asciichem 0.3.1 → 0.3.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: c092bfffa44620c0bb2ef20abdba849732eaaaa01ae2f0039bf8c22a4d57baad
+  metadata.gz: 9dcc9efdb2f096fa1b8e71fa12f23df5ff2c7246d017d71fe3cf87309ed65504
+  data.tar.gz: f64ddf08f74a2c38fcce98bae1cd4010b4ae55ede0f38bbf0f248fea475dead6
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+  metadata.gz: 283b735f960be1ab4cc2f3d4b98977dc8ef49dab16e19305ab64cd5054ac09a6f69e942c56a93705c48f6e9710ecf7c3e6f462bdd12e0a0081a58eea8b7bc8aa
+  data.tar.gz: 2c9d3f021372984bd52177269bcae201f2b176393883c774533232a2e21b3498e083d2874b1ccb1c06a8d6596cf8d309c88aed2fd457e92b8a0b6c78ea714423

data/lib/asciichem/cml/translator.rb

@@ -23,6 +23,8 @@ module AsciiChem
           translation = AsciiChem::ModelAdapter.to_canonical_with_mapping(formula)
           xml = translation.document.to_xml
           xml = inject_atom_extensions(xml, translation.atom_mapping)
+          xml = inject_reaction_conditions(xml, formula)
+          xml = inject_metadata(xml, formula)
           inject_molecule_extensions(xml, formula, translation)
         end
 
@@ -31,10 +33,14 @@ module AsciiChem
           top_level = Extensions.extract_top_level(xml)
           atom_extensions = Extensions.extract(xml)
           group_extensions = GroupExtensions.extract(xml)
+          metadata_map = extract_metadata(xml)
+          reaction_conditions = extract_reaction_conditions(xml)
           wire_doc = Chemicalml::Cml::Document.from_xml(xml)
           formula = AsciiChem::ModelAdapter.from_canonical(wire_doc)
           Extensions.restore(formula, wire_doc, atom_extensions)
           GroupExtensions.restore(formula, wire_doc, group_extensions)
+          restore_reaction_conditions(formula, reaction_conditions)
+          restore_metadata(formula, metadata_map)
           Extensions.restore_top_level(formula, top_level)
           formula
         end
@@ -57,6 +63,120 @@ module AsciiChem
           Extensions.inject(xml, extensions)
         end
 
