Hi,
I have an idea as to how this multi-column formatted file can be
handled. What could be done is simply to expand the scope of the user
function args - increasing the flexibility of relax. The relax_fit and
int_col arguments could be allowed to be lists rather than just a float
and an int. Then you could use:
relax_fit.read(file="generic.txt", dir=sys.path[-1] +
"/test_suite/shared_data/peak_lists", format='generic', int_col=[5, 6,
7], relax_time=[0.0109016, 0.0218032, 0.0436064])
This allows a single file to be read and all data extracted by one user
function call. Of course the argument tests would be more complex. If
one arg is a list, then so must the other be. They must both be the
same size. And the elements of the int_col list must all be integers
and those of relax_time must be floats. This idea is similar to what
the value.set() user function employs. I would highly recommend setting
up unit tests for this argument checking in
test_suite/unit_tests/_prompt/ before even thinking of implementing
this. Alternatively the current user function can be used as is but
just called 10 times, changing the int_col and relax_time args each
time. I think the list args would be the best solution to match how
relax currently operates.
Regards,
Edward
P.S. As another test, maybe the spin name column can be completely
removed to see if the user function can handle missing elements.
On Fri, 2008-10-17 at 18:23 +0000, sebastien.morin.1@xxxxxxxxx wrote:
Author: semor
Date: Fri Oct 17 20:22:59 2008
New Revision: 7799
URL: http://svn.gna.org/viewcvs/relax?rev=7799&view=rev
Log:
Added prototypes for the generic peak intensities file.
Only two files will be needed, instead of one file per delay. The first
file (generic_delay.txt)
will contain the different delays. The second file (generic_intensity.txt)
will contain the peak
intensities.
There may also be a way of including all this information in one single
file... maybe by putting
the delays in the header ? This would be even simpler for the user who
would only need to input 1
single file.
Added:
1.3/test_suite/shared_data/peak_lists/generic_delays.txt
1.3/test_suite/shared_data/peak_lists/generic_intensity.txt
Added: 1.3/test_suite/shared_data/peak_lists/generic_delays.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/generic_delays.txt?rev=7799&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/generic_delays.txt (added)
+++ 1.3/test_suite/shared_data/peak_lists/generic_delays.txt Fri Oct 17
20:22:59 2008
@@ -1,0 +1,10 @@
+intensity_1 0.0109016
+intensity_2 0.0218032
+intensity_3 0.0436064
+intensity_4 0.0436064
+intensity_5 0.0872128
+intensity_6 0.1744260
+intensity_7 0.3488510
+intensity_8 0.6977020
+intensity_9 1.3954000
+intensity_10 1.9949900
Added: 1.3/test_suite/shared_data/peak_lists/generic_intensity.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/generic_intensity.txt?rev=7799&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/generic_intensity.txt (added)
+++ 1.3/test_suite/shared_data/peak_lists/generic_intensity.txt Fri Oct 17
20:22:59 2008
@@ -1,0 +1,7 @@
+mol_name res_num res_name spin_num spin_name intensity_1
intensity_2 intensity_3 intensity_4 intensity_5 intensity_6
intensity_7 intensity_8 intensity_9 intensity_10
+
+None 20 GLY None N 1.0000
0.9714 0.9602 0.9626 0.8839 0.8327
0.7088 0.5098 0.2410 0.1116
+None 23 ALA None N 1.0000
0.9789 0.9751 0.9762 0.9074 0.8532
0.7089 0.5170 0.2444 0.1537
+None 34 CYS None N 1.0000
0.9659 0.9580 0.9559 0.9325 0.8460
0.7187 0.5303 0.2954 0.1683
+None 35 MET None N 1.0000
0.9657 0.9389 0.9366 0.9331 0.8683
0.7169 0.5357 0.2769 0.1625
+None 36 LYS None N 1.0000
1.0060 0.9556 0.9456 0.9077 0.8411
0.6788 0.4558 0.2448 0.1569
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How to handle the generic peak intensity file.