ScoreFile¶

class visualife.data.ScoreFile(input_file: str = None, **kwargs)¶

Bases: object

Score file is a tabular data format, originally used by Rosetta to store energy values

This class loads .sc / .fsc (these two are identical) and .fasc files; saves .sc. Data is stored column-wise to facilitate plotting and conversion to JSON.

Creates an empty object

Keyword Arguments:
Parameters:	input_file – input file to load once this object is constructed (optional) kwargs – see below
	columns (`list(string)`) – provide a list of columns this score file will have; this data should be provided when new rows are to be added with `add_row()` method skip_columns (`list(string)`) – when loading data from a file, skip columns given their names rename_columns (`list(tuple(string,string)`) – when loading data from a file, rename given columns

Attributes Summary

`field_width`
`n_rows`	Provides the number of data entries (rows) in this score file

Methods Summary

`add_row`(row)	Adds a new data row to this score file :param row: (`iterable`) an iterable of values, that will be appended to the relevant columns (the values must be given in the same order as columns defined in this object) :return: None
`column`(col_name)	Returns a column by its name
`column_names`()	Provides an iterable of column names :return: names of all the data columns
`detect_pdb_name_column`([structure_names])
`find_row`(tag)	Find a row identified by a given tag :param tag: decoy / structure / data row name :return: row number (`int`) or `-1` if this tag was not yet inserted into this score file
`is_relevant_column`(col_name)	Returns False if column is not relevant meaning has all values identical
`merge_in`(other_sf)	Merges data from `other_sf` into this object
`read_fasc_file`(fname)	Reads a file in .fast (JSON) format
`read_score_file`(fname)	Reads data in the Rosetta’s score-file format
`replace_value`(column_name, row_tag, new_value)	Replaces a value in this score file table.
`row`(index)	Returns a row of data requested by its index (from 0 to n_rows - 1) :param index: (`int`) row index :return: a of row data (as a list)
`write`(fname)	Writes all data stored in this object in score-file format

Attributes Documentation

field_width = 8¶

n_rows¶

Provides the number of data entries (rows) in this score file

Returns:	number of rows

Methods Documentation

add_row(row)¶

Adds a new data row to this score file :param row: (iterable) an iterable of values, that will be appended to the relevant columns

(the values must be given in the same order as columns defined in this object)

Returns:	None

column(col_name)¶

Returns a column by its name

Parameters:	col_name – column name
Returns:	data column

column_names()¶: Provides an iterable of column names :return: names of all the data columns

detect_pdb_name_column(structure_names=['protein', 'tag', 'decoy', 'description'])¶

find_row(tag)¶: Find a row identified by a given tag :param tag: decoy / structure / data row name :return: row number (int) or -1 if this tag was not yet inserted into this score file

is_relevant_column(col_name)¶: Returns False if column is not relevant meaning has all values identical

merge_in(other_sf)¶

Merges data from other_sf into this object

Columns from other_sf object will be added to rows of this object for these rows where tag columns hold the same row names :param other_sf: other score file object :return: None

read_fasc_file(fname)¶

Reads a file in .fast (JSON) format

Parameters:	fname – input file name
Returns:	None

read_score_file(fname)¶

Reads data in the Rosetta’s score-file format

Parameters:	fname – input file name or input data as multi-line string
Returns:	None

replace_value(column_name, row_tag, new_value)¶

Replaces a value in this score file table.

The cell is represent by a tag (to identify a row) and a column name. Both tag and column must be already defined in this score file

Parameters:	column_name – (`string`) points to the column an updated cell belong to row_tag – (`string`) points to the row an updated cell belong to new_value – the new value
Returns:	`None`

row(index)¶: Returns a row of data requested by its index (from 0 to n_rows - 1) :param index: (int) row index :return: a of row data (as a list)

write(fname)¶

Writes all data stored in this object in score-file format

Parameters:	fname – output file name or an opened stream; use None to print on stdout
Returns:	None