Re: r9650 - /1.3/sample_scripts/ -- October 07, 2009 - 22:21

Seb,

Thanks for picking these up.  I'd forgotten that these would need to be 
updated!

Cheers,

Edward


2009/10/7  <sebastien.morin.1@xxxxxxxxx>:
> Author: semor
> Date: Wed Oct  7 20:37:57 2009
> New Revision: 9650
>
> URL: http://svn.gna.org/viewcvs/relax?rev=9650&view=rev
> Log:
>
> Modified the relax_data.read() entries in order to reflect the new design.
>
> The relax_data.read() function now absolutely needs arguments for 
> 'res_num_col', 'data_col' and
> 'error_col'. Hence, this argument is now shown in the sample script in 
> order to avoid the users
> lose time figuring out where their script went bad...
>
>
> Modified:
>    1.3/sample_scripts/consistency_tests.py
>    1.3/sample_scripts/dasha.py
>    1.3/sample_scripts/diff_min.py
>    1.3/sample_scripts/jw_mapping.py
>    1.3/sample_scripts/map.py
>    1.3/sample_scripts/mf_multimodel.py
>    1.3/sample_scripts/model-free.py
>    1.3/sample_scripts/palmer.py
>    1.3/sample_scripts/remap.py
>
> Modified: 1.3/sample_scripts/consistency_tests.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/consistency_tests.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/consistency_tests.py (original)
> +++ 1.3/sample_scripts/consistency_tests.py Wed Oct  7 20:37:57 2009
> @@ -31,9 +31,9 @@
>  sequence.read('noe.600.out', res_num_col=1)
>
>  # Load the relaxation data.
> -relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
> -relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
> -relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
> +relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out', res_num_col=1, 
> data_col=3, error_col=4)
>
>  # Set the nuclei types
>  value.set('15N', 'heteronucleus')
>
> Modified: 1.3/sample_scripts/dasha.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/dasha.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/dasha.py (original)
> +++ 1.3/sample_scripts/dasha.py Wed Oct  7 20:37:57 2009
> @@ -19,12 +19,12 @@
>     #structure.read_pdb('example.pdb')
>
>     # Load the relaxation data.
> -    relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
> -    relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
> -    relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
> -    relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out')
> -    relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out')
> -    relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out')
> +    relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +    relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out', 
> res_num_col=1, data_col=3, error_col=4)
>
>     # Setup other values.
>     diffusion_tensor.init(10e-9, fixed=1)
>
> Modified: 1.3/sample_scripts/diff_min.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/diff_min.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/diff_min.py (original)
> +++ 1.3/sample_scripts/diff_min.py Wed Oct  7 20:37:57 2009
> @@ -25,12 +25,12 @@
>     structure.read_pdb('example.pdb')
>
>     # Load the relaxation data.
> -    relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
> -    relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
> -    relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
> -    relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out')
> -    relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out')
> -    relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out')
> +    relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +    relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out', 
> res_num_col=1, data_col=3, error_col=4)
>
>     # Setup other values.
>     diffusion_tensor.init((1e-8, 1.0, 60, 290), param_types=1, 
> spheroid_type='oblate', fixed=1)
>
> Modified: 1.3/sample_scripts/jw_mapping.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/jw_mapping.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/jw_mapping.py (original)
> +++ 1.3/sample_scripts/jw_mapping.py Wed Oct  7 20:37:57 2009
> @@ -7,9 +7,9 @@
>  sequence.read('noe.600.out', res_num_col=1)
>
>  # Load the relaxation data.
> -relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
> -relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
> -relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
> +relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out', res_num_col=1, 
> data_col=3, error_col=4)
>
>  # Set the nuclei types.
>  value.set('15N', 'heteronucleus')
>
> Modified: 1.3/sample_scripts/map.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/map.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/map.py (original)
> +++ 1.3/sample_scripts/map.py Wed Oct  7 20:37:57 2009
> @@ -11,12 +11,12 @@
>  sequence.read(name, 'noe.500.out', res_num_col=1)
>
>  # Load the relaxation data.
> -relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
> -relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'r2.600.out')
> -relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'noe.600.out')
> -relax_data.read(name, 'R1', '500', 500.0 * 1e6, 'r1.500.out')
> -relax_data.read(name, 'R2', '500', 500.0 * 1e6, 'r2.500.out')
> -relax_data.read(name, 'NOE', '500', 500.0 * 1e6, 'noe.500.out')
