schrodinger.application.mopac.results2012 module

This module parses and stores the results of a MOPAC2012 calculation. A MopacResults2012 class is populated with data from the MOPAC2012 output files using a text parser.

class schrodinger.application.mopac.results2012.Mopac2012TextParser(filename)

Bases: object

Parser for the MOPAC2012 .out and .aux files. Using decorators, the callback() function below populates the “callbacks” dictionary in this class with key-value pairs of the form (regex,func) where “regex” is a regular expression to catch patterns in the output file, and “func” is the callback function which is triggered when the regex is matched.

In this way, each specific callback is triggered by a given pattern such as ‘HOMO LUMO ENERGIES (EV) =’, and the callback function processes the matched lines.

Note that multiple regex’s can be associated with a given callback function by associating it with two or more decorators. In this way, the same callback can be triggered multiple times. e.g. for both the .aux and .out files, perhaps for consistency checking etc.

Typically, however, only one regex is associated with each callback so that data for a given property is grepped from either the .out file OR the .aux file, but not both.

callbacks = OrderedDict([(<_sre.SRE_Pattern object at 0x4ad98c0>, <function func>), (<_sre.SRE_Pattern object at 0x8ce10d0>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object at 0x8e33e60>, <function func>), (<_sre.SRE_Pattern object at 0x7ed54a0>, <function func>), (<_sre.SRE_Pattern object at 0x7b83f60>, <function func>), (<_sre.SRE_Pattern object at 0xae3cc20>, <function func>), (<_sre.SRE_Pattern object at 0x975eec0>, <function func>), (<_sre.SRE_Pattern object at 0x54bb700>, <function func>), (<_sre.SRE_Pattern object at 0xa2ac870>, <function func>), (<_sre.SRE_Pattern object at 0xa71e120>, <function func>), (<_sre.SRE_Pattern object at 0x5964030>, <function func>), (<_sre.SRE_Pattern object at 0xa7fa340>, <function func>), (<_sre.SRE_Pattern object at 0xaa009b0>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object at 0xb3bbed0>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>), (<_sre.SRE_Pattern object>, <function func>)])

parse_file(properties)

Loop over self.file_iter and trigger the callbacks.

exception schrodinger.application.mopac.results2012.MopacBasisError1

Bases: exceptions.Exception

exception schrodinger.application.mopac.results2012.MopacBasisError2

Bases: exceptions.Exception

exception schrodinger.application.mopac.results2012.MopacBasisError3

Bases: exceptions.Exception

exception schrodinger.application.mopac.results2012.MopacBasisError4

Bases: exceptions.Exception

exception schrodinger.application.mopac.results2012.MopacBasisError5

Bases: exceptions.Exception

exception schrodinger.application.mopac.results2012.MopacNumericalError

Bases: exceptions.Exception

exception schrodinger.application.mopac.results2012.MopacPropertyError

Bases: exceptions.Exception

class schrodinger.application.mopac.results2012.MopacResults2012

Bases: schrodinger.application.mopac.mopac_results.MopacResults

A class to parse and store the results of a MOPAC2012 calculation.

get_error_text()

Needed to be consistent with legacy code

method

output_file

populate_from_file(filename)

Parse “filename” containing MOPAC2012 output data.

set_final_structure(structure, filename)

Compile parsed results into the structure.properties dictionary.

set_method(value)

set_output_file(value)

set_status(value)

statusOk()

Needed to be consistent with legacy code

structure

write_vis_files(jobname, nplot, gridres, gridext)

This function will call the Fortran routines to generate the 3D data and .vis files for plotting surfaces.

Parameters:nplot (int) – number of MOs to plot around HOMO/LUMO gap.

schrodinger.application.mopac.results2012.callback(regex)

This decorator is just a convenient way to populate the callbacks dictionary in the Mopac2012TextParser. The associated functions themselves are not actually decorated.

schrodinger.application.mopac.results2012.check_memory_use(nvals, name)

Check memory requirment for a long list of floats. Print message if size exceeds MEMORY_WARNING.

schrodinger.application.mopac.results2012.fortfloat(val)

Convert a floating point number in Fortran notation to a regular float.

schrodinger.application.mopac.results2012.func(props, match, it)

schrodinger.application.mopac.results2012.update_props(props, key, value, precision=5)

Update the props dictionary with the key-value pair, performing consistency checks if the key already exists.