swamp.wrappers.phenixcc module

class PhenixCC(workdir, pdbin, mtzin, logger=None, silent_start=False)[source]

Bases: swamp.wrappers.wrapper.Wrapper

Wrapper around phenix.get_cc_mtz_pdb

Parameters:
  • workdir (str) – working directory
  • mtzin (str) – file name of the mtz with the phase information to calculate correlation coefficient
  • pdbin (str) – pdb file name to calculate correlation coefficient
  • logger (SwampLogger) – logging interface for the wrapper (default None)
  • silent_start (bool) – if True, the logger will not display the start banner (default False)
Variables:
  • error (bool) – if True an error has occurred along the process
  • ovarall_CC (str) – overall correlation coefficient between the phases in the mtz file and the pdb file
  • local_CC (str) – local correlation coefficient between the phases in the mtz file and the pdb file
Example: 
>>> from swamp.wrappers import PhenixCC
>>> my_pehnix = PhenixCC('<workdir>', '<pdbin>', '<mtzin>')
>>> my_pehnix.run()
cmd

Command to be executed on the shell

get_scores(logfile=None)[source]

Use PhenixParser to parse the log file and obtain values for local_CC and overall_CC

Parameters:logfile – Not in use
keywords

No keywords are used through stdin in phenix.get_cc_mtz_pdb

source

Override source to include PHENIX/build/bin instead of CCP4/bin

summary_results

A summary with the obtained figures of merit

wrapper_name

The name of this ~swamp.wrapper.wrapper.Wrapper child class (phenix_cc)