Package schrodinger :: Package application :: Package jaguar :: Module textparser :: Class TextParser

Class TextParser

object --+
         |
        TextParser

Known Subclasses:

qsite.output.QSiteTextParser

A parser to create a JaguarOutput object from a Jaguar output file.

The basic organization of this parser is that of a number of line processing callback functions triggered by regular expressions.

Instance Methods

[hide private]

__init__(self, jaguar_output, file_iter=None)
Parameters

_newResults(self, jo)
Add a new results object for a new geometry or scan step.

endGeopt(self, jo)
Clean up at the end of a geopt step.

endScan(self, jo)
Clean up at the end of a scan step.

endIRC(self, direction)
Set state indicating the end of an IRC step and its direction.

parse(self, file_iter=None, jaguar_output=None)
Parse the provided file iterator.

_finalize(self, jo)
Actions to be taken at the end of the file.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

callback = {None: {re.compile(r'ERROR *(\d+)?: fatal error( --...

first_line_re = re.compile(r'^Job \S+ started on (\S+) at (\w....

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, jaguar_output, file_iter=None)
(Constructor)

Parameters

file_iter (iterator returning lines of Jaguar output file)

jaguar_output (JaguarOutput instance)

Overrides: object.__init__

_newResults(self, jo)

Add a new results object for a new geometry or scan step.

Caller is responsible for storing jo._results before calling this if it needs to be kept. For example, storing results from a geometry in a geopt sequence of results.

endGeopt(self, jo)

Clean up at the end of a geopt step.

Adds the current results to the geopt list and creates a new current results object if appropriate.

endScan(self, jo)

Clean up at the end of a scan step.

Adds the current results to the scan list and creates a new current results object. Or, if this a relaxed scan, archives the geopt steps to the scan list and creates an empty geopt_step list.

endIRC(self, direction)


Set state indicating the end of an IRC step and its direction.

direction (str)
    Must be 'Forward' or 'Reverse'.

parse(self, file_iter=None, jaguar_output=None)


Parse the provided file iterator.

Return a JaguarOutput instance populated with properties parsed from
the output file.

Parameters

file_iter (iterator returning lines of Jaguar output)

jaguar_output (JaguarOutput instance)
    If jaguar_output is provided, that instance will be populated
    with the properties parsed from the output file. Otherwise,
    the object provided to the TextParser constructor will be used.

Class Variable Details

[hide private]

callback

Value:

{}

first_line_re

Value:

re.compile(r'^Job \S+ started on (\S+) at (\w.*)$')

Class TextParser

__init__(self, jaguar_output, file_iter=None) (Constructor)

_newResults(self, jo)

endGeopt(self, jo)

endScan(self, jo)

endIRC(self, direction)

parse(self, file_iter=None, jaguar_output=None)

callback

first_line_re

init(self, jaguar_output, file_iter=None)
(Constructor)