rdkit_chem 2019.03.3.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: 16d4c3253c524fed6350543655d42c6bc31282ad7d2d3427f2d3caaa6d509801
+  data.tar.gz: 3be48c571b7fd47a6623b5050ec466c4b5d6771d645f369f105cffc2744f1a05
+SHA512:
+  metadata.gz: 9c743b77d31914166e44381cea20f6e46cf5177bc07e24679990731c954561beb25a29e81e20afbd6cb46bba8d803bf9a841f1845eeda77fe2ca3a185f3e25eb
+  data.tar.gz: 137c9762b8257d5e638f325eb66005ff10bf9e292413e16526c61768a7e91ba14b4cbd360039f56720964e9fa3108dc054b08de618cd2cc17a29ac8ce9d8272f

data/Rakefile

@@ -0,0 +1,9 @@
+require "bundler/gem_tasks"
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+end
+
+desc "Run tests"
+task :default => :test

data/ext/rdkit_chem/extconf.rb

@@ -0,0 +1,54 @@
+require 'fileutils'
+require 'rbconfig'
+require 'mkmf'
+
+main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
+
+# install OpenBabel
+
+rdkit_dir = File.join main_dir, 'rdkit'
+src_dir = rdkit_dir
+
+build_dir = File.join src_dir, 'build'
+install_dir = rdkit_dir
+
+begin
+  nr_processors = `getconf _NPROCESSORS_ONLN`.to_i # should be POSIX compatible
+rescue StandardError
+  nr_processors = 1
+end
+
+FileUtils.mkdir_p rdkit_dir
+Dir.chdir main_dir do
+  FileUtils.rm_rf src_dir
+  puts 'Downloading RDKit sources'
+  git = "git clone https://github.com/CamAnNguyen/rdkit.git \
+          --branch 'ruby-binding'"
+  system git
+end
+
+FileUtils.mkdir_p build_dir
+FileUtils.mkdir_p install_dir
+Dir.chdir build_dir do
+  puts 'Configuring RDKit'
+
+  cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} " \
+          '-DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_PYTHON_WRAPPERS=OFF ' \
+          '-DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON ' \
+          '-DBOOST_ROOT=/usr/include/'
+  system cmake
+end
+
+# local installation in gem directory
+Dir.chdir build_dir do
+  puts 'Compiling RDKit sources.'
+  system "make -j#{nr_processors}"
+  system 'make install'
+end
+
+# create a fake Makefile
+File.open(File.join(File.dirname(__FILE__), 'Makefile'), "w+") do |makefile|
+  makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
+end
+
+$makefile_created = true

data/lib/rdkit_chem.rb

@@ -0,0 +1,2 @@
+require_relative '../rdkit/Code/lib/RDKitChem'
+require 'rdkit_chem/version'

data/lib/rdkit_chem/version.rb

@@ -0,0 +1,4 @@
+module RDKitChem
+  VERSION = '2019.03.3'.freeze
+  GEMVERSION = VERSION + '.1'
+end

data/test/test_rdkit_chem.rb

@@ -0,0 +1,19 @@
+require 'test/unit'
+
+require 'rdkit_chem'
+include RDKit
+
+class RDKitTest < Test::Unit::TestCase
+  def test_ROMol
+    # smi2mol = OBConversion.new
+    # smi2mol.set_in_format("smi")
+
+    # mol = OBMol.new
+    # smi2mol.read_string(mol, 'CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C') # cholesterol, no chirality
+    # mol.add_hydrogens
+
+    # assert_equal(mol.num_atoms, 74)
+    # assert_in_delta(mol.get_mol_wt, 386.65, 0.1)
+    # assert_equal(mol.get_formula, "C27H46O")
+  end
+end

metadata

@@ -0,0 +1,51 @@
+--- !ruby/object:Gem::Specification
+name: rdkit_chem
+version: !ruby/object:Gem::Version
+  version: 2019.03.3.1
+platform: ruby
+authors:
+- An Nguyen
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2019-07-15 00:00:00.000000000 Z
+dependencies: []
+description: RDKit as a GEM
+email:
+- annguyen@kit.edu
+executables: []
+extensions:
+- ext/rdkit_chem/extconf.rb
+extra_rdoc_files: []
+files:
+- Rakefile
+- ext/rdkit_chem/extconf.rb
+- lib/rdkit_chem.rb
+- lib/rdkit_chem/version.rb
+- test/test_rdkit_chem.rb
+homepage: https://github.com/CamAnNguyen/rdkit-chem
+licenses:
+- BSD
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.7.9
+signing_key: 
+specification_version: 4
+summary: Ruby gem for RDKit !
+test_files:
+- test/test_rdkit_chem.rb