chemruby 0.9.3
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/sample/images/mol/adenine.mol +26 -0
- data/sample/images/mol/atp.mol +69 -0
- data/sample/images/temp/ex5.mol +344 -0
- data/sample/kegg_db.rb +116 -0
- data/setup.rb +1551 -0
- data/test/all.rb +6 -0
- data/test/coord_test.rb +17 -0
- data/test/ctab_test.rb +31 -0
- data/test/data/A_21.tar.gz +0 -0
- data/test/data/A_21/aceanthrylene.cdx +0 -0
- data/test/data/A_21/aceanthrylene.mol +40 -0
- data/test/data/A_21/acenaphthylene.cdx +0 -0
- data/test/data/A_21/acenaphthylene.mol +31 -0
- data/test/data/A_21/acephenanthrylene.cdx +0 -0
- data/test/data/A_21/acephenanthrylene.mol +40 -0
- data/test/data/A_21/anthracene.cdx +0 -0
- data/test/data/A_21/anthracene.mol +35 -0
- data/test/data/A_21/as-indacene.cdx +0 -0
- data/test/data/A_21/as-indacene.mol +31 -0
- data/test/data/A_21/azulene.cdx +0 -0
- data/test/data/A_21/azulene.mol +26 -0
- data/test/data/A_21/biphenylene.cdx +0 -0
- data/test/data/A_21/biphenylene.mol +31 -0
- data/test/data/A_21/chrysene.cdx +0 -0
- data/test/data/A_21/chrysene.mol +44 -0
- data/test/data/A_21/coronen.cdx +0 -0
- data/test/data/A_21/coronen.mol +59 -0
- data/test/data/A_21/fluoranthene.cdx +0 -0
- data/test/data/A_21/fluoranthene.mol +40 -0
- data/test/data/A_21/fluorene.cdx +0 -0
- data/test/data/A_21/fluorene.mol +33 -0
- data/test/data/A_21/heptacene.cdx +0 -0
- data/test/data/A_21/heptacene.mol +71 -0
- data/test/data/A_21/heptalene.cdx +0 -0
- data/test/data/A_21/heptalene.mol +30 -0
- data/test/data/A_21/heptaphene.cdx +0 -0
- data/test/data/A_21/heptaphene.mol +71 -0
- data/test/data/A_21/hexacene.cdx +0 -0
- data/test/data/A_21/hexacene.mol +62 -0
- data/test/data/A_21/hexaphene.cdx +0 -0
- data/test/data/A_21/hexaphene.mol +62 -0
- data/test/data/A_21/indene.cdx +0 -0
- data/test/data/A_21/indene.mol +24 -0
- data/test/data/A_21/iupac.txt +41 -0
- data/test/data/A_21/naphthacene.cdx +0 -0
- data/test/data/A_21/naphthacene.mol +44 -0
- data/test/data/A_21/naphthalene.cdx +0 -0
- data/test/data/A_21/naphthalene.mol +26 -0
- data/test/data/A_21/ovalene.cdx +0 -0
- data/test/data/A_21/ovalene.mol +78 -0
- data/test/data/A_21/pentacene.cdx +0 -0
- data/test/data/A_21/pentacene.mol +53 -0
- data/test/data/A_21/pentalene.cdx +0 -0
- data/test/data/A_21/pentalene.mol +22 -0
- data/test/data/A_21/pentaphene.cdx +0 -0
- data/test/data/A_21/pentaphene.mol +53 -0
- data/test/data/A_21/perylene.cdx +0 -0
- data/test/data/A_21/perylene.mol +49 -0
- data/test/data/A_21/phenalene.cdx +0 -0
- data/test/data/A_21/phenalene.mol +33 -0
