schrodinger.application.matsci.bandshape_utils module

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

Bases: object

Manage a bandshape spectrum file.

COLUMNS = OrderedDict([('r_j_Excitation_Energy_(eV)', 'Excitation Energy (eV)'), ('r_j_Intensity', 'Intensity'), ('s_j_Symmetry', 'Symmetry')])

DEFAULT_TRIM_PCT = 5.0

ENERGY_KEY = 'r_j_Excitation_Energy_(eV)'

ENERGY_TITLE = 'Excitation Energy (eV)'

EXT = '.uvv.spm'

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')])

INTENSITY_KEY = 'r_j_Intensity'

INTENSITY_TITLE = 'Intensity'

SPECTRUM_KEY = 's_j_spectrum_type'

SPECTRUM_TITLE = 'Electronic Transition w/ Bandshape'

SYMMETRY_KEY = 's_j_Symmetry'

SYMMETRY_TITLE = 'Symmetry'

X_ALIAS = 'r_j_Excitation_Energy_(eV)'

X_KEY = 's_j_x_label'

Y_ALIAS = 'r_j_Intensity'

Y_KEY = 's_j_y_label'

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

static getTrimmedTable(filepath, trim_pct=None)

Return a table of trimmed data for the given file path and trim percent.

Parameters:

• filepath (str) – the file path to the file with the data
• trim_pct (float) – the trim percent, it is the percent of the maximum y-value, i.e. intensity value, that is used when trimming

Raises:

ValueError – if there isn’t any data

Return type:

table.Table

Returns:

table of trimmed data

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

write()

Write the *spm file.

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

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.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