Module relax_data

Module for the manipulation of relaxation data.

Functions

back_calc(ri_id=None, ri_type=None, frq=None)
Back calculate the relaxation data.

bmrb_read(star, sample_conditions=None)
Read the relaxation data from the NMR-STAR dictionary object.

bmrb_write(star)
Generate the relaxation data saveframes for the NMR-STAR dictionary object.

copy(pipe_from=None, pipe_to=None, ri_id=None)
Copy the relaxation data from one data pipe to another.

str create_frq_label(frq)
Generate a frequency label in MHz, rounded to the nearest factor of 10.

delete(ri_id=None)
Delete relaxation data corresponding to the relaxation data ID.

display(ri_id=None)
Display relaxation data corresponding to the ID.

list of str get_data_names(global_flag=False, sim_names=False)
Return a list of names of data structures associated with relaxation data.

list of str get_ids()
Return the list of all relaxation data IDs.

pack_data(ri_id, ri_type, frq, values, errors, spin_ids=None, mol_names=None, res_nums=None, res_names=None, spin_nums=None, spin_names=None, spin_id=None, gen_seq=False, verbose=True)
Pack the relaxation data into the data pipe and spin containers.

peak_intensity_type(ri_id=None, type=None)
Set the type of intensity measured for the peaks.

read(ri_id=None, ri_type=None, frq=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 R1, R2, or NOE, or R2eff relaxation data from a file.

return_data_desc(name)
Return a description of the spin specific object.

return_value(spin, data_type, bc=False)
Return the value and error corresponding to 'data_type'.

temp_calibration(ri_id=None, method=None)
Set the temperature calibration method.

temp_control(ri_id=None, method=None)
Set the temperature control method.

type(ri_id=None, ri_type=None)
Set or reset the frequency associated with the ID.

write(ri_id=None, file=None, dir=None, bc=False, force=False)
Write relaxation data to a file.

Variables

ds = The relax data storage obje...

VALID_TYPES = ['R1', 'R2', 'NOE', 'R2eff']

__package__ = 'pipe_control'

Imports: int32, ones, zeros, string, sys, warn, Relax_data_store, ExpInfo, RelaxError, RelaxMultiSpinIDError, RelaxNoRiError, RelaxNoSequenceError, RelaxNoSpinError, RelaxRiError, write_data, element_from_isotope, number_from_isotope, read_spin_data, RelaxWarning, bmrb, pipes, value, define_dipole_pair, return_interatom, return_interatom_list, Selection, exists_mol_res_spin_data, find_index, generate_spin_id_unique, get_molecule_names, return_spin, return_spin_from_selection, spin_index_loop, spin_loop, check_pipe, copy_frequencies, delete_frequencies, frequency_checks, loop_frequencies, set_frequency, return_api

Function Details

back_calc(ri_id=None, ri_type=None, frq=None)

Back calculate the relaxation data.

If no relaxation data currently exists, then the ri_id, ri_type, and frq args are required.

Parameters:

• ri_id (None or str) - The relaxation data ID string. If not given, all relaxation data will be back calculated.
• ri_type (None or str) - The relaxation data type. This should be one of 'R1', 'R2', or 'NOE'.
• frq (None or float) - The spectrometer proton frequency in Hz.

bmrb_read(star, sample_conditions=None)

Read the relaxation data from the NMR-STAR dictionary object.

Parameters:

• star (NMR_STAR instance) - The NMR-STAR dictionary object.
• sample_conditions (None or str) - The sample condition label to read. Only one sample condition can be read per data pipe.

bmrb_write(star)

Generate the relaxation data saveframes for the NMR-STAR dictionary object.

Parameters:

• star (NMR_STAR instance) - The NMR-STAR dictionary object.

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

Copy the relaxation data from one data pipe to another.

Parameters:

• pipe_from (str) - The data pipe to copy the relaxation data from. This defaults to the current data pipe.
• pipe_to (str) - The data pipe to copy the relaxation data to. This defaults to the current data pipe.
• ri_id (str) - The relaxation data ID string.

create_frq_label(frq)

Generate a frequency label in MHz, rounded to the nearest factor of 10.

Parameters:

• frq (float) - The frequency in Hz.

Returns: str

The MHz frequency label.

delete(ri_id=None)

Delete relaxation data corresponding to the relaxation data ID.

Parameters:

• ri_id (str) - The relaxation data ID string.

display(ri_id=None)

Display relaxation data corresponding to the ID.

Parameters:

• ri_id (str) - The relaxation data ID string.

get_data_names(global_flag=False, sim_names=False)

Return a list of names of data structures associated with relaxation data.

