Module xplor

Module containing functions for the parsing and creation of Xplor formatted files.

Functions

str __convert_to_id(string)
Convert the string into a relax atom id representation.

list of lists of str, str, float, float parse_noe_restraints(lines)
Parse and return the NOE restraints from the Xplor lines.

str, str, float, float, float first_parse(lines)
Generator function to parse and extract the 2 atom IDs and NOE info from the lines.

str or list of str second_parse(id)
Split up pseudoatoms.

list of str strip_comments(lines)
Remove all Xplor comments from the data.

Variables

__package__ = 'lib.software'

Imports: search, RelaxError

Function Details

__convert_to_id(string)

Convert the string into a relax atom id representation.

Parameters:

• string (str) - The Xplor atom string.

Returns: str

The relax atom id.

parse_noe_restraints(lines)

Parse and return the NOE restraints from the Xplor lines.

Parameters:

• lines (list of str) - The Xplor formatted file, or file fragment, split into lines.

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

The NOE restraint list in the format of two atom identification strings (or list of str for pseudoatoms) and the lower and upper restraints.

first_parse(lines)

Generator function to parse and extract the 2 atom IDs and NOE info from the lines.

The first parse loops over and returns the data from assign statements, returning pseudo atoms as single strings. The second parse splits the pseudoatoms.

Parameters:

• lines (list of str) - The Xplor formatted file, or file fragment, split into lines.

Returns: str, str, float, float, float

The 2 atom IDs, and NOE info (NOE, upper, and lower bounds).

second_parse(id)

Split up pseudoatoms.

Parameters:

• id (str) - The Xplor atom id without outer brackets, i.e. a single atom or a list of atoms in the case of pseudoatoms.

Returns: str or list of str

For normal atoms, the id string is returned unmodified. For pseudoatoms, a list of strings, with brackets removed, is returned.

strip_comments(lines)

Remove all Xplor comments from the data.

Parameters:

• lines (list of str) - The Xplor formatted file, or file fragment, split into lines.

Returns: list of str

The file data with all comments removed.