asciichem 0.3.0

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Files changed (68) hide show
  1. checksums.yaml +7 -0
  2. data/.github/workflows/ci.yml +21 -0
  3. data/.gitignore +14 -0
  4. data/.rubocop.yml +50 -0
  5. data/ARCHITECTURE.adoc +239 -0
  6. data/CHANGELOG.md +17 -0
  7. data/CLAUDE.md +318 -0
  8. data/Gemfile +14 -0
  9. data/LICENSE +24 -0
  10. data/README.adoc +55 -0
  11. data/RELEASING.md +102 -0
  12. data/Rakefile +8 -0
  13. data/asciichem.gemspec +39 -0
  14. data/benchmarks/RESULTS.md +49 -0
  15. data/benchmarks/benchmark.rb +106 -0
  16. data/exe/asciichem +6 -0
  17. data/lib/asciichem/cli.rb +96 -0
  18. data/lib/asciichem/cml/extensions.rb +360 -0
  19. data/lib/asciichem/cml/group_extensions.rb +290 -0
  20. data/lib/asciichem/cml/translator.rb +69 -0
  21. data/lib/asciichem/cml.rb +40 -0
  22. data/lib/asciichem/errors.rb +9 -0
  23. data/lib/asciichem/formatter/base.rb +21 -0
  24. data/lib/asciichem/formatter/html.rb +111 -0
  25. data/lib/asciichem/formatter/latex.rb +173 -0
  26. data/lib/asciichem/formatter/mathml.rb +309 -0
  27. data/lib/asciichem/formatter/structural_svg.rb +286 -0
  28. data/lib/asciichem/formatter/svg.rb +141 -0
  29. data/lib/asciichem/formatter/text.rb +143 -0
  30. data/lib/asciichem/formatter.rb +43 -0
  31. data/lib/asciichem/grammar.rb +344 -0
  32. data/lib/asciichem/greek.rb +80 -0
  33. data/lib/asciichem/layout.rb +313 -0
  34. data/lib/asciichem/linter/balance_check.rb +103 -0
  35. data/lib/asciichem/linter/base.rb +52 -0
  36. data/lib/asciichem/linter/bracket_balance_check.rb +44 -0
  37. data/lib/asciichem/linter/diagnostic.rb +16 -0
  38. data/lib/asciichem/linter/element_validation_check.rb +39 -0
  39. data/lib/asciichem/linter/isotope_sanity_check.rb +47 -0
  40. data/lib/asciichem/linter/registry.rb +31 -0
  41. data/lib/asciichem/linter/unclosed_ring_check.rb +27 -0
  42. data/lib/asciichem/linter/valence_check.rb +91 -0
  43. data/lib/asciichem/linter.rb +40 -0
  44. data/lib/asciichem/model/atom.rb +73 -0
  45. data/lib/asciichem/model/bond.rb +41 -0
  46. data/lib/asciichem/model/electron_configuration.rb +36 -0
  47. data/lib/asciichem/model/embedded_math.rb +26 -0
  48. data/lib/asciichem/model/formula.rb +31 -0
  49. data/lib/asciichem/model/group.rb +50 -0
  50. data/lib/asciichem/model/identifier.rb +14 -0
  51. data/lib/asciichem/model/molecule.rb +70 -0
  52. data/lib/asciichem/model/name.rb +15 -0
  53. data/lib/asciichem/model/node.rb +100 -0
  54. data/lib/asciichem/model/reaction.rb +49 -0
  55. data/lib/asciichem/model/reaction_cascade.rb +33 -0
  56. data/lib/asciichem/model/text.rb +23 -0
  57. data/lib/asciichem/model.rb +23 -0
  58. data/lib/asciichem/model_adapter/from_canonical.rb +272 -0
  59. data/lib/asciichem/model_adapter/to_canonical.rb +429 -0
  60. data/lib/asciichem/model_adapter.rb +56 -0
  61. data/lib/asciichem/parser.rb +36 -0
  62. data/lib/asciichem/periodic_table.rb +112 -0
  63. data/lib/asciichem/ring_bonds.rb +68 -0
  64. data/lib/asciichem/transform.rb +513 -0
  65. data/lib/asciichem/version.rb +5 -0
  66. data/lib/asciichem/xml_builder.rb +9 -0
  67. data/lib/asciichem.rb +34 -0
  68. metadata +197 -0
metadata ADDED
@@ -0,0 +1,197 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: asciichem
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.3.0
5
+ platform: ruby
6
+ authors:
7
+ - Ribose Inc.
