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/test/all.rb +6 -0
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- data/test/ctab_test.rb +31 -0
- data/test/data/A_21.tar.gz +0 -0
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- data/test/data/A_21/phenalene.cdx +0 -0
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- data/test/data/A_21/phenanthrene.cdx +0 -0
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- data/test/data/A_21/picene.cdx +0 -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
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- data/test/data/hypericin.ct +85 -0
- data/test/data/hypericin.f1d +0 -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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- data/test/heavy_test_pubchem.rb +16 -0
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- data/test/test_canonical_smiles.rb +46 -0
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|
+
60 Hexacontane
|
|
37
|
+
70 Heptacontane
|
|
38
|
+
80 Octacontane
|
|
39
|
+
90 Nonacontane
|
|
40
|
+
100 Hectane
|
|
41
|
+
132 Dotriacontahectane
|
|
Binary file
|
|
@@ -0,0 +1,44 @@
|
|
|
1
|
+
naphthacene.mol
|
|
2
|
+
ChemDraw06220510362D
|
|
3
|
+
|
|
4
|
+
18 21 0 0 0 0 0 0 0 0999 V2000
|
|
5
|
+
2.1434 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6
|
+
2.8579 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7
|
+
2.8579 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
8
|
+
2.1434 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9
|
+
1.4289 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10
|
+
0.7145 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11
|
+
-0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
12
|
+
-0.7145 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
13
|
+
-1.4289 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
14
|
+
-2.1434 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
15
|
+
-2.8579 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
16
|
+
-2.8579 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
17
|
+
-2.1434 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
18
|
+
-1.4289 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
19
|
+
-0.7145 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
20
|
+
0.0000 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
21
|
+
0.7145 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
22
|
+
1.4289 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
23
|
+
1 2 1 0
|
|
24
|
+
2 3 2 0
|
|
25
|
+
3 4 1 0
|
|
26
|
+
4 5 2 0
|
|
27
|
+
5 6 1 0
|
|
28
|
+
6 7 2 0
|
|
29
|
+
7 8 1 0
|
|
30
|
+
8 9 2 0
|
|
31
|
+
9 10 1 0
|
|
32
|
+
10 11 2 0
|
|
33
|
+
11 12 1 0
|
|
34
|
+
12 13 2 0
|
|
35
|
+
13 14 1 0
|
|
36
|
+
9 14 1 0
|
|
37
|
+
14 15 2 0
|
|
38
|
+
15 16 1 0
|
|
39
|
+
7 16 1 0
|
|
40
|
+
16 17 2 0
|
|
41
|
+
17 18 1 0
|
|
42
|
+
5 18 1 0
|
|
43
|
+
1 18 2 0
|
|
44
|
+
M END
|