- data/test/data/A_21/phenanthrene.cdx +0 -0
- data/test/data/A_21/phenanthrene.mol +35 -0
- data/test/data/A_21/picene.cdx +0 -0
- data/test/data/A_21/picene.mol +53 -0
- data/test/data/A_21/pleiadene.cdx +0 -0
- data/test/data/A_21/pleiadene.mol +44 -0
- data/test/data/A_21/pyranthrene.cdx +0 -0
- data/test/data/A_21/pyranthrene.mol +72 -0
- data/test/data/A_21/pyrene.cdx +0 -0
- data/test/data/A_21/pyrene.mol +40 -0
- data/test/data/A_21/rubicene.cdx +0 -0
- data/test/data/A_21/rubicene.mol +63 -0
- data/test/data/A_21/s-indacene.cdx +0 -0
- data/test/data/A_21/s-indacene.mol +31 -0
- data/test/data/A_21/tetraphenylene.cdx +0 -0
- data/test/data/A_21/tetraphenylene.mol +57 -0
- data/test/data/A_21/trinaphthylene.cdx +0 -0
- data/test/data/A_21/trinaphthylene.mol +71 -0
- data/test/data/A_21/triphenylene.cdx +0 -0
- data/test/data/A_21/triphenylene.mol +44 -0
- 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
- data/test/data/hypericin.f1q +0 -0
- data/test/data/hypericin.gif +0 -0
- data/test/data/hypericin.mol +88 -0
- data/test/data/hypericin.mol2 +159 -0
- data/test/data/hypericin.msm +123 -0
- data/test/data/hypericin.pdf +359 -0
- data/test/data/hypericin.png +0 -0
- data/test/data/hypericin.ps +0 -0
- data/test/data/hypericin.skc +0 -0
- data/test/data/hypericin2.gif +0 -0
- data/test/data/hypericin2.ps +0 -0
- 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
- data/test/data/reaction +14 -0
- data/test/data/reaction.lst +1 -0
- 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
- data/test/data/rxn/C01010.mol +18 -0
- data/test/data/rxn/sample.rxn +50 -0
- data/test/data/rxn/substitution.rxn +45 -0
- data/test/data/test.eps +0 -0
- data/test/data/test.mol +28 -0
- data/test/data/test.sdf +143 -0
- data/test/data/test.skc +0 -0
- data/test/data/test.xyz +4 -0
- data/test/data/test_lf.sdf +143 -0
- data/test/heavy_test_pubchem.rb +16 -0
- data/test/multiple_test.rb +22 -0
- data/test/test_adj.rb +54 -0
- data/test/test_canonical_smiles.rb +46 -0
- data/test/test_cdx.rb +32 -0
- data/test/test_chem.rb +18 -0
- data/test/test_cluster.rb +19 -0
- data/test/test_db.rb +11 -0
- data/test/test_eps.rb +24 -0
- data/test/test_geometry.rb +11 -0
- data/test/test_gspan.rb +28 -0
- data/test/test_iupac.rb +36 -0
- data/test/test_kcf.rb +24 -0
- data/test/test_kcf_glycan.rb +10 -0
- data/test/test_kegg.rb +118 -0
- data/test/test_linucs.rb +21 -0
- data/test/test_mdl.rb +45 -0
- data/test/test_mol2.rb +62 -0
- data/test/test_morgan.rb +21 -0
- data/test/test_pdf.rb +12 -0
- data/test/test_prop.rb +86 -0
- data/test/test_rmagick.rb +15 -0
