Package pipe_control :: Module j_coupling
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Module j_coupling

source code

Module for the manipulation of J coupling data.

Functions [hide private]
 
check_pipe_setup(pipe=None, sequence=False, j=False)
Check that the current data pipe has been setup sufficiently.
source code
 
copy(pipe_from=None, pipe_to=None)
Copy the J coupling data from one data pipe to another.
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delete()
Delete all J coupling data.
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display()
Display the J coupling data.
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read(file=None, dir=None, file_data=None, spin_id1_col=None, spin_id2_col=None, data_col=None, error_col=None, sign_col=None, sep=None)
Read the J coupling data from file.
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write(file=None, dir=None, force=False)
Write the J coupling data to file.
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Variables [hide private]
  __package__ = 'pipe_control'

Imports: sys, warn, is_float, RelaxError, RelaxNoJError, RelaxNoSequenceError, extract_data, open_write_file, strip, write_data, RelaxWarning, pipes, consistent_interatomic_data, create_interatom, interatomic_loop, return_interatom, exists_mol_res_spin_data, return_spin


Function Details [hide private]

check_pipe_setup(pipe=None, sequence=False, j=False)

source code 

Check that the current data pipe has been setup sufficiently.

Parameters:
  • pipe (None or str) - The data pipe to check, defaulting to the current pipe.
  • sequence (bool) - A flag which when True will invoke the sequence data check.
  • j (bool) - A flag which if True will check that J couplings exist.

copy(pipe_from=None, pipe_to=None)

source code 

Copy the J coupling data from one data pipe to another.

Parameters:
  • pipe_from (str) - The data pipe to copy the J coupling data from. This defaults to the current data pipe.
  • pipe_to (str) - The data pipe to copy the J coupling data to. This defaults to the current data pipe.

read(file=None, dir=None, file_data=None, spin_id1_col=None, spin_id2_col=None, data_col=None, error_col=None, sign_col=None, sep=None)

source code 

Read the J coupling data from file.

Parameters:
  • file (str) - The name of the file to open.
  • dir (str or None) - The directory containing the file (defaults to the current directory if None).
  • file_data (list of lists) - An alternative to opening a file, if the data already exists in the correct format. The format is a list of lists where the first index corresponds to the row and the second the column.
  • spin_id1_col (int) - The column containing the spin ID strings of the first spin.
  • spin_id2_col (int) - The column containing the spin ID strings of the second spin.
  • data_col (int or None) - The column containing the J coupling data in Hz.
  • error_col (int or None) - The column containing the J coupling errors.
  • sign_col (int or None) - The optional column containing the sign of the J coupling.
  • sep (str or None) - The column separator which, if None, defaults to whitespace.

write(file=None, dir=None, force=False)

source code 

Write the J coupling data to file.

Parameters:
  • file (str or file object) - The file name or object to write to.
  • dir (str) - The name of the directory to place the file into (defaults to the current directory).
  • force (bool) - A flag which if True will cause any pre-existing file to be overwritten.