Hi,
This patch (patch_consistency_tests__l1.2_r3342) adds missing lines for
variables 'orientation' and 'tc' in the 'specific_fnx/consistency_tests.py'
and
'test_suite/consistency.py' files. The consistency_tests code was inspired by
the jw_mapping code and, at some places, only the two variables 'r' and 'csa'
were present (as in jw mapping) instead of the four variables 'r', 'csa',
'orientation' and 'tc' (as in consistency testing). Also, there is a
correction
for the run type ('ct') in the test suite which was left to the original type
from jw mapping ('jw').
Cheers.
Séb :)
Selon Sebastien Morin <sebastien.morin.1@xxxxxxxxx>, 16.07.2007:
> Hi,
>
> When I adapted the jw_mapping code to yield the consistency_test code, I
> didn't understand why, in the test suite, the following lines :
>
> if abs(self.relax.data.res[self.run][index].j0 -
> j0[index]) > j0[index]/1e6:
> print 'Error in residue',
> self.relax.data.res[self.run][index].num, 'j0 calculated value'
> return
> if abs(self.relax.data.res[self.run][index].f_eta -
> f_eta[index]) > f_eta[index]/1e6:
> print 'Error in residue',
> self.relax.data.res[self.run][index].num, 'f_eta calculated value'
> return
> if abs(self.relax.data.res[self.run][index].f_r2 -
> f_r2[index]) > f_r2[index]/1e6:
> print 'Error in residue',
> self.relax.data.res[self.run][index].num, 'f_r2 calculated value'
> return
>
> had a '/1e6' in the end and why those lines were not simply :
>
> if abs(self.relax.data.res[self.run][index].j0 -
> j0[index]) > j0[index]:
> print 'Error in residue',
> self.relax.data.res[self.run][index].num, 'j0 calculated value'
> return
> if abs(self.relax.data.res[self.run][index].f_eta -
> f_eta[index]) > f_eta[index]:
> print 'Error in residue',
> self.relax.data.res[self.run][index].num, 'f_eta calculated value'
> return
> if abs(self.relax.data.res[self.run][index].f_r2 -
> f_r2[index]) > f_r2[index]:
> print 'Error in residue',
> self.relax.data.res[self.run][index].num, 'f_r2 calculated value'
> return
>
> I tried to modify those lines and the test-suite code still works, anyway.
> Could you explain this issue to me, please ? Or is it a mistake and
> should the '/1e6' part be taken off..?
>
> Thanks !
>
>
> Séb :)
>
>
>
>
> Edward d'Auvergne wrote:
> > Oh well, it doesn't matter if it's not documented in the code then.
> >
> > Regards,
> >
> > Edward
> >
> >
> > On 7/13/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> >>
> >> Hi,
> >>
> >> For the eta value calculated in the consistency_tests code, I don't
> >> know if
> >> it is the eta_z or eta_xy value. In the original paper by Fushman &
> >> Cowburn
> >> (1998, JACS, 120: 7109-7110) as well as in the consistency tests paper
> >> (Fushman et al., 1998, JACS, 120: 10947-10952), eta is only described
> >> as the
> >> cross-correlation rate between 15N CSA and 15N-1H dipolar interaction.
> >>
> >> Cheers
> >>
> >>
> >> Séb :)
> >>
> >>
> >>
> >>
> >>
> >> Sébastien Morin wrote:
> >> Hi Ed,
> >>
> >> Here is the first part of the split patch as you asked for.
> >>
> >> This one if for docstrings and comments in files :
> >> /branches/consistency_tests_1.2/prompt/consistency_tests.py
> >> /branches/consistency_tests_1.2/maths_fns/consistency_tests.py
> >> /branches/consistency_tests_1.2/test_suite/consistency_tests.py
> >> /branches/consistency_tests_1.2/sample_scripts/consistency_tests.py
> >> /branches/consistency_tests_1.2/specific_fns/consistency_tests.py
> >>
> >> Should the commit log be something like what follows ?
