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jlec 13/11/29 10:58:25 |
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|
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Added: relax-3.1.0-sample-script-backport.patch |
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Log: |
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sci-chemistry/relax: Add another backport for sample scripts; add live ebuild |
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|
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(Portage version: 2.2.7/cvs/Linux x86_64, RepoMan options: --force, signed Manifest commit with key B9D4F231BD1558AB!) |
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|
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Revision Changes Path |
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1.1 sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/relax/files/relax-3.1.0-sample-script-backport.patch?rev=1.1&content-type=text/plain |
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|
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Index: relax-3.1.0-sample-script-backport.patch |
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=================================================================== |
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--- trunk/sample_scripts/relax_disp/R1rho_analysis.py 2013/11/29 09:40:25 21705 |
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+++ trunk/sample_scripts/relax_disp/R1rho_analysis.py 2013/11/29 09:42:22 21706 |
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@@ -58,16 +58,16 @@ |
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# Set up the data pipe. |
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####################### |
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|
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+# The path to the data files. |
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+DATA_PATH = '../../test_suite/shared_data/dispersion/r1rho_off_res_tp02' |
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+ |
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# Create the data pipe. |
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pipe_name = 'base pipe' |
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pipe_bundle = 'relax_disp' |
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pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp') |
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|
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-# The path to the data files. |
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-data_path = 'r1rho_off_res_tp02' |
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- |
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# Load the sequence. |
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-sequence.read('fake_sequence.in', res_num_col=1, res_name_col=2) |
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+sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1, res_name_col=2) |
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|
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# Name the spins so they can be matched to the assignments. |
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spin.name(name='N') |
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@@ -77,37 +77,37 @@ |
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|
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# 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). |
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data = [ |
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- ['ref_500MHz', 'ref_500MHz.list', None, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, 500e6, 200000.0] |
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- ['ref_800MHz', 'ref_800MHz.list', None, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6, 200000.0] |
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- ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6, 200000.0] |
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+ ['ref_500MHz', 'ref_500MHz.list', None, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, 500e6, 200000.0], |
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+ ['ref_800MHz', 'ref_800MHz.list', None, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6, 200000.0], |
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+ ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6, 200000.0], |
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['nu_6000.0_800MHz', 'nu_6000.0_800MHz.list', 6000.0, 110.0, 0.1, 800e6, 200000.0] |
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] |
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|
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# Loop over the spectra. |
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for id, file, field, offset, relax_time, H_frq, rmsd in data: |
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# Load the peak intensities and set the errors. |
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- spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id, int_method='height') |
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- spectrum.baseplane_rmsd(spectrum_id=id, error=error) |
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+ spectrum.read_intensities(file=file, dir=DATA_PATH, spectrum_id=id, int_method='height') |
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+ spectrum.baseplane_rmsd(spectrum_id=id, error=rmsd) |
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|
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# Set the relaxation dispersion experiment type. |
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relax_disp.exp_type(spectrum_id=id, exp_type='R1rho') |
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@@ -125,18 +125,17 @@ |
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spectrometer.frequency(id=id, frq=H_frq) |
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|
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# Load the R1 data. |
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-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) |
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-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) |
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+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) |
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+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) |
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|
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-# Clustering. |
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-relax_disp.cluster(cluster_id='cluster', spin_id=':1-50') |
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+# Clustering (only to be activated after an initial analysis without clustering). |
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+#relax_disp.cluster(cluster_id='cluster', spin_id=':1-50') |
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|
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# Read the chemical shift data. |
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-chemical_shift.read(file='ref_500MHz.list', dir=data_path) |
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+chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH) |
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|
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# Deselect unresolved spins. |
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-deselect.read(file='unresolved', dir='500_MHz', res_num_col=1) |
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-deselect.read(file='unresolved', dir='800_MHz', res_num_col=1) |
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+deselect.read(file='unresolved', dir=DATA_PATH, res_num_col=1) |
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