asciichem 0.4.0 → 0.4.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: 1272affa5aa88924aaa06424dbc59bb115255963b675f596b58fd9588cd94fdc
+  data.tar.gz: bc6e6da1096c7a1c4e404d23036ec9513eae0f2866feeff9bd54a31c04540473
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+  data.tar.gz: c0c694ec1edf82c9d7dfc57adaa8853cf37c1d94dca7a1288e0587f669776e5d68275345ebcc89717628b12711acd88feb3adcc885aeb945b53bf4d7f8f08d42

data/lib/asciichem/formatter/text.rb

@@ -140,6 +140,24 @@ module AsciiChem
         parts.join
       end
 
+      def visit_spectrum(spectrum)
+        parts = ["spectrum"]
+        parts << "[#{spectrum.type}]" if spectrum.type
+        params = spectrum.params.map { |k, v| "#{k}=#{v}" }.join(',')
+        parts << "(#{params})" unless params.empty?
+        peak_lines = spectrum.peaks.map do |peak|
+          line = "#{peak[:position]}: #{peak[:intensity]}"
+          line += " #{peak[:multiplicity]}" if peak[:multiplicity]
+          line += %( "#{peak[:assignment]}") if peak[:assignment]
+          line
+        end
+        unless peak_lines.empty?
+          body = peak_lines.join("\n  ")
+          parts << "{\n  #{body}\n}"
+        end
+        parts.join
+      end
+
       private
 
       def render_node(node)

data/lib/asciichem/grammar.rb

@@ -27,16 +27,16 @@ module AsciiChem
 
     rule(:nodes) { node >> (spaces? >> node).repeat }
 
-    rule(:node)  { reaction_cascade | reaction | electron_config | crystal | annotated_molecule | molecule | embedded_math | text_run.as(:text_run) }
+    rule(:node)  { reaction_cascade | reaction | electron_config | crystal | spectrum | annotated_molecule | molecule | embedded_math | text_run.as(:text_run) }
 
     # -- crystallography -------------------------------------------------
 
     # crystal[Name](a=X,b=Y,...,sg=SG){atoms with @f(x,y,z)}
     rule(:crystal) do
-      str('crystal') >>
+      (str('crystal') >>
         crystal_name.maybe >>
         crystal_params.maybe >>
-        crystal_body.maybe
+        crystal_body.maybe).as(:crystal_node)
     end
 
     rule(:crystal_name) do
@@ -51,6 +51,28 @@ module AsciiChem
       str('{') >> (str('}').absent? >> any).repeat.as(:crystal_body) >> str('}')
     end
 
+    # -- spectroscopy ---------------------------------------------------
+
+    # spectrum[type](params){peak data}
+    rule(:spectrum) do
+        (str('spectrum') >>
+        spectrum_type.maybe >>
+        spectrum_params.maybe >>
+        spectrum_body.maybe).as(:spectrum_node)
+    end
+
+    rule(:spectrum_type) do
+      str('[') >> (str(']').absent? >> any).repeat.as(:spectrum_type) >> str(']')
+    end
+
+    rule(:spectrum_params) do
+      str('(') >> (str(')').absent? >> any).repeat.as(:spectrum_params) >> str(')')
+    end
+
+    rule(:spectrum_body) do
+      str('{') >> (str('}').absent? >> any).repeat.as(:spectrum_body) >> str('}')
+    end
+
     # Annotated molecule: a molecule followed by one or more
     # `@key("value")` annotations for CML metadata (names,
     # identifiers, title, formula, labels).

data/lib/asciichem/model/spectrum.rb

@@ -0,0 +1,46 @@
+# frozen_string_literal: true
+
+module AsciiChem
+  module Model
+    # A spectroscopy result: NMR, IR, MS, UV-Vis peaks.
+    #
+    # Syntax:
+    #   spectrum[nmr](type=1H,solvent=CDCl3){
+    #     1.2: 3H s "CH3"
+    #     7.2: 5H m "C6H5"
+    #   }
+    #
+    #   spectrum[ir]{
+    #     3300: broad "O-H stretch"
+    #   }
+    #
+    #   spectrum[ms]{
+    #     18: 100% "M+"
+    #   }
+    class Spectrum < Node
+      attr_accessor :type, :params, :peaks
+
+      def initialize(type: nil, params: {}, peaks: [])
+        @type = type
+        @params = params
+        @peaks = peaks
+      end
+
+      def value_attributes
+        { type: type, params: params, peaks: peaks }
+      end
+
+      def children
+        []
+      end
+
+      def diagnostic_label
+        "Spectrum(#{type || 'unknown'})"
+      end
+
+      def to_s
+        "spectrum[#{type}](#{params.map { |k, v| "#{k}=#{v}" }.join(',')})"
+      end
+    end
+  end
+end