- data/test/test_sbdb.rb +23 -0
- data/test/test_sdf.rb +30 -0
- data/test/test_smiles.rb +84 -0
- data/test/test_sssr.rb +18 -0
- data/test/test_sub.rb +47 -0
- data/test/test_subcomp.rb +37 -0
- data/test/test_traverse.rb +29 -0
- data/test/test_writer.rb +13 -0
- data/test/test_xyz.rb +15 -0
- data/test/type_test.rb +25 -0
- metadata +290 -0
@@ -0,0 +1,37 @@
|
|
1
|
+
# $Id: test_subcomp.rb 101 2006-01-06 22:26:49Z tanaka $
|
2
|
+
|
3
|
+
require 'test/unit'
|
4
|
+
require 'test/all'
|
5
|
+
|
6
|
+
require 'chem'
|
7
|
+
|
8
|
+
class SubcompTest < Test::Unit::TestCase
|
9
|
+
|
10
|
+
def setup
|
11
|
+
@mol = Chem.open_mol($data_dir + 'hypericin.mol')
|
12
|
+
end
|
13
|
+
|
14
|
+
# def test_mol
|
15
|
+
# mol = Chem.open_mol($data_dir + 'hypericin.mol')
|
16
|
+
# #assert_equal(mol.nodes.length, mol.match_by_ullmann(mol).length)
|
17
|
+
# end
|
18
|
+
|
19
|
+
# def test_match_by_atom
|
20
|
+
# mol2 = Chem.parse_smiles("CCCBrCC")
|
21
|
+
# mol = Chem.parse_smiles("CCBr")
|
22
|
+
# assert_equal(mol.nodes.length, mol.match_by_ullmann(mol2).length);
|
23
|
+
# end
|
24
|
+
|
25
|
+
def test_search
|
26
|
+
@mol.match_by_ullmann(@mol)
|
27
|
+
end
|
28
|
+
|
29
|
+
# def test_exhaustive
|
30
|
+
# cyclopropane = SMILES("C1CCC1")
|
31
|
+
# match = cyclopropane.match_by_ullmann(cyclopropane)
|
32
|
+
# assert_equal([0, 1, 2, 3], match)
|
33
|
+
# match = cyclopropane.match_exhaustively(cyclopropane)
|
34
|
+
# end
|
35
|
+
|
36
|
+
end
|
37
|
+
|
@@ -0,0 +1,29 @@
|
|
1
|
+
# $Id: test_traverse.rb 65 2005-10-25 17:17:36Z tanaka $
|
2
|
+
|
3
|
+
require 'test/all'
|
4
|
+
|
5
|
+
class TraverseTest < Test::Unit::TestCase
|
6
|
+
|
7
|
+
def setup
|
8
|
+
@cyclohexane = Chem.open_mol($data_dir + 'cyclohexane.mol')
|
9
|
+
end
|
10
|
+
|
11
|
+
def test_bfs
|
12
|
+
i = 0
|
13
|
+
@cyclohexane.bfs do |from, to|
|
14
|
+
i += 1
|
15
|
+
# Block should return true if you want to continue traversing this branch!
|
16
|
+
true
|
17
|
+
end
|
18
|
+
assert_equal(i, 6)
|
19
|
+
end
|
20
|
+
|
21
|
+
def test_dfs
|
22
|
+
i = 0
|
23
|
+
@cyclohexane.dfs do |from, to, bond|
|
24
|
+
i += 1
|
25
|
+
end
|
26
|
+
assert_equal(i, 6)
|
27
|
+
end
|
28
|
+
|
29
|
+
end
|
data/test/test_writer.rb
ADDED
data/test/test_xyz.rb
ADDED
@@ -0,0 +1,15 @@
|
|
1
|
+
# $Id: test_xyz.rb 156 2006-02-09 02:00:47Z tanaka $
|
2
|
+
|
3
|
+
require 'test/all'
|
4
|
+
require 'test/type_test'
|
5
|
+
|
6
|
+
class XyzTest < Test::Unit::TestCase
|
7
|
+
include Chem::TypeTest
|
8
|
+
|
9
|
+
def setup
|
10
|
+
(@entries = []).push Chem.open_mol($data_dir + "test.xyz")
