From f84708d7740e22c3b476da897345c4079a861551 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Tue, 2 Apr 2024 23:55:42 -0600
Subject: add autodock-vina and chemicalite

---
 Formula/autodock-vina.rb | 43 +++++++++++++++++++++++++++++++++++++++++++
 Formula/chemicalite.rb   | 29 +++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+)
 create mode 100644 Formula/autodock-vina.rb
 create mode 100644 Formula/chemicalite.rb

diff --git a/Formula/autodock-vina.rb b/Formula/autodock-vina.rb
new file mode 100644
index 0000000..284873d
--- /dev/null
+++ b/Formula/autodock-vina.rb
@@ -0,0 +1,43 @@
+class AutodockVina < Formula
+  desc "Open-source program for doing molecular docking"
+  homepage "http://vina.scripps.edu"
+  url "https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.2.3.tar.gz"
+  sha256 "22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0"
+  license "Apache-2.0"
+
+  depends_on "swig" => :build
+  depends_on "boost"
+
+  def install
+    if OS.mac?
+      cd "build/mac/release" do
+        inreplace "Makefile" do |s|
+          s.gsub! "C_OPTIONS= -O3 -DNDEBUG -std=c++11", "C_OPTIONS= -O3 -DNDEBUG \
+          -std=c++14 -DBOOST_TIMER_ENABLE_DEPRECATED"
+          s.gsub! "BASE=/usr/local", "BASE=#{HOMEBREW_PREFIX}"
+        end
+        system "make"
+        system "make"
+        bin.install "vina"
+        bin.install "vina_split"
+      end
+    else
+      cd "build/linux/release" do
+        inreplace "Makefile" do |s|
+          s.gsub! "C_OPTIONS= -O3 -DNDEBUG -std=c++11", "C_OPTIONS= -O3 -DNDEBUG \
+          -std=c++14 -DBOOST_TIMER_ENABLE_DEPRECATED"
+          s.gsub! "BASE=/usr/local", "BASE=#{HOMEBREW_PREFIX}"
+        end
+        system "make"
+        system "make"
+        bin.install "vina"
+        bin.install "vina_split"
+      end
+    end
+  end
+
+  test do
+    system "#{HOMEBREW_PREFIX}/bin/vina", "--version"
+    system "#{HOMEBREW_PREFIX}/bin/vina_split", "--version"
+  end
+end
diff --git a/Formula/chemicalite.rb b/Formula/chemicalite.rb
new file mode 100644
index 0000000..6c94a38
--- /dev/null
+++ b/Formula/chemicalite.rb
@@ -0,0 +1,29 @@
+class Chemicalite < Formula
+  desc "SQLite extension for chemoinformatics applications"
+  homepage "https://chemicalite.readthedocs.io/en/latest/"
+  url "https://github.com/rvianello/chemicalite/archive/refs/tags/2024.02.1.tar.gz"
+  sha256 "fa254bb9a9b15b8fb4befefc28ff12225fdf99ddcf3ee0a5bd749be72283c9e7"
+  license "BSD-3-Clause"
+
+  depends_on "catch2" => [:build, :test]
+  depends_on "cmake" => :build
+  depends_on "sqlite" => [:build, :test]
+  depends_on "python3" => [:test]
+  depends_on "boost"
+  depends_on "rdkit"
+
+  def install
+    system "cmake", "-S", ".", "-B", "build", "-DCHEMICALITE_ENABLE_TESTS=OFF", *std_cmake_args
+    system "cmake", "--build", "build"
+    system "cmake", "--install", "build"
+  end
+
+  test do
+    system "python3", "-c", "import sqlite3; \
+    con = sqlite3.connect('chembldb.sql'); \
+    con.enable_load_extension(True); \
+    con.load_extension('chemicalite'); \
+    con.execute( \
+    'CREATE TABLE chembl(id INTEGER PRIMARY KEY, chembl_id TEXT, molecule MOL)')"
+  end
+end
-- 
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