Help! My script crashes!

Getting more logs from BioShell library

There are nine levels of importance for log messages reported by BioShell methods. Seven of them are used for general reporting, in the order of decreasing importance: CRITICAL, SEVERE, WARNING, INFO, FINE, FINER and FINEST. The two additional levels: HTTP and FILE are used to report HTTP messages and information about disk I/O, respectively. By default, loggging level is set to INFO which means that only INFO and more important messages show up. To see more logs, increase the verbosity as follows:

from pybioshell.utils import LogManager

Checking C++ excpetion from Python

Occasionally PyBioShell library throws an exception, which stops a Python script. To find out the reason, wrap a bioshell call into a try / except block and print out execution information as below:

  pdb = find_pdb(pdb_fname, path, True, False)
  sys.stderr.write(str(sys.exc_info()[0])+" "+str(sys.exc_info()[1]))