pestifer.logparsers.pdb2pqrlogparser module

PDB2PQR log parsing utility

class pestifer.logparsers.pdb2pqrlogparser.PDB2PQRLogParser(basename='pdb2pqr-logparser')

Bases: LogParser

A class for parsing PDB2PQR log files. This class is a subclass of LogParser and provides methods for reading, updating, and dumping PDB2PQR log data.

Parameters:

basename (str) – The base name for the log parser. This is used to name the output log file.

finalize()

Finalize the PDB2PQR log parser by saving the metadata to a YAML file. This method writes the metadata to a YAML file with the base name of the log parser.

process_section(bytes: str)

Process a section of the PDB2PQR log file. This method identifies the type of section and processes it accordingly.

process_summary(bytes: str)

Process the summary section of the PDB2PQR log file. This method extracts information from the summary section and updates the metadata attribute with relevant data.

Parameters:

bytes (bytes) – The bytes representing the summary section to be processed. This can be a string or bytes object containing the summary data.

section_separator = '--------------------------------------------------------------------------------'

The separator used to identify sections in the PDB2PQR log file.

update(bytes: str)

Update the PDB2PQR log parser with new bytes of data. This method appends the new bytes to the byte collector and processes the sections in the log file.

Parameters:

bytes (bytes) – The bytes to update the log parser with.