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Rename "Tests" directory for consistency.

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This commit is contained in:
Nathan Baker
2020-05-21 10:39:08 -07:00
parent fa4a547f1f
commit 393f5cee50
18 changed files with 1 additions and 1 deletions
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7
tests/.gitignore vendored Normal file
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# Compiled python files
*.pka
*.out
*.propka_input

0
tests/__init__.py Normal file
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tests/hybrid36.py Normal file
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import unittest
import propka.hybrid36 as hybrid36
class Hybrid36Test(unittest.TestCase):
def testDecode(self):
test_values = {
"99999": 99999,
"A0000": 100000,
"0": 0,
"9": 9,
"A": 10,
" ZZZZY": 43770014,
"ZZZZZ": 43770015, # ZZZZZ - A0000 + 100000
"a0000": 43770016,
"zzzzz": 87440031,
"zzzzy": 87440030,
"99": 99,
"A0": 100,
"ZZ": 1035,
"zz": 1971,
"-99999": -99999,
"-A0000": -100000,
"-0": 0,
"-9": -9,
"-A": -10,
"-ZZZZY": -43770014,
"-ZZZZZ": -43770015, # ZZZZZ - A0000 + 100000
"-a0000": -43770016,
"-zzzzz": -87440031,
"-zzzzy": -87440030,
"-99": -99,
"-A0": -100,
"-ZZ": -1035,
"-zz": -1971,
"PROPKA": 954495146,
"A001Z": 100071,
"B0000": 1779616,
}
for k, v in test_values.iteritems():
self.assertEqual(hybrid36.decode(k), v)
def testErrors(self):
test_values = [
"99X99",
"X9-99",
"XYZa",
"",
"-",
"!NotOk",
]
for v in test_values:
with self.assertRaises(ValueError) as e:
hybrid36.decode(v)
self.assertTrue(v in str(e.exception))

2073
tests/pdb/1FTJ-Chain-A.pdb Normal file
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tests/pdb/1HPX-warn.pdb Normal file
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ATOM 1 N PRO A 1 12.435 14.677 30.369 1.00 35.93 N
ATOM 2 CA PRO A 1 11.739 15.379 29.269 1.00 34.94 C
ATOM 2 CA PRO A 1 11.739 15.379 29.269 1.00 34.94 C
ATOM 3 C PRO A 1 10.309 14.853 29.143 1.00 32.24 C
ATOM 4 O PRO A 1 10.035 13.743 29.578 1.00 32.11 O
ATOM 5 CB PRO A 1 12.566 15.121 27.988 1.00 34.34 C
ATOM 6 CG PRO A 1 13.973 14.970 28.518 1.00 35.36 C
ATOM 7 CD PRO A 1 13.768 14.261 29.859 1.00 35.14 C
ATOM 8 N GLN A 2 9.436 15.666 28.552 1.00 29.85 N
ATOM 9 CA GLN A 2 8.117 15.184 28.193 1.00 29.27 C
ATOM 10 C GLN A 2 7.939 15.392 26.711 1.00 28.61 C
ATOM 11 O GLN A 2 8.147 16.506 26.246 1.00 31.02 O
ATOM 12 CB GLN A 2 7.108 15.981 28.932 1.00 28.24 C
ATOM 13 CG GLN A 2 5.789 15.599 28.365 1.00 32.41 C
ATOM 14 CD GLN A 2 4.735 16.247 29.153 1.00 37.59 C
ATOM 15 OE1 GLN A 2 4.403 15.796 30.243 1.00 39.05 O
ATOM 16 NE2 GLN A 2 4.210 17.303 28.540 1.00 39.28 N
END

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tests/pdb/1HPX.pdb Normal file
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tests/pdb/3SGB-subset.pdb Normal file
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tests/pdb/3SGB.pdb Normal file
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tests/pdb/4DFR.pdb Normal file
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tests/pkacalc_test.py Normal file
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"""Reproduce tests from original PROPKA."""
import os
import re
from subprocess import call
import sys
import unittest
import logging
import propka.lib
import propka.molecular_container
# This error tolerance was chosen to make Ubuntu 18.04 pass under Windows
# Subsystem Linux.
ACCEPTABLE_ERROR = 0.001
def run_propka(args):
"""Run PROPKA.
Args:
args: command-line arguments for PROPKA
"""
options = propka.lib.loadOptions()
raise NotImplementedError("Need to incorporated command-line arguments")
pdbfiles = options.filenames
for pdbfile in pdbfiles:
my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
my_molecule.calculate_pka()
my_molecule.write_pka()
# Setting this up as a direct translation of the original runtest.py script
# that will be run as part of 'python setup.py test'. This takes on the
# order of 10s to run.
class SystemTest(unittest.TestCase):
"""
Run the program and compare against reference results.
"""
def test_pka_calc(self):
pdbs = ['1FTJ-Chain-A',
'1HPX',
'4DFR']
test_dir = os.path.dirname(__file__)
base_dir = os.path.dirname(test_dir)
executable = os.path.join(base_dir, "scripts", "propka31.py")
env = { "PYTHONPATH" : base_dir }
for pdb in pdbs:
input_filename = os.path.join(test_dir, "pdb", pdb + ".pdb")
output_filename = os.path.join(test_dir, pdb + ".out")
output_file = open(output_filename, "w")
call([sys.executable, executable, input_filename],
stdout=output_file, env=env)
output_file.close()
# Check pka predictions.
ref = open(os.path.join(test_dir, "results", pdb + ".dat"))
output = open(output_filename)
atpka = False
errors = []
for line in output:
if not atpka:
# Start testing pka values.
if "model-pKa" in line:
atpka = True
continue
m = re.search('([0-9]+\.[0-9]+)', line)
if not m:
break
expected_value = float(ref.readline())
value = float(m.group(0))
value_error = (value-expected_value)/expected_value
if abs(value_error) > ACCEPTABLE_ERROR:
logging.error(value_error)
identity = line[:m.start()].strip()
errors.append("%12s %8.2f %8.2f" %
(identity, expected_value, value))
os.remove("%s.pka" % pdb)
os.remove("%s.propka_input" % pdb)
ref.close()
output.close()
if errors:
error_header = " Group Expected Calculated\n"
self.fail("Unexpected pKa values:\n" + error_header +
"\n".join(errors))

