From d0fa4b60be562d9a77f660452f7713de0b7375e4 Mon Sep 17 00:00:00 2001
From: Jason Swails <jason.swails@gmail.com>
Date: Mon, 16 Jan 2023 22:18:28 -0500
Subject: [PATCH] Fix bug for nbfix/chamber in ParmEd v3.4 (#1282)

* Fix bug for nbfix/chamber in ParmEd v3.4

* Remove visualization tests
---
 .github/workflows/Test.yaml       |  2 ++
 parmed/amber/_chamberparm.py      |  4 +--
 test/test_parmed_visualization.py | 55 -------------------------------
 3 files changed, 4 insertions(+), 57 deletions(-)
 delete mode 100644 test/test_parmed_visualization.py

diff --git a/.github/workflows/Test.yaml b/.github/workflows/Test.yaml
index 998328599..e76e2b000 100644
--- a/.github/workflows/Test.yaml
+++ b/.github/workflows/Test.yaml
@@ -28,6 +28,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/environment-dev.yaml
         activate-environment: parmed-dev
+        channels: conda-forge,bioconda
+        # mamba-version: "*"
 
     - name: Environment Information
       shell: bash -l {0}
diff --git a/parmed/amber/_chamberparm.py b/parmed/amber/_chamberparm.py
index 199b24516..1af391f5c 100644
--- a/parmed/amber/_chamberparm.py
+++ b/parmed/amber/_chamberparm.py
@@ -579,10 +579,10 @@ def _set_nonbonded_tables(self, nbfixes=None):
             for i, fix in enumerate(nbfixes):
                 for terms in fix:
                     j, rmin, eps, rmin14, eps14 = terms
-                    i, j = min(i, j-1), max(i, j-1)
+                    k, l = min(i, j-1), max(i, j-1)
                     eps = abs(eps)
                     eps14 = abs(eps14)
-                    idx = data['NONBONDED_PARM_INDEX'][ntypes*i+j] - 1
+                    idx = data['NONBONDED_PARM_INDEX'][ntypes*k+l] - 1
                     data['LENNARD_JONES_ACOEF'][idx] = eps * rmin**12
                     data['LENNARD_JONES_BCOEF'][idx] = 2 * eps * rmin**6
                     data['LENNARD_JONES_14_ACOEF'][idx] = eps14 * rmin14**12
diff --git a/test/test_parmed_visualization.py b/test/test_parmed_visualization.py
deleted file mode 100644
index 54539a90e..000000000
--- a/test/test_parmed_visualization.py
+++ /dev/null
@@ -1,55 +0,0 @@
-from __future__ import print_function
-import sys
-import parmed as pmd
-import unittest
-
-from utils import get_fn
-
-try:
-    from ipywidgets import Widget
-    from ipykernel.comm import Comm
-    import nglview
-    has_nglview = True
-
-    #------------------------------------------------------
-    # Utility stuff from ipywidgets tests: create DummyComm
-    # we dont need Jupyter notebook for testing
-    #------------------------------------------------------
-    class DummyComm(Comm):
-        comm_id = 'a-b-c-d'
-    
-        def open(self, *args, **kwargs):
-            pass
-    
-        def send(self, *args, **kwargs):
-            pass
-    
-        def close(self, *args, **kwargs):
-            pass
-    
-    _widget_attrs = {}
-    displayed = []
-    undefined = object()
-
-    _widget_attrs['_comm_default'] = getattr(Widget, '_comm_default', undefined)
-    Widget._comm_default = lambda self: DummyComm()
-    _widget_attrs['_ipython_display_'] = Widget._ipython_display_
-    def raise_not_implemented(*args, **kwargs):
-        raise NotImplementedError()
-    Widget._ipython_display_ = raise_not_implemented
-except ImportError:
-    has_nglview = False
-    nglview = Comm = DummyComm = _widget_attrs = displayed = undefined = Widget  = None
-
-@unittest.skipUnless(has_nglview, "Only test if having nglview")
-class TestVisualization(unittest.TestCase):
-    """ Test visualization """
-
-    def test_visualization(self):
-        """ Test visualization with nglview """
-        parm = pmd.load_file(get_fn('2koc.pdb'))
-        view = parm.visualize()
-        self.assertIsInstance(view, nglview.NGLWidget)
-        # test None
-        parm.coordinates = None
-        self.assertRaises(ValueError, parm.visualize)