+        # Inject reaction conditions via aci: attributes. Each Reaction
+        # in the formula with conditions produces aci:conditionsAbove
+        # and aci:conditionsBelow attributes on its <reaction> element.
+        def inject_reaction_conditions(xml, formula)
+          require 'nokogiri'
+          doc = Nokogiri::XML(xml)
+          root = doc.root
+          reactions = formula.nodes.select { |n| n.is_a?(AsciiChem::Model::Reaction) }
+          return xml if reactions.empty?
+
+          root.add_namespace(Extensions::PREFIX, Extensions::NAMESPACE) unless root.namespaces.value?(Extensions::NAMESPACE)
+          reactions.each_with_index do |reaction, idx|
+            next unless reaction.conditions
+
+            reaction_el = root.at_xpath("//cml:reaction[@id='r#{idx + 1}']", cml: Extensions::CML_NS)
+            next unless reaction_el
+
+            reaction_el["#{Extensions::PREFIX}:conditionsAbove"] = reaction.conditions.above if reaction.conditions.above
+            reaction_el["#{Extensions::PREFIX}:conditionsBelow"] = reaction.conditions.below if reaction.conditions.below
+          end
+          doc.to_xml
+        end
+
+        def extract_reaction_conditions(xml)
+          require 'nokogiri'
+          doc = Nokogiri::XML(xml)
+          result = {}
+          doc.xpath("//cml:reaction", cml: Extensions::CML_NS).each do |el|
+            id = el['id']
+            next unless id
+
+            above = el["#{Extensions::PREFIX}:conditionsAbove"]
+            below = el["#{Extensions::PREFIX}:conditionsBelow"]
+            result[id] = { above: above, below: below } if above || below
+          end
+          result
+        end
+
+        def restore_reaction_conditions(formula, conditions)
+          return formula if conditions.empty?
+
+          formula.nodes.each_with_index do |node, idx|
+            next unless node.is_a?(AsciiChem::Model::Reaction)
+
+            data = conditions["r#{idx + 1}"]
+            next unless data
+
+            node.conditions = AsciiChem::Model::Reaction::Conditions.new(
+              above: data[:above],
+              below: data[:below]
+            )
+          end
+          formula
+        end
+
+        # Inject molecule metadata via aci: attributes on <molecule>.
+        # Each {name: "k", content: "v"} produces aci:meta-k="v".
+        def inject_metadata(xml, formula)
+          require 'nokogiri'
+          doc = Nokogiri::XML(xml)
+          root = doc.root
+          molecules = formula.nodes.select { |n| n.is_a?(AsciiChem::Model::Molecule) }
+          has_meta = molecules.any? { |m| !m.metadata.empty? }
+          return xml unless has_meta
+
+          root.add_namespace(Extensions::PREFIX, Extensions::NAMESPACE) unless root.namespaces.value?(Extensions::NAMESPACE)
+          molecules.each_with_index do |mol, idx|
+            next if mol.metadata.empty?
+
+            mol_el = root.at_xpath("//cml:molecule[@id='m#{idx + 1}']", cml: Extensions::CML_NS)
+            next unless mol_el
+
+            mol.metadata.each do |m|
+              mol_el["#{Extensions::PREFIX}:meta-#{m[:name]}"] = m[:content]
+            end
+          end
+          doc.to_xml
+        end
+
+        def extract_metadata(xml)
+          require 'nokogiri'
+          doc = Nokogiri::XML(xml)
+          result = {}
+          doc.xpath("//cml:molecule", cml: Extensions::CML_NS).each do |el|
+            id = el['id']
+            next unless id
+
+            meta = {}
+            el.attributes.each do |name, attr|
+              next unless name.start_with?('meta-')
+              next unless attr.namespace && attr.namespace.prefix == Extensions::PREFIX
+
+              key = name.sub('meta-', '')
+              meta[key] = attr.value
+            end
+            result[id] = meta unless meta.empty?
+          end
+          result
+        end
+
+        def restore_metadata(formula, metadata_map)
+          return formula if metadata_map.empty?
+
+          formula.nodes.each_with_index do |node, idx|
+            next unless node.is_a?(AsciiChem::Model::Molecule)
+
+            meta = metadata_map["m#{idx + 1}"]
+            next unless meta
+
+            meta.each { |name, content| node.metadata << { name: name, content: content } }
+          end
+          formula
+        end
+
         def inject_molecule_extensions(xml, formula, translation)
           xml = inject_groups(xml, formula, translation)
           inject_top_level(xml, formula)

data/lib/asciichem/model_adapter/from_canonical.rb

@@ -104,7 +104,7 @@ module AsciiChem
         canonical_properties.map do |p|
           {
             title: p.title,
-            value: extract_scalar_value(p.value),
+            value: extract_scalar_value(p.scalar),
             dict_ref: p.dict_ref,
             convention: p.convention
           }
@@ -113,7 +113,7 @@ module AsciiChem
 
       def extract_scalar_value(value)
         return nil if value.nil?
-        return value.value if value.is_a?(Chemicalml::Cml::Scalar)
+        return value.content if value.is_a?(Chemicalml::Cml::Scalar)
 
         value.to_s
       end

data/lib/asciichem/model_adapter/to_canonical.rb

@@ -130,7 +130,7 @@ module AsciiChem
         properties.map do |p|
           Chemicalml::Cml::Property.new(
             title: p[:title],
-            value: build_scalar(p[:value]),
+            scalar: build_scalar(p[:value]),
             dict_ref: p[:dict_ref],
             convention: p[:convention]
           )
@@ -141,7 +141,7 @@ module AsciiChem
         return nil if value.nil?
 
         Chemicalml::Cml::Scalar.new(
-          value: value.to_s,
+          content: value.to_s,
           dict_ref: nil
         )
       end

data/lib/asciichem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module AsciiChem
-  VERSION = "0.3.1"
+  VERSION = "0.3.3"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.3
 platform: ruby
 authors:
 - Ribose Inc.