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Re: Octave's and Matlab's limitations
From: |
Dimitri Maziuk |
Subject: |
Re: Octave's and Matlab's limitations |
Date: |
Wed, 21 Nov 2012 16:22:29 -0600 |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:10.0.10) Gecko/20121030 Thunderbird/10.0.10 |
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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- Re: Octave's and Matlab's limitations, (continued)
- Re: Octave's and Matlab's limitations, Sergei Steshenko, 2012/11/22
- Re: Octave's and Matlab's limitations, Kjetil brinchmann Halvorsen, 2012/11/22
- Re: Octave's and Matlab's limitations, Francesco Potortì, 2012/11/22
- Re: Octave's and Matlab's limitations, Freddy López, 2012/11/22
- Re: Octave's and Matlab's limitations, Francesco Potortì, 2012/11/22
- Re: Octave's and Matlab's limitations, Martin Helm, 2012/11/22
- Re: Octave's and Matlab's limitations, Kjetil brinchmann Halvorsen, 2012/11/22
- Re: Octave's and Matlab's limitations, Sergei Steshenko, 2012/11/22
- Re: Octave's and Matlab's limitations, Dimitri Maziuk, 2012/11/21
- Re: Octave's and Matlab's limitations, c., 2012/11/21
- Re: Octave's and Matlab's limitations,
Dimitri Maziuk <=
- Re: Octave's and Matlab's limitations, Jordi Gutiérrez Hermoso, 2012/11/21
- Re: Octave's and Matlab's limitations, Dimitri Maziuk, 2012/11/21
- Re: Octave's and Matlab's limitations, Sergei Steshenko, 2012/11/21
- Re: Octave's and Matlab's limitations, Salva Ardid, 2012/11/21
- Re: Octave's and Matlab's limitations, Francesco Potortì, 2012/11/21