@@ -2244,6 +2244,37 @@ (define-public python-parabam
defined rule on an input file.")
(license license:gpl3)))
+(define-public python-pdbfixer
+ (package
+ (name "python-pdbfixer")
+ (version "1.9")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openmm/pdbfixer")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags '(list "-k"
+ ;; These tests fail because they require internet access.
+ (string-append "not test_build_and_simulate.py"
+ " and not test_cli.py"
+ " and not test_mutate.py"))))
+ (propagated-inputs (list python-numpy openmm))
+ (native-inputs (list python-pytest))
+ (home-page "https://github.com/openmm/pdbfixer")
+ (synopsis "Application for fixing problems in Protein Data Bank")
+ (description
+ "PDBFixer is designed to rectify issues in Protein Data Bank files.
+Its intuitive interface simplifies the process of resolving problems
+encountered in PDB files prior to simulation tasks.")
+ (license license:expat)))
+
(define-public python-peaks2utr
(package
(name "python-peaks2utr")