asciichem 0.3.3 → 0.3.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9dcc9efdb2f096fa1b8e71fa12f23df5ff2c7246d017d71fe3cf87309ed65504
-  data.tar.gz: f64ddf08f74a2c38fcce98bae1cd4010b4ae55ede0f38bbf0f248fea475dead6
+  metadata.gz: 82e379bdd585e67154ee2ac11685d34d343fc7603dad41c8e629d27610f66a0e
+  data.tar.gz: 443e0c865b127e706b61ec9d8781b3516aecb8dfb86a83630e1363af5ae52779
 SHA512:
-  metadata.gz: 283b735f960be1ab4cc2f3d4b98977dc8ef49dab16e19305ab64cd5054ac09a6f69e942c56a93705c48f6e9710ecf7c3e6f462bdd12e0a0081a58eea8b7bc8aa
-  data.tar.gz: 2c9d3f021372984bd52177269bcae201f2b176393883c774533232a2e21b3498e083d2874b1ccb1c06a8d6596cf8d309c88aed2fd457e92b8a0b6c78ea714423
+  metadata.gz: 1dca3abf1149dbbeb1166053cdc6afd58e90c4ad1635c5d13a8884aa11e00b1f43dbdadda6a860d5110dc3924f1ce8f01cba41992faaabbe5bd8a5b05382cdf6
+  data.tar.gz: 2fb960db615687093e7cb30f70752303d1b143fc9c3af8cd582d0fef7afcff00e45feabe88769bbb8f6af6431171b3b431d2689339a1d52903f21f397acc23a3

data/lib/asciichem/formatter/text.rb

@@ -57,15 +57,19 @@ module AsciiChem
       end
 
       def atom_annotation(atom)
-        annotation = +""
+        parts = []
         if atom.x2 && atom.y2
-          annotation << "@(#{format_coord(atom.x2)},#{format_coord(atom.y2)}"
-          annotation << ",#{format_coord(atom.z2)}" if atom.z2
-          annotation << ")"
-        elsif atom.atom_parity
-          annotation << "@#{atom.atom_parity}"
+          coord = "@(#{format_coord(atom.x2)},#{format_coord(atom.y2)}"
+          coord << ",#{format_coord(atom.z2)}" if atom.z2
+          parts << "#{coord})"
+        end
+        parts << "@#{atom.atom_parity}" if atom.atom_parity
+        parts << "@m(#{atom.spin_multiplicity})" if atom.spin_multiplicity
+        parts << %(@t("#{atom.atom_title}")) if atom.atom_title
+        if atom.x_fract && atom.y_fract && atom.z_fract
+          parts << "@f(#{format_coord(atom.x_fract)},#{format_coord(atom.y_fract)},#{format_coord(atom.z_fract)})"
         end
-        annotation
+        parts.join
       end
 
       def format_coord(value)

data/lib/asciichem/grammar.rb

@@ -182,7 +182,7 @@ module AsciiChem
         atom_suffix >>
         lewis_radicals.maybe >>
         ring_closures.maybe.as(:ring_closures) >>
-        atom_annotation.maybe).as(:atom)
+        atom_annotation).as(:atom)
     end
 
     rule(:plain_atom) do
@@ -191,15 +191,18 @@ module AsciiChem
         atom_suffix >>
         lewis_radicals.maybe >>
         ring_closures.maybe.as(:ring_closures) >>
-        atom_annotation.maybe).as(:atom)
+        atom_annotation).as(:atom)
     end
 
