data/lib/chem/db/types/type_cdx.rb +24 -0
- data/lib/chem/db/types/type_gspan.rb +31 -0
- data/lib/chem/db/types/type_kcf.rb +28 -0
- data/lib/chem/db/types/type_kcf_glycan.rb +26 -0
- data/lib/chem/db/types/type_kegg.rb +92 -0
- data/lib/chem/db/types/type_mdl.rb +31 -0
- data/lib/chem/db/types/type_pdf.rb +33 -0
- data/lib/chem/db/types/type_png.rb +31 -0
- data/lib/chem/db/types/type_rxn.rb +25 -0
- data/lib/chem/db/types/type_sdf.rb +25 -0
- data/lib/chem/db/types/type_sybyl.rb +30 -0
- data/lib/chem/db/types/type_xyz.rb +26 -0
- data/lib/chem/db/vector.rb +128 -0
- data/lib/chem/db/xyz.rb +39 -0
- data/lib/chem/model.rb +119 -0
- data/lib/chem/model/skeleton.rb +37 -0
- data/lib/chem/utils.rb +11 -0
- data/lib/chem/utils/geometry.rb +27 -0
- data/lib/chem/utils/graph_db.rb +146 -0
- data/lib/chem/utils/math.rb +17 -0
- data/lib/chem/utils/prop.rb +123 -0
- data/lib/chem/utils/sssr.rb +101 -0
- data/lib/chem/utils/sub.rb +78 -0
- data/lib/chem/utils/transform.rb +110 -0
- data/lib/chem/utils/traverse.rb +37 -0
- data/lib/chem/utils/ullmann.rb +134 -0
- data/lib/graph.rb +41 -0
- data/lib/graph/cluster.rb +20 -0
- data/lib/graph/morgan.rb +38 -0
- data/sample/frequent_subgraph.rb +46 -0
- data/sample/images/ex1.rb +11 -0
- data/sample/images/ex2.rb +4 -0
- data/sample/images/ex3.rb +5 -0
- data/sample/images/ex4.rb +17 -0
- data/sample/images/ex5.rb +10 -0
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- data/setup.rb +1551 -0
- data/test/all.rb +6 -0
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- data/test/ctab_test.rb +31 -0
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- data/test/data/A_21/triphenylene.cdx +0 -0
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- data/test/data/C00147.kcf +25 -0
- data/test/data/G00147.kcf +13 -0
- data/test/data/atp.mol +69 -0
- data/test/data/cyclohexane.mol +17 -0
- data/test/data/cyclohexane.ps +485 -0
- data/test/data/fullerene.mol +155 -0
- data/test/data/glycan +33 -0
- data/test/data/hypericin.cdx +0 -0
- data/test/data/hypericin.cdxml +596 -0
- data/test/data/hypericin.chm +0 -0
- data/test/data/hypericin.ct +85 -0
- data/test/data/hypericin.f1d +0 -0
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- data/test/data/hypericin.gif +0 -0
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- data/test/data/hypericin.mol2 +159 -0
- data/test/data/hypericin.msm +123 -0
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- data/test/data/kegg/genomes/hsa/hsa_enzyme.list +4 -0
- data/test/data/kegg/genomes/hsa/hsa_pfam.list +4 -0
- data/test/data/kegg/ligand/mol/C00147.mol +26 -0
- data/test/data/kegg/ligand/reaction +14 -0
- data/test/data/kegg/ligand/reaction.lst +1 -0
- data/test/data/kegg/ligand/reaction_mapformula.lst +3 -0
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- data/test/data/reaction_mapformula.lst +3 -0
- data/test/data/rxn/C00001.mol +6 -0
- data/test/data/rxn/C00011.mol +10 -0
- data/test/data/rxn/C00014.mol +6 -0
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- data/test/data/rxn/sample.rxn +50 -0
- data/test/data/rxn/substitution.rxn +45 -0
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- data/test/data/test.sdf +143 -0
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ENTRY C00147 Compound
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///
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data/test/data/atp.mol
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2.4765 0.9902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
20
|
+
2.9582 0.3213 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
|
21
|
+
3.7432 0.5727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
22
|
+
3.7468 1.3970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
23
|
+
4.4519 2.6378 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
24
|
+
-1.1542 -0.5208 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0
|
25
|
+
-1.9792 -0.5208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
26
|
+
-1.1583 0.3042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
27
|
+
-1.1583 -1.3458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
28
|
+
-2.8042 -0.5167 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0
|
29
|
+
-3.6292 -0.5125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
30
|
+
-2.8000 0.3083 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
31
|
+
-2.8083 -1.3417 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
32
|
+
-4.4542 -0.5125 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0
|
33
|
+
-5.2792 -0.5125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
34
|
+
-4.4542 0.3125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
35
|
+
-4.4542 -1.3375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
36
|
+
8 9 1 1 0 0 0
|
37
|
+
9 4 1 0 0 0 0
|
38
|
+
6 1 1 6 0 0 0
|
39
|
+
14 15 2 0 0 0 0
|
40
|
+
16 17 1 0 0 0 0
|
41
|
+
18 14 1 0 0 0 0
|
42
|
+
15 16 1 0 0 0 0
|
43
|
+
5 16 1 1 0 0 0
|
44
|
+
7 2 1 6 0 0 0
|
45
|
+
13 19 1 0 0 0 0
|
46
|
+
4 20 1 0 0 0 0
|
47
|
+
17 10 1 0 0 0 0
|
48
|
+
20 21 1 0 0 0 0
|
49
|
+
8 3 1 0 0 0 0
|
50
|
+
20 22 2 0 0 0 0
|
51
|
+
10 11 2 0 0 0 0
|
52
|
+
20 23 1 0 0 0 0
|
53
|
+
8 7 1 0 0 0 0
|
54
|
+
21 24 1 0 0 0 0
|
55
|
+
11 12 1 0 0 0 0
|
56
|
+
24 25 1 0 0 0 0
|
57
|
+
3 5 1 0 0 0 0
|
58
|
+
24 26 2 0 0 0 0
|
59
|
+
12 13 2 0 0 0 0
|
60
|
+
24 27 1 0 0 0 0
|
61
|
+
13 18 1 0 0 0 0
|
62
|
+
25 28 1 0 0 0 0
|
63
|
+
17 18 2 0 0 0 0
|
64
|
+
28 29 1 0 0 0 0
|
65
|
+
7 6 1 0 0 0 0
|
66
|
+
28 30 2 0 0 0 0
|
67
|
+
5 6 1 0 0 0 0
|
68
|
+
28 31 1 0 0 0 0
|
69
|
+
M END
|