src package

Submodules

src.bond_angles module

The BondAngles class calculates or searches for and stores bond angle data from an ORCA .out file.

class src.bond_angles.BondAngles(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores bond angle data from an ORCA .out file.

Methods

_search

Search the .out file for bond angle data.

__calc_atom_angle

Manually calcs the “bond angle” of the 3 atoms in the input angle tuple.

get_datum

Gives the bond angle from _data for a certain bond.

get_datum(angle_tuple)

Gives the bond angle from _data for a certain bond.

Parameters

angle_tupletuple

Tuple containing three atom labels, representing the desired bond.

Returns

str

String consisting of the angle of the corresponding bond in degrees.

Raises

KeyError

This occurs when the input ‘bond’ tuple can’t be found as a key in the dict containing the bond angle data.

src.bond_lengths module

The BondLengths class calculates or searches for and stores bond length data from an ORCA .out file.

class src.bond_lengths.BondLengths(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores bond length data from an ORCA .out file.

Methods

_search

Search the .out file for bond length data.

__calc_atom_angle

Manually calcs the “bond length” of the 2 atoms in the input bond tuple.

get_datum

Gives the bond length from _data for a certain bond.

get_datum(bond_tuple)

Gives the bond length from _data for a certain bond.

Parameters

bond_tupletuple

Tuple containing two atom labels, representing the desired bond.

Returns

str

String consisting of the length of the corresponding bond in Angstroms.

Raises

KeyError

This occurs when the input ‘bond’ tuple can’t be found as a key in the dict containing the bond length data.

src.data_section module

Structures subclasses that represent types of data from ORCA .out file.

The DataSection abstract class provides an interface for creating subclasses that represent different types of data from an ORCA .out file. These subclasses use regular expressions to search the contents of the .out file and find a particular type of data (e.g. input geometry coordinates for a series of atoms) and then stores these data using an appropriate structure. These subclasses also have a method to return these data to the user.

class src.data_section.DataSection(out_filename, outfile_contents)

Bases: ABC

Searches and stores a particular type of data from an ORCA .out file.

Attributes

_out_filenamestr

Name of the ORCA .out file that will be searched.

_outfile_contentsstr

String containing the full text of the ORCA .out file.

_datadict

Dictionary containing the desired data, with relevant categories as keys (e.g. atom labels, bond tuples, polarizability parameters, etc.) and their corresponding values as values. Conventionally both are strs.

Methods

_find_data

Searches the .out file for the desired data, which is used to store these data in the _data attribute.

get_data

Getter method that returns the _data attribute.

get_datum

Getter method that returns a ‘datum’ (one entry in the _data dict).

get_section_name

Getter method that returns the name of the DataSection subclass.

get_out_filename

Getter method that returns name of the .out file that the data is from.

get_data()

Getter method that returns the _data attribute.

Returns

dict

The _data attribute.

get_datum(datum_label)

Return the value associated with a particular key (datum_label) from the _data dict attribute.

Parameters

datum_labelstr

Key for the _data dictionary.

Returns

Value from the _data dictionary corresponding to param.

get_out_filename()

Returns string of the filename of the ORCA .out file associated with this instance.

Returns

str

String of the filename of the ORCA .out file.

get_section_name()

Getter method that returns the _section_name attribute.

Returns

str

_section_name attribute.

src.data_section_with_inputs module

An abstract class for DataSection subclasses that need to take inputs.

Inputs (e.g. tuples of strings of atom labels, or tuples of tuples of atom labels) specify which pieces of data should be searched for. The result of the search is a dictionary with each element from the inputs as keys and the resulting data from the search as values.

class src.data_section_with_inputs.DataSectionWithInputs(out_filename, outfile_contents, inputs)

Bases: DataSection, ABC

A subclass of DataSection for data that takes a set of inputs to search for.

Attributes

_inputstuple

A tuple of information (e.g. strings of atom labels, or of tuples that contain strings of atom labels) which signify which pieces of information should be searched for.

Methods

_find_data

Searches the .out file for the desired data, which is used to store these data in the _data attribute.

_search

Abstract method which defines how each subclass of this class should go about searching the .out file for its particular type of data.

get_inputs

Returns a copy of the _inputs attribute.

get_inputs()

Returns the inputs used for this instance.

Returns

tuple

_inputs attribute.

src.dipole_moments module

The DipoleMoments class searches for and stores dipole moment data from an ORCA .out file.

class src.dipole_moments.DipoleMoments(out_filename, outfile_contents)

Bases: DataSection

Finds and stores dipole moment data from a ORCA .out file.

Attributes

_regexstr

Regular expression string used to search the .out file for the dipole moments data.

Methods

_find_data

Search the .out file for polarizability data, return as dict.

src.final_geom module

The FinalGeometry class searches for and stores the final structure geometry data (i.e., after geometry optimization is complete) from an ORCA .out file.

class src.final_geom.FinalGeometry(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores the final geometry data from an ORCA .out file.

