Package generic_fns :: Module pcs
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Module pcs

source code

Module for the manipulation of pseudocontact shift data.

Functions [hide private]
 
back_calc(align_id=None)
Back calculate the PCS from the alignment tensor.
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centre(pos=None, atom_id=None, pipe=None, verbosity=1, ave_pos=False, force=False)
Specify the atom in the loaded structure corresponding to the paramagnetic centre.
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corr_plot(format=None, file=None, dir=None, force=False)
Generate a correlation plot of the measured vs.
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delete(align_id=None)
Delete the PCS data corresponding to the alignment ID.
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display(align_id=None, bc=False)
Display the PCS data corresponding to the alignment ID.
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q_factors(spin_id=None)
Calculate the Q-factors for the PCS data.
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read(align_id=None, file=None, dir=None, file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None)
Read the PCS data from file.
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weight(align_id=None, spin_id=None, weight=1.0)
Set optimisation weights on the PCS data.
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write(align_id=None, file=None, dir=None, bc=False, force=False)
Display the PCS data corresponding to the alignment ID.
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Variables [hide private]
  __package__ = 'generic_fns'

Imports: deepcopy, pi, sqrt, array, float64, ones, zeros, norm, sys, warn, grace, pipes, get_tensor_index, exists_mol_res_spin_data, return_spin, spin_loop, ave_pcs_tensor, g1H, pcs_constant, RelaxError, RelaxNoPdbError, RelaxNoSequenceError, open_write_file, read_spin_data, write_spin_data, RelaxWarning, RelaxNoSpinWarning


Function Details [hide private]

back_calc(align_id=None)

source code 

Back calculate the PCS from the alignment tensor.

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

centre(pos=None, atom_id=None, pipe=None, verbosity=1, ave_pos=False, force=False)

source code 

Specify the atom in the loaded structure corresponding to the paramagnetic centre.

Parameters:
  • pos (list of float) - The atomic position. If set, the atom_id string will be ignored.
  • atom_id (str) - The atom identification string.
  • pipe (None or str) - An alternative data pipe to extract the paramagnetic centre from.
  • verbosity (int) - The amount of information to print out. The bigger the number, the more information.
  • ave_pos (bool) - A flag which if True causes the atomic positions from multiple models to be averaged.
  • force - A flag which if True will cause the current PCS centre to be overwritten.

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

source code 

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

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 PCS 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 PCS 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 PCS 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, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None)

source code 

Read the PCS 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 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_id_col (int or None) - The column containing the spin ID strings. If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
  • mol_name_col (int or None) - The column containing the molecule name information. If supplied, spin_id_col must be None.
  • res_name_col (int or None) - The column containing the residue name information. If supplied, spin_id_col must be None.
  • res_num_col (int or None) - The column containing the residue number information. If supplied, spin_id_col must be None.
  • spin_name_col (int or None) - The column containing the spin name information. If supplied, spin_id_col must be None.
  • spin_num_col (int or None) - The column containing the spin number information. If supplied, spin_id_col must be None.
  • data_col (int or None) - The column containing the PCS data in Hz.
  • error_col (int or None) - The column containing the PCS errors.
  • sep (str or None) - The column separator which, if None, defaults to whitespace.
  • spin_id (None or str) - The spin ID string used to restrict data loading to a subset of all spins.

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

source code 

Set optimisation weights on the PCS 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 PCS will have.

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

source code 

Display the PCS 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.