> +relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'r2.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'noe.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'R1', '500', 500.0 * 1e6, 'r1.500.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'R2', '500', 500.0 * 1e6, 'r2.500.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'NOE', '500', 500.0 * 1e6, 'noe.500.out', 
> res_num_col=1, data_col=3, error_col=4)
>
>  # Setup other values.
>  diffusion_tensor.init(name, 1e-8)
>
> Modified: 1.3/sample_scripts/mf_multimodel.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/mf_multimodel.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/mf_multimodel.py (original)
> +++ 1.3/sample_scripts/mf_multimodel.py Wed Oct  7 20:37:57 2009
> @@ -39,12 +39,12 @@
>     #structure.read_pdb('example.pdb')
>
>     # Load the relaxation data.
> -    relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
> -    relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
> -    relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
> -    relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out')
> -    relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out')
> -    relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out')
> +    relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +    relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +    relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out', 
> res_num_col=1, data_col=3, error_col=4)
>
>     # Setup other values.
>     diffusion_tensor.init(1e-8, fixed=True)
>
> Modified: 1.3/sample_scripts/model-free.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model-free.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/model-free.py (original)
> +++ 1.3/sample_scripts/model-free.py Wed Oct  7 20:37:57 2009
> @@ -34,12 +34,12 @@
>  #structure.read_pdb('example.pdb')
>
>  # Load the relaxation data.
> -relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
> -relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
> -relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
> -relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out')
> -relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out')
> -relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out')
> +relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out', res_num_col=1, 
> data_col=3, error_col=4)
> +relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out', res_num_col=1, 
> data_col=3, error_col=4)
>
>  # Setup other values.
>  diffusion_tensor.init(10e-9, fixed=True)
>
> Modified: 1.3/sample_scripts/palmer.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/palmer.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/palmer.py (original)
> +++ 1.3/sample_scripts/palmer.py Wed Oct  7 20:37:57 2009
> @@ -55,12 +55,12 @@
>         #structure.read_pdb('Ap4Aase_new_3.pdb')
>
>         # Load the relaxation data.
> -        relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
> -        relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
> -        relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
> -        relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out')
> -        relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out')
> -        relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out')
> +        relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +        relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +        relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +        relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out', 
> res_num_col=1, data_col=3, error_col=4)
> +        relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out', 
> res_num_col=1, data_col=3, error_col=4)
> +        relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out', 
> res_num_col=1, data_col=3, error_col=4)
>
>         # Setup other values.
>         diffusion_tensor.init(1e-8)
>
> Modified: 1.3/sample_scripts/remap.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/remap.py?rev=9650&r1=9649&r2=9650&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/remap.py (original)
> +++ 1.3/sample_scripts/remap.py Wed Oct  7 20:37:57 2009
> @@ -35,12 +35,12 @@
>  sequence.read(name, 'noe.500.out', res_num_col=1)
>
>  # Load the relaxation data.
> -relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
> -relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'r2.600.out')
> -relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'noe.600.out')
> -relax_data.read(name, 'R1', '500', 500.0 * 1e6, 'r1.500.out')
> -relax_data.read(name, 'R2', '500', 500.0 * 1e6, 'r2.500.out')
> -relax_data.read(name, 'NOE', '500', 500.0 * 1e6, 'noe.500.out')
> +relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'r2.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'noe.600.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'R1', '500', 500.0 * 1e6, 'r1.500.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'R2', '500', 500.0 * 1e6, 'r2.500.out', 
> res_num_col=1, data_col=3, error_col=4)
> +relax_data.read(name, 'NOE', '500', 500.0 * 1e6, 'noe.500.out', 
> res_num_col=1, data_col=3, error_col=4)
>
>  # Setup other values.
>  diffusion_tensor.init(name, 1e-8)
>
>
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