8
+ bindir: exe
9
+ cert_chain: []
10
+ date: 1980-01-02 00:00:00.000000000 Z
11
+ dependencies:
12
+ - !ruby/object:Gem::Dependency
13
+ name: chemicalml
14
+ requirement: !ruby/object:Gem::Requirement
15
+ requirements:
16
+ - - '='
17
+ - !ruby/object:Gem::Version
18
+ version: 0.2.0
19
+ type: :runtime
20
+ prerelease: false
21
+ version_requirements: !ruby/object:Gem::Requirement
22
+ requirements:
23
+ - - '='
24
+ - !ruby/object:Gem::Version
25
+ version: 0.2.0
26
+ - !ruby/object:Gem::Dependency
27
+ name: elkrb
28
+ requirement: !ruby/object:Gem::Requirement
29
+ requirements:
30
+ - - "~>"
31
+ - !ruby/object:Gem::Version
32
+ version: '1.0'
33
+ type: :runtime
34
+ prerelease: false
35
+ version_requirements: !ruby/object:Gem::Requirement
36
+ requirements:
37
+ - - "~>"
38
+ - !ruby/object:Gem::Version
39
+ version: '1.0'
40
+ - !ruby/object:Gem::Dependency
41
+ name: nokogiri
42
+ requirement: !ruby/object:Gem::Requirement
43
+ requirements:
44
+ - - "~>"
45
+ - !ruby/object:Gem::Version
46
+ version: '1.16'
47
+ type: :runtime
48
+ prerelease: false
49
+ version_requirements: !ruby/object:Gem::Requirement
50
+ requirements:
51
+ - - "~>"
52
+ - !ruby/object:Gem::Version
53
+ version: '1.16'
54
+ - !ruby/object:Gem::Dependency
55
+ name: parslet
56
+ requirement: !ruby/object:Gem::Requirement
57
+ requirements:
58
+ - - "~>"
59
+ - !ruby/object:Gem::Version
60
+ version: '2.0'
61
+ type: :runtime
62
+ prerelease: false
63
+ version_requirements: !ruby/object:Gem::Requirement
64
+ requirements:
65
+ - - "~>"
66
+ - !ruby/object:Gem::Version
67
+ version: '2.0'
68
+ - !ruby/object:Gem::Dependency
69
+ name: plurimath
70
+ requirement: !ruby/object:Gem::Requirement
71
+ requirements:
72
+ - - "~>"
73
+ - !ruby/object:Gem::Version
74
+ version: '0.8'
75
+ type: :runtime
76
+ prerelease: false
77
+ version_requirements: !ruby/object:Gem::Requirement
78
+ requirements:
79
+ - - "~>"
80
+ - !ruby/object:Gem::Version
81
+ version: '0.8'
82
+ - !ruby/object:Gem::Dependency
83
+ name: thor
84
+ requirement: !ruby/object:Gem::Requirement
85
+ requirements:
86
+ - - "~>"
87
+ - !ruby/object:Gem::Version
88
+ version: '1.3'
89
+ type: :runtime
90
+ prerelease: false
91
+ version_requirements: !ruby/object:Gem::Requirement
92
+ requirements:
93
+ - - "~>"
94
+ - !ruby/object:Gem::Version
95
+ version: '1.3'
96
+ description: AsciiChem is an ASCII syntax for representing chemical formulae, reactions,
97
+ electron configurations, and bonds. It parses to a semantic model and renders to
98
+ MathML, HTML, LaTeX, and SVG. Math embedding uses Plurimath.
