def special_mtz_mode(args):
print('Usage: %s' % USAGE_SHORT)
check_ccp4_envvars()
wf = workflow.Workflow('')
wf.enable_logs = False
try:
mtz_meta = wf.read_mtz_metadata(args[0])
print('Basic MTZ file info:')
print(mtz_meta.info())
contam_info = contaminants.get_info(mtz_meta)
if contam_info:
print(contam_info)
except (IOError, RuntimeError) as e:
put_error(e)
def special_pdb_mode(args):
print('Proper usage: %s' % USAGE_SHORT)
check_ccp4_envvars()
print('...actually we can run rwcontents for you')
wf = workflow.Workflow('')
wf.enable_logs = False
for p in args:
try:
wf.read_pdb_metadata(p, print_errors=True)
_comment_summary_line(os.path.basename(p), wf.file_info[p])
wf.rwcontents(xyzin=p).run()
except (IOError, RuntimeError) as e:
put_error(e)
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
print('\n\n...but this is NOT how dimple is supposed to be run.')
def main(args):
if workflow.parse_workflow_commands():
return
options = parse_dimple_commands(args)
check_ccp4_envvars()
try:
wf = workflow.Workflow(options.output_dir, from_job=options.from_step)
utils.start_log(os.path.join(options.output_dir, 'dimple.log'),
output_dir=options.output_dir)
utils.log_value('version', __version__)
utils.start_log_screen(os.path.join(options.output_dir, 'screen.log'))
dimple(wf=wf, opt=options)
check_contaminants_if_bad(wf, mtz=options.mtz)
exit_status = 0
except workflow.JobError as e:
put_error(e.msg, comment=e.note)
try:
utils.report_disk_space([wf.output_dir, os.getenv('CCP4_SCR')])
except KeyboardInterrupt:
comment('\nok, exiting...')
exit_status = 1
except (RuntimeError, IOError, OSError) as e:
put_error(e)
exit_status = 1
finally:
comment('\n')
if options.cleanup:
wf.delete_files(wf.temporary_files)
wf.options = options
try:
wf.dump_pickle()
except IOError as e:
put_error(e)
exit_status = 1
return exit_status