Methods

_search

Search the .out file for bond length data.

src.homo_lumo_energies module

The HOMOLUMOEnergies class searches for and stores the HOMO and LUMO energy data from an ORCA .out file.

class src.homo_lumo_energies.HOMOLUMOEnergies(out_filename, outfile_contents)

Bases: DataSection

Finds and stores HOMO and LUMO energy data from a ORCA .out file.

Attributes

__regexstr

Regular expression string used to search the .out file for the HOMO and LUMO energy data.

Methods

_find_data

Search the .out file for HOMO and LUMO energy data, return as dict.

src.initial_geom module

The FinalGeometry class searches for and stores the initial (i.e., input by the user) geometry data from an ORCA .out file.

class src.initial_geom.InitialGeometry(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores initial geometry data from an ORCA .out file.

Methods

_search

Search the .out file for bond length data.

src.input_reader module

Structures subclasses that represent “Input Readers”.

For our purposes, “Input Readers” read in information from the user related to what data they want to extract from the ORCA .out file.

class src.input_reader.InputReader(input_filename)

Bases: ABC

Finds and stores input data for DataSection subclasses from an input file.

abstract get_bond_angle_inputs()

Returns bond angle inputs.

abstract get_bond_length_inputs()

Returns of bond length inputs.

abstract get_final_geom_inputs()

Returns final geometry inputs.

abstract get_initial_geom_inputs()

Returns initial geometry inputs.

abstract get_loewdin_charge_inputs()

Returns Loewdin charge inputs.

abstract get_loewdin_charge_sum_inputs()

Returns Loewdin charge sum inputs.

abstract get_mulliken_charge_inputs()

Returns Mulliken charge inputs.

abstract get_mulliken_charge_sum_inputs()

Returns Mulliken charge sum inputs.

src.loewdin_charge_sums module

The LoewdinChargeSums class searches for and stores sums of Loewdin charges from an ORCA .out file.

The LoewdinCharges class searches for the Loewdin charge data for a series of atoms from a ORCA .out file, as specified by input (tuple of) tuples which contains a series of LEXICOGRAPHICALLY SORTED atom labels to search for.

class src.loewdin_charge_sums.LoewdinChargeSums(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores Loewdin charge sum data from a ORCA .out file.

Methods

_search

Search the .out file for Loewdin charge sum data.

get_datum

Gives the sum of Loewdin charges from _data for a set of atoms.

get_datum(atoms_tuple)

Gives the sum of Loewdin charges from _data for a set of atoms.

Parameters

atoms_tupletuple

A tuple containing strings of the desired atom labels.

Returns

str

String consisting of the sum of Loewdin charges of the atoms in atoms_tuple.

Raises

KeyError

This occurs when the input atoms tuple can’t be found as a key in the dict containing the Loewdin charge sum data.

src.loewdin_charges module

The LoewdinCharges class searches for and stores Loewdin charge data from an ORCA .out file.

class src.loewdin_charges.LoewdinCharges(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores Loewdin charge data from an ORCA .out file.

Methods

_search

Search .out file for Loewdin charge data.

src.mulliken_charge_sums module

The MullikenChargeSums class searches for and stores sums of Mulliken charges from an ORCA .out file.

The MullikenCharges class searches for the Mulliken charge data for a series of atoms from a ORCA .out file, as specified by input (tuple of) tuples which contains a series of LEXICOGRAPHICALLY SORTED atom labels to search for.

class src.mulliken_charge_sums.MullikenChargeSums(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores Mulliken charge sum data from a ORCA .out file.

Methods

_search

Search the .out file for Mulliken charge sum data.

get_datum

Gives the sum of Mulliken charges from _data for a set of atoms.

get_datum(atoms_tuple)

Gives the sum of Mulliken charges from _data for a set of atoms.

Parameters

atoms_tupletuple

A tuple containing strings of the desired atom labels.

Returns

str

String consisting of the sum of Mulliken charges of the atoms in atoms_tuple.

Raises

KeyError

This occurs when the input atoms tuple can’t be found as a key in the dict containing the Mulliken charge sum data.

src.mulliken_charges module

The MullikenCharges class searches for and stores Mulliken charge data from an ORCA .out file.

class src.mulliken_charges.MullikenCharges(out_filename, outfile_contents, inputs)

Bases: DataSectionWithInputs

Finds and stores Mulliken charge data from an ORCA .out file.

Methods

_search

Search .out file for Mulliken charge data.

src.orca_out_to_csv module

src.orca_out_to_excel module

src.orca_out_to_json module

A script to quickly pull desired data from an ORCA .out file and compile it into a JSON file.

