rubabel 0.1.0 → 0.1.1
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- data/README.rdoc +13 -9
- data/Rakefile +10 -2
- data/VERSION +1 -1
- data/bin/rubabel +229 -0
- data/lib/rubabel.rb +46 -14
- data/lib/rubabel/atom.rb +78 -0
- data/lib/rubabel/bond.rb +18 -0
- data/lib/rubabel/molecule.rb +187 -59
- data/lib/rubabel/molecule/fragmentable.rb +209 -0
- data/lib/rubabel/molecule_data.rb +89 -0
- data/reference/arity_method_list.txt +1564 -1294
- data/rubabel.gemspec +100 -0
- data/spec/chemistry_toolkit_rosetta/README.txt +1 -0
- data/spec/chemistry_toolkit_rosetta/benzodiazepine.sdf.gz +0 -0
- data/spec/chemistry_toolkit_rosetta/benzodiazepine.smi.gz +0 -0
- data/spec/chemistry_toolkit_rosetta/chemistry_toolkit_rosetta_spec.rb +225 -0
- data/spec/chemistry_toolkit_rosetta/key/benzodiazepine_heavy_atom_counts.output.10.txt +10 -0
- data/spec/chemistry_toolkit_rosetta/key/benzodiazepine_ring_counts.output.10.txt +10 -0
- data/spec/chemistry_toolkit_rosetta/key/rule5.10.sdf +1924 -0
- data/spec/rubabel/atom_spec.rb +35 -0
- data/spec/rubabel/molecule/fragmentable_spec.rb +51 -0
- data/spec/rubabel/molecule_data_spec.rb +76 -0
- data/spec/rubabel/molecule_spec.rb +131 -1
- data/spec/rubabel_spec.rb +33 -3
- data/spec/spec_helper.rb +24 -0
- data/spec/testfiles/Samples.sdf.gz +0 -0
- metadata +65 -4
- data/lib/rubabel/fragmentation.rb +0 -23
Binary file
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: rubabel
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.1.
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4
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+
version: 0.1.1
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5
5
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prerelease:
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6
6
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platform: ruby
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7
7
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authors:
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@@ -9,8 +9,56 @@ authors:
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9
9
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autorequire:
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10
10
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bindir: bin
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11
11
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cert_chain: []
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12
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-
date: 2012-05-
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12
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+
date: 2012-05-31 00:00:00.000000000 Z
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13
13
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dependencies:
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14
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+
- !ruby/object:Gem::Dependency
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15
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+
name: openbabel
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16
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+
requirement: !ruby/object:Gem::Requirement
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17
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+
none: false
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18
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+
requirements:
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19
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+
- - ~>
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20
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+
- !ruby/object:Gem::Version
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21
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+
version: 2.3.1.2
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22
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+
type: :runtime
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23
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+
prerelease: false
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24
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+
version_requirements: !ruby/object:Gem::Requirement
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25
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+
none: false
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26
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+
requirements:
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27
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+
- - ~>
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28
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+
- !ruby/object:Gem::Version
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29
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+
version: 2.3.1.2
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30
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+
- !ruby/object:Gem::Dependency
|
31
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+
name: commander
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32
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+
requirement: !ruby/object:Gem::Requirement
|
33
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+
none: false
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34
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+
requirements:
|
35
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+
- - ~>
|
36
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+
- !ruby/object:Gem::Version
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37
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+
version: 4.1.2
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+
type: :runtime
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+
prerelease: false
|
40
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+
version_requirements: !ruby/object:Gem::Requirement
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41
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+
none: false
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+
requirements:
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43
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+
- - ~>
|
44
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+
- !ruby/object:Gem::Version
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45
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+
version: 4.1.2
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46
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+
- !ruby/object:Gem::Dependency
|
47
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+
name: andand
|
48
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+
requirement: !ruby/object:Gem::Requirement
|
49
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+
none: false
|
50
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+
requirements:
|
51
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+
- - ~>
|
52
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+
- !ruby/object:Gem::Version
|
53
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+
version: 1.3.3
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54
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+
type: :runtime
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55
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+
prerelease: false
|
56
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+
version_requirements: !ruby/object:Gem::Requirement
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57
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+
none: false
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58
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+
requirements:
|
59
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+
- - ~>
|
60
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+
- !ruby/object:Gem::Version
|
61
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+
version: 1.3.3
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14
62
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- !ruby/object:Gem::Dependency
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15
63
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name: rspec
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16
64
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requirement: !ruby/object:Gem::Requirement
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@@ -63,7 +111,8 @@ description: ! 'Ruby interface to the openbabel ruby bindings (or the openbabel
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63
111
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64
112
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interface attempts to be a ruby-ish analogue of pybel.'