> >>
> >> "This patch
> >> (patch_consistency_tests__l1.2_r3340__docstrings_and_comments)
> >> corrects docstrings and comments errors which were remnants of the
> >> jw_mapping
> >> code from which the consistency_tests code was inspired. Also, this
> >> patch
> >> adds
> >> docstrings and comments to the code for making it easier for users to
> >> understand what the code actually does."
> >>
> >> Cheers
> >>
> >>
> >> Séb :)
> >>
> >>
> >>
> >>
> >> Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 13.07.2007:
> >>
> >>
> >>
> >> Hi,
> >>
> >> This patch will need a few small changes before being committed. The
> >> first is the docstring of the set_frq function of
> >> 'prompt/consistency_tests.py'. In the user function docstrings, the
> >> list of keyword arguments need to be separated by newlines. This is a
> >> relax convention as can be seen in the equivalent function of
> >> 'prompt/jw_mapping.py'. One problem with this is that the docstring
> >> parser used to generate the relax manual might fail in this keyword
> >> argument section. An additional formatting convention is the use of
> >> two blank lines in front of the section titles in the docstring. This
> >> allows easier reading of the much longer docstrings.
> >>
> >> This isn't important but for the eta value, do you know if this is
> >> eta_z or eta_xy? A more important point is that the patch should be
> >> split up so that there are different patches for different types of
> >> fixes. For example there are docstring and comment changes which
> >> could be grouped together into a single patch. Then there are
> >> modifications to the test suite for the consistency tests which should
> >> be separate. In 'specific_fns/consistency_tests.py' there
> >> is a change
> >> to the default value of the CSA and a number of other fundamental
> >> changes. These should all be separate.
> >>
> >> It would be a good exercise in preparation for having full commit
> >> access to the relax repository to split this patch into a number of
> >> small patches. No patch or commit to the relax repository should
> >> contain two unrelated changes, even if these are tiny one line
> >> changes. For each commit to the repository, a detailed description of
> >> the changes should be placed into the commit log (which is
> >> automatically emailed to the relax-commits mailing list but remains in
> >> the repository and is important for repository maintenance). You can
> >> see these messages by typing something like 'svn log -v --limit=100 |
> >> less' within your checked out copy. So if you could prepare a similar
> >> commit message for the patches, it would be much appreciated.
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >> P.S. A small fix is needed in 'prompt/consistency_tests.py' at line
> >> 4. And as for the self.__relax_help_ string, this isn't actually a
> >> docstring but is used by the relax prompt help system. These
> >> __init__() functions don't have docstrings, and I don't remember if
> >> this was deliberate because of the special help system or not.
> >>
> >>
> >> On 7/13/07, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> >>
> >>
> >> Hi,
> >>
> >> Here is a patch for the consistency tests branch of the 1.2 line
> >> (r3340).
> >>
> >> Some comments and docstrings were added as well as errors corrected from
> >>
> >> the
> >>
> >>
> >> adaptation of this code from the jw_mapping code...
> >>
> >> The following file are modified :
> >> prompt/consistency_tests.py
> >> maths_fns/consistency_tests.py
> >> test_suite/consistency_tests.py
> >> sample_scripts/consistency_tests.py
> >> specific_fns/consistency_tests.py
> >>
> >> Formating should be OK in these files except maybe for one thing for
> >> which
> >>
> >> I'm
> >>
> >>
> >> not sure. It's between lines 29 and 33 of
> >> prompt/consistency_tests.py where
> >>
> >> I
> >>
> >>
> >> don't know if the docstring should be below the line 'def
> >> __init__(self,
> >> relax):' or below the line 'self.__relax_help__ = \' as it is now...
> >> Note
> >>
> >> that
> >>
> >>
> >> this is seen in many other code files...
> >>
> >> Cheers
> >>
> >>
> >> Sébastien :)
> >>
> >>
> >>
> >> Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 09.07.2007:
> >>
> >>
> >>
> >> Hi,
> >>
> >> Both patches have been applied to the repository. The patch
> >> 'patch_sample_scripts_consistency_tests' was committed at
> >> r3331.