Before running, the user should specify what information they want to look for in a .txt file (see example). When executed, the script checks each file in the working directory. If the file ends in .out, it exports the desired data into a JSON file.

src.orca_out_to_json.create_json_from_sds(sd_list, json_name)

Writes the data in a list of StructureData instances to a JSON file.

Parameters

sd_listlist

List containing the set of StructureData instances that each come from the ORCA .out files.

json_namestr

Name of the JSON file where the data will be stored.

src.orca_out_to_json.main()

src.orca_out_to_json.make_json_list(sd_list)

Converts the data in a list of StructureData instances to a dict for JSON.

Parameters

sd_listlist

List containing the set of StructureData instances that each come from the ORCA .out files.

Returns

list

List with the data from sd_list configured to be compatible with JSON (i.e., tuples are converted to strings).

src.polarizability module

The Polarizability class searches for and stores polarizability data from an ORCA .out file.

class src.polarizability.Polarizability(out_filename, outfile_contents)

Bases: DataSection

Finds and stores polarizability data from a ORCA .out file.

Attributes

__regexstr

Regular expression string used to search the .out file for the polarizability data.

Methods

_find_data

Search the .out file for polarizability data, return as dict.

src.structure_data module

Provides the StructureData class for use with other scripts.

The StructureData class holds information from an ORCA .out file, as specified by an input .txt file. It holds these data in a dictionary with the names of data sections as keys and corresponding DataSection subclasses as values. It contains methods to get data from these sections.

class src.structure_data.StructureData(out_filename, input_filename, data_sections)

Bases: object

Associates a desired subset of data from an ORCA .out file.

Attributes

__out_filenamestr

String of the filename of the ORCA .out file this object represents.

__input_filenamestr

String of filename of .txt file that contains lists of desired atom labels for each type of data that will be pulled from the .out file.

__data_sectionsdict

Dictionary mapping strings of the names of DataSection subclasses to instances those subclasses associated with this .out file.

Methods

__read_file

Converts a text file to a single string using .read().

__check_coord_system

Determines whether the coordinate system was set up correctly.

get_out_filename

Gives the filename of the .out file from which the data was taken.

get_input_filename

Gives the filename of the input .txt file.

get_std_error_msg

Gives the standard error message used by this class.

get_data_sections

Gives __data_sections attribute, a dictionary that maps names of DataSection subclasses to their corresponding instances.

get_data_section

Gives a DataSection subclass (value) from the __data_sections dict given its name (key).

get_data_section_data

Gives dict containing the data from a particular DataSection subclass instance.

get_data_section_datum

Gives ‘datum’ (value from DataSection subclass data dictionary) corresponding to a given label (key for said dict).

get_data_section(section_name)

Gives a DataSection subclass (value) from the __data_sections dict given its name (key).

Parameters

section_namestr

Name of a DataSection subclass.

Returns

DataSection subclass

Instance of a DataSection subclass corresponding to the passed name.

get_data_section_data(section_name)

Gives dict containing the data from a particular DataSection subclass instance.

Parameters

section_namestr

Name of the DataSection, should be a key in __data_sections attribute.

Returns

dict

Data found by a DataSection subclass instance.

get_data_section_datum(section_name, datum_label)

Gives ‘datum’ (value from DataSection subclass data dictionary) corresponding to a given label (key for said dict).

Parameters

section_namestr

Name of the DataSection, should be a key in __data_sections attribute.

datum_labelstr or tuple

Key to the DataSection subclass data dictionary for the desired datum.

Returns

str or dict

‘Datum’ corresponding to the datum label key in the DataSection data dictionary.

get_data_sections()

Gives __data_sections attribute, a dictionary that maps names of DataSection subclasses to their corresponding instances.

Returns

dict

__data_sections attribute.

get_input_filename()

Gives the filename of the input .txt file.

Returns

str

__input_filename attribute.

get_out_filename()

Gives the filename of the .out file from which the data was taken.

Returns

str

__out_filename attribute.

static get_std_error_msg()

Gives the standard error message used by this class.

Returns

str

__std_error_msg attribute.

src.structure_data_builder module

Provides a Builder which creates StructureData instances.

This class uses the Builder design pattern to create instances of the StructureData class based on a given filename for an input .txt file.

class src.structure_data_builder.StructureDataBuilder(input_filename)

Bases: object

A Builder which creates StructureData instances.

Attributes

__input_filenamestr

String of filename of .txt file that contains lists of desired atom labels for each type of data that will be pulled from the .out file.

__input_readerInputReaderJSON

Instance of InputReader used to retrieve the inputs for the StructureData objects this instance builds.

build(out_filename)

Creates and returns an instance of StructureData based on the passed .out filename and the input filename attribute.

Parameters

out_filenamestr

String of filename of desired .out file.

Returns

StructureData

Instance of StructureData based on the passed .out filename and the input filename attribute.

Module contents