Class Relax_data

Class for manipulating R1, R2, and NOE relaxation data.

Instance Methods

back_calc(self, ri_id=None, ri_type=None, frq=None)
Back calculate the relaxation data at the given frequency.

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

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

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

peak_intensity_type(self, ri_id=None, type=None)
Specify the type of peak intensity measurement used - i.e.

read(self, ri_id=None, ri_type=None, frq=None, file=None, dir=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 relaxation data from a file.

temp_calibration(self, ri_id=None, method=None)
Specify the temperature calibration method used.

temp_control(self, ri_id=None, method=None)
Specify the temperature control method used.

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

Inherited from base_class.User_fn_class: __init__

Method Details

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

Back calculate the relaxation data at the given frequency.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.

ri_type:  The relaxation data type, ie 'R1', 'R2', or 'NOE'.

frq:  The spectrometer frequency in Hz.


Description
~~~~~~~~~~~

This allows relaxation data of the given type and frequency to be back calculated from the model
parameter values.

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

Copy relaxation data from one pipe to another.

Keyword Arguments
~~~~~~~~~~~~~~~~~

pipe_from:  The name of the pipe to copy the relaxation data from.

pipe_to:  The name of the pipe to copy the relaxation data to.

ri_id:  The relaxation data ID string.


Description
~~~~~~~~~~~

This will copy relaxation data from one data pipe to another.  If the relaxation ID data string is
not given then all relaxation data will be copied, otherwise only a specific data set will be
copied.


Examples
~~~~~~~~

To copy all relaxation data from pipe 'm1' to pipe 'm9', type one of:

relax> relax_data.copy('m1', 'm9')
relax> relax_data.copy(pipe_from='m1', pipe_to='m9')
relax> relax_data.copy('m1', 'm9', None)
relax> relax_data.copy(pipe_from='m1', pipe_to='m9', ri_id=None)

To copy only the NOE relaxation data with the ID string of 'NOE_800' from 'm3' to 'm6', type
one of:

relax> relax_data.copy('m3', 'm6', 'NOE_800')
relax> relax_data.copy(pipe_from='m3', pipe_to='m6', ri_id='NOE_800')

delete(self, ri_id=None)

Delete the data corresponding to the relaxation data ID string.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.


Description
~~~~~~~~~~~

The relaxation data corresponding to the given relaxation data ID string will be removed from the
current data pipe.


Examples
~~~~~~~~

To delete the relaxation data corresponding to the ID 'NOE_600', type:

relax> relax_data.delete('NOE_600')

display(self, ri_id=None)

Display the data corresponding to the relaxation data ID string.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.



Examples
~~~~~~~~

To display the NOE relaxation data at 600 MHz with the ID string 'NOE_600', type:

relax> relax_data.display('NOE_600')

peak_intensity_type(self, ri_id=None, type=None)

Specify the type of peak intensity measurement used - i.e. height or volume.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.

type:  The peak intensity type.


Description
~~~~~~~~~~~

This is essential for BMRB data deposition.  It is used to specify whether peak heights or peak
volumes were measured.  The two currently allowed values for the type argument are 'height' and
'volume'.

read(self, ri_id=None, ri_type=None, frq=None, file=None, dir=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 relaxation data from a file.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.  This must be a unique identifier.

ri_type:  The relaxation data type, i.e. 'R1', 'R2', or 'NOE'.

frq:  The exact proton frequency of the spectrometer in Hertz.  See the 'sfrq' parameter in the
Varian procpar file or the 'SFO1' parameter in the Bruker acqus file.

file:  The name of the file containing the relaxation data.

dir:  The directory where the file is located.

spin_id_col:  The spin ID string column (an alternative to the mol, res, and spin name and number
columns).

mol_name_col:  The molecule name column (alternative to the spin_id_col).

res_num_col:  The residue number column (alternative to the spin_id_col).

res_name_col:  The residue name column (alternative to the spin_id_col).

spin_num_col:  The spin number column (alternative to the spin_id_col).

spin_name_col:  The spin name column (alternative to the spin_id_col).

data_col:  The relaxation data column.

error_col:  The experimental error column.

sep:  The column separator (the default is white space).

spin_id:  The spin ID string to restrict the loading of data to certain spin subsets.


Description
~~~~~~~~~~~

The spin system can be identified in the file using two different formats.  The first is the spin ID
string column which can include the molecule name, the residue name and number, and the spin name
and number.  Alternatively the molecule name, residue number, residue name, spin number and/or spin
name columns can be supplied allowing this information to be in separate columns.  Note that the
numbering of columns starts at one.  The spin ID string can be used to restrict the reading to
certain spin types, for example only 15N spins when only residue information is in the file.


Examples
~~~~~~~~

The following commands will read the protein NOE relaxation data collected at 600 MHz out of
a file called 'noe.600.out' where the residue numbers, residue names, data, errors are in
the first, second, third, and forth columns respectively.

relax> relax_data.read('NOE_600', 'NOE', 599.7 * 1e6, 'noe.600.out', res_num_col=1,
                       res_name_col=2, data_col=3, error_col=4)
relax> relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0 * 1e6, file='noe.600.out',
                       res_num_col=1, res_name_col=2, data_col=3, error_col=4)


The following commands will read the R2 data out of the file 'r2.out' where the residue
numbers, residue names, data, errors are in the second, third, fifth, and sixth columns
respectively.  The columns are separated by commas.

relax> relax_data.read('R2_800', 'R2', 8.0 * 1e8, 'r2.out', res_num_col=2, res_name_col=3,
                       data_col=5, error_col=6, sep=',')
relax> relax_data.read(ri_id='R2_800', ri_type='R2', frq=8.0*1e8, file='r2.out',
                       res_num_col=2, res_name_col=3, data_col=5, error_col=6, sep=',')


The following commands will read the R1 data out of the file 'r1.out' where the columns are
separated by the symbol '%'

relax> relax_data.read('R1_300', 'R1', 300.1 * 1e6, 'r1.out', sep='%')

temp_calibration(self, ri_id=None, method=None)

Specify the temperature calibration method used.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.

method:  The calibration method.


Description
~~~~~~~~~~~

This is essential for BMRB data deposition.  The currently allowed methods are:

    'methanol',
    'monoethylene glycol',
    'no calibration applied'.

Other strings will be accepted if supplied.

temp_control(self, ri_id=None, method=None)

Specify the temperature control method used.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.

method:  The control method.


Description
~~~~~~~~~~~

This is essential for BMRB data deposition.  The currently allowed methods are:

    'single scan interleaving',
    'temperature compensation block',
    'single scan interleaving and temperature compensation block',
    'single fid interleaving',
    'single experiment interleaving',
    'no temperature control applied'.

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

Write relaxation data to a file.

Keyword Arguments
~~~~~~~~~~~~~~~~~

ri_id:  The relaxation data ID string.

file:  The name of the file.

dir:  The directory name.

force:  A flag which if True will cause the file to be overwritten.


Description
~~~~~~~~~~~

If no directory name is given, the file will be placed in the current working directory.  The
relaxation data ID string is required for selecting which relaxation data to write to file.