Module j_coupling
source code
Module for the manipulation of J coupling data.
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copy(pipe_from=None,
pipe_to=None)
Copy the J coupling data from one data pipe to another. |
source code
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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. |
source code
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write(file=None,
dir=None,
force=False)
Write the J coupling data to file. |
source code
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__package__ = ' pipe_control '
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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
check_pipe_setup(pipe=None,
sequence=False,
j=False)
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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.
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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.
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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)
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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.
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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.
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