Re: Octave's and Matlab's limitations

[Dimitri Maziuk]

On 11/21/2012 03:39 PM, c. wrote:
> 
> On 21 Nov 2012, at 22:04, Dimitri Maziuk wrote:
> 
>> It's all fine but how often and how well do you document matrices in
>> your matlab scripts? You can't use "other tools" to convert data to
>> load()'able format if nobody knows what that format is supposed to be.
>
> sorry, I don't think I get the meaning of this sentence, are you 
> asking for 
> matlab file format specification?
> 

I have an input file like this

1 M     HE    2.140
1 M     CE   16.600
2 Q     HA    4.410
...
10 P     HA    4.480
10 P    HB2    1.840
10 P    HB3    2.280
10 P    HG2    2.100
10 P    HG3    2.030
10 P    HD2    3.920
10 P    HD3    3.750
10 P      C  175.850
10 P     CA   62.280
10 P     CB   32.150
10 P     CG   27.400
10 P     CD   51.100
11 A      H    8.500
11 A     HA    3.920
11 A     HB    1.060
11 A     CA   49.600
11 A     CB   16.280
11 A      N  121.750
12 P     HA    4.590
12 P    HB2    1.970
12 P    HB3    1.870

I see that matlab script uses matrix like this:

10 13 62.28   32.15  4.48  175.85  -100.00    -100.00     2.06
11  1 49.60   16.28  3.92 -100.00     8.50     121.75     1.06
12 13 59.90 -100.00  4.59 -100.00  -100.00    -100.00     1.92

-- explain to me how one converts to the other.

What I mean is if it had

% first 9 residues (always 9) are excluded because blah
% residues are mapped to numbers (2nd col) using foo.m
% from 3rd col on: alpha and beta carbon, alpha proton, ...,
% if beta-hydrogen is a methylene group, average of the 2 vals is stored
% missing values are set to -100
% if both alpha an beta carbons are missing, the residue is excluded

That'd be easy. How often do you put something like that in your scripts?

> so, it'd be really nice if you would give Pytave a try, it should allow you
> to run Octave functions from within Octave. If you do try it, I'd be really 
> interested in knowing your impressions.

I don't have any octave code to try (like I said, I only have matlab 7.3
scripts) and anyway pytave is not available from the standard rpm
repositories for redhat 6.

I don't quite see the point: you can always run actual octave in a
popen() call, the advantage of "pytave.eval( 'matlab code' )" over
"os.popen( ['octave', '--eval', 'matlab code'] )" is lost on me -- if
that's what they're trying to do: there seems to be zero documentation
on the site, so who knows.


-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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