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Raise error for ligand pKa errors.

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Fixes https://github.com/jensengroup/propka/pull/109#discussion_r532735233 per @orbeckst.
This commit is contained in:
Nathan Baker
2020-11-30 15:21:47 -08:00
parent c281623078
commit de020599d3
1 changed files with 15 additions and 17 deletions
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32
propka/ligand_pka_values.py
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@@ -163,23 +163,21 @@ class LigandPkaValues:
[self.cxcalc, filename]+options.split(), stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()
if len(errors) > 0:
_LOGGER.error(
'***********************************************************'
'*********************************************')
_LOGGER.error(
'* Error: Marvin execution failed: '
' *')
_LOGGER.error('* {0:<100s} *'.format(errors))
_LOGGER.error(
'* '
' *')
_LOGGER.error(
'* Please edit the ligand mol2 file and re-run PropKa with '
'the -l option: {0:>29s} *'.format(filename))
_LOGGER.error(
'***********************************************************'
'*********************************************')
sys.exit(-1)
err = (
f'***********************************************************'
f'*********************************************'
f'* Error: Marvin execution failed: '
f' *'
f'* {errors:<100s} *'
f'* '
f' *'
f'* Please edit the ligand mol2 file and re-run PropKa with '
f'the -l option: {filename:>29s} *'
f'***********************************************************'
f'*********************************************'
)
_LOGGER.error(err)
raise OSError(err)
# extract calculated pkas
indices, pkas, types = self.extract_pkas(output)
# store calculated pka values