|
11
|
+
@parser = Chem::XYZ::XyzMolecule
|
12
|
+
@file_type = Chem::Type::XyzType
|
13
|
+
end
|
14
|
+
|
15
|
+
end
|
data/test/type_test.rb
ADDED
@@ -0,0 +1,25 @@
|
|
1
|
+
# $Id: type_test.rb 61 2005-10-12 09:17:39Z tanaka $
|
2
|
+
|
3
|
+
module Chem
|
4
|
+
# A test module for testing ``autodetect'' mechanism
|
5
|
+
# Modules that test autodetection must conform this test.
|
6
|
+
|
7
|
+
module TypeTest
|
8
|
+
|
9
|
+
def test_db_mod
|
10
|
+
assert(@file_type.respond_to?(:parse),
|
11
|
+
"Type modules must respond to parse(file) method")
|
12
|
+
assert(@file_type.respond_to?(:detect_file),
|
13
|
+
"Type modules must respond to detect_file method")
|
14
|
+
assert(@file_type.respond_to?(:detect_type),
|
15
|
+
"Type modules must respond to detect_type method")
|
16
|
+
end
|
17
|
+
|
18
|
+
def test_autodetect
|
19
|
+
@entries.each do |entry|
|
20
|
+
# assert_instance_of(@parser, entry)
|
21
|
+
end
|
22
|
+
end
|
23
|
+
|
24
|
+
end
|
25
|
+
end
|
metadata
ADDED
@@ -0,0 +1,290 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
rubygems_version: 0.8.10
|
3
|
+
specification_version: 1
|
4
|
+
name: chemruby
|
5
|
+
version: !ruby/object:Gem::Version
|
6
|
+
version: 0.9.3
|
7
|
+
date: 2006-02-12
|
8
|
+
summary: A framework program for cheminformatics
|
9
|
+
require_paths:
|
10
|
+
- lib
|
11
|
+
email:
|
12
|
+
homepage:
|
13
|
+
rubyforge_project:
|
14
|
+
description:
|
15
|
+
autorequire: chem
|
16
|
+
default_executable:
|
17
|
+
bindir: bin
|
18
|
+
has_rdoc: false
|
19
|
+
required_ruby_version: !ruby/object:Gem::Version::Requirement
|
20
|
+
requirements:
|
21
|
+
- - ">"
|
22
|
+
- !ruby/object:Gem::Version
|
23
|
+
version: 0.0.0
|
24
|
+
version:
|
25
|
+
platform: ruby
|
26
|
+
authors: []
|
27
|
+
|
28
|
+
files:
|
29
|
+
- Rakefile
|
30
|
+
- README
|
31
|
+
- setup.rb
|
32
|
+
- lib/chem.rb
|
33
|
+
- lib/graph.rb
|
34
|
+
- lib/chem/appl.rb
|
35
|
+
- lib/chem/data.rb
|
36
|
+
- lib/chem/db.rb
|
37
|
+
- lib/chem/model.rb
|
38
|
+
- lib/chem/utils.rb
|
39
|
+
- lib/chem/appl/chem3dole.rb
|
40
|
+
- lib/chem/appl/tinker/nucleic.rb
|
41
|
+
- lib/chem/appl/tinker/tinker_reader.rb
|
42
|
+
- lib/chem/data/atomic_weight.rb
|
43
|
+
- lib/chem/data/character.rb
|
44
|
+
- lib/chem/data/electronegativity.rb
|
45
|
+
- lib/chem/data/periodic_table.rb
|
46
|
+
- lib/chem/data/prime_numbers.rb
|
47
|
+
- lib/chem/data/vdw_radii.rb
|
48
|
+
- lib/chem/db/cansmi.rb
|
49
|
+
- lib/chem/db/cdx.rb
|
50
|
+
- lib/chem/db/eps.rb
|
51
|
+
- lib/chem/db/g98.rb
|
52
|
+
- lib/chem/db/gspan.rb
|
53
|
+
- lib/chem/db/iupac.rb
|
54
|
+
- lib/chem/db/kcf.rb
|
55
|
+
- lib/chem/db/kcf_glycan.rb
|
56
|
+
- lib/chem/db/kegg.rb
|
57
|
+
- lib/chem/db/mdl.rb
|
58
|
+
- lib/chem/db/molconnz.rb
|
59
|
+
- lib/chem/db/mopac.rb
|
60
|
+
