first add

CMakeLists.txt

@@ -0,0 +1,95 @@
+# Copyright 2024 DeepMind Technologies Limited
+#
+# AlphaFold 3 source code is licensed under CC BY-NC-SA 4.0. To view a copy of
+# this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/
+#
+# To request access to the AlphaFold 3 model parameters, follow the process set
+# out at https://github.com/google-deepmind/alphafold3. You may only use these
+# if received directly from Google. Use is subject to terms of use available at
+# https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
+
+cmake_minimum_required(VERSION 3.28)
+project(
+  "${SKBUILD_PROJECT_NAME}"
+  LANGUAGES CXX
+  VERSION "${SKBUILD_PROJECT_VERSION}")
+
+include(FetchContent)
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
+set(ABSL_PROPAGATE_CXX_STD ON)
+
+# Remove support for scan deps, which is only useful when using C++ modules.
+unset(CMAKE_CXX_SCANDEP_SOURCE)
+
+FetchContent_Declare(
+  abseil-cpp
+  GIT_REPOSITORY https://github.com/abseil/abseil-cpp
+  GIT_TAG d7aaad83b488fd62bd51c81ecf16cd938532cc0a # 20240116.2
+  EXCLUDE_FROM_ALL)
+
+FetchContent_Declare(
+  pybind11
+  GIT_REPOSITORY https://github.com/pybind/pybind11
+  GIT_TAG 2e0815278cb899b20870a67ca8205996ef47e70f # v2.12.0
+  EXCLUDE_FROM_ALL)
+
+FetchContent_Declare(
+  pybind11_abseil
+  GIT_REPOSITORY https://github.com/pybind/pybind11_abseil
+  GIT_TAG bddf30141f9fec8e577f515313caec45f559d319 # HEAD @ 2024-08-07
+  EXCLUDE_FROM_ALL)
+
+FetchContent_Declare(
+  cifpp
+  GIT_REPOSITORY https://github.com/pdb-redo/libcifpp
+  GIT_TAG ac98531a2fc8daf21131faa0c3d73766efa46180 # v7.0.3
+  # Don't `EXCLUDE_FROM_ALL` as necessary for build_data.
+)
+
+FetchContent_Declare(
+  dssp
+  GIT_REPOSITORY https://github.com/PDB-REDO/dssp
+  GIT_TAG 57560472b4260dc41f457706bc45fc6ef0bc0f10 # v4.4.7
+  EXCLUDE_FROM_ALL)
+
+FetchContent_MakeAvailable(pybind11 abseil-cpp pybind11_abseil cifpp dssp)
+
+find_package(
+  Python3
+  COMPONENTS Interpreter Development NumPy
+  REQUIRED)
+
+include_directories(${PYTHON_INCLUDE_DIRS})
+include_directories(src/)
+
+file(GLOB_RECURSE cpp_srcs src/alphafold3/*.cc)
+list(FILTER cpp_srcs EXCLUDE REGEX ".*\(_test\|_main\|_benchmark\).cc$")
+
+add_compile_definitions(NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
+
+pybind11_add_module(cpp ${cpp_srcs})
+
+target_link_libraries(
+  cpp
+  PRIVATE absl::check
+          absl::flat_hash_map
+          absl::node_hash_map
+          absl::strings
+          absl::status
+          absl::statusor
+          absl::log
+          pybind11_abseil::absl_casters
+          Python3::NumPy
+          dssp::dssp
+          cifpp::cifpp)
+
+target_compile_definitions(cpp PRIVATE VERSION_INFO=${PROJECT_VERSION})
+install(TARGETS cpp LIBRARY DESTINATION alphafold3)
+install(
+  FILES LICENSE
+        OUTPUT_TERMS_OF_USE.md
+        WEIGHTS_PROHIBITED_USE_POLICY.md
+        WEIGHTS_TERMS_OF_USE.md
+  DESTINATION alphafold3)