Module nmrpipe

Module containing functions for handling NMRPipe SeriesTab files.

Functions

read_seriestab(peak_list=None, file_data=None, int_col=None)
Extract the intensity information from the NMRPipe SeriesTab peak intensity file.

list of lines show_apod_extract(file_name=None, dir=None, path_to_command='showApod')
Extract showApod information for spectrum fourier transformed with NMRPipe.

float show_apod_rmsd(file_name=None, dir=None, path_to_command='showApod')
Extract showApod 'Noise Std Dev' for spectrum fourier transformed with NMRPipe.

str show_apod_rmsd_to_file(file_name=None, dir=None, path_to_command='showApod', outdir=None, force=False)
Extract showApod 'Noise Std Dev' from showApod, and write to file with same filename and ending '.rmsd'

list of str show_apod_rmsd_dir_to_files(file_ext='.ft2', dir=None, path_to_command='showApod', outdir=None, force=False)
Searches 'dir' for files with extension 'file_ext'.

Variables

subprocess_module = True

__package__ = 'lib.spectrum'

Imports: re, glob, sep, abspath, subprocess, warn, RelaxError, file_root, get_file_path, open_write_file, sort_filenames, write_data, RelaxWarning

Function Details

read_seriestab(peak_list=None, file_data=None, int_col=None)

Extract the intensity information from the NMRPipe SeriesTab peak intensity file.

Parameters:

• peak_list (lib.spectrum.objects.Peak_list instance) - The peak list object to place all data into.
• file_data (list of lists of str) - The data extracted from the file converted into a list of lists.
• int_col (int) - The column which to multiply the peak intensity data (used by the SeriesTab intensity file format).

Raises:

• RelaxError - When the expected peak intensity is not a float.

show_apod_extract(file_name=None, dir=None, path_to_command='showApod')

Extract showApod information for spectrum fourier transformed with NMRPipe.

Parameters:

• file (str) - The filename of the NMRPipe fourier transformed file.
• dir (str) - The directory where the file is located.
• path_to_command (str) - If showApod not in PATH, then specify absolute path as: /path/to/showApod

Returns: list of lines

The output from showApod as list of lines.

show_apod_rmsd(file_name=None, dir=None, path_to_command='showApod')

Extract showApod 'Noise Std Dev' for spectrum fourier transformed with NMRPipe.

Parameters:

• file (str) - The filename of the NMRPipe fourier transformed file.
• dir (str) - The directory where the file is located.
• path_to_command (str) - If showApod not in PATH, then specify absolute path as: /path/to/showApod

Returns: float

The Noise Std Dev from line: 'REMARK Automated Noise Std Dev in Processed Data'

show_apod_rmsd_to_file(file_name=None, dir=None, path_to_command='showApod', outdir=None, force=False)

Extract showApod 'Noise Std Dev' from showApod, and write to file with same filename and ending '.rmsd'

Parameters:

• file (str) - The filename of the NMRPipe fourier transformed file.
• dir (str) - The directory where the file is located.
• path_to_command (str) - If showApod not in PATH, then specify absolute path as: /path/to/showApod
• outdir (str) - The directory where to write the file. If 'None', then write in same directory.
• force (bool) - Boolean argument which if True causes the file to be overwritten if it already exists.

Returns: str

Write the 'Noise Std Dev' from showApod to a file with same file filename, with ending '.rmsd'. This will be a file path.

show_apod_rmsd_dir_to_files(file_ext='.ft2', dir=None, path_to_command='showApod', outdir=None, force=False)

Searches 'dir' for files with extension 'file_ext'. Extract showApod 'Noise Std Dev' from showApod, and write to file with same filename and ending '.rmsd'.

Parameters:

• file_ext (str) - The extension for files which is NMRPipe fourier transformed file.
• dir (str) - The directory where the files is located.
• path_to_command (str) - If showApod not in PATH, then specify absolute path as: /path/to/showApod
• outdir (str) - The directory where to write the files. If 'None', then write in same directory.
• force (bool) - Boolean argument which if True causes the file to be overwritten if it already exists.

Returns: list of str

Write the 'Noise Std Dev' from showApod to a file with same file filename, with ending '.rmsd'. This will be a list of file paths.