-    # Atom annotations: stereo parity (@R / @S) or 2D/3D coordinates
-    # (@(x,y) / @(x,y,z)). Both use the `@` prefix. An atom can carry
-    # at most one annotation in the grammar; multiple annotations
-    # would require compound syntax (deferred).
+    # Atom annotations: each is independently optional via .maybe.
+    # Order matters: @(x,y) → @R/@S → @m(N) → @t("...") → @f(x,y,z).
+    # Example: C@(10,20)@R@m(2)@t("C1")@f(0.5,0.5,0.5)
     rule(:atom_annotation) do
-      coordinate_annotation | parity_annotation
+      coordinate_annotation.maybe >>
+      parity_annotation.maybe >>
+      multiplicity_annotation.maybe >>
+      atom_title_annotation.maybe >>
+      fractional_annotation.maybe
     end
 
     rule(:parity_annotation) do
@@ -214,6 +217,27 @@ module AsciiChem
         str(')')
     end
 
+    # Spin multiplicity: @m(2) for doublet, @m(1) for singlet
+    rule(:multiplicity_annotation) do
+      str('@m(') >> match('[0-9]').repeat(1).as(:spin_multiplicity) >> str(')')
+    end
+
+    # Atom title/label: @t("C1")
+    rule(:atom_title_annotation) do
+      str('@t(') >> str('"') >>
+      (str('"').absent? >> any).repeat.as(:atom_title) >>
+      str('"') >> str(')')
+    end
+
+    # Fractional coordinates (crystallographic): @f(0.5,0.25,0.75)
+    rule(:fractional_annotation) do
+      str('@f(') >>
+        float_number.as(:x_fract) >> str(',') >>
+        float_number.as(:y_fract) >> str(',') >>
+        float_number.as(:z_fract) >>
+      str(')')
+    end
+
     rule(:float_number) do
       str('-').maybe >> match('[0-9]').repeat(1) >> (str('.') >> match('[0-9]').repeat(0)).maybe
     end

data/lib/asciichem/model/atom.rb

@@ -20,13 +20,17 @@ module AsciiChem
                     :charge, :oxidation_state,
                     :lone_pairs, :radical_electrons,
                     :ring_closures,
-                    :x2, :y2, :z2, :atom_parity
+                    :x2, :y2, :z2, :atom_parity,
+                    :spin_multiplicity, :atom_title,
+                    :x_fract, :y_fract, :z_fract
 
       def initialize(element:, isotope: nil, subscript: nil,
                      superscript: nil, charge: nil, oxidation_state: nil,
                      lone_pairs: nil, radical_electrons: nil,
                      ring_closures: nil,
-                     x2: nil, y2: nil, z2: nil, atom_parity: nil)
+                     x2: nil, y2: nil, z2: nil, atom_parity: nil,
+                     spin_multiplicity: nil, atom_title: nil,
+                     x_fract: nil, y_fract: nil, z_fract: nil)
         @element = element
         @isotope = isotope
         @subscript = subscript
@@ -40,6 +44,11 @@ module AsciiChem
         @y2 = y2
         @z2 = z2
         @atom_parity = atom_parity
+        @spin_multiplicity = spin_multiplicity
+        @atom_title = atom_title
+        @x_fract = x_fract
+        @y_fract = y_fract
+        @z_fract = z_fract
       end
 
       def value_attributes
@@ -48,7 +57,9 @@ module AsciiChem
           oxidation_state: oxidation_state,
           lone_pairs: lone_pairs, radical_electrons: radical_electrons,
           ring_closures: ring_closures,
-          x2: x2, y2: y2, z2: z2, atom_parity: atom_parity }
+          x2: x2, y2: y2, z2: z2, atom_parity: atom_parity,
+          spin_multiplicity: spin_multiplicity, atom_title: atom_title,
+          x_fract: x_fract, y_fract: y_fract, z_fract: z_fract }
       end
 
       def diagnostic_label

data/lib/asciichem/model_adapter/from_canonical.rb

@@ -215,7 +215,10 @@ module AsciiChem
             isotope: atom.isotope,
             subscript: subscript_from_count(atom.count),
             charge: atom.formal_charge,
-            **extract_coordinates(atom)
+            spin_multiplicity: atom.spin_multiplicity,
+            atom_title: atom.title,
+            **extract_coordinates(atom),
+            **extract_fractional(atom)
           )
         end
 