> >> Change from 5000 to 500 simulations is reasonable. The large number
> >> of simulations was because the calculation was so quick, but 500
> >> should be more than sufficient. The addition of Grace plotting
> >> functions to the Reduced Spectral Density Mapping sample script is
> >> very useful and I will probably port this commit very soon to the 1.3
> >> line. The patch 'patch_sample_scripts_jw_mapping' was
> >> applied (at
> >> r3332) directly to the 1.2 line rather than the
> >> 'consistency_tests_1.2' branch.
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >> On 7/9/07, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> >>
> >>
> >> Hi again !
> >>
> >> I added lines for plotting using grace in the sample script. Since this
> >>
> >> sample
> >>
> >>
> >> script was inspired by the jw_mapping sample script, I also submit a
> >>
> >> patch
> >>
> >>
> >>
> >> for
> >>
> >>
> >> this file (adding lines for plotting, changing the number of Monte
> >>
> >> Carlo
> >>
> >>
> >>
> >>
> >> simulations from 5000 to 500 and changing the sequence file from
> >>
> >> noe.500.out to
> >>
> >>
> >> noe.600.out for more consistency)...
> >>
> >> Ciao !
> >>
> >>
> >> Sébastien :)
> >>
> >>
> >>
> >>
> >> Selon Sébastien Morin <sebastien.morin.1@xxxxxxxxx>, 09.07.2007:
> >>
> >>
> >>
> >> Hi Ed
> >>
> >> Tell me if this works better. I'm now using the mail server directly
> >>
> >> from
> >>
> >>
> >>
> >> the
> >>
> >>
> >>
> >> internet GUI... (not with Thuderbird).
> >>
> >> If this does not work neither, maybe we could try with the task...
> >>
> >> Ciao !
> >>
> >>
> >> Sébastien
> >>
> >>
> >> Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 09.07.2007:
> >>
> >>
> >>
> >> I've tried cutting an pasting the patch but I get the following:
> >>
> >> edau@klymene:/media/usbdisk/relax/branches/consistency_tests_1.2>
> >> patch -p0 < patch
> >> patching file prompt/consistency_tests.py
> >> Hunk #2 FAILED at 26.
> >> Hunk #3 FAILED at 40.
> >> Hunk #4 FAILED at 49.
> >> Hunk #5 FAILED at 74.
> >> 4 out of 5 hunks FAILED -- saving rejects to file
> >> prompt/consistency_tests.py.rej
> >> edau@klymene:/media/usbdisk/relax/branches/consistency_tests_1.2>
> >>
> >> I don't know why, but thunderbird is destroying the attachment.
> >>
> >> The
> >>
> >>
> >>
> >>
> >>
> >>
> >> failed 'hunks' are the wrapped lines. Maybe there is a way to
> >>
> >> prevent
> >>
> >>
> >>
> >>
> >>
> >>
> >> thunderbird from doing this. Otherwise using another email client
> >>
> >> (or
> >>
> >>
> >>
> >>
> >>
> >>
> >> webmail) may work. I could also create a task for this consistency
> >> test work and these could be attached to the task. It's best that,
> >> for the record, the files are located within the permanent relax
> >> infrastructure.
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >>
> >>
> >> On 7/9/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> >>
> >>
> >> Hi again !
> >>
> >> Here is again the first patch for the file
> >>
> >> 'prompt/consistency_tests.py'.
> >>
> >>
> >>
> >>
> >>
> >> I modified the header for the copyrights.
> >>
> >> Also, the former patches were not copied-pasted, but attached
> >>
> >> using
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Thunderbird after their creation using a command like 'svn diff >
> >>
> >> patch'
> >>
> >>
> >>
> >>
> >>
> >> under Linux. When I send those kinds of files as attachment, I
> >>
> >> usually
> >>
> >>
> >>
> >>
> >>
> >> see them as text in the e-mail, but also as an attachment that
> >>
> >> can be
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> save. Tell me if it is okay and if it is still a problem, I'll
> >>
> >> put
> >>
> >>
> >>
> >> them
> >>
> >>
> >>
> >>
> >>
> >> on my lab's website...
