Package generic_fns :: Module rdc
[hide private]
[frames] | no frames]

Module rdc

source code

Module for the manipulation of RDC data.

Functions [hide private]
 
back_calc(align_id=None)
Back calculate the RDC from the alignment tensor and unit bond vectors.
source code
 
check_pipe_setup(pipe=None, rdc_id=None, sequence=False, N=False, tensors=False, rdc=False)
Check that the current data pipe has been setup sufficiently.
source code
float or None
convert(value, align_id, to_intern=False)
Convert the RDC based on the 'D' or '2D' data type.
source code
 
copy(pipe_from=None, pipe_to=None, align_id=None)
Copy the RDC data from one data pipe to another.
source code
 
corr_plot(format=None, file=None, dir=None, force=False)
Generate a correlation plot of the measured vs.
source code
 
delete(align_id=None)
Delete the RDC data corresponding to the alignment ID.
source code
 
display(align_id=None, bc=False)
Display the RDC data corresponding to the alignment ID.
source code
 
q_factors(spin_id=None)
Calculate the Q-factors for the RDC data.
source code
 
read(align_id=None, file=None, dir=None, file_data=None, data_type='D', spin_id1_col=None, spin_id2_col=None, data_col=None, error_col=None, sep=None, neg_g_corr=False, absolute=False)
Read the RDC data from file.
source code
 
set_errors(align_id=None, spin_id1=None, spin_id2=None, sd=None)
Set the RDC errors if not already present.
source code
 
weight(align_id=None, spin_id=None, weight=1.0)
Set optimisation weights on the RDC data.
source code
 
write(align_id=None, file=None, dir=None, bc=False, force=False)
Display the RDC data corresponding to the alignment ID.
source code
Variables [hide private]
  __package__ = 'generic_fns'

Imports: deepcopy, pi, sqrt, float64, ones, zeros, norm, sys, warn, is_float, nan, grace, pipes, get_tensor_index, consistent_interatomic_data, create_interatom, interatomic_loop, return_interatom, exists_mol_res_spin_data, return_spin, ave_rdc_tensor, dipolar_constant, return_gyromagnetic_ratio, RelaxError, RelaxNoAlignError, RelaxNoRDCError, RelaxNoSequenceError, RelaxSpinTypeError, extract_data, open_write_file, write_data, RelaxWarning


Function Details [hide private]

back_calc(align_id=None)

source code 

Back calculate the RDC from the alignment tensor and unit bond vectors.

Parameters:
  • align_id (str) - The alignment tensor ID string.

check_pipe_setup(pipe=None, rdc_id=None, sequence=False, N=False, tensors=False, rdc=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.
  • rdc_id (None or str) - The RDC ID string to check for in cdp.rdc_ids.
  • sequence (bool) - A flag which when True will invoke the sequence data check.
  • N (bool) - A flag which if True will check that cdp.N is set.
  • tensors (bool) - A flag which if True will check that alignment tensors exist.
  • rdc (bool) - A flag which if True will check that RDCs exist.

convert(value, align_id, to_intern=False)

source code 

Convert the RDC based on the 'D' or '2D' data type.

Parameters:
  • value (float or None) - The value or error to convert.
  • align_id (str) - The alignment tensor ID string.
  • to_intern (bool) - A flag which if True will convert to the internal D notation if needed, or if False will convert from the internal D notation to the external D or 2D format.
Returns: float or None
The converted value.

copy(pipe_from=None, pipe_to=None, align_id=None)

source code 

Copy the RDC data from one data pipe to another.

Parameters:
  • pipe_from (str) - The data pipe to copy the RDC data from. This defaults to the current data pipe.
  • pipe_to (str) - The data pipe to copy the RDC data to. This defaults to the current data pipe.
  • align_id (str) - The alignment ID string.

corr_plot(format=None, file=None, dir=None, force=False)

source code 

Generate a correlation plot of the measured vs. back-calculated RDCs.

Parameters:
  • format (str or None) - The format for the plot file. The following values are accepted: 'grace', a Grace plot; None, a plain text file.
  • 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.

delete(align_id=None)

source code 

Delete the RDC data corresponding to the alignment ID.

Parameters:
  • align_id (str or None) - The alignment tensor ID string. If not specified, all data will be deleted.

display(align_id=None, bc=False)

source code 

Display the RDC data corresponding to the alignment ID.

Parameters:
  • align_id (str) - The alignment tensor ID string.
  • bc (bool) - The back-calculation flag which if True will cause the back-calculated rather than measured data to be displayed.

q_factors(spin_id=None)

source code 

Calculate the Q-factors for the RDC data.

Parameters:
  • spin_id (None or str) - The spin ID string used to restrict the Q-factor calculation to a subset of all spins.

read(align_id=None, file=None, dir=None, file_data=None, data_type='D', spin_id1_col=None, spin_id2_col=None, data_col=None, error_col=None, sep=None, neg_g_corr=False, absolute=False)

source code 

Read the RDC data from file.

Parameters:
  • align_id (str) - The alignment tensor ID string.
  • 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.
  • data_type - A string which is set to 'D' means that the splitting in the aligned sample was assumed to be J + D, or if set to '2D' then the splitting was taken as J + 2D.
  • 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 RDC data in Hz.
  • error_col (int or None) - The column containing the RDC errors.
  • sep (str or None) - The column separator which, if None, defaults to whitespace.
  • neg_g_corr (bool) - A flag which is used to correct for the negative gyromagnetic ratio of 15N. If True, a sign inversion will be applied to all RDC values to be loaded.
  • absolute (bool) - A flag which if True indicates that the RDCs to load are signless. All RDCs will then be converted to positive values.

set_errors(align_id=None, spin_id1=None, spin_id2=None, sd=None)

source code 

Set the RDC errors if not already present.

Parameters:
  • align_id (str) - The optional alignment tensor ID string.
  • spin_id1 (None or str) - The optional spin ID string of the first spin.
  • spin_id2 (None or str) - The optional spin ID string of the second spin.
  • sd (float or int.) - The RDC standard deviation in Hz.

weight(align_id=None, spin_id=None, weight=1.0)

source code 

Set optimisation weights on the RDC data.

Parameters:
  • align_id (str) - The alignment tensor ID string.
  • spin_id (None or str) - The spin ID string.
  • weight (float or int.) - The optimisation weight. The higher the value, the more importance the RDC will have.

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

source code 

Display the RDC data corresponding to the alignment ID.

Parameters:
  • align_id (str) - The alignment tensor ID string.
  • 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).
  • bc (bool) - The back-calculation flag which if True will cause the back-calculated rather than measured data to be written.
  • force (bool) - A flag which if True will cause any pre-existing file to be overwritten.