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Fix protein-rna test

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Curtis, Darren S
2020-05-07 08:50:21 -07:00
parent e91246f1cb
commit 0f9558aedf
4 changed files with 27 additions and 20 deletions
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5
.gitignore vendored
View File

@@ -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

38
apbs/examples/protein-rna/apbs_dx.py
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@@ -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)

2
apbs/examples/protein-rna/test.sh
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@@ -8,7 +8,7 @@ fi
if [[ "$3" = "ocd" ]]; then
ocd='ocd'
else
ocd='noocd'
ocd='noocd'
fi
logfile=TESTRESULTS.log

2
apbs/tests/test_cases.cfg
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@@ -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