nafkhamdc wrote 1 years ago
(address . guix-patches@gnu.org)(name . nafkhamdc)(address . navid.afkhami@mdc-berlin.de)
6b3d0b29311e02f801f0990ccb88033763f00e56.1707560088.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-pdbfixer): New variable.
Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a
---
gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
Toggle diff (48 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 56709c0332..2c1917be95 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")
base-commit: 10dba10fd6551ab480a38d00301e6f102def674d
prerequisite-patch-id: 3a59afadab83198b19921e19197e26925523b4a3
prerequisite-patch-id: 116b12264d1713957eef349460a71f04b0757a9e
--
2.34.1