omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

Raise error for ligand pKa errors.

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files

32
propka/ligand_pka_values.py
View File

@@ -163,23 +163,21 @@ class LigandPkaValues:
[self.cxcalc, filename]+options.split(), stdout=subprocess.PIPE, [self.cxcalc, filename]+options.split(), stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate() stderr=subprocess.PIPE).communicate()
if len(errors) > 0: if len(errors) > 0:
_LOGGER.error( err = (
'***********************************************************' f'***********************************************************'
'*********************************************') f'*********************************************'
_LOGGER.error( f'* Error: Marvin execution failed: '
'* Error: Marvin execution failed: ' f' *'
' *') f'* {errors:<100s} *'
_LOGGER.error('* {0:<100s} *'.format(errors)) f'* '
_LOGGER.error( f' *'
'* ' f'* Please edit the ligand mol2 file and re-run PropKa with '
' *') f'the -l option: {filename:>29s} *'
_LOGGER.error( f'***********************************************************'
'* Please edit the ligand mol2 file and re-run PropKa with ' f'*********************************************'
'the -l option: {0:>29s} *'.format(filename)) )
_LOGGER.error( _LOGGER.error(err)
'***********************************************************' raise OSError(err)
'*********************************************')
sys.exit(-1)
# extract calculated pkas # extract calculated pkas
indices, pkas, types = self.extract_pkas(output) indices, pkas, types = self.extract_pkas(output)
# store calculated pka values # store calculated pka values