rdkit-rb 0.1.3 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 5ddcfc7d66cb137fe609094a7d0a0a964cb72e42803084e56b0b55ce8994d988
+  metadata.gz: c0a8054f7d7636d54bb74c37a0767f39c5ac39618f56b634bfc0deac77c7be13
+  data.tar.gz: 9fc6f39cfc0f9b683d538fb8e7ce567ed147513085b6b6e06053a1ec5551ce8c
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-  data.tar.gz: 8f18f2ce745ba8ec893f4e95ada45130a4a65b6b6e9a3e4aac39209bf961d07cc50d533d8db03235f213588350cb862201f010a714ccef62540d270e5eb8c8c1
+  metadata.gz: 0a000053252d7c363f5e24f2c7670650d5097c808372cd93de6fa6c8723382f3a918baef986dbd21db3d83a77125352a9bf6efbd7690c31492dc9d80551f27a3
+  data.tar.gz: 47de8c95416133f86cc9abde50778939536e12a2d10cc74bfb90df72547b0572d670b1013c136f8e7aaa0b13fa7cc46fa26cb29eeccb3f8bfe13840c920901be

data/CHANGELOG.md

@@ -1,3 +1,7 @@
+## 0.1.4 (2025-05-04)
+
+- Fixed memory leaks
+
 ## 0.1.3 (2024-12-29)
 
 - Fixed warning with Ruby 3.4

data/lib/rdkit/ffi.rb

@@ -70,7 +70,7 @@ module RDKit
 
     # housekeeping
     # treat as void *ptr since calls free() internally
-    FREE = extern "void free_ptr(char *ptr)"
+    extern "void free_ptr(char *ptr)"
 
     # other
     extern "char *version()"

data/lib/rdkit/molecule.rb

@@ -46,15 +46,19 @@ module RDKit
     end
 
     def fragments(sanitize: true)
-      sz_arr = Fiddle::Pointer.malloc(Fiddle::SIZEOF_VOIDP)
-      num_frags = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T)
+      sz_arr = Fiddle::Pointer.malloc(Fiddle::SIZEOF_VOIDP, Fiddle::RUBY_FREE)
+      num_frags = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T, Fiddle::RUBY_FREE)
       details = {
         sanitizeFrags: sanitize
       }
-      arr = FFI.get_mol_frags(@ptr, @sz, sz_arr.ref, num_frags.ref, to_details(details), nil)
+      arr = FFI.get_mol_frags(@ptr, @sz, sz_arr, num_frags, to_details(details), nil)
       check_ptr(arr)
+      arr.free = FFI["free_ptr"]
+      sz_arr = sz_arr.ptr
+      sz_arr.free = FFI["free_ptr"]
 
-      num_frags.to_i.times.map do |i|
+      num = num_frags.to_str(Fiddle::SIZEOF_SIZE_T).unpack1(Fiddle::SIZEOF_SIZE_T == 4 ? "L" : "Q")
+      num.times.map do |i|
         ptr = (arr + i * Fiddle::SIZEOF_VOIDP).ptr
         sz = (sz_arr + i * Fiddle::SIZEOF_SIZE_T).ptr
 
@@ -62,9 +66,6 @@ module RDKit
         mol.send(:load_ptr, ptr, sz)
         mol
       end
-    ensure
-      free_ptr(sz_arr)
-      free_ptr(arr)
     end
 
     def rdkit_fingerprint(min_path: 1, max_path: 7, length: 2048, bits_per_hash: 2, use_hs: true, branched_paths: true, use_bond_order: true)
@@ -145,8 +146,7 @@ module RDKit
     end
 
     def add_hs!
-      check_status(FFI.add_hs(@ptr.ref, @sz.ref))
-      self
+      modify(:add_hs)
     end
 
     def remove_hs
@@ -154,8 +154,7 @@ module RDKit
     end
 
     def remove_hs!
-      check_status(FFI.remove_all_hs(@ptr.ref, @sz.ref))
-      self
+      modify(:remove_all_hs)
     end
 
     def cleanup
@@ -163,8 +162,7 @@ module RDKit
     end
 
     def cleanup!
-      check_status(FFI.cleanup(@ptr.ref, @sz.ref, to_details({})))
-      self
+      modify(:cleanup, to_details({}))
     end
 
     def normalize
@@ -172,8 +170,7 @@ module RDKit
     end
 
     def normalize!
-      check_status(FFI.normalize(@ptr.ref, @sz.ref, to_details({})))
-      self
+      modify(:normalize, to_details({}))
     end
 
     def neutralize
@@ -181,8 +178,7 @@ module RDKit
     end
 
     def neutralize!
-      check_status(FFI.neutralize(@ptr.ref, @sz.ref, to_details({})))
-      self
+      modify(:neutralize, to_details({}))
     end
 
     def reionize
@@ -190,8 +186,7 @@ module RDKit
     end
 
     def reionize!
-      check_status(FFI.reionize(@ptr.ref, @sz.ref, to_details({})))
-      self
+      modify(:reionize, to_details({}))
     end
 
     def canonical_tautomer
@@ -199,8 +194,7 @@ module RDKit
     end
 
     def canonical_tautomer!
-      check_status(FFI.canonical_tautomer(@ptr.ref, @sz.ref, to_details({})))
-      self
+      modify(:canonical_tautomer, to_details({}))
     end
 
     def charge_parent
@@ -208,8 +202,7 @@ module RDKit
     end
 
     def charge_parent!
-      check_status(FFI.charge_parent(@ptr.ref, @sz.ref, to_details({})))
-      self
+      modify(:charge_parent, to_details({}))
     end
 
