asciichem 0.31.8 → 0.31.10

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -3,6 +3,29 @@
 All notable changes to AsciiChem are documented here.
 This project follows [Semantic Versioning](https://semver.org/).
 
+## [0.31.10] - 2026-11-05
+
+### Changed
+- The native engine binding points at the renamed **chemomer** crate
+  (chemomer/chemomer): the dylib is `libchemomer.dylib` with
+  `chemomer_*` symbols and `CHEMOMER_LIB` replaces `INCHI_RS_LIB`.
+  Same contract, new spelling.
+- moxml is pinned to the 0.6 line from 0.6.1 (resolves to 0.6.2);
+  the full suite runs green against it.
+
+## [0.31.9] - 2026-10-24
+
+### Added
+- `AsciiChem::Inchi::NativeEngine`: the identity engine drives the
+  native inchi-rs Rust engine through its C ABI (model → molfile →
+  identifier + InChIKey). The library is an external artifact built
+  from the inchi-rs checkout and located via `INCHI_RS_LIB`; the
+  `ffi` gem loads lazily, so the core gem stays dependency-free.
+  Opt-in registration matches the BinaryEngine:
+  `AsciiChem::Inchi.engine = AsciiChem::Inchi::NativeEngine.new`.
+- The install guide mentions the native path alongside the IUPAC
+  binary.
+
 ## [0.31.8] - 2026-10-22
 
 ### Fixed

data/asciichem.gemspec

@@ -39,7 +39,7 @@ Gem::Specification.new do |spec|
   spec.add_dependency "elkrb", "~> 2.0"
   spec.add_dependency "lutaml-model", "~> 0.8"
   spec.add_dependency "mml", "~> 2.3"
-  spec.add_dependency "moxml", "~> 0.5"
+  spec.add_dependency "moxml", "~> 0.6.1"
   spec.add_dependency "parslet", "~> 2.0"
   spec.add_dependency "relaton-bib", "~> 2.1"
   spec.add_dependency "plurimath", "~> 0.11"

data/lib/asciichem/inchi/binary_engine.rb

@@ -33,7 +33,7 @@ module AsciiChem
       # the pipe: atom coordinates, charges and isotopes cross into
       # the engine through the V2000 block.
       def identity(molecule)
-        molfile = AsciiChem::Molfile.write(molecule)
+        molfile = AsciiChem::Molfile.write(molecule, layout: false)
         out = execute(molfile)
         inchi = out[/^InChI=\S+/]
         raise AsciiChem::Error, "#{bin} produced no InChI:\n#{out}" unless inchi

data/lib/asciichem/inchi/native_engine.rb

@@ -0,0 +1,80 @@
+# frozen_string_literal: true
+
+module AsciiChem
+  module Inchi
+    # Engine that drives the native chemomer engine (the Rust port)
+    # through its C ABI. The library is a documented external
+    # artifact — nothing is vendored: build it once from the chemomer
+    # checkout (`cargo build --release`) and point CHEMOMER_LIB at
+    # the cdylib, the same opt-in shape as the BinaryEngine's
+    # ASCIICHEM_INCHI_BIN. The `ffi` gem loads lazily — the core gem
+    # stays dependency-free.
+    #
+    #   AsciiChem::Inchi.engine = AsciiChem::Inchi::NativeEngine.new
+    #   AsciiChem::Inchi.engine = AsciiChem::Inchi::NativeEngine.new(lib: "/path/libchemomer.dylib")
+    class NativeEngine < Engine
+      DEFAULT_LIB = ENV.fetch('CHEMOMER_LIB', nil)
+
+      attr_reader :lib
+
+      def initialize(lib: DEFAULT_LIB)
+        super()
+        @lib = lib
+        unless @lib
+          raise AsciiChem::Error,
+                'chemomer native engine: set CHEMOMER_LIB to the built cdylib ' \
+                '(cargo build --release in the chemomer checkout)'
+        end
+        return if File.readable?(@lib)
+
+        raise AsciiChem::Error, "chemomer native engine: #{@lib} is not readable"
+      end
+
+      # model → molfile → chemomer → Identity. The molfile emission is
+      # the pipe, exactly as in the BinaryEngine.
+      def identity(molecule)
+        molfile = AsciiChem::Molfile.write(molecule, layout: false)
+        inchi = call(molfile, :chemomer_from_molfile)
+        inchikey = call(molfile, :chemomer_inchikey)
+        Identity.new(inchi: inchi, inchikey: inchikey)
+      end
+
+      private
+
+      def call(molfile, function)
+        binding_class = self.class.binding_class(@lib)
+        pointer = binding_class.public_send(function, molfile)
+        unless pointer
+          message = binding_class.last_error
+          raise AsciiChem::Error, "chemomer native engine: #{message || 'call failed'}"
+        end
+        value = pointer.read_string
+        binding_class.chemomer_string_free(pointer)
+        value
+      end
+
+      # One FFI module per library path, cached: attach_function
+      # defines the symbol bindings once.
+      def self.binding_class(path)
+        @binding_classes ||= {}
+        @binding_classes[path] ||= begin
+          require 'ffi'
+          Module.new do
+            extend FFI::Library
+
+            ffi_lib path
+            attach_function :chemomer_from_molfile, %i[string], :pointer
+            attach_function :chemomer_inchikey, %i[string], :pointer
+            attach_function :chemomer_string_free, %i[pointer], :void
+            attach_function :chemomer_last_error, [], :pointer
+
+            def self.last_error
+              pointer = chemomer_last_error
+              pointer.null? ? nil : pointer.read_string
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/asciichem/inchi.rb