> >>
> >> Cheers
> >>
> >>
> >> Séb :)
> >>
> >>
> >>
> >> Edward d'Auvergne wrote:
> >>
> >>
> >> Hi,
> >>
> >> Just add some text such as 'Copyright (C) 2007 Sebastien Morin
> >> <sebastien.morin.1 at ulaval.ca>' underneath the already
> >>
> >> existent
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> copyright text. The can be changed later, for example I can
> >>
> >> give
> >>
> >>
> >>
> >> you
> >>
> >>
> >>
> >>
> >>
> >>
> >> a ???@nmr-relax.com email address which is an alias for any
> >>
> >> other
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> email address (once voted in as a relax developer). Could you
> >>
> >> add
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> this and then resend the patches? Ta. If they are attached
> >>
> >> rather
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> than cut and paste that would be much easier for applying the
> >>
> >> patches
> >>
> >>
> >>
> >>
> >>
> >>
> >> (as email wraps lines). Also, maybe responding to your
> >>
> >> original
> >>
> >>
> >>
> >> posts
> >>
> >>
> >>
> >>
> >>
> >>
> >> will allow the patches to be more easily tracked in the mailing
> >>
> >> list
> >>
> >>
> >>
> >>
> >>
> >>
> >> https://mail.gna.org/public/relax-devel/.
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >> On 7/9/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> >>
> >>
> >> Hi !
> >>
> >> I'm about to create the patches to merge the consistency tests
> >>
> >> code
> >>
> >>
> >>
> >> into
> >>
> >>
> >>
> >>
> >>
> >> the 1.2 branch.
> >>
> >> However, I have one question. How do I treat the copyrights ?
> >>
> >> Do I
> >>
> >>
> >>
> >>
> >>
> >> leave
> >>
> >>
> >>
> >>
> >>
> >> the original author from which I copied the code and then
> >>
> >> modified
> >>
> >>
> >>
> >> it
> >>
> >>
> >>
> >> or
> >>
> >>
> >>
> >>
> >>
> >> do I had my name to the code headers..?
> >>
> >> Thanks !
> >>
> >>
> >> Sébastien :)
> >>
> >>
> >>
> >>
> >> Edward d'Auvergne wrote:
> >>
> >>
> >> Oh, I've committed your patch at
> >>
> >>
> >>
>
http://maple.rsvs.ulaval.ca/mediawiki/index.php/Patch_consistency_tests_2007-06-26
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> as revision r3324, applying it to the 1.2 branch. I've
> >>
> >> carefully
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> checked the code and none of the changes are detrimental or
> >>
> >> could
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> affect the stability of the stable 1.2 relax codebase. Note
> >>
> >> however
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> that the code in the branch will not run as the
> >>
> >> consistency_test.py
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> files are still identical copies of the jw_mapping.py files.
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >> On 7/9/07, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>
> >>
> >> wrote:
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Hi,
> >>
> >> I've now created two branches within the relax repository
> >>
> >> for
> >>
> >>
> >>
> >> you
> >>
> >>
> >>
> >> to
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> play with. The first is a copy of the 1.2 line and is
> >>
> >> located
> >>
> >>
> >>
> >> at
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> svn.gna.org/svn/relax/branches/consistency_tests_1.2/. The
> >>
> >> second
> >>
> >>
> >>
> >> is
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> a copy of the 1.3 line and is located at
> >> svn.gna.org/svn/relax/branches/consistency_tests_1.3/.
> >>
> >> I've
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> initially
> >>
> >>
> >>
> >> used 'svn cp' to create the 5 consistency_tests.py files as
> >>
> >> described
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> in
> >>
> >> https://mail.gna.org/public/relax-devel/2007-07/msg00001.html
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> (Message-id:
> >>
> >>
> >> <7f080ed10707090251ve1c4a8fl7f8618843e5c9459@xxxxxxxxxxxxxx>).