- lib/chem/db/msi.rb
|
61
|
+
- lib/chem/db/pdb_dic.rb
|
62
|
+
- lib/chem/db/pdf.rb
|
63
|
+
- lib/chem/db/pubchem.rb
|
64
|
+
- lib/chem/db/rmagick.rb
|
65
|
+
- lib/chem/db/sdf.rb
|
66
|
+
- lib/chem/db/smbl.rb
|
67
|
+
- lib/chem/db/smiles.rb
|
68
|
+
- lib/chem/db/swf.rb
|
69
|
+
- lib/chem/db/sybyl.rb
|
70
|
+
- lib/chem/db/tinker.rb
|
71
|
+
- lib/chem/db/vector.rb
|
72
|
+
- lib/chem/db/xyz.rb
|
73
|
+
- lib/chem/db/iupac/a_1.rb
|
74
|
+
- lib/chem/db/iupac/iuparser.rb
|
75
|
+
- lib/chem/db/iupac/postfix.rb
|
76
|
+
- lib/chem/db/linucs/linparser.rb
|
77
|
+
- lib/chem/db/smiles/smiparser.rb
|
78
|
+
- lib/chem/db/types/type_cansmi.rb
|
79
|
+
- lib/chem/db/types/type_cdx.rb
|
80
|
+
- lib/chem/db/types/type_gspan.rb
|
81
|
+
- lib/chem/db/types/type_kcf.rb
|
82
|
+
- lib/chem/db/types/type_kcf_glycan.rb
|
83
|
+
- lib/chem/db/types/type_kegg.rb
|
84
|
+
- lib/chem/db/types/type_mdl.rb
|
85
|
+
- lib/chem/db/types/type_pdf.rb
|
86
|
+
- lib/chem/db/types/type_png.rb
|
87
|
+
- lib/chem/db/types/type_rxn.rb
|
88
|
+
- lib/chem/db/types/type_sdf.rb
|
89
|
+
- lib/chem/db/types/type_sybyl.rb
|
90
|
+
- lib/chem/db/types/type_xyz.rb
|
91
|
+
- lib/chem/model/skeleton.rb
|
92
|
+
- lib/chem/utils/geometry.rb
|
93
|
+
- lib/chem/utils/graph_db.rb
|
94
|
+
- lib/chem/utils/math.rb
|
95
|
+
- lib/chem/utils/prop.rb
|
96
|
+
- lib/chem/utils/sssr.rb
|
97
|
+
- lib/chem/utils/sub.rb
|
98
|
+
- lib/chem/utils/transform.rb
|
99
|
+
- lib/chem/utils/traverse.rb
|
100
|
+
- lib/chem/utils/ullmann.rb
|
101
|
+
- lib/graph/cluster.rb
|
102
|
+
- lib/graph/morgan.rb
|
103
|
+
- lib/chem/db/iupac/iuparser.ry
|
104
|
+
- lib/chem/db/linucs/linucs.ry
|
105
|
+
- lib/chem/db/smiles/smiles.ry
|
106
|
+
- test/all.rb
|
107
|
+
- test/coord_test.rb
|
108
|
+
- test/ctab_test.rb
|
109
|
+
- test/data
|
110
|
+
- test/heavy_test_pubchem.rb
|
111
|
+
- test/multiple_test.rb
|
112
|
+
- test/test_adj.rb
|
113
|
+
- test/test_canonical_smiles.rb
|
114
|
+
- test/test_cdx.rb
|
115
|
+
- test/test_chem.rb
|
116
|
+
- test/test_cluster.rb
|
117
|
+
- test/test_db.rb
|
118
|
+
- test/test_eps.rb
|
119
|
+
- test/test_geometry.rb
|
120
|
+
- test/test_gspan.rb
|
121
|
+
- test/test_iupac.rb
|
122
|
+
- test/test_kcf.rb
|
123
|
+
- test/test_kcf_glycan.rb
|
124
|
+
- test/test_kegg.rb
|
125
|
+
- test/test_linucs.rb
|
126
|
+
- test/test_mdl.rb
|
127
|
+
- test/test_mol2.rb
|
128
|
+
- test/test_morgan.rb
|
129
|
+
- test/test_pdf.rb
|
130
|
+
- test/test_prop.rb
|
131
|
+
- test/test_rmagick.rb
|
132
|
+
- test/test_sbdb.rb
|
133
|
+
- test/test_sdf.rb
|
134
|
+
- test/test_smiles.rb
|
135
|
+
- test/test_sssr.rb
|
136
|
+
- test/test_sub.rb
|
137
|
+
- test/test_subcomp.rb
|
138
|
+
- test/test_traverse.rb
|
139
|
+
- test/test_writer.rb
|
140
|
+
- test/test_xyz.rb
