def autodetect_start_structure():
"""
Autodetect a lone PDB file in the inputs folder if the user has not changed the default "start_structure"
setting. This function is useful for starting batches of protein simulations or homology modeling in
e.g. the factory codes.
"""
if wordspace.requires == 'homology':
wordspace.start_structure = wordspace.template
if not 'start_structure' in wordspace:
raise Exception(
'\n[ERROR] this autodect function requires the start_structure setting\n'
+
'[ERROR] (set start_structure to inputs/STRUCTURE.pdb to autodetect a lone pdb in inputs.'
)
if wordspace.start_structure == 'inputs/STRUCTURE.pdb':
pdbs = glob.glob('inputs/*.pdb')
if len(pdbs) == 1:
wordspace.start_structure = pdbs[0]
wordspace.system_name = re.findall('^inputs/([\w\.-]+)\.pdb$',
pdbs[0])[0]
else:
if 'watch_file' not in wordspace:
wordspace.watch_file = 'ERROR.log'
report(
'multiple PDBs in inputs/ and start_structure is still default',
tag='warning')
else:
print "OOPS"
import pdb
pdb.set_trace()
def equilibrate_check(name):
"""
Check if the gro file for this step has been written.
"""
found = False
fn = wordspace['step'] + 'md-%s.gro' % name
if os.path.isfile(fn):
report('found %s' % fn, tag='RETURN')
found = True
return found
def equilibrate_check(name):
"""
Check if the gro file for this step has been written.
"""
found = False
fn = wordspace['step']+'md-%s.gro'%name
if os.path.isfile(fn):
report('found %s'%fn,tag='RETURN')
found = True
return found
def autodetect_start_structure():
"""
Autodetect a lone PDB file in the inputs folder if the user has not changed the default "start_structure"
setting. This function is useful for starting batches of protein simulations or homology modeling in
e.g. the factory codes.
"""
if wordspace.requires=='homology':
wordspace.start_structure=wordspace.template
if not 'start_structure' in wordspace:
raise Exception('\n[ERROR] this autodect function requires the start_structure setting\n'+
'[ERROR] (set start_structure to inputs/STRUCTURE.pdb to autodetect a lone pdb in inputs.')
if wordspace.start_structure == 'inputs/STRUCTURE.pdb':
pdbs = glob.glob('inputs/*.pdb')
if len(pdbs)==1:
wordspace.start_structure = pdbs[0]
wordspace.system_name = re.findall('^inputs/([\w\.-]+)\.pdb$',pdbs[0])[0]
else:
if 'watch_file' not in wordspace: wordspace.watch_file = 'ERROR.log'
report('multiple PDBs in inputs/ and start_structure is still default',tag='warning')
else:
print "OOPS"
import pdb;pdb.set_trace()
def exception_handler(e,wordspace,all=False,outfile=None):
"""
Report an error concisely to the terminal to avoid overwhelming the user.
"""
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
from amx.base.journal import report
report('%s in %s at line %d'%(str(exc_type),fname,exc_tb.tb_lineno),tag='error')
report('%s'%e,tag='error')
if all:
import traceback
report(re.sub('\n','\n[TRACEBACK] ',traceback.format_exc()),tag='traceback')
write_wordspace(wordspace,outfile=outfile)
sys.exit(1)
def exception_handler(e, wordspace, all=False, outfile=None):
"""
Report an error concisely to the terminal to avoid overwhelming the user.
"""
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
from amx.base.journal import report
report('%s in %s at line %d' % (str(exc_type), fname, exc_tb.tb_lineno),
tag='error')
report('%s' % e, tag='error')
if all:
import traceback
report(re.sub('\n', '\n[TRACEBACK] ', traceback.format_exc()),
tag='traceback')
write_wordspace(wordspace, outfile=outfile)
sys.exit(1)
