Module noesy

Module for NOESY related operations.

Functions

str __file_format(lines)
Determine the format of the NOE restraints data.

list of lists of [str, str, float, float] parse_noe_restraints(lines, proton1_col=None, proton2_col=None, lower_col=None, upper_col=None, sep=None)
Parse and return the NOE restraints from the generic formatted file.

read_restraints(file=None, dir=None, proton1_col=None, proton2_col=None, lower_col=None, upper_col=None, sep=None)
Load NOESY or ROESY constraint information from file.

Variables

__package__ = 'pipe_control'

Imports: search, warn, RelaxError, RelaxNoSequenceError, open_read_file, xplor, RelaxWarning, exists_mol_res_spin_data, return_spin, tokenise, check_pipe

Function Details

__file_format(lines)

Determine the format of the NOE restraints data.

Parameters:

• lines (list of str) - The file data converted to a list of file lines.

Returns: str

The format of the file.

parse_noe_restraints(lines, proton1_col=None, proton2_col=None, lower_col=None, upper_col=None, sep=None)

Parse and return the NOE restraints from the generic formatted file.

Parameters:

• lines (list of str) - The file, or file fragment, split into lines.
• proton1_col (None or int) - The column containing the first proton of the NOE or ROE cross peak.
• proton2_col (None or int) - The column containing the second proton of the NOE or ROE cross peak.
• lower_col (None or int) - The column containing the lower NOE bound.
• upper_col (None or int) - The column containing the upper NOE bound.
• sep (None or str) - The column separator (the default is white space).

Returns: list of lists of [str, str, float, float]

The NOE restraint list in the format of two atom identification strings and the lower and upper restraints.

read_restraints(file=None, dir=None, proton1_col=None, proton2_col=None, lower_col=None, upper_col=None, sep=None)

Load NOESY or ROESY constraint information from file.

If the input file is a pre-formatted Xplor file, the column number and separator arguments will be ignored.

Parameters:

• file (str) - The name of the file containing the relaxation data.
• dir (None or str) - The directory where the file is located.
• proton1_col (None or int) - The column containing the first proton of the NOE or ROE cross peak.
• proton2_col (None or int) - The column containing the second proton of the NOE or ROE cross peak.
• lower_col (None or int) - The column containing the lower NOE bound.
• upper_col (None or int) - The column containing the upper NOE bound.
• sep (None or str) - The column separator (the default is white space).