99
+ email:
100
+ - open.source@ribose.com
101
+ executables:
102
+ - asciichem
103
+ extensions: []
104
+ extra_rdoc_files: []
105
+ files:
106
+ - ".github/workflows/ci.yml"
107
+ - ".gitignore"
108
+ - ".rubocop.yml"
109
+ - ARCHITECTURE.adoc
110
+ - CHANGELOG.md
111
+ - CLAUDE.md
112
+ - Gemfile
113
+ - LICENSE
114
+ - README.adoc
115
+ - RELEASING.md
116
+ - Rakefile
117
+ - asciichem.gemspec
118
+ - benchmarks/RESULTS.md
119
+ - benchmarks/benchmark.rb
120
+ - exe/asciichem
121
+ - lib/asciichem.rb
122
+ - lib/asciichem/cli.rb
123
+ - lib/asciichem/cml.rb
124
+ - lib/asciichem/cml/extensions.rb
125
+ - lib/asciichem/cml/group_extensions.rb
126
+ - lib/asciichem/cml/translator.rb
127
+ - lib/asciichem/errors.rb
128
+ - lib/asciichem/formatter.rb
129
+ - lib/asciichem/formatter/base.rb
130
+ - lib/asciichem/formatter/html.rb
131
+ - lib/asciichem/formatter/latex.rb
132
+ - lib/asciichem/formatter/mathml.rb
133
+ - lib/asciichem/formatter/structural_svg.rb
134
+ - lib/asciichem/formatter/svg.rb
135
+ - lib/asciichem/formatter/text.rb
136
+ - lib/asciichem/grammar.rb
137
+ - lib/asciichem/greek.rb
138
+ - lib/asciichem/layout.rb
139
+ - lib/asciichem/linter.rb
140
+ - lib/asciichem/linter/balance_check.rb
141
+ - lib/asciichem/linter/base.rb
142
+ - lib/asciichem/linter/bracket_balance_check.rb
143
+ - lib/asciichem/linter/diagnostic.rb
144
+ - lib/asciichem/linter/element_validation_check.rb
145
+ - lib/asciichem/linter/isotope_sanity_check.rb
146
+ - lib/asciichem/linter/registry.rb
147
+ - lib/asciichem/linter/unclosed_ring_check.rb
148
+ - lib/asciichem/linter/valence_check.rb
149
+ - lib/asciichem/model.rb
150
+ - lib/asciichem/model/atom.rb
151
+ - lib/asciichem/model/bond.rb
152
+ - lib/asciichem/model/electron_configuration.rb
153
+ - lib/asciichem/model/embedded_math.rb
154
+ - lib/asciichem/model/formula.rb
155
+ - lib/asciichem/model/group.rb
156
+ - lib/asciichem/model/identifier.rb
157
+ - lib/asciichem/model/molecule.rb
158
+ - lib/asciichem/model/name.rb
159
+ - lib/asciichem/model/node.rb
160
+ - lib/asciichem/model/reaction.rb
161
+ - lib/asciichem/model/reaction_cascade.rb
162
+ - lib/asciichem/model/text.rb
163
+ - lib/asciichem/model_adapter.rb
164
+ - lib/asciichem/model_adapter/from_canonical.rb
165
+ - lib/asciichem/model_adapter/to_canonical.rb
166
+ - lib/asciichem/parser.rb
167
+ - lib/asciichem/periodic_table.rb
168
+ - lib/asciichem/ring_bonds.rb
169
+ - lib/asciichem/transform.rb
170
+ - lib/asciichem/version.rb
171
+ - lib/asciichem/xml_builder.rb
172
+ homepage: https://www.asciichem.org
173
+ licenses:
174
+ - BSD-2-Clause
175
+ metadata:
176
+ homepage_uri: https://www.asciichem.org
177
+ source_code_uri: https://github.com/asciichem/asciichem-ruby
178
+ changelog_uri: https://github.com/asciichem/asciichem-ruby/blob/main/CHANGELOG.md
179
+ rubygems_mfa_required: 'true'
180
+ rdoc_options: []
181
+ require_paths:
182
+ - lib
183
+ required_ruby_version: !ruby/object:Gem::Requirement
184
+ requirements:
185
+ - - ">="
186
+ - !ruby/object:Gem::Version
187
+ version: 3.3.0
188
+ required_rubygems_version: !ruby/object:Gem::Requirement
189
+ requirements:
190
+ - - ">="
191
+ - !ruby/object:Gem::Version
192
+ version: '0'
193
+ requirements: []
194
+ rubygems_version: 4.0.16
195
+ specification_version: 4
196
+ summary: ASCII syntax for chemistry formulae, reactions, and structures.
197
+ test_files: []