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Would you be able to create patches for these files (in
> >>
> >> the
> >>
> >>
> >>
> >> 1.2
> >>
> >>
> >>
> >> line
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> first, no need to worry about the 1.3 line yet), and then
> >>
> >> post
> >>
> >>
> >>
> >> the
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> individual patches as text file attachments to the mailing
> >>
> >> list?
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Thanks. I will then be able to commit these patches
> >>
> >> individually,
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> checking them in fine detail.
> >>
> >> Things to note in creating the patches from the code at
> >>
> >>
> >> http://maple.rsvs.ulaval.ca/mediawiki/index.php/Relax_development
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> include the copyright preservation, a number of integers in
> >> 'maths_fns/consistency_tests.py' which should be floating
> >>
> >> point
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> numbers (just add '.0' to the end of the number), the
> >>
> >> addition
> >>
> >>
> >>
> >> of
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Grace plots as an output in the
> >>
> >> 'sample_scripts/consistency_tests.py'
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> script to be able to create a picture similar to that on
> >>
> >> your
> >>
> >>
> >>
> >> relax
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> development site, maybe only allowing 'Tc' and 'tc' in the
> >> return_data_name() function and not 'TC', and 'degrees'
> >>
> >> instead
> >>
> >>
> >>
> >> of
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> 'degree' in the return_units() function.
> >>
> >> One bug includes:
> >>
> >> setattr(self.relax.data.res[self.run][index],
> >>
> >> 'csa',
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> float(value[0]))
> >> setattr(self.relax.data.res[self.run][index],
> >>
> >> 'r',
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> float(value[1]))
> >> + setattr(self.relax.data.res[self.run][index],
> >> 'orientation', float(value[1]))
> >> + setattr(self.relax.data.res[self.run][index],
> >>
> >> 'tc',
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> float(value[1]))
> >>
> >> value[1] has been used twice. I have a feeling there is
> >>
> >> another
> >>
> >>
> >>
> >> bug
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> somewhere where an index has been repeated a few times when
> >>
> >> it
> >>
> >>
> >>
> >>
> >>
> >> should
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> be different indices, but I can't find it at the moment.
> >>
> >> The
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> individual patches should help. Finally, I have a feeling
> >>
> >> that
> >>
> >>
> >>
> >>
> >>
> >> there
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> is unused code which can be deleted as it is a relic from
> >>
> >> the
> >>
> >>
> >>
> >> copy
> >>
> >>
> >>
> >> of
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> the J(w) mapping code and is not needed. For the 1.3 line
> >>
> >> code
> >>
> >>
> >>
> >> I
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> would recommend that identical functions are shifted into
> >>
> >> files
> >>
> >>
> >>
> >>
> >>
> >> such
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> as 'specific_fns/base_class.py', but for the 1.2 line code
> >>
> >> I
> >>
> >>
> >>
> >> would
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> prefer the duplication as this means that the current
> >>
> >> stable
> >>
> >>
> >>
> >> code
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> base
> >>
> >>
> >>
> >> remains stable.
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >>
> >> On 6/26/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx>
> >>
> >> wrote:
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Hi,
> >>
> >> I started working on implementing the consistency tests
> >>
> >> last
> >>
> >>
> >>
> >> week
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> before
> >>
> >>
> >> the last post was made and, hence, I worked on repository
> >>
> >> line
> >>
> >>
> >>
> >> 1.2
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> (revision 3303).
> >>
> >> I implemented the consistency tests as a new type of run
> >>
> >> ('ct')
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> similar
> >>
> >>
> >> to the one for Jw mapping.
> >>
> >> The calculations are made for J(0), F_eta and F_R2
> >>
> >> separately
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> for each
> >>
> >>
> >>
> >>
> >> magnetic field (one at a time). The output results file
> >>
> >> is
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> similar to
> >>
> >>
> >>
> >>
> >> the one for Jw mapping. The user then needs to plot them
> >>
> >> and
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> look for
> >>
> >>
> >>
> >>
> >> consistency with its own criteria (calculation
> >>
> >> correlation
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> coefficients, mean ratios and standard deviations, etc).
