diff options
Diffstat (limited to 'sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch')
| -rw-r--r-- | sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch | 111 |
1 files changed, 111 insertions, 0 deletions
diff --git a/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch b/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch new file mode 100644 index 000000000000..7c82da50aaa0 --- /dev/null +++ b/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch @@ -0,0 +1,111 @@ +--- trunk/sample_scripts/relax_disp/R1rho_analysis.py 2013/11/29 09:40:25 21705 ++++ trunk/sample_scripts/relax_disp/R1rho_analysis.py 2013/11/29 09:42:22 21706 +@@ -58,16 +58,16 @@ + # Set up the data pipe. + ####################### + ++# The path to the data files. ++DATA_PATH = '../../test_suite/shared_data/dispersion/r1rho_off_res_tp02' ++ + # Create the data pipe. + pipe_name = 'base pipe' + pipe_bundle = 'relax_disp' + pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp') + +-# The path to the data files. +-data_path = 'r1rho_off_res_tp02' +- + # Load the sequence. +-sequence.read('fake_sequence.in', res_num_col=1, res_name_col=2) ++sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1, res_name_col=2) + + # Name the spins so they can be matched to the assignments. + spin.name(name='N') +@@ -77,37 +77,37 @@ + + # The spectral data - spectrum ID, peak list file name, spin-lock field strength (Hz), the spin-lock offset (ppm), the relaxation time (s), spectrometer frequency (Hz), and experimental error (RMSD of the base plane noise for each spectrum). + data = [ +- ['ref_500MHz', 'ref_500MHz.list', None, 110.0, 0.1, 500e6, 200000.0] +- ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, 500e6, 200000.0] +- ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, 500e6, 200000.0] +- ['ref_800MHz', 'ref_800MHz.list', None, 110.0, 0.1, 800e6, 200000.0] +- ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6, 200000.0] +- ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6, 200000.0] ++ ['ref_500MHz', 'ref_500MHz.list', None, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, 500e6, 200000.0], ++ ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, 500e6, 200000.0], ++ ['ref_800MHz', 'ref_800MHz.list', None, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6, 200000.0], ++ ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6, 200000.0], + ['nu_6000.0_800MHz', 'nu_6000.0_800MHz.list', 6000.0, 110.0, 0.1, 800e6, 200000.0] + ] + + # Loop over the spectra. + for id, file, field, offset, relax_time, H_frq, rmsd in data: + # Load the peak intensities and set the errors. +- spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id, int_method='height') +- spectrum.baseplane_rmsd(spectrum_id=id, error=error) ++ spectrum.read_intensities(file=file, dir=DATA_PATH, spectrum_id=id, int_method='height') ++ spectrum.baseplane_rmsd(spectrum_id=id, error=rmsd) + + # Set the relaxation dispersion experiment type. + relax_disp.exp_type(spectrum_id=id, exp_type='R1rho') +@@ -125,18 +125,17 @@ + spectrometer.frequency(id=id, frq=H_frq) + + # Load the R1 data. +-relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6, file='R1_500MHz.out', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) +-relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) ++relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6, file='R1_500MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) ++relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) + +-# Clustering. +-relax_disp.cluster(cluster_id='cluster', spin_id=':1-50') ++# Clustering (only to be activated after an initial analysis without clustering). ++#relax_disp.cluster(cluster_id='cluster', spin_id=':1-50') + + # Read the chemical shift data. +-chemical_shift.read(file='ref_500MHz.list', dir=data_path) ++chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH) + + # Deselect unresolved spins. +-deselect.read(file='unresolved', dir='500_MHz', res_num_col=1) +-deselect.read(file='unresolved', dir='800_MHz', res_num_col=1) ++deselect.read(file='unresolved', dir=DATA_PATH, res_num_col=1) + + + |