Package generic_fns :: Module noesy
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Module noesy

source code

Module for NOESY related operations.

Functions [hide private]
str
__file_format(lines)
Determine the format of the NOE restraints data.
source code
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.
source code
 
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.
source code
Variables [hide private]
  __package__ = 'generic_fns'

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


Function Details [hide private]

__file_format(lines)

source code 

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)

source code 

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)

source code 

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).