> >>
> >> Please look at the followinr URL for a listing of the
> >>
> >> modifications to
> >>
> >>
> >>
> >>
> >> old files and also necessary new files.
> >>
> >>
> >>
> >> http://maple.rsvs.ulaval.ca/mediawiki/index.php/Relax_development
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> The file 'sample_scripts/consistency_tests.py' should be
> >>
> >> useful
> >>
> >>
> >>
> >> to
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> understand how the new procedure works.
> >>
> >> Even if this was done on repository line 1.2, I think it
> >>
> >> is
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> quite fine
> >>
> >>
> >>
> >>
> >> since nothing was deleted but only things added (maybe
> >>
> >> too
> >>
> >>
> >>
> >> much,
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> as I
> >>
> >>
> >>
> >>
> >> reproduced the Jw mapping approach, maybe too much as I
> >>
> >> added
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> lines in
> >>
> >>
> >>
> >>
> >> the codes for grace, molmol, etc, maybe too much also
> >>
> >> since
> >>
> >>
> >>
> >> some
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> code is
> >>
> >>
> >> duplicated from the Jw mapping code). The test-suite
> >>
> >> still
> >>
> >>
> >>
> >> works
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> perfectly and, so, I think it could be fine to add the
> >>
> >> tests
> >>
> >>
> >>
> >> to
> >>
> >>
> >>
> >> the
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> 1.2
> >>
> >>
> >> line as well... However, if necessary, I could implement
> >>
> >> the
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> consistency
> >>
> >>
> >> testing procedure on line 1.3, following your comments as
> >>
> >> I
> >>
> >>
> >>
> >> am
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> quite new
> >>
> >>
> >> to Python and maybe made things somehow not perfectly...
> >>
> >> Please tell me what you think about this.
> >>
> >> Cheers,
> >>
> >>
> >> Sébastien :)
> >>
> >>
> >>
> >> Edward d'Auvergne wrote:
> >>
> >>
> >> Hi,
> >>
> >> I have previously talked about data set consistency.
> >>
> >> For
> >>
> >>
> >>
> >>
> >>
> >> example
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> see
> >>
> >>
> >>
> >> the post at
> >>
> >> https://mail.gna.org/public/relax-users/2007-06/msg00001.html
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> in which a few reasons for inconsistencies have been
> >>
> >> explained. I
> >>
> >>
> >>
> >>
> >>
> >> have, from experience, noticed that small changes in
> >>
> >> protein
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> concentration can change the collected relaxation rates
> >>
> >> significantly
> >>
> >>
> >>
> >> - most likely because of packing interactions. All
> >>
> >> samples
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> should
> >>
> >>
> >>
> >>
> >>
> >> essentially be identical in all respects for the
> >>
> >> relaxation
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> rates to
> >>
> >>
> >>
> >>
> >>
> >> be compared. And the temperate should always be fine
> >>
> >> tuned
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> between
> >>
> >>
> >>
> >>
> >>
> >> experiments and spectrometers using methanol (and
> >>
> >> always
> >>
> >>
> >>
> >>
> >>
> >> checked
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> later
> >>
> >>
> >>
> >> on if there is a large time between collecting the same
> >>
> >> experiment).
