From 0f9558aedf5f496520000062c25fc4b48e8cdd34 Mon Sep 17 00:00:00 2001
From: "Curtis, Darren S" <>
Date: Thu, 7 May 2020 08:50:21 -0700
Subject: [PATCH] Fix protein-rna test

---
 .gitignore                           |  5 +++-
 apbs/examples/protein-rna/apbs_dx.py | 38 +++++++++++++++-------------
 apbs/examples/protein-rna/test.sh    |  2 +-
 apbs/tests/test_cases.cfg            |  2 +-
 4 files changed, 27 insertions(+), 20 deletions(-)

diff --git a/.gitignore b/.gitignore
index 17a5cd32b..8918326d9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,10 +22,13 @@
 **/.ipynb_checkpoints
 **/.pytest_cache
 **/.vscode
+**/apbs*.in
 **/apbslib.py
 **/build
 **/c_cpp_properties.json
-apbs**.in
+**/dxmath*.in
+**/ndens*.dx
+**/qdens*.dx
 apbs/externals/fetk
 include/maloc
 io.mc
diff --git a/apbs/examples/protein-rna/apbs_dx.py b/apbs/examples/protein-rna/apbs_dx.py
index 1fd2841dd..7dc8ca53b 100644
--- a/apbs/examples/protein-rna/apbs_dx.py
+++ b/apbs/examples/protein-rna/apbs_dx.py
@@ -1,25 +1,29 @@
 #!/bin/python
 
-my_list = ('0.025', '0.050', '0.075', '0.100', '0.125', '0.150', '0.175',
-	'0.200', '0.225', '0.250', '0.275', '0.300', '0.325', '0.400', '0.500',
-	'0.600', '0.700', '0.800')
+"""
+Create files for the protein-rna tests
+"""
+
+MY_LIST = ('0.025', '0.050', '0.075', '0.100', '0.125', '0.150', '0.175',
+           '0.200', '0.225', '0.250', '0.275', '0.300', '0.325', '0.400', '0.500',
+           '0.600', '0.700', '0.800')
 
 with open("template.txt", "r") as temp:
-	template_text = temp.read()
+    TEMPLATE_TEXT = temp.read()
 
-for item in my_list:
-	input_txt = template_text.replace("IONSTR", item)
-	file_name = "apbs-" + item + ".in"
-	print("Creating file now:", file_name)
-	with open(file_name, "w") as temp:
-		temp.write(input_txt)
+for item in MY_LIST:
+    input_txt = TEMPLATE_TEXT.replace("IONSTR", item)
+    file_name = "apbs-" + item + ".in"
+    print("Creating file now:", file_name)
+    with open(file_name, "w") as temp:
+        temp.write(input_txt)
 
 with open("dxmath.txt", "r") as temp:
-	template_2_text = temp.read()
+    TEMPLATE_2_TEXT = temp.read()
 
-for item in my_list:
-	input_2_txt = template_2_text.replace("IONSTR", item)
-	file_2_name = "dxmath-" + item + ".in"
-	print "Creating file_2 now:", file_2_name
-	with open(file_2_name, "w") as temp:
-		temp.write(input_2_txt)
+for item in MY_LIST:
+    input_2_txt = TEMPLATE_2_TEXT.replace("IONSTR", item)
+    file_2_name = "dxmath-" + item + ".in"
+    print("Creating file_2 now: %s" % file_2_name)
+    with open(file_2_name, "w") as temp:
+        temp.write(input_2_txt)
diff --git a/apbs/examples/protein-rna/test.sh b/apbs/examples/protein-rna/test.sh
index 388a7edd4..56b9655e5 100644
--- a/apbs/examples/protein-rna/test.sh
+++ b/apbs/examples/protein-rna/test.sh
@@ -8,7 +8,7 @@ fi
 if [[ "$3" = "ocd" ]]; then
     ocd='ocd'
 else
-	ocd='noocd'
+    ocd='noocd'
 fi
 
 logfile=TESTRESULTS.log
diff --git a/apbs/tests/test_cases.cfg b/apbs/tests/test_cases.cfg
index 2e13840fa..2e3354915 100644
--- a/apbs/tests/test_cases.cfg
+++ b/apbs/tests/test_cases.cfg
@@ -109,7 +109,7 @@ gly_energyforce : 6.176608555569E-05 6.210593742215E-05
 
 [protein-rna]
 input_dir  : ../examples/protein-rna
-setup      : python apbs_unix_dx.py
+setup      : python apbs_dx.py
 apbs-0.025 : 3.186122223752E+04 3.662855899462E+04 8.477786964834E+03 1.000545153104E+04 2.329205982055E+04 2.653636629928E+04 8.674116429353E+01
 apbs-0.050 : 3.184763478312E+04 3.661493366846E+04 8.475252516617E+03 1.000292179294E+04 2.327168361816E+04 2.651594350839E+04 9.606836713866E+01
 apbs-0.075 : 3.184033569905E+04 3.660761530545E+04 8.473669396547E+03 1.000134276339E+04 2.326088212207E+04 2.650511882057E+04 1.011537214883E+02