From 948c4c26e15a834e02c0e2b4b2a0a84b0671bd88 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 6 Feb 2024 16:16:23 +0100
Subject: [PATCH] gnu: Add openmm.

* gnu/packages/machine-learning.scm (openmm): New variable.

Change-Id: I2a296471881ffbd9356fcdd27d349aa4a7bb5132
---
 gnu/packages/machine-learning.scm | 48 +++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 92cc468871..7653608fd9 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -73,6 +73,7 @@ (define-module (gnu packages machine-learning)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dejagnu)
+  #:use-module (gnu packages documentation)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
@@ -660,6 +661,53 @@ (define-public ocaml-mcl
 algorithm.")
     (license license:gpl3)))
 
+(define-public openmm
+  (package
+    (name "openmm")
+    (version "8.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/openmm/openmm")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "064vv6zaci30pj38z5lwfqscxssm67jqxkz30hcya9vm4ng831d5"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      '(list "-DOPENMM_BUILD_SHARED_LIB=TRUE"
+             "-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=TRUE"
+             "-DOPENMM_BUILD_PYTHON_WRAPPERS=TRUE"
+             "-DOPENMM_BUILD_CUDA_LIB=FALSE")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-python-build-system
+            (lambda _
+              (substitute* "wrappers/python/CMakeLists.txt"
+                (("install --root=\\\\\\$ENV\\{DESTDIR\\}/")
+                 (string-append "install --prefix=" #$output
+                                " --root=/ --single-version-externally-managed")))))
+          (add-after 'install 'install-python
+            (lambda _
+              (invoke "make" "PythonInstall"))))))
+    (inputs
+     (list python-wrapper))
+    (propagated-inputs
+     (list python-numpy))
+    (native-inputs
+     (list doxygen gfortran opencl-headers python-cython swig))
+    (home-page "https://github.com/openmm/openmm/")
+    (synopsis "Toolkit for molecular simulation")
+    (description
+     "OpenMM is a toolkit for molecular simulation.  It can be used either as
+a stand-alone application for running simulations, or as a library you call
+from your own code.")
+    ;; See https://github.com/openmm/openmm/issues/4278#issuecomment-1772982471
+    (license license:expat)))
+
 (define-public randomjungle
   (package
     (name "randomjungle")