schrodinger.application.matsci.bandshape_utils module

Utilities for bandshape calculations.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.bandshape_utils.is_bs_spectrum_file_key(key)

Return True if the given structure property key is a bandshape spectrum file key.

Parameters:key (str) – the structure property key to check Return type:bool Returns:True if the given key is a bandshape spectrum file key

schrodinger.application.matsci.bandshape_utils.get_temp_from_bs_spectrum_file_key(key)

Return the temperature from the given bandshape spectrum file structure property key.

Parameters:key (str) – the structure property key containing the temperature Return type:float Returns:the temperature in K

schrodinger.application.matsci.bandshape_utils.get_bs_spectrum_file_temps_keys(struct)

Return the bandshape spectrum file structure property keys and associated temperatures for the given structure.

Parameters:struct (schrodinger.structure.Structure) – the structure with the property keys Return type:list Returns:pair tuples of temperatures in K and bandshape spectrum file structure property keys

class schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile(data_file_name, spm_file_name)

Bases: object

Manage a bandshape spectrum file.

ENERGY_KEY = 'r_j_Excitation_Energy_(eV)'

ENERGY_TITLE = 'Excitation Energy (eV)'

INTENSITY_KEY = 'r_j_Intensity'

INTENSITY_TITLE = 'Intensity'

SYMMETRY_KEY = 's_j_Symmetry'

SYMMETRY_TITLE = 'Symmetry'

SPECTRUM_KEY = 's_j_spectrum_type'

SPECTRUM_TITLE = 'Electronic Transition w/ Bandshape'

X_KEY = 's_j_x_label'

X_ALIAS = 'r_j_Excitation_Energy_(eV)'

Y_KEY = 's_j_y_label'

Y_ALIAS = 'r_j_Intensity'

HEADERS = {'s_j_spectrum_type': 'Electronic Transition w/ Bandshape', 's_j_x_label': 'r_j_Excitation_Energy_(eV)', 's_j_y_label': 'r_j_Intensity'}

COLUMNS = {'r_j_Excitation_Energy_(eV)': 'Excitation Energy (eV)', 'r_j_Intensity': 'Intensity', 's_j_Symmetry': 'Symmetry'}

EXT = '.uvv.spm'

DEFAULT_BIN_WIDTH = 400.0

__init__(data_file_name, spm_file_name)

Create an instance.

Parameters:

• data_file_name (str) – the text file containing whitespace separated energies and intensities, one pair per line, energies in eV
• spm_file_name (str) – the name of the *spm file to create

static getData(data_file_name)

Return the data from the given data file.

Parameters:data_file_name (str) – the text file containing whitespace separated energies and intensities, one pair per line, energies in eV Return type:list Returns:contains (energy, intensity) tuples

write()

Write the *spm file.

static isBandshapeTable(atable)

Return True if the given table is a bandshape table.

Parameters:atable (table.Table) – the table to check Return type:bool Returns:True if the given table is a bandshape table

static getTrimmedTable(filepath, bin_width=None)

Return a table of trimmed data for the given file path and bin width.

Parameters:

• filepath (str) – the file path to the file with the data
• bin_width (float) – the bin width in wavenumbers (cm-1) used for binning

Raises:

ValueError – if there isn’t any data

Return type:

table.Table

Returns:

table of trimmed data

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.bandshape_utils', '__doc__': '\n Manage a bandshape spectrum file.\n ', 'ENERGY_KEY': 'r_j_Excitation_Energy_(eV)', 'ENERGY_TITLE': 'Excitation Energy (eV)', 'INTENSITY_KEY': 'r_j_Intensity', 'INTENSITY_TITLE': 'Intensity', 'SYMMETRY_KEY': 's_j_Symmetry', 'SYMMETRY_TITLE': 'Symmetry', 'SPECTRUM_KEY': 's_j_spectrum_type', 'SPECTRUM_TITLE': 'Electronic Transition w/ Bandshape', 'X_KEY': 's_j_x_label', 'X_ALIAS': 'r_j_Excitation_Energy_(eV)', 'Y_KEY': 's_j_y_label', 'Y_ALIAS': 'r_j_Intensity', 'HEADERS': OrderedDict([('s_j_spectrum_type', 'Electronic Transition w/ Bandshape'), ('s_j_x_label', 'r_j_Excitation_Energy_(eV)'), ('s_j_y_label', 'r_j_Intensity')]), 'COLUMNS': OrderedDict([('r_j_Excitation_Energy_(eV)', 'Excitation Energy (eV)'), ('r_j_Intensity', 'Intensity'), ('s_j_Symmetry', 'Symmetry')]), 'EXT': '.uvv.spm', 'DEFAULT_BIN_WIDTH': 400.0, '__init__': <function BandshapeSpectrumFile.__init__>, 'getData': <staticmethod object>, '_setUp': <function BandshapeSpectrumFile._setUp>, '_buildTable': <function BandshapeSpectrumFile._buildTable>, '_createFile': <function BandshapeSpectrumFile._createFile>, '_tearDown': <function BandshapeSpectrumFile._tearDown>, 'write': <function BandshapeSpectrumFile.write>, 'isBandshapeTable': <staticmethod object>, 'getTrimmedTable': <staticmethod object>, '__dict__': <attribute '__dict__' of 'BandshapeSpectrumFile' objects>, '__weakref__': <attribute '__weakref__' of 'BandshapeSpectrumFile' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.bandshape_utils'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)