> >>
> >>
> >>
> >>
> >>
> >> Therefore these tests would be quite useful. Data
> >>
> >> consistency
> >>
> >>
> >>
> >> is
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> essential for the model-free results to be correct (as
> >>
> >> well
> >>
> >>
> >>
> >> as
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> reduced
> >>
> >>
> >>
> >> spectral density mapping, SRLS, etc.) as this affects
> >>
> >> both
> >>
> >>
> >>
> >> the
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> optimisation and model selection and can result in
> >>
> >> artificial
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> motions
> >>
> >>
> >>
> >> appearing. However I don't know how these test would
> >>
> >> currently fit
> >>
> >>
> >>
> >>
> >>
> >> within relax. Maybe a new type of analysis should be
> >>
> >> created
> >>
> >>
> >>
> >> for
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> this
> >>
> >>
> >>
> >> (see the pipe.create() user function in the 1.3 line or
> >>
> >> the
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> run.create() user function in the 1.2 line). These
> >>
> >> ideas
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> should all
> >>
> >>
> >>
> >>
> >>
> >> go into the 1.3 line (via a branch) as the 1.2 line is
> >>
> >> stable
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> and no
> >>
> >>
> >>
> >>
> >>
> >> new major features will be added to this code. What
> >>
> >> are
> >>
> >>
> >>
> >> the
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> ideas you
> >>
> >>
> >>
> >> have been playing with?
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >> On 6/15/07, Sebastien Morin
> >>
> >> <sebastien.morin.1@xxxxxxxxx>
> >>
> >>
> >>
> >>
> >>
> >> wrote:
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Hi everyone
> >>
> >> During the last months, I was astonished to realize
> >>
> >> that
> >>
> >>
> >>
> >> some
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> spin
> >>
> >>
> >>
> >>
> >>
> >>
> >> relaxation data I had acquired at different fields
> >>
> >> were
> >>
> >>
> >>
> >> not
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> consistent
> >>
> >>
> >>
> >>
> >> between each other. The way I realized that was by
> >>
> >> seeing
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> discrepancy
> >>
> >>
> >>
> >>
> >> between J(0) values calculated with those different
> >>
> >> datasets.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> I looked a little bit in the litterature and found
> >>
> >> some
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> interesting
> >>
> >>
> >>
> >>
> >>
> >>
> >> consistency tests in a paper by Fushman (Fushman et
> >>
> >> al.,
> >>
> >>
> >>
> >> JACS,
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> 1998,
> >>
> >>
> >>
> >>
> >> 120:10947-10952).
> >>
> >> This paper present 2 consistency tests to compare
> >>
> >> datasets
> >>
> >>
> >>
> >>
> >>
> >> from
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> different magnetic fields / samples / time / etc.
> >>
> >> I think it would be interesting to implement those
> >>
> >> simple
> >>
> >>
> >>
> >>
> >>
> >> tests
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> in relax
> >>
> >>
> >>
> >>
> >> so the user can, before trying to fit their data, know
> >>
> >> the
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> quality of
> >>
> >>
> >>
> >>
> >> those... Regrettably, very few people look at the
> >>
> >> consistency
> >>
> >>
> >>
> >> of
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> their
> >>
> >>
> >>
> >>
> >> datasets before analysis...
> >>
> >> The underlying principle is the same as when looking
> >>
> >> at
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> consistency for
> >>
> >>
> >>
> >>
> >> J(0). Thus, I think that those two tests and a J(0)
> >>
> >> test
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> should be
> >>
> >>
> >>
> >>
> >>
> >>
> >> implemented altogether...
> >>
> >> I'll try to work a bit on this. Mimicking the code for
> >>
> >> ...
> >>
> >> [Message clipped]
> >
>
> --
> ______________________________________
> _______________________________________________
> | |
> || Sebastien Morin ||
> ||| Etudiant au PhD en biochimie |||
> |||| Laboratoire de resonance magnetique nucleaire ||||
> ||||| Dr Stephane Gagne |||||
> |||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
> ||| 1-418-656-2131 #4530 |||
> || ||
> |_______________________________________________|
> ______________________________________
>
>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
> This is the relax-devel mailing list
> relax-devel@xxxxxxx
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-devel
>
>
------------------------
Sébastien Morin
Étudiant M.Sc. Biochimie
Laboratoire S. Gagné
3252 Pav. Marchand (Université Laval)
Tél : (418) 656-2131 #4530
Fax : (418) 656-7176
e-mail : sebastien.morin.1@xxxxxxxxx
Re: Consistency tests