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tests/results/1FTJ-Chain-A.dat Normal file
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3.56
3.25
2.87
3.52
3.77
3.26
3.82
3.92
3.08
3.65
4.01
4.01
6.38
4.58
4.49
4.90
3.62
4.52
5.36
4.67
3.61
3.88
4.58
4.66
4.27
3.84
4.95
4.68
3.44
6.11
5.61
12.90
10.65
99.99
99.99
15.10
10.44
14.06
11.43
19.83
9.71
12.57
10.97
12.75
15.63
11.13
21.84
12.00
10.43
10.31
10.34
10.49
10.08
10.45
10.37
10.25
10.37
11.44
9.30
10.41
10.31
10.00
10.44
10.31
10.60
10.37
11.35
10.41
10.21
10.33
9.25
11.16
10.02
12.52
12.28
13.22
13.43
12.31
12.20
12.24
12.73
7.93
11.90
1.20
7.39

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tests/results/1HPX-warn.dat Normal file
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7.95

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tests/results/1HPX.dat Normal file
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5.07
3.11
4.62
2.55
9.28
1.78
4.91
2.13
4.78
3.93
3.65
3.89
4.73
3.36
4.07
3.70
2.08
2.11
6.98
7.11
9.41
11.68
9.82
11.61
9.67
9.54
10.43
10.32
11.41
10.54
10.42
10.92
10.55
11.01
11.43
10.47
10.41
11.07
13.96
12.41
14.39
12.35
12.76
12.42
13.73
12.28
8.96
8.96
4.60

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tests/results/3SGB-subset.dat Normal file
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3.51
12.80

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tests/results/3SGB.dat Normal file
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3.21
4.29
3.47
3.85
4.22
4.59
3.55
2.61
4.48
5.27
4.26
5.11
4.60
3.63
3.24
8.04
6.15
7.14
99.99
99.99
99.99
99.99
99.99
99.99
99.99
99.99
99.99
99.99
10.27
10.00
10.33
10.82
13.96
13.90
10.28
10.96
12.23
12.62
10.25
10.52
12.31
9.50
10.92
10.35
10.44
10.67
11.74
12.84
11.95
12.36
11.05
12.89
12.19
12.17
12.16
7.38
7.56

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tests/results/4DFR.dat Normal file
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3.86
5.05
3.99
2.02
3.71
4.00
3.85
4.30
3.89
3.74
4.05
4.02
2.82
3.88
4.03
3.98
2.05
4.01
3.79
3.90
3.93
4.07
3.70
4.15
4.01
2.65
4.50
4.77
3.71
2.85
3.90
4.71
4.59
4.86
4.47
4.63
4.86
4.52
3.73
2.91
4.57
4.83
4.62
4.16
3.73
4.70
3.38
3.26
6.77
4.89
6.85
5.95
4.91
6.50
4.87
6.69
7.15
4.99
10.86
9.04
10.91
9.07
14.10
13.22
11.24
11.58
14.07
13.23
11.19
11.76
10.47
10.50
10.23
10.04
10.32
10.46
10.50
10.30
10.26
10.54
10.21
10.23
12.34
12.17
12.29
12.66
11.95
13.80
13.21
11.90
12.49
12.41
12.09
12.51
12.06
13.97
12.55
12.10
12.39
7.70
7.63
4.86
4.83
4.05
4.26
4.03
4.47

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tests/runtest.py Normal file
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#!/usr/bin/env python
""" Run test for test pdbs """
from __future__ import division
from __future__ import print_function
from subprocess import call
import os, re
import sys
if __name__ == "__main__":
# A list of input structures and command-line arguments to be passed in
# to PROPKA for each:
pdbs = [('1FTJ-Chain-A', []),
('1HPX', []),
('4DFR', []),
('3SGB', []),
('3SGB-subset', ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139']),
('1HPX-warn', ['--quiet']),
]
for pdb, args in pdbs:
print('')
print('RUNNING '+pdb)
# Run pka calculation
fh = open(pdb + '.out', 'w')
cmd = [sys.executable, '../scripts/propka31.py','pdb/%s.pdb' % pdb] + args
ret = call(cmd, stdout=fh, stderr=fh)
if ret != 0:
print(" ERR:")
print(" Failed to execute PROPKA on %s" % pdb)
print(" See: %s.out" % pdb)
sys.exit(1)
# Test pka predictions
result_file = 'results/%s.dat' % pdb
if not os.path.isfile(result_file):
print(" ERR:")
print(" file not found: %s" % result_file)
sys.exit(1)
result = open(result_file,'r')
atpka = False
for line in open(pdb+'.pka', 'r').readlines():
if not atpka:
if "model-pKa" in line:
# test pka
atpka = True
continue
else:
continue
if "-" in line:
# done testing
atpka = False
continue
expected_value = float(result.readline())
m = re.search('([0-9]+\.[0-9]+)', line)
value = float(m.group(0))
if value != expected_value:
print(" ERR:")
print(line)
print(" %s should be: %s" % (value, expected_value))
sys.exit(1)