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65
113
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email: jtprince@gmail.com
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66
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-
executables:
|
114
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+
executables:
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115
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+
- rubabel
|
67
116
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extensions: []
|
68
117
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extra_rdoc_files:
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69
118
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- LICENSE
|
@@ -75,12 +124,13 @@ files:
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75
124
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- README.rdoc
|
76
125
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- Rakefile
|
77
126
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- VERSION
|
127
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+
- bin/rubabel
|
78
128
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- lib/rubabel.rb
|
79
129
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- lib/rubabel/atom.rb
|
80
130
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- lib/rubabel/bond.rb
|
81
131
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- lib/rubabel/fingerprint.rb
|
82
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-
- lib/rubabel/fragmentation.rb
|
83
132
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- lib/rubabel/molecule.rb
|
133
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+
- lib/rubabel/molecule/fragmentable.rb
|
84
134
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- lib/rubabel/molecule_data.rb
|
85
135
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- lib/rubabel/pm.rb
|
86
136
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- lib/rubabel/smarts.rb
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@@ -91,14 +141,25 @@ files:
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91
141
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- reference/bond_methods.txt
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92
142
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- reference/get_methods.rb
|
93
143
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- reference/mol_methods.txt
|
144
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+
- rubabel.gemspec
|
145
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+
- spec/chemistry_toolkit_rosetta/README.txt
|
146
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+
- spec/chemistry_toolkit_rosetta/benzodiazepine.sdf.gz
|
147
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+
- spec/chemistry_toolkit_rosetta/benzodiazepine.smi.gz
|
148
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+
- spec/chemistry_toolkit_rosetta/chemistry_toolkit_rosetta_spec.rb
|
149
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+
- spec/chemistry_toolkit_rosetta/key/benzodiazepine_heavy_atom_counts.output.10.txt
|
150
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+
- spec/chemistry_toolkit_rosetta/key/benzodiazepine_ring_counts.output.10.txt
|
151
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+
- spec/chemistry_toolkit_rosetta/key/rule5.10.sdf
|
94
152
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- spec/rubabel/atom_spec.rb
|
95
153
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- spec/rubabel/bond_spec.rb
|
154
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+
- spec/rubabel/molecule/fragmentable_spec.rb
|
155
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+
- spec/rubabel/molecule_data_spec.rb
|
96
156
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- spec/rubabel/molecule_spec.rb
|
97
157
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- spec/rubabel_spec.rb
|
98
158
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- spec/spec_helper.rb
|
99
159
|
- spec/testfiles/7-oxocholesterol-d7.mol
|
100
160
|
- spec/testfiles/7-oxocholesterol-d7.sdf
|
101
161
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- spec/testfiles/Samples.sdf
|
162
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+
- spec/testfiles/Samples.sdf.gz
|
102
163
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- spec/testfiles/cholesterol.mol
|
103
164
|
- spec/testfiles/cholesterol.sdf
|
104
165
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- spec/testfiles/two.sdf
|
@@ -1,23 +0,0 @@
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1
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-
|
2
|
-
module Rubabel
|
3
|
-
class Fragmentation
|
4
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-
|
5
|
-
ADDUCTS = [:lioh, :nh4cl, :nh4oh]
|
6
|
-
|
7
|
-
DEFAULTS = {
|
8
|
-
ph: 7.4,
|
9
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-
adducts: [],
|
10
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-
}
|
11
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-
|
12
|
-
def initialize(mol, options)
|
13
|
-
@mol = mol
|
14
|
-
@options = options
|
15
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-
end
|
16
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-
|
17
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-
def fragment(rules=[:co])
|
18
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-
end
|
19
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-
|
20
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-
|
21
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-
|
22
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-
end
|
23
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-
end
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