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
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- 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
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- data/lib/chem/db/linucs/linparser.rb +144 -0
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- data/lib/chem/db/mdl.rb +379 -0
- data/lib/chem/db/molconnz.rb +12 -0
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- data/lib/chem/db/rmagick.rb +70 -0
- data/lib/chem/db/sdf.rb +37 -0
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- data/lib/chem/db/smiles.rb +2 -0
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- data/lib/chem/db/types/type_cansmi.rb +9 -0
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- 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
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- data/lib/chem/db/types/type_sdf.rb +25 -0
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- data/lib/chem/utils.rb +11 -0
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- data/lib/chem/utils/graph_db.rb +146 -0
- data/lib/chem/utils/math.rb +17 -0
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- data/lib/chem/utils/sssr.rb +101 -0
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- data/lib/chem/utils/transform.rb +110 -0
- data/lib/chem/utils/traverse.rb +37 -0
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- 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/data/kegg/genomes/hsa/hsa_enzyme.list +4 -0
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ISISHOST03240423012D 1 1.00000 0.00000 145
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10 11 0 0 0 999 V2000
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M END
|
@@ -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
|
+
///
|
@@ -0,0 +1 @@
|
|
1
|
+
R00001: 2 C00890 + C00001 <=> 2 C02174
|
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
|
+
///
|
@@ -0,0 +1 @@
|
|
1
|
+
R00001: 2 C00890 + C00001 <=> 2 C02174
|