Re: r26144 - /trunk/test_suite/system_tests/relax_disp.py -- October 06, 2014 - 14:15

Hi Troels,

This will not work as the relaxation dispersion API functions
bmrb_read() and bmrb_write() need to be implemented.  But this will
require discussions with Eldon Ulrich from the BMRB to jointly develop
this (http://thread.gmane.org/gmane.science.nmr.relax.devel/7144/focus=7152).

Regards,

Edward

On 3 October 2014 18:30,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Fri Oct  3 18:30:36 2014
> New Revision: 26144
>
> URL: http://svn.gna.org/viewcvs/relax?rev=26144&view=rev
> Log:
> Added systemtest Relax_disp.test_bmrb_sub_cpmg() to try calling the bmrb 
> functions in relax.
>
> task #7858 (https://gna.org/task/?7858): Make it possible to submit CPMG 
> experiments for BMRB
>
> Modified:
>     trunk/test_suite/system_tests/relax_disp.py
>
> Modified: trunk/test_suite/system_tests/relax_disp.py
> URL: 
> http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=26144&r1=26143&r2=26144&view=diff
> ==============================================================================
> --- trunk/test_suite/system_tests/relax_disp.py (original)
> +++ trunk/test_suite/system_tests/relax_disp.py Fri Oct  3 18:30:36 2014
> @@ -1223,6 +1223,43 @@
>          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].dw, dw_ppm, 6)
>          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].pA, 1-pb, 6)
>          self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].kex, kex, 2)
> +
> +
> +    def test_bmrb_sub_cpmg(self):
> +        """U{Task #7858: <https://gna.org/task/?7858>} Make it possible to 
> submit CPMG experiments for BMRB.
> +        This uses CPMG data from:
> +
> +            Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, 
> Soendergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE
> +            Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, 
> analysis, accuracy, and implications for theoretical pK(a) calculations.
> +            (2011), Proteins: Struct, Funct, Bioinf 79(3):685-702, DOI 
> 10.1002/prot.22886
> +        """
> +
> +        # Define path to data
> +        prev_data_path = status.install_path + 
> sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'HWebb_KTeilum_Proteins_Struct_Funct_Bioinf_2011'
> +
> +        # Read data.
> +        self.interpreter.results.read(prev_data_path + sep + 
> 'FT_-_CR72_-_min_-_128_-_free_spins')
> +
> +        # Set element
> +        self.interpreter.spin.element(element='N', spin_id=':*@N', 
> force=False)
> +        #self.interpreter.spin.isotope(isotope='15N', spin_id=':*@N', 
> force=False)
> +        # Rename molecule from None to 'HEWL'
> +        self.interpreter.molecule.name(mol_id=None, name='HEWL', 
> force=True)
> +        self.interpreter.molecule.type(mol_id='#HEWL', type='protein', 
> force=False)
> +
> +        for cur_spin, mol_name, resi, resn, spin_id in 
> spin_loop(full_info=True, return_id=True, skip_desel=True):
> +            print(spin_id)
> +            if resn == 'C':
> +                print(resi, resn)
> +
> +        # Select the thiol state of the system.
> +        # 'all disulfide bound', 'all free', 'all other bound', 'disulfide 
> and other bound', 'free and disulfide bound', 'free and other bound', 'free 
> disulfide and other bound', 'not available', 'not present', 'not reported', 
> 'unknown'
> +        self.interpreter.bmrb.thiol_state(state='not reported')
> +
> +        # relax_data.temp_calibration(ri_id=None, method=None)
> +
> +        # Call display of bmrb.
> +        self.interpreter.bmrb.display()
>
>
>      def test_bug_21081_disp_cluster_fail(self):
>
>
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