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Class for handling residual dipolar coulpings.
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Inherited from |
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Back calculate RDCs. Keyword Arguments ~~~~~~~~~~~~~~~~~ align_id: The alignment ID string. |
Calculate the RDC Q-factor for the selected spins.
Keyword Arguments
~~~~~~~~~~~~~~~~~
spin_id: The spin ID string for restricting to subset of all selected spins.
Description
~~~~~~~~~~~
For this function to work, the back-calculated RDC data must first be generated by the
analysis specific code. Otherwise a warning will be given.
Examples
~~~~~~~~
To calculate the RDC Q-factor for only the spins '@H26', '@H27', and '@H28', type one of:
relax> rdc.calc_q_factors('@H26 & @H27 & @H28')
relax> rdc.calc_q_factors(spin_id='@H26 & @H27 & @H28')
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Copy RDC data from pipe_from to pipe_to.
Keyword Arguments
~~~~~~~~~~~~~~~~~
pipe_from: The name of the pipe to copy the RDC data from.
pipe_to: The name of the pipe to copy the RDC data to.
align_id: The alignment ID string.
Description
~~~~~~~~~~~
This function will copy RDC data from 'pipe_from' to 'pipe_to'. If align_id is not given
then all RDC data will be copied, otherwise only a specific data set will be.
Examples
~~~~~~~~
To copy all RDC data from pipe 'm1' to pipe 'm9', type one of:
relax> rdc.copy('m1', 'm9')
relax> rdc.copy(pipe_from='m1', pipe_to='m9')
relax> rdc.copy('m1', 'm9', None)
relax> rdc.copy(pipe_from='m1', pipe_to='m9', align_id=None)
To copy only the 'Th' RDC data from 'm3' to 'm6', type one of:
relax> rdc.copy('m3', 'm6', 'Th')
relax> rdc.copy(pipe_from='m3', pipe_to='m6', align_id='Th')
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Generate a correlation plot of the measured vs. the back-calculated RDCs. Keyword Arguments ~~~~~~~~~~~~~~~~~ format: The format of the plot data. file: The name of the file. dir: The directory name. force: A flag which if True will cause the file to be overwritten. Description ~~~~~~~~~~~ Two formats are currently supported. If format is set to 'grace', then a Grace plot file will be created. If the format arg is set to None, then a plain text list of the measured and back-calculated data will be created. Examples ~~~~~~~~ To create a Grace plot of the data, type: relax> rdc.corr_plot() To create a plain text list of the measured and back-calculated data, type one of: relax> rdc.corr_plot(None) relax> rdc.corr_plot(format=None) |
Delete the RDC data corresponding to the alignment ID.
Keyword Arguments
~~~~~~~~~~~~~~~~~
align_id: The alignment ID string.
Examples
~~~~~~~~
To delete the RDC data corresponding to align_id='PH_gel', type:
relax> rdc.delete('PH_gel')
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Display the RDC data corresponding to the alignment ID.
Keyword Arguments
~~~~~~~~~~~~~~~~~
align_id: The alignment ID string.
bc: A flag which if set will display the back-calculated rather than measured RDCs.
Examples
~~~~~~~~
To display the 'phage' RDC data, type:
relax> rdc.display('phage')
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Read the RDC data from file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
align_id: The alignment ID string.
file: The name of the file containing the RDC data.
dir: The directory where the file is located.
data_type: Whether the RDC data is in the D or 2D format.
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 RDC 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.
neg_g_corr: A flag which is used to correct for the negative gyromagnetic ratio of 15N.
Description
~~~~~~~~~~~
The data_type argument is used to specify how the RDC is defined. It is a string which can
be set to two values:
- 'D' means that the splitting in the aligned sample was taken as J + D.
- '2D' means that the splitting in the aligned sample was assumed to be J + 2D.
Internally, relax uses the D notation. Therefore if set to '2D', the values will be doubled
when read in.
If neg_g_corr is set to True, a sign inversion will be applied to all RDC values to be
loaded. This is sometimes needed for 15N if the data is not compensated for the negative
gyromagnetic ratio.
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 mol_name_col, res_num_col, res_name_col,
spin_num_col, and/or spin_name_col arguments can be supplied allowing this information to be
in separate columns. Note that the numbering of columns starts at one. The spin_id
argument 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 RDC data out of the file 'Tb.txt' where the columns are
separated by the symbol ',', and store the RDCs under the ID 'Tb':
relax> rdc.read('Tb', 'Tb.txt', sep=',')
If the individual spin RDC errors are located in the file 'rdc_err.txt' in column number 5,
then to read these values into relax, assuming J + D was measured, type one of:
relax> rdc.read('phage', 'rdc_err.txt', data_type='D', error_col=5)
relax> rdc.read(align_id='phage', file='rdc_err.txt', data_type='D', error_col=5)
If the RDCs correspond to the 'N' spin and other spin types such as 1H, 13C, etc. are loaded
into relax, then type:
relax> rdc.read('Tb', 'Tb.txt', spin_id='@N')
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Set optimisation weights on the RDC data. Keyword Arguments ~~~~~~~~~~~~~~~~~ align_id: The alignment ID string. spin_id: The spin ID string. weight: The weighting value. Description ~~~~~~~~~~~ This function can be used to force the RDC to contribute more or less to the chi-squared optimisation statistic. The higher the value, the more importance the RDC will have. |
Write the RDC data to file. Keyword Arguments ~~~~~~~~~~~~~~~~~ align_id: The alignment ID string. file: The name of the file. dir: The directory name. bc: A flag which if set will write out the back-calculated rather than measured RDCs. 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 'align_id' argument are required for selecting which RDC data set will be written to file. |
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