schrodinger.application.bioluminate.propka_parse module

Module used to parse the output from a propka job.

schrodinger.application.bioluminate.propka_parse.get_detailed(pka_file, headers=None)

Get the detailed report from the PROPKA output file. This will return a list of lists. The first list is the “header” and the remaining lists will be the values corresponding to the headers.

Parameters

  • pka_file (string) – The name of the propka output (usually <jobname>.pka)

  • headers – A list of header to return in the summary. Only these headers and their corresponding data are returned. If this is None, all headers and values are returned.

See

DETAILED_HEADERS

schrodinger.application.bioluminate.propka_parse.get_summary(pka_file, headers=None)

Get the summary from the PROPKA output file. This will return a list of headers and a list of lists. The list of lists will be the values corresponding to the headers.

Parameters

  • pka_file (string) – The name of the propka output (usually <jobname>.pka)

  • headers – A list of header to return in the summary. Only these headers and their corresponding data are returned. If this is None, all headers and values are returned.

See

SUMMARY_HEADERS

schrodinger.application.bioluminate.propka_parse.get_free_energy(pka_file, headers=None)

Get the free energy of folding (kcal/mol) as a function of pH from the PROPKA output file. This will return a list of headers and a list of lists. The list of lists will be the values corresponding to the headers.This will return a list of lists. The first list is the “header” and the remaining lists will be the values corresponding to the headers.

Parameters

  • pka_file (string) – The name of the propka output (usually <jobname>.pka)

  • headers – A list of header to return in the summary. Only these headers and their corresponding data are returned. If this is None, all headers and values are returned.

See

FREE_ENERGY_HEADERS

schrodinger.application.bioluminate.propka_parse.get_charge(pka_file, headers=None)

Get the protein charge of folded and unfolded state as a function of pH from the PROPKA output file. This will return a list of headers, a list of lists containing the data, and a list of pI values for folded and unfolded states.

Parameters

  • pka_file (string) – The name of the propka output (usually <jobname>.pka)

  • headers – A list of header to return in the summary. Only these headers and their corresponding data are returned. If this is None, all headers and values are returned.

See

CHARGE_HEADERS