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unittesting and readme update

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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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41
README.md
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# PROPKA 3.1
PROPKA predicts the pKa values of ionizable groups in
proteins (version 3.0) and
protein-ligand complexes (version 3.1)
based in the 3D structure.
See [propka.ki.ku.dk](http://propka.ki.ku.dk/)
for more information.
For proteins without ligands both version should produce the same result.
The method is described in the following papers, which you should cite
in publications:
* Søndergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
* Olsson, Mats HM, Chresten R. Søndergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
See [propka.ki.ku.dk](http://propka.ki.ku.dk/) for the PROPKA web server,
using the [tutorial](http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial)
## Installation
@@ -19,22 +32,26 @@ No installation needed. Just clone and run.
## Examples
Calculate
Calculate using pdb file
propka.py 1hpx.pdb
./propka.py 1hpx.pdb
If for some reason your setup with python3.1+ is
not located in '/usr/bin/python3', run the script
If you don't have Python 3.1 installed, but
Python 3.2 (most Ubuntu distributions), then run
propka like;
python3.2 propka.py 1hpx.pdb
python3.2 propka.py 1hpx.pdb
## Testing (for developers)
Please run test before pushing commits.
Please run 'Tests/runtest.py/ after changes before pushing commits.
## References / Citations
Please cite these references in publications:
* Søndergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
* Olsson, Mats HM, Chresten R. Søndergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.

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Tests/.gitignore vendored Normal file
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# Compiled python files
*.pka
*.out
*.propka_input

2073
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))

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propka.py
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#!/usr/bin/env python3.1
#!/usr/bin/python3
import string,re,sys,os,math
import Source.lib, Source.molecular_container