data/lib/asciichem/model.rb

@@ -19,6 +19,7 @@ module AsciiChem
     autoload :Node, "asciichem/model/node"
     autoload :Reaction, "asciichem/model/reaction"
     autoload :ReactionCascade, "asciichem/model/reaction_cascade"
+    autoload :Spectrum, "asciichem/model/spectrum"
     autoload :Text, "asciichem/model/text"
   end
 end

data/lib/asciichem/transform.rb

@@ -151,10 +151,24 @@ module AsciiChem
     # Grammar captures crystal_name, crystal_params, and crystal_body
     # as optional strings. CrystalBuilder parses them into the model.
 
-    rule(crystal_name: subtree(:name),
-         crystal_params: subtree(:params),
-         crystal_body: subtree(:body)) do
-      CrystalBuilder.new(name, params, body).build
+    rule(crystal_node: subtree(:data)) do
+      hash = data.is_a?(Hash) ? data : {}
+      CrystalBuilder.new(
+        hash[:crystal_name],
+        hash[:crystal_params],
+        hash[:crystal_body]
+      ).build
+    end
+
+    # -- spectra --------------------------------------------------------
+
+    rule(spectrum_node: subtree(:data)) do
+      hash = data.is_a?(Hash) ? data : {}
+      SpectrumBuilder.new(
+        hash[:spectrum_type],
+        hash[:spectrum_params],
+        hash[:spectrum_body]
+      ).build
     end
 
     # -- internal helpers ------------------------------------------------
@@ -215,6 +229,69 @@ module AsciiChem
       end
     end
 
+    # Builds a Spectrum from parsed grammar captures. Parses peak
+    # lines from the body string.
+    class SpectrumBuilder
+      def initialize(type_str, params_str, body_str)
+        @type = strip_value(type_str)
+        @params_str = strip_value(params_str)
+        @body_str = strip_value(body_str)
+      end
+
+      def build
+        Model::Spectrum.new(
+          type: @type,
+          params: parse_params(@params_str),
+          peaks: parse_peaks(@body_str)
+        )
+      end
+
+      private
+
+      def strip_value(value)
+        return nil if value.nil?
+
+        s = value.to_s.strip
+        s.empty? ? nil : s
+      end
+
+      def parse_params(str)
+        return {} unless str
+
+        str.split(',').each_with_object({}) do |pair, memo|
+          key, val = pair.strip.split('=', 2)
+          memo[key] = val&.strip if key
+        end
+      end
+
+      def parse_peaks(str)
+        return [] unless str
+
+        str.split("\n").filter_map { |line| parse_peak(line.strip) }
+      end
+
+      def parse_peak(line)
+        return nil if line.empty?
+
+        assignment = nil
+        match = line.match(/"([^"]*)"/)
+        if match
+          assignment = match[1]
+          line = line.sub(/"[^"]*"/, '').strip
+        end
+
+        pos, rest = line.split(':', 2)
+        tokens = rest&.strip&.split(/\s+/) || []
+
+        {
+          position: pos&.strip,
+          intensity: tokens[0],
+          multiplicity: tokens[1],
+          assignment: assignment
+        }
+      end
+    end
+
     # Strips the surrounding `"..."` quotes from a quoted text match.
     # Used by both `text_run` and `group_text_run` rules so the
     # model never carries the delimiters — the formatter re-adds them

data/lib/asciichem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module AsciiChem
-  VERSION = "0.4.0"
+  VERSION = "0.4.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.1
 platform: ruby
 authors:
 - Ribose Inc.
@@ -166,6 +166,7 @@ files:
 - lib/asciichem/model/node.rb
 - lib/asciichem/model/reaction.rb
 - lib/asciichem/model/reaction_cascade.rb
+- lib/asciichem/model/spectrum.rb
 - lib/asciichem/model/text.rb
 - lib/asciichem/model_adapter.rb
 - lib/asciichem/model_adapter/from_canonical.rb