|
141
|
+
- test/type_test.rb
|
142
|
+
- test/data/A_21
|
143
|
+
- test/data/A_21.tar.gz
|
144
|
+
- test/data/atp.mol
|
145
|
+
- test/data/C00147.kcf
|
146
|
+
- test/data/cyclohexane.mol
|
147
|
+
- test/data/cyclohexane.ps
|
148
|
+
- test/data/fullerene.mol
|
149
|
+
- test/data/G00147.kcf
|
150
|
+
- test/data/glycan
|
151
|
+
- test/data/hypericin.cdx
|
152
|
+
- test/data/hypericin.cdxml
|
153
|
+
- test/data/hypericin.chm
|
154
|
+
- test/data/hypericin.ct
|
155
|
+
- test/data/hypericin.f1d
|
156
|
+
- test/data/hypericin.f1q
|
157
|
+
- test/data/hypericin.gif
|
158
|
+
- test/data/hypericin.mol
|
159
|
+
- test/data/hypericin.mol2
|
160
|
+
- test/data/hypericin.msm
|
161
|
+
- test/data/hypericin.pdf
|
162
|
+
- test/data/hypericin.png
|
163
|
+
- test/data/hypericin.ps
|
164
|
+
- test/data/hypericin.skc
|
165
|
+
- test/data/hypericin2.gif
|
166
|
+
- test/data/hypericin2.ps
|
167
|
+
- test/data/kegg
|
168
|
+
- test/data/reaction
|
169
|
+
- test/data/reaction.lst
|
170
|
+
- test/data/reaction_mapformula.lst
|
171
|
+
- test/data/rxn
|
172
|
+
- test/data/test.eps
|
173
|
+
- test/data/test.mol
|
174
|
+
- test/data/test.sdf
|
175
|
+
- test/data/test.skc
|
176
|
+
- test/data/test.xyz
|
177
|
+
- test/data/test_lf.sdf
|
178
|
+
- test/data/A_21/aceanthrylene.cdx
|
179
|
+
- test/data/A_21/aceanthrylene.mol
|
180
|
+
- test/data/A_21/acenaphthylene.cdx
|
181
|
+
- test/data/A_21/acenaphthylene.mol
|
182
|
+
- test/data/A_21/acephenanthrylene.cdx
|
183
|
+
- test/data/A_21/acephenanthrylene.mol
|
184
|
+
- test/data/A_21/anthracene.cdx
|
185
|
+
- test/data/A_21/anthracene.mol
|
186
|
+
- test/data/A_21/as-indacene.cdx
|
187
|
+
- test/data/A_21/as-indacene.mol
|
188
|
+
- test/data/A_21/azulene.cdx
|
189
|
+
- test/data/A_21/azulene.mol
|
190
|
+
- test/data/A_21/biphenylene.cdx
|
191
|
+
- test/data/A_21/biphenylene.mol
|
192
|
+
- test/data/A_21/chrysene.cdx
|
193
|
+
- test/data/A_21/chrysene.mol
|
194
|
+
- test/data/A_21/coronen.cdx
|
195
|
+
- test/data/A_21/coronen.mol
|
196
|
+
- test/data/A_21/fluoranthene.cdx
|
197
|
+
- test/data/A_21/fluoranthene.mol
|
198
|
+
- test/data/A_21/fluorene.cdx
|
199
|
+
- test/data/A_21/fluorene.mol
|
200
|
+
- test/data/A_21/heptacene.cdx
|
201
|
+
- test/data/A_21/heptacene.mol
|
202
|
+
- test/data/A_21/heptalene.cdx
|
203
|
+
- test/data/A_21/heptalene.mol
|
204
|
+
- test/data/A_21/heptaphene.cdx
|
205
|
+
- test/data/A_21/heptaphene.mol
|
206
|
+
- test/data/A_21/hexacene.cdx
|
207
|
+
- test/data/A_21/hexacene.mol
|
208
|
+
- test/data/A_21/hexaphene.cdx
|
209
|
+
- test/data/A_21/hexaphene.mol
|
210
|
+
- test/data/A_21/indene.cdx
|
211
|
+
- test/data/A_21/indene.mol
|
212
|
+
- test/data/A_21/iupac.txt
|
213
|
+
- test/data/A_21/naphthacene.cdx
|
214
|
+
- test/data/A_21/naphthacene.mol
