Package schrodinger :: Package application :: Package bioluminate :: Module propka_parse

Module propka_parse

Module used to parse the output from a propka job.

Functions

get_detailed(pka_file, headers=None)
Get the detailed report from the PROPKA output file.

get_summary(pka_file, headers=None)
Get the summary from the PROPKA output file.

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.

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.

Variables

[hide private]

REGEXS = {'break': re.compile(r'(^---+|\s*$)'), 'charge': re.c...

DETAILED_HEADER = ['resname', 'resnum', 'chain', 'pKa', 'burie...

SUMMARY_HEADER = ['resname', 'resnum', 'chain', 'pKa', 'pKmode...

FREE_ENERGY_HEADER = ['pH', 'free energy']

CHARGE_HEADER = ['pH', 'unfolded', 'folded']

__package__ = 'schrodinger.application.bioluminate'

Function Details

[hide private]

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 Also: DETAILED_HEADERS

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 Also: SUMMARY_HEADERS

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 Also: FREE_ENERGY_HEADERS

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 Also: CHARGE_HEADERS

Variables Details

[hide private]

REGEXS

Value:

{'break': re.compile(r'(^---+|\s*$)'),
 'charge': re.compile(r'^\s*pH\s+unfolded\s+folded\s*$'),
 'detailed': re.compile(r'^\s*RESIDUE\s+pKa\s+BURIED[ \t\w]\n$'),
 'free_ene': re.compile(r'^Free energy of'),
 'pI': re.compile(r'^\s*The\s+pI\s+is\s+(?P<folded_pI>-?\d*\.\d*)\s+\(
folded\)\s+and\s+(?P<unfolded_pI>-?\d*\.\d*)\s+\(unfolded\)\s*$'),
 'summary': re.compile(r'^\s*Group\s+pKa\s+model-pKa\s+ligand atom-typ
e\s*$')}

DETAILED_HEADER

Value:

['resname',
 'resnum',
 'chain',
 'pKa',
 'buried',
 'desolvation regular',
 'effects re',
 'sidechain h-bond',
...

SUMMARY_HEADER

Value:

['resname', 'resnum', 'chain', 'pKa', 'pKmodel', 'ligand atom-type']