From 1076b460a18ec2a415198a9da6b8881fcdc6afb2 Mon Sep 17 00:00:00 2001
From: Yoshitaka Moriwaki <virgospica93@gmail.com>
Date: Wed, 14 Aug 2024 02:08:52 +0900
Subject: [PATCH] alphafill 2.1.0 (new formula) (#1825)

---
 Formula/alphafill.rb | 52 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 Formula/alphafill.rb

diff --git a/Formula/alphafill.rb b/Formula/alphafill.rb
new file mode 100644
index 000000000..56dc02587
--- /dev/null
+++ b/Formula/alphafill.rb
@@ -0,0 +1,52 @@
+class Alphafill < Formula
+  # cite Hekkelman_2023: "https://doi.org/10.1038/s41592-022-01685-y"
+  desc "Transplant missing compounds to the AlphaFold models"
+  homepage "https://github.com/PDB-REDO/alphafill"
+  url "https://github.com/PDB-REDO/alphafill/archive/refs/tags/v2.1.0.tar.gz"
+  sha256 "30b554a936fcf052c562020ac6dd516386863dfc710ac91be3a11b83bb4c69d1"
+  license "BSD-2-Clause"
+  head "https://github.com/PDB-REDO/alphafill.git", branch: "trunk"
+
+  depends_on "cmake" => :build
+  depends_on "pkg-config" => :build
+  depends_on "boost"
+  depends_on "brewsci/bio/libcifpp"
+  depends_on "brewsci/bio/libmcfp"
+  depends_on "brewsci/bio/libzeep"
+
+  uses_from_macos "bzip2"
+  uses_from_macos "zlib"
+
+  def install
+    inreplace "CMakeLists.txt" do |s|
+      s.gsub! "find_package(libmcfp 1.2.4 QUIET)", "find_package(libmcfp REQUIRED)"
+      s.gsub! "find_package(libpqxx 7.8.0 QUIET)",
+              "find_package(PkgConfig)\npkg_check_modules(libpqxx REQUIRED libpqxx>=7.8.0)"
+      s.gsub! "libpqxx::pqxx", "${LIBPQXX_LIBRARIES}"
+    end
+    # WEB_APPLICATION and BUILD_DOCUMENTATION were OFF because they failed to build
+    system "cmake", "-S", ".", "-B", "build",
+                    "-DBUILD_DOCUMENTATION=OFF",
+                    "-DBUILD_WEB_APPLICATION=OFF",
+                    "-DALPHAFILL_DATA_DIR=#{pkgshare}",
+                    *std_cmake_args
+    system "cmake", "--build", "build"
+    system "cmake", "--install", "build"
+    prefix.install "test"
+  end
+
+  test do
+    (testpath/"alphafill.conf").write <<~EOS
+      pdb-dir=#{prefix}/test/mini-pdb-redo/
+      pdb-fasta=#{testpath}/pdb-redo.fa
+      ligands=#{share}/alphafill/af-ligands.cif
+    EOS
+    system "#{bin}/alphafill", "create-index"
+    assert_match ">pdb-entity|2CBS|1|R13\nPNFSGNW", File.read("#{testpath}/pdb-redo.fa")
+    system "#{bin}/alphafill", "process", "--config", "#{testpath}/alphafill.conf",
+           "#{prefix}/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz",
+           "#{testpath}/out.cif.gz"
+    assert_predicate testpath/"out.cif.gz", :exist?
+    assert_match "RETINOIC ACID", shell_output("gunzip -c #{testpath}/out.cif.gz")
+  end
+end