|
215
|
+
- test/data/A_21/naphthalene.cdx
|
216
|
+
- test/data/A_21/naphthalene.mol
|
217
|
+
- test/data/A_21/ovalene.cdx
|
218
|
+
- test/data/A_21/ovalene.mol
|
219
|
+
- test/data/A_21/pentacene.cdx
|
220
|
+
- test/data/A_21/pentacene.mol
|
221
|
+
- test/data/A_21/pentalene.cdx
|
222
|
+
- test/data/A_21/pentalene.mol
|
223
|
+
- test/data/A_21/pentaphene.cdx
|
224
|
+
- test/data/A_21/pentaphene.mol
|
225
|
+
- test/data/A_21/perylene.cdx
|
226
|
+
- test/data/A_21/perylene.mol
|
227
|
+
- test/data/A_21/phenalene.cdx
|
228
|
+
- test/data/A_21/phenalene.mol
|
229
|
+
- test/data/A_21/phenanthrene.cdx
|
230
|
+
- test/data/A_21/phenanthrene.mol
|
231
|
+
- test/data/A_21/picene.cdx
|
232
|
+
- test/data/A_21/picene.mol
|
233
|
+
- test/data/A_21/pleiadene.cdx
|
234
|
+
- test/data/A_21/pleiadene.mol
|
235
|
+
- test/data/A_21/pyranthrene.cdx
|
236
|
+
- test/data/A_21/pyranthrene.mol
|
237
|
+
- test/data/A_21/pyrene.cdx
|
238
|
+
- test/data/A_21/pyrene.mol
|
239
|
+
- test/data/A_21/rubicene.cdx
|
240
|
+
- test/data/A_21/rubicene.mol
|
241
|
+
- test/data/A_21/s-indacene.cdx
|
242
|
+
- test/data/A_21/s-indacene.mol
|
243
|
+
- test/data/A_21/tetraphenylene.cdx
|
244
|
+
- test/data/A_21/tetraphenylene.mol
|
245
|
+
- test/data/A_21/trinaphthylene.cdx
|
246
|
+
- test/data/A_21/trinaphthylene.mol
|
247
|
+
- test/data/A_21/triphenylene.cdx
|
248
|
+
- test/data/A_21/triphenylene.mol
|
249
|
+
- test/data/kegg/genomes
|
250
|
+
- test/data/kegg/ligand
|
251
|
+
- test/data/kegg/genomes/hsa
|
252
|
+
- test/data/kegg/genomes/hsa/hsa_enzyme.list
|
253
|
+
- test/data/kegg/genomes/hsa/hsa_pfam.list
|
254
|
+
- test/data/kegg/ligand/mol
|
255
|
+
- test/data/kegg/ligand/reaction
|
256
|
+
- test/data/kegg/ligand/reaction.lst
|
257
|
+
- test/data/kegg/ligand/reaction_mapformula.lst
|
258
|
+
- test/data/kegg/ligand/mol/C00147.mol
|
259
|
+
- test/data/rxn/C00001.mol
|
260
|
+
- test/data/rxn/C00011.mol
|
261
|
+
- test/data/rxn/C00014.mol
|
262
|
+
- test/data/rxn/C01010.mol
|
263
|
+
- test/data/rxn/sample.rxn
|
264
|
+
- test/data/rxn/substitution.rxn
|
265
|
+
- sample/frequent_subgraph.rb
|
266
|
+
- sample/kegg_db.rb
|
267
|
+
- sample/images/ex1.rb
|
268
|
+
- sample/images/ex2.rb
|
269
|
+
- sample/images/ex3.rb
|
270
|
+
- sample/images/ex4.rb
|
271
|
+
- sample/images/ex5.rb
|
272
|
+
- sample/images/mol/adenine.mol
|
273
|
+
- sample/images/mol/atp.mol
|
274
|
+
- sample/images/temp/ex5.mol
|
275
|
+
- ext/subcomp.c
|
276
|
+
- ext/extconf.rb
|
277
|
+
test_files: []
|
278
|
+
|
279
|
+
rdoc_options: []
|
280
|
+
|
281
|
+
extra_rdoc_files: []
|
282
|
+
|
283
|
+
executables: []
|
284
|
+
|
285
|
+
extensions:
|
286
|
+
- ext/extconf.rb
|
287
|
+
requirements: []
|
288
|
+
|
289
|
+
dependencies: []
|
290
|
+
|