rdkit_chem 2019.03.3.1
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +7 -0
- data/Rakefile +9 -0
- data/ext/rdkit_chem/extconf.rb +54 -0
- data/lib/rdkit_chem.rb +2 -0
- data/lib/rdkit_chem/version.rb +4 -0
- data/test/test_rdkit_chem.rb +19 -0
- metadata +51 -0
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA256:
|
3
|
+
metadata.gz: 16d4c3253c524fed6350543655d42c6bc31282ad7d2d3427f2d3caaa6d509801
|
4
|
+
data.tar.gz: 3be48c571b7fd47a6623b5050ec466c4b5d6771d645f369f105cffc2744f1a05
|
5
|
+
SHA512:
|
6
|
+
metadata.gz: 9c743b77d31914166e44381cea20f6e46cf5177bc07e24679990731c954561beb25a29e81e20afbd6cb46bba8d803bf9a841f1845eeda77fe2ca3a185f3e25eb
|
7
|
+
data.tar.gz: 137c9762b8257d5e638f325eb66005ff10bf9e292413e16526c61768a7e91ba14b4cbd360039f56720964e9fa3108dc054b08de618cd2cc17a29ac8ce9d8272f
|
data/Rakefile
ADDED
@@ -0,0 +1,54 @@
|
|
1
|
+
require 'fileutils'
|
2
|
+
require 'rbconfig'
|
3
|
+
require 'mkmf'
|
4
|
+
|
5
|
+
main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
|
6
|
+
|
7
|
+
# install OpenBabel
|
8
|
+
|
9
|
+
rdkit_dir = File.join main_dir, 'rdkit'
|
10
|
+
src_dir = rdkit_dir
|
11
|
+
|
12
|
+
build_dir = File.join src_dir, 'build'
|
13
|
+
install_dir = rdkit_dir
|
14
|
+
|
15
|
+
begin
|
16
|
+
nr_processors = `getconf _NPROCESSORS_ONLN`.to_i # should be POSIX compatible
|
17
|
+
rescue StandardError
|
18
|
+
nr_processors = 1
|
19
|
+
end
|
20
|
+
|
21
|
+
FileUtils.mkdir_p rdkit_dir
|
22
|
+
Dir.chdir main_dir do
|
23
|
+
FileUtils.rm_rf src_dir
|
24
|
+
puts 'Downloading RDKit sources'
|
25
|
+
git = "git clone https://github.com/CamAnNguyen/rdkit.git \
|
26
|
+
--branch 'ruby-binding'"
|
27
|
+
system git
|
28
|
+
end
|
29
|
+
|
30
|
+
FileUtils.mkdir_p build_dir
|
31
|
+
FileUtils.mkdir_p install_dir
|
32
|
+
Dir.chdir build_dir do
|
33
|
+
puts 'Configuring RDKit'
|
34
|
+
|
35
|
+
cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} " \
|
36
|
+
'-DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_PYTHON_WRAPPERS=OFF ' \
|
37
|
+
'-DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON ' \
|
38
|
+
'-DBOOST_ROOT=/usr/include/'
|
39
|
+
system cmake
|
40
|
+
end
|
41
|
+
|
42
|
+
# local installation in gem directory
|
43
|
+
Dir.chdir build_dir do
|
44
|
+
puts 'Compiling RDKit sources.'
|
45
|
+
system "make -j#{nr_processors}"
|
46
|
+
system 'make install'
|
47
|
+
end
|
48
|
+
|
49
|
+
# create a fake Makefile
|
50
|
+
File.open(File.join(File.dirname(__FILE__), 'Makefile'), "w+") do |makefile|
|
51
|
+
makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
|
52
|
+
end
|
53
|
+
|
54
|
+
$makefile_created = true
|
data/lib/rdkit_chem.rb
ADDED
@@ -0,0 +1,19 @@
|
|
1
|
+
require 'test/unit'
|
2
|
+
|
3
|
+
require 'rdkit_chem'
|
4
|
+
include RDKit
|
5
|
+
|
6
|
+
class RDKitTest < Test::Unit::TestCase
|
7
|
+
def test_ROMol
|
8
|
+
# smi2mol = OBConversion.new
|
9
|
+
# smi2mol.set_in_format("smi")
|
10
|
+
|
11
|
+
# mol = OBMol.new
|
12
|
+
# smi2mol.read_string(mol, 'CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C') # cholesterol, no chirality
|
13
|
+
# mol.add_hydrogens
|
14
|
+
|
15
|
+
# assert_equal(mol.num_atoms, 74)
|
16
|
+
# assert_in_delta(mol.get_mol_wt, 386.65, 0.1)
|
17
|
+
# assert_equal(mol.get_formula, "C27H46O")
|
18
|
+
end
|
19
|
+
end
|
metadata
ADDED
@@ -0,0 +1,51 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: rdkit_chem
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 2019.03.3.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- An Nguyen
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2019-07-15 00:00:00.000000000 Z
|
12
|
+
dependencies: []
|
13
|
+
description: RDKit as a GEM
|
14
|
+
email:
|
15
|
+
- annguyen@kit.edu
|
16
|
+
executables: []
|
17
|
+
extensions:
|
18
|
+
- ext/rdkit_chem/extconf.rb
|
19
|
+
extra_rdoc_files: []
|
20
|
+
files:
|
21
|
+
- Rakefile
|
22
|
+
- ext/rdkit_chem/extconf.rb
|
23
|
+
- lib/rdkit_chem.rb
|
24
|
+
- lib/rdkit_chem/version.rb
|
25
|
+
- test/test_rdkit_chem.rb
|
26
|
+
homepage: https://github.com/CamAnNguyen/rdkit-chem
|
27
|
+
licenses:
|
28
|
+
- BSD
|
29
|
+
metadata: {}
|
30
|
+
post_install_message:
|
31
|
+
rdoc_options: []
|
32
|
+
require_paths:
|
33
|
+
- lib
|
34
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
35
|
+
requirements:
|
36
|
+
- - ">="
|
37
|
+
- !ruby/object:Gem::Version
|
38
|
+
version: '0'
|
39
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
40
|
+
requirements:
|
41
|
+
- - ">="
|
42
|
+
- !ruby/object:Gem::Version
|
43
|
+
version: '0'
|
44
|
+
requirements: []
|
45
|
+
rubyforge_project:
|
46
|
+
rubygems_version: 2.7.9
|
47
|
+
signing_key:
|
48
|
+
specification_version: 4
|
49
|
+
summary: Ruby gem for RDKit !
|
50
|
+
test_files:
|
51
|
+
- test/test_rdkit_chem.rb
|