rdkit_chem 2025.09.3.1-x86_64-linux → 2025.09.3.3-x86_64-linux

checksums.yaml

@@ -1,7 +1,7 @@
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data/Code/RubyWrappers/MolOps.i

@@ -45,9 +45,10 @@
 %newobject RDKit::MolOps::adjustQueryProperties;
 
 %ignore RDKit::MolOps::detectChemistryProblems;
-// Ignore all native sanitizeMol overloads - we provide a custom wrapper below
-%ignore RDKit::MolOps::sanitizeMol;
 %include <GraphMol/MolOps.h>
+// Ignore only the 3-arg overload that uses reference parameters (incompatible with SWIG)
+// This keeps the 1-arg sanitizeMol(RWMol &) available from the header
+%ignore RDKit::MolOps::sanitizeMol(RWMol &,unsigned int &,unsigned int &);
 %template(BoolPair) std::pair<bool, bool>;
 
 %inline %{

data/Code/RubyWrappers/ROMol.i

@@ -189,9 +189,12 @@ unsigned int getDefaultPickleProperties();
     return res;
   }
 
-  /* Used in the addConformer modifications described above */
-  unsigned int RDKit::ROMol::addConf(RDKit::Conformer * ownedConf, bool assignId=false) {
-    return self->addConformer(ownedConf, assignId);
+  /* Create a copy of the conformer before adding it to the molecule.
+     This avoids the double-free issue since Ruby owns the original and C++ owns the copy.
+     The original DISOWN approach doesn't work with shared_ptr wrappers. */
+  unsigned int RDKit::ROMol::addConf(RDKit::Conformer *conf, bool assignId=false) {
+    RDKit::Conformer *confCopy = new RDKit::Conformer(*conf);
+    return self->addConformer(confCopy, assignId);
   }
 
   std::string MolToSmiles(bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true,

data/Rakefile

@@ -10,6 +10,12 @@ require 'rdkit_chem/version'
 VERSION = RDKitChem::GEMVERSION
 NATIVE_DIR = 'rdkit_chem/lib'
 
+# System libraries that need to be bundled for portability
+BUNDLED_SYSTEM_LIBS = %w[
+  libboost_serialization.so*
+  libboost_iostreams.so*
+].freeze
+
 desc 'Run tests'
 Rake::TestTask.new(:test) do |t|
   t.libs << 'lib'
@@ -69,6 +75,40 @@ task :build_native do
   puts "\nBuilt: rdkit_chem-#{VERSION}-#{Gem::Platform.local}.gem"
 end
 
+desc 'Bundle system libraries (Boost) into native directory'
+task :bundle_system_libs do
+  so_file = File.join(NATIVE_DIR, 'RDKitChem.so')
+  unless File.exist?(so_file)
+    abort "ERROR: #{so_file} not found"
+  end
+
+  puts "Finding and bundling system library dependencies..."
+
+  # Find library paths using ldd
+  ldd_output = `ldd #{so_file} 2>/dev/null`
+
+  BUNDLED_SYSTEM_LIBS.each do |lib_pattern|
+    lib_name = lib_pattern.gsub('*', '')
+    # Extract actual library path from ldd output
+    match = ldd_output.match(/#{Regexp.escape(lib_name)}[^\s]* => ([^\s]+)/)
+    if match
+      src_path = match[1]
+      if File.exist?(src_path)
+        dest = File.join(NATIVE_DIR, File.basename(src_path))
+        unless File.exist?(dest)
+          FileUtils.cp(src_path, dest, verbose: true)
+        else
+          puts "Already exists: #{dest}"
+        end
+      end
+    else
+      puts "WARNING: Could not find #{lib_pattern} in ldd output"
+    end
+  end
+
+  puts "Done bundling system libraries."
+end
+
 desc 'Apply RPATH fix to existing native extension (no recompile needed)'
 task :fix_rpath do
   so_file = File.join(NATIVE_DIR, 'RDKitChem.so')

data/lib/rdkit_chem/version.rb

@@ -1,4 +1,4 @@
 module RDKitChem
-  VERSION = '2025.09.3'.freeze
-  GEMVERSION = VERSION + '.1'
+  VERSION = "2025.09.3".freeze
+  GEMVERSION = VERSION + ".3"
 end

data/test/test_rdkit_chem.rb

@@ -44,4 +44,41 @@ class RDKitTest < Test::Unit::TestCase
     assert_not_nil(rw_mol)
     assert_equal(28, rw_mol.get_num_atoms)  # C27H46O has 28 heavy atoms (27 C + 1 O)
   end
+
+  def test_conformer_ownership
+    # Test that conformer ownership is properly transferred to the molecule.
+    # This verifies the DISOWN directive works - without it, Ruby GC and C++
+    # destructor both try to free the Conformer, causing a double-free segfault.
+    smiles = 'CCO'  # ethanol
+    rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
+
+    # Create a conformer with 3D coordinates
+    conf = RDKitChem::Conformer.new(rw_mol.get_num_atoms)
+    conf.set_atom_pos(0, RDKitChem::Point3D.new(0.0, 0.0, 0.0))
+    conf.set_atom_pos(1, RDKitChem::Point3D.new(1.5, 0.0, 0.0))
+    conf.set_atom_pos(2, RDKitChem::Point3D.new(2.0, 1.0, 0.0))
+
+    # Add conformer to molecule (ownership transfers to C++)
+    conf_id = rw_mol.addConf(conf, true)
+    assert(conf_id >= 0, "Conformer should be added successfully")
+
+    # Verify conformer was added
+    assert_equal(1, rw_mol.get_num_conformers)
+
+    # Access the conformer through the molecule
+    retrieved_conf = rw_mol.get_conformer(conf_id)
+    assert_not_nil(retrieved_conf)
+
+    # Verify coordinates
+    pos = retrieved_conf.get_atom_pos(0)
+    assert_in_delta(0.0, pos.x, 0.001)
+    assert_in_delta(0.0, pos.y, 0.001)
+    assert_in_delta(0.0, pos.z, 0.001)
+
+    # Force garbage collection to ensure no double-free occurs
+    GC.start
+
+    # The molecule should still be valid after GC
+    assert_equal(3, rw_mol.get_num_atoms)
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rdkit_chem
 version: !ruby/object:Gem::Version
-  version: 2025.09.3.1
+  version: 2025.09.3.3
 platform: x86_64-linux
 authors:
 - An Nguyen
@@ -337,6 +337,8 @@ files:
 - lib/rdkit_chem/3.3.0/libRDKitpubchem_align3d.so
 - lib/rdkit_chem/3.3.0/libRDKitpubchem_align3d.so.1
 - lib/rdkit_chem/3.3.0/libRDKitpubchem_align3d.so.1.2026.03.1pre
+- lib/rdkit_chem/3.3.0/libboost_iostreams.so.1.83.0
+- lib/rdkit_chem/3.3.0/libboost_serialization.so.1.83.0
 - lib/rdkit_chem/version.rb
 - test/test_rdkit_chem.rb
 homepage: https://github.com/CamAnNguyen/rdkit-chem