Description

The names are as follows:

ri_data: Relaxation data.

ri_data_err: Relaxation data error.

ri_data_bc: The back calculated relaxation data.

ri_type: The relaxation data type, i.e. one of ['NOE', 'R1', 'R2']

frq: NMR frequencies in Hz, eg [600.0 * 1e6, 500.0 * 1e6]

Parameters:

• global_flag (bool) - A flag which if True corresponds to the pipe specific data structures and if False corresponds to the spin specific data structures.
• sim_names (bool) - A flag which if True will add the Monte Carlo simulation object names as well.

Returns: list of str

The list of object names.

get_ids()

Return the list of all relaxation data IDs.

Returns: list of str

The list of all relaxation data IDs.

pack_data(ri_id, ri_type, frq, values, errors, spin_ids=None, mol_names=None, res_nums=None, res_names=None, spin_nums=None, spin_names=None, spin_id=None, gen_seq=False, verbose=True)

Pack the relaxation data into the data pipe and spin containers.

The values, errors, and spin_ids arguments must be lists of equal length or None. Each element i corresponds to a unique spin.

Parameters:

• ri_id (str) - The relaxation data ID string.
• ri_type (str) - The relaxation data type, ie 'R1', 'R2', or 'NOE'.
• frq (float) - The spectrometer proton frequency in Hz.
• values (None or list of float or float array) - The relaxation data for each spin.
• errors (None or list of float or float array) - The relaxation data errors for each spin.
• spin_ids (None or list of str) - The list of spin ID strings. If the other spin identifiers are given, i.e. mol_names, res_nums, res_names, spin_nums, and/or spin_names, then this argument is not necessary.
• mol_names (None or list of str) - The list of molecule names used for creating the spin IDs (if not given) or for generating the sequence data.
• res_nums (None or list of str) - The list of residue numbers used for creating the spin IDs (if not given) or for generating the sequence data.
• res_names (None or list of str) - The list of residue names used for creating the spin IDs (if not given) or for generating the sequence data.
• spin_nums (None or list of str) - The list of spin numbers used for creating the spin IDs (if not given) or for generating the sequence data.
• spin_names (None or list of str) - The list of spin names used for creating the spin IDs (if not given) or for generating the sequence data.
• gen_seq (bool) - A flag which if True will cause the molecule, residue, and spin sequence data to be generated.
• verbose (bool) - A flag which if True will cause all relaxation data loaded to be printed out.

peak_intensity_type(ri_id=None, type=None)

Set the type of intensity measured for the peaks.

Parameters:

• ri_id (str) - The relaxation data ID string.
• type (str) - The peak intensity type, one of 'height' or 'volume'.

read(ri_id=None, ri_type=None, frq=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 R1, R2, or NOE, or R2eff relaxation data from a file.

Parameters:

• ri_id (str) - The relaxation data ID string.
• ri_type (str) - The relaxation data type, ie 'R1', 'R2', 'NOE', or 'R2eff'.
• frq (float) - The spectrometer proton frequency in Hz.
• 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 relaxation data.
• error_col (int or None) - The column containing the relaxation data 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.

return_data_desc(name)

Return a description of the spin specific object.

Parameters:

• name (str) - The name of the spin specific object.

return_value(spin, data_type, bc=False)

Return the value and error corresponding to 'data_type'.

Parameters:

• spin (SpinContainer instance) - The spin container.
• data_type (str) - The relaxation data ID string.
• bc (bool) - A flag which if True will cause the back calculated relaxation data to be written.

temp_calibration(ri_id=None, method=None)

Set the temperature calibration method.

Parameters:

• ri_id (str) - The relaxation data type, ie 'R1', 'R2', or 'NOE'.
• method (str) - The temperature calibration method.

temp_control(ri_id=None, method=None)

Set the temperature control method.

Parameters:

• ri_id (str) - The relaxation data ID string.
• method (str) - The temperature control method.

type(ri_id=None, ri_type=None)

Set or reset the frequency associated with the ID.

Parameters:

• ri_id (str) - The relaxation data ID string.
• ri_type (str) - The relaxation data type, ie 'R1', 'R2', or 'NOE'.

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

Write relaxation data to a file.

Parameters:

• ri_id (str) - The relaxation data ID string.
• file (str) - The name of the file to create.
• dir (str or None) - The directory to write to.
• bc (bool) - A flag which if True will cause the back calculated relaxation data to be written.
• force (bool) - A flag which if True will cause any pre-existing file to be overwritten.

Variables Details

ds

Value:

The relax data storage object.

Data pipes:
  None

Data store objects:
  __dict__ <type 'dict'>: dict() -> new empty dictionary
  __doc__ <type 'str'>: The relax data storage object.
...