@@ -232,6 +235,14 @@ module AsciiChem
           end
         end
 
+        def extract_fractional(atom)
+          return {} unless atom.xFract && atom.yFract && atom.zFract
+
+          { x_fract: atom.xFract.to_f,
+            y_fract: atom.yFract.to_f,
+            z_fract: atom.zFract.to_f }
+        end
+
         def subscript_from_count(count)
           return nil if count.nil? || count.to_s == "1"
 

data/lib/asciichem/model_adapter/to_canonical.rb

@@ -330,9 +330,12 @@ module AsciiChem
             formal_charge: atom.charge,
             count: effective_count(atom, multiplier),
             lone_pairs: atom.lone_pairs,
-            radical_electrons: atom.radical_electrons
+            radical_electrons: atom.radical_electrons,
+            spin_multiplicity: atom.spin_multiplicity,
+            title: atom.atom_title
           }
           merge_coordinates(attrs, atom)
+          merge_fractional_coords(attrs, atom)
           @atoms << Chemicalml::Cml::Atom.new(**attrs)
           emit_pending_bond(id) if @pending_bond_kind && @last_atom_id
           @last_atom_id = id
@@ -386,6 +389,14 @@ module AsciiChem
           end
         end
 
+        def merge_fractional_coords(attrs, atom)
+          return unless atom.x_fract && atom.y_fract && atom.z_fract
+
+          attrs[:xFract] = atom.x_fract
+          attrs[:yFract] = atom.y_fract
+          attrs[:zFract] = atom.z_fract
+        end
+
         def combine(left, right)
           lv = integer_or_nil(left)
           rv = integer_or_nil(right)

data/lib/asciichem/transform.rb

@@ -272,7 +272,12 @@ module AsciiChem
           x2: float_or_nil(hash[:x2]),
           y2: float_or_nil(hash[:y2]),
           z2: float_or_nil(hash[:z2]),
-          atom_parity: hash[:atom_parity]&.to_s
+          atom_parity: hash[:atom_parity]&.to_s,
+          spin_multiplicity: hash[:spin_multiplicity]&.to_s,
+          atom_title: hash[:atom_title]&.to_s,
+          x_fract: float_or_nil(hash[:x_fract]),
+          y_fract: float_or_nil(hash[:y_fract]),
+          z_fract: float_or_nil(hash[:z_fract])
         )
       end
 
@@ -305,7 +310,9 @@ module AsciiChem
       def initialize(element, isotope: nil, subscript: nil, superscript: nil,
                      lone_pairs: nil, radical_electrons: nil,
                      ring_closures: nil,
-                     x2: nil, y2: nil, z2: nil, atom_parity: nil)
+                     x2: nil, y2: nil, z2: nil, atom_parity: nil,
+                     spin_multiplicity: nil, atom_title: nil,
+                     x_fract: nil, y_fract: nil, z_fract: nil)
         @element = element
         @isotope = isotope
         @subscript = subscript
@@ -317,6 +324,11 @@ module AsciiChem
         @y2 = y2
         @z2 = z2
         @atom_parity = atom_parity
+        @spin_multiplicity = spin_multiplicity
+        @atom_title = atom_title
+        @x_fract = x_fract
+        @y_fract = y_fract
+        @z_fract = z_fract
       end
 
       def build
@@ -335,7 +347,12 @@ module AsciiChem
           x2: @x2,
           y2: @y2,
           z2: @z2,
-          atom_parity: @atom_parity
+          atom_parity: @atom_parity,
+          spin_multiplicity: @spin_multiplicity,
+          atom_title: @atom_title,
+          x_fract: @x_fract,
+          y_fract: @y_fract,
+          z_fract: @z_fract
         )
       end
 

data/lib/asciichem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module AsciiChem
-  VERSION = "0.3.3"
+  VERSION = "0.3.4"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.3.3
+  version: 0.3.4
 platform: ruby
 authors:
 - Ribose Inc.