@@ -14,11 +14,15 @@ module AsciiChem
     autoload :BinaryEngine, 'asciichem/inchi/binary_engine'
     autoload :Engine, 'asciichem/inchi/engine'
     autoload :Identity, 'asciichem/inchi/identity'
+    autoload :NativeEngine, 'asciichem/inchi/native_engine'
 
     INSTALL_GUIDE = 'install the IUPAC InChI software ' \
                     '(https://www.inchi-trust.org/downloads/) and set ' \
                     'AsciiChem::Inchi.engine = AsciiChem::Inchi::BinaryEngine.new ' \
-                    '(or pass bin: "path/to/inchi-1")'
+                    '(or pass bin: "path/to/inchi-1") — or, for the native ' \
+                    'Rust engine, build chemomer and set ' \
+                    'AsciiChem::Inchi.engine = AsciiChem::Inchi::NativeEngine.new ' \
+                    '(pointing CHEMOMER_LIB at the built cdylib)'
 
     class << self
       attr_accessor :engine

data/lib/asciichem/molfile/writer.rb

@@ -24,13 +24,16 @@ module AsciiChem
       BOND_STEREO = { wedge: 1, hash: 6 }.freeze
       CHIRALITY_PARITY = { 'TH1' => 1, 'TH2' => 2 }.freeze
 
-      def initialize(molecule, name: nil)
+      def initialize(molecule, name: nil, layout: true)
         @molecule = molecule
         @name = name
+      @layout = layout
       end
 
       def write
-        atoms, edges = Structure::Graph.build!(@molecule)
+        @atoms, @edges = Structure::Graph.build!(@molecule)
+        atoms = @atoms
+        edges = @edges
         raise ParseError, "molecule has no bonds — a formula is not a structure" if edges.empty? && atoms.length > 1
 
         lines = []
@@ -100,11 +103,11 @@ module AsciiChem
 
       # Authored coordinates win; otherwise positions from the
       # deterministic 2D layout (same walk order as the graph).
-      def coordinates(atom, index, atoms)
-        return [atom.x2, atom.y2] if atom.x2 && atom.y2
+      def coordinates(atom, index, _atoms)
+        return [0.0, 0.0] unless @layout
 
-        @layout ||= AsciiChem::Layout.layout(@molecule)
-        placed = @layout.atoms[index]
+        @layout_positions ||= AsciiChem::Layout.layout(@molecule).atoms
+        placed = @layout_positions[index]
         placed ? [placed.x, placed.y] : [0.0, 0.0]
       end
 

data/lib/asciichem/molfile.rb

@@ -18,8 +18,8 @@ module AsciiChem
 
       # Emits a V2000 molfile. Uses authored x2/y2 coordinates;
       # computes a 2D layout otherwise.
-      def write(molecule, name: nil)
-        Writer.new(molecule, name: name).write
+      def write(molecule, name: nil, layout: true)
+        Writer.new(molecule, name: name, layout: layout).write
       end
     end
   end

data/lib/asciichem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module AsciiChem
-  VERSION = "0.31.8"
+  VERSION = "0.31.10"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.31.8
+  version: 0.31.10
 platform: ruby
 authors:
 - Ribose Inc.
@@ -71,14 +71,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: 0.6.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: 0.6.1
 - !ruby/object:Gem::Dependency
   name: parslet
   requirement: !ruby/object:Gem::Requirement
@@ -220,6 +220,7 @@ files:
 - lib/asciichem/inchi/binary_engine.rb
 - lib/asciichem/inchi/engine.rb
 - lib/asciichem/inchi/identity.rb
+- lib/asciichem/inchi/native_engine.rb
 - lib/asciichem/layout.rb
 - lib/asciichem/linter.rb
 - lib/asciichem/linter/balance_check.rb