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Added --titrate_only option and tests for it.

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This option makes it possible for PROPKA to treat only a subset of protein
residues as titratable.
This commit is contained in:
Matvey Adzhigirey
2014-08-13 11:13:55 -07:00
committed by Mike Beachy
parent c420b4c2a5
commit 8084b31393
5 changed files with 112 additions and 28 deletions
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40
Tests/runtest.py
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@@ -10,19 +10,37 @@ import os, re
import sys
if __name__ == "__main__":
pdbs = ['1FTJ-Chain-A',
'1HPX',
'4DFR']
# 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']),
]
for pdb in pdbs:
for pdb, args in pdbs:
print('')
print('RUNNING '+pdb)
# Run pka calculation
call([sys.executable, '../scripts/propka31.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
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 predictiona
result = open('results/'+pdb+'.dat','r')
# 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:
@@ -37,11 +55,13 @@ if __name__ == "__main__":
atpka = False
continue
r = float(result.readline())
expected_value = float(result.readline())
m = re.search('([0-9]+\.[0-9]+)', line)
value = float(m.group(0))
if(float(m.group(0)) != r):
if value != expected_value:
print(" ERR:")
print(line)
print(" "+"should be: "+str(r))
print(" %s should be: %s" % (value, expected_value))
sys.exit(1)