From b4f2b681ad9c01b99f36d3c2f6af78234b41d745 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 11 Oct 2023 15:40:54 +0200
Subject: [PATCH] gnu: Add r-chemmineob.

* gnu/packages/bioconductor.scm (r-chemmineob): New variable.
---
 gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9358e75aba..f6946b72c8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -37,10 +37,12 @@ (define-module (gnu packages bioconductor)
   #:use-module (guix git-download)
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages chemistry)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
@@ -18852,6 +18854,47 @@ (define-public r-bigpint
 visualizing RNA-sequencing datasets and differentially expressed genes.")
     (license license:gpl3)))
 
+(define-public r-chemmineob
+  (package
+    (name "r-chemmineob")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ChemmineOB" version))
+       (sha256
+        (base32 "0l44d6l078k1w5nf7i4sarah1zn30zqjmcj9qpy4hhg97dfy45ci"))))
+    (properties `((upstream-name . "ChemmineOB")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-makefile
+            (lambda _
+              (substitute* "src/Makevars.in"
+                (("/usr/include/openbabel3")
+                 (string-append #$(this-package-input "openbabel")
+                                "/include/openbabel3"))
+                (("/usr/include/eigen3")
+                 (string-append #$(this-package-input "eigen")
+                                "/include/eigen3"))))))))
+    (inputs (list eigen openbabel))
+    (propagated-inputs (list r-bh r-biocgenerics r-rcpp r-zlibbioc))
+    (native-inputs (list pkg-config r-knitr))
+    (home-page "https://github.com/girke-lab/ChemmineOB")
+    (synopsis "R interface to a subset of OpenBabel functionalities")
+    (description
+     "@code{ChemmineOB} provides an R interface to a subset of cheminformatics
+functionalities implemented by the @code{OpelBabel} C++ project.
+@code{OpenBabel} is an open source cheminformatics toolbox that includes
+utilities for structure format interconversions, descriptor calculations,
+compound similarity searching and more. @code{ChemineOB} aims to make a subset
+of these utilities available from within R.  For non-developers,
+@code{ChemineOB} is primarily intended to be used from @code{ChemmineR} as an
+add-on package rather than used directly.")
+    (license license:asl2.0)))
+
 (define-public r-chemminer
   (package
     (name "r-chemminer")