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unittesting and readme update

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This commit is contained in:
Jimmy Charnley Kromann, lat13
2012-11-19 18:36:24 +01:00
parent d882a2f5d1
commit 6886db9697
10 changed files with 8373 additions and 14 deletions
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7
Tests/.gitignore vendored Normal file
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# Compiled python files
*.pka
*.out
*.propka_input

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Tests/pdb/1FTJ-Chain-A.pdb Normal file
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Tests/pdb/1HPX.pdb Normal file
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Tests/pdb/4DFR.pdb Normal file
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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.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/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 Executable file
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#!/usr/bin/python3
""" Run test for test pdbs """
from subprocess import call
import os, re
pdbs = ['1FTJ-Chain-A',
'1HPX',
'4DFR']
for pdb in pdbs:
print('')
print('RUNNING '+pdb)
# Run pka calculation
call(['../propka.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
# Test pka predictiona
result = open('results/'+pdb+'.dat','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
r = float(result.readline())
m = re.search('([0-9]+\.[0-9]+)', line)
if(float(m.group(0)) != r):
print(" ERR:")
print(line)
print(" "+"should be: "+str(r))