From ba4d8923791880fc46f78eb625b28f489b8ddbcf Mon Sep 17 00:00:00 2001
From: Irfan Alibay <IAlibay@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:47:52 +0100
Subject: [PATCH] Pymbar duecredit (#753)

* Add pymbar duecredit sections

* Add rever entry

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
---
 news/pymbar_duecredit.rst                     | 24 ++++++++++++++
 .../openmm_utils/multistate_analysis.py       | 31 +++++++++++++++++++
 openfe/tests/utils/test_duecredit.py          |  4 +++
 3 files changed, 59 insertions(+)
 create mode 100644 news/pymbar_duecredit.rst

diff --git a/news/pymbar_duecredit.rst b/news/pymbar_duecredit.rst
new file mode 100644
index 000000000..5cfa09038
--- /dev/null
+++ b/news/pymbar_duecredit.rst
@@ -0,0 +1,24 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Add duecredit citations for pymbar when calling
+  `openfe.protocols.openmm_utils.multistate_analysis`.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/openfe/protocols/openmm_utils/multistate_analysis.py b/openfe/protocols/openmm_utils/multistate_analysis.py
index a5dd647b5..49c2102b5 100644
--- a/openfe/protocols/openmm_utils/multistate_analysis.py
+++ b/openfe/protocols/openmm_utils/multistate_analysis.py
@@ -13,6 +13,37 @@
 from pymbar.utils import ParameterError
 from openfe.analysis import plotting
 from typing import Optional, Union
+from openfe.due import due, Doi
+
+
+due.cite(Doi("10.5281/zenodo.596622"),
+         description="OpenMMTools",
+         path="openfe.protocols.openmm_utils.multistate_analysis",
+         cite_module=True)
+
+
+due.cite(Doi("10.1063/1.2978177"),
+         description="MBAR paper",
+         path="openfe.protocols.openmm_utils.multistate_analysis",
+         cite_module=True)
+
+
+due.cite(Doi("10.1021/ct0502864"),
+         description="MBAR timeseries algorithms",
+         path="openfe.protocols.openmm_utils.multistate_analysis",
+         cite_module=True)
+
+
+due.cite(Doi("10.1021/acs.jctc.5b00784"),
+         description="Automatic equilibration detection method",
+         path="openfe.protocols.openmm_utils.multistate_analysis",
+         cite_module=True)
+
+
+due.cite(Doi("10.5281/zenodo.596220"),
+         description="pyMBAR zenodo",
+         path="openfe.protocols.openmm_utils.multistate_analysis",
+         cite_module=True)
 
 
 class MultistateEquilFEAnalysis:
diff --git a/openfe/tests/utils/test_duecredit.py b/openfe/tests/utils/test_duecredit.py
index dad7b9966..e3b3283f8 100644
--- a/openfe/tests/utils/test_duecredit.py
+++ b/openfe/tests/utils/test_duecredit.py
@@ -20,6 +20,10 @@ class TestDuecredit:
         ['openfe.protocols.openmm_rfe.equil_rfe_methods',
          ['10.5281/zenodo.1297683', '10.5281/zenodo.596622',
           '10.1371/journal.pcbi.1005659']],
+        ['openfe.protocols.openmm_utils.multistate_analysis',
+         ["10.5281/zenodo.596622", "10.1063/1.2978177",
+          "10.1021/ct0502864", "10.1021/acs.jctc.5b00784",
+          "10.5281/zenodo.596220"]],
     ])
     def test_duecredit_protocol_collection(self, module, dois):
         importlib.import_module(module)