     def fragment_parent
@@ -217,8 +210,7 @@ module RDKit
     end
 
     def fragment_parent!
-      check_status(FFI.fragment_parent(@ptr.ref, @sz.ref, to_details({})))
-      self
+      modify(:fragment_parent, to_details({}))
     end
 
     def to_smiles
@@ -262,20 +254,20 @@ module RDKit
     end
 
     def load_smiles(input, sanitize: true, kekulize: true, remove_hs: true)
-      sz = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T)
+      sz = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T, Fiddle::RUBY_FREE)
       details = {
         sanitize: sanitize,
         kekulize: kekulize,
         removeHs: remove_hs
       }
-      ptr = FFI.get_mol(input.to_str, sz.ref, to_details(details))
-      load_ptr(ptr, sz)
+      ptr = FFI.get_mol(+input.to_str, sz, to_details(details))
+      load_ptr(ptr, Utils.read_size(sz))
     end
 
     def load_smarts(input)
-      sz = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T)
-      ptr = FFI.get_qmol(input.to_str, sz.ref, to_details({}))
-      load_ptr(ptr, sz)
+      sz = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T, Fiddle::RUBY_FREE)
+      ptr = FFI.get_qmol(+input.to_str, sz, to_details({}))
+      load_ptr(ptr, Utils.read_size(sz))
     end
 
     def load_ptr(ptr, sz)
@@ -284,7 +276,7 @@ module RDKit
       end
 
       @ptr = ptr
-      @ptr.free = FFI::FREE
+      @ptr.free = FFI["free_ptr"]
       @sz = sz
     end
 
@@ -313,22 +305,15 @@ module RDKit
     end
 
     def check_ptr(ptr)
-      if ptr.nil? || ptr.null?
+      if ptr.null?
         raise Error, "bad pointer"
       end
     end
 
-    def free_ptr(ptr)
-      FFI.free_ptr(ptr) if ptr
-    end
-
     def check_string(ptr)
       check_ptr(ptr)
-      begin
-        ptr.to_s
-      ensure
-        free_ptr(ptr)
-      end
+      ptr.free = FFI["free_ptr"]
+      ptr.to_s
     end
 
     def check_status(status)
@@ -336,5 +321,13 @@ module RDKit
         raise Error, "bad status: #{status}"
       end
     end
+
+    def modify(op, *args)
+      # TODO write as size_t
+      sz = Fiddle::Pointer.new(@sz)
+      check_status(FFI[op.to_s].call(@ptr.ref, sz.ref, *args))
+      @sz = Utils.read_size(sz.ref)
+      self
+    end
   end
 end

data/lib/rdkit/reaction.rb

@@ -24,10 +24,10 @@ module RDKit
     private
 
     def load_rxn(input)
-      sz = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T)
+      sz = Fiddle::Pointer.malloc(Fiddle::SIZEOF_SIZE_T, Fiddle::RUBY_FREE)
       @input = input.to_str
-      ptr = FFI.get_rxn(@input, sz.ref, to_details({}))
-      load_ptr(ptr, sz)
+      ptr = FFI.get_rxn(+@input, sz, to_details({}))
+      load_ptr(ptr, Utils.read_size(sz))
     end
 
     def load_ptr(ptr, sz)
@@ -36,7 +36,7 @@ module RDKit
       end
 
       @ptr = ptr
-      @ptr.free = FFI::FREE
+      @ptr.free = FFI["free_ptr"]
       @sz = sz
     end
 
@@ -45,22 +45,15 @@ module RDKit
     end
 
     def check_ptr(ptr)
-      if ptr.nil? || ptr.null?
+      if ptr.null?
         raise Error, "bad pointer"
       end
     end
 
-    def free_ptr(ptr)
-      FFI.free_ptr(ptr) if ptr
-    end
-
     def check_string(ptr)
       check_ptr(ptr)
-      begin
-        ptr.to_s
-      ensure
-        free_ptr(ptr)
-      end
+      ptr.free = FFI["free_ptr"]
+      ptr.to_s
     end
   end
 end

data/lib/rdkit/utils.rb

@@ -0,0 +1,8 @@
+module RDKit
+  module Utils
+    def self.read_size(ptr)
+      # TODO read as size_t
+      ptr.ptr.to_i
+    end
+  end
+end

data/lib/rdkit/version.rb

@@ -1,3 +1,3 @@
 module RDKit
-  VERSION = "0.1.3"
+  VERSION = "0.1.4"
 end

data/lib/rdkit.rb

@@ -6,6 +6,7 @@ require "json"
 require_relative "rdkit/molecule"
 require_relative "rdkit/reaction"
 require_relative "rdkit/version"
+require_relative "rdkit/utils"
 
 module RDKit
   class Error < StandardError; end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: rdkit-rb
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
 platform: ruby
 authors:
 - Andrew Kane
 bindir: bin
 cert_chain: []
-date: 2024-12-29 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: fiddle
@@ -36,6 +36,7 @@ files:
 - lib/rdkit/ffi.rb
 - lib/rdkit/molecule.rb
 - lib/rdkit/reaction.rb
+- lib/rdkit/utils.rb
 - lib/rdkit/version.rb
 - vendor/aarch64-linux/ChemReactions-license.txt
 - vendor/aarch64-linux/librdkitcffi.so
@@ -75,7 +76,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.6.2
+rubygems_version: 3.6.7
 specification_version: 4
 summary: Cheminformatics for Ruby, powered by RDKit
 test_files: []