Hi
Here the patch for the file 'maths_fns/consistency.py'
Séb :)
Sebastien Morin 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 [EMAIL PROTECTED] 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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:
>>>>> <[EMAIL PROTECTED]>).
>>>>> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 spectral
>>>>>>>>
>>>>> density
>>>>>
>>>>>>>> should be a good starting point.
>>>>>>>>
>>>>>>>> Am I right ?
>>>>>>>> Do you see any value in those tests ?
>>>>>>>>
>>>>>>>> Cheers
>>>>>>>>
>>>>>>>>
>>>>>>>> Sébastien :)
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> relax (http://nmr-relax.com)
>>>>>>>>
>>>>>>>> This is the relax-devel mailing list
>>>>>>>> relax-devel@gna.org
>>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>> --
>>>>>> ______________________________________
>>>>>> _______________________________________________
>>>>>> | |
>>>>>> || 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 |||
>>>>>> || ||
>>>>>> |_______________________________________________|
>>>>>> ______________________________________
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>> --
>>> ______________________________________
>>> _______________________________________________
>>> | |
>>> || 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@gna.org
>
> 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
--
______________________________________
_______________________________________________
| |
|| 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 |||
|| ||
|_______________________________________________|
______________________________________
Index: maths_fns/consistency_tests.py
===================================================================
--- maths_fns/consistency_tests.py (revision 3324)
+++ maths_fns/consistency_tests.py (working copy)
@@ -1,6 +1,7 @@
###############################################################################
# #
# Copyright (C) 2004 Edward d'Auvergne #
+# Copyright (C) 2007 Sebastien Morin <sebastien.morin.1 at ulaval.ca> #
# #
# This file is part of the program relax. #
# #
@@ -21,14 +22,14 @@
###############################################################################
from Numeric import Float64, zeros
-from math import pi
+from math import pi, cos
from ri_comps import calc_fixed_csa, calc_fixed_dip, comp_csa_const_func,
comp_dip_const_func
-class Mapping:
+class Consistency:
def __init__(self, frq=None, gx=None, gh=None, mu0=None, h_bar=None):
- """Reduced spectral density mapping."""
+ """Consistency tests for data acquired at different magnetic fields."""
# Initialise the data container.
self.data = Data()
@@ -67,10 +68,10 @@
return (noe - 1.0) * r1 * self.data.gx / self.data.gh
- def func(self, r=None, csa=None, r1=None, r2=None, noe=None):
- """Function for calculating the three spectal density values.
+ def func(self, orientation=None, tc=None, r=None, csa=None, r1=None,
r2=None, noe=None):
+ """Function for calculating the three consistency testing values.
- Three values are returned, J(0), J(wX), and J(wH) (or J(0.87wH)).
+ Three values are returned, J(0), F_eta and F_R2.
"""
# Calculate the fixed component of the dipolar and CSA constants.
@@ -94,11 +95,23 @@
# Calculate J(wX).
jwx = 1.0 / (3.0*d + c) * (r1 - 1.4*sigma_noe)
- # Calculate J(wH).
- jwh = sigma_noe / (5.0*d)
+ # Calculate P_2.
+ p_2 = 0.5 * ((3.0 * (cos(orientation * pi / 180)) ** 2) -1)
+ # Calculate eta.
+ eta = ((d * c) ** 0.5) * (4.0 * j0 + 3.0 * jwx) * p_2
+
+ # Calculate F_eta.
+ f_eta = eta * self.data.gh / (self.data.frq_list[0, 3] * (4.0 + 3.0 /
(1 + (self.data.frq_list[0, 1] * tc) ** 2)))
+
+ # Calculate P_HF.
+ p_hf = 1.3 * (self.data.gx / self.data.gh) * (1.0 - noe) * r1
+
+ # Calculate F_R2.
+ f_r2 = (r2 - p_hf) / ((4.0 + 3.0 / (1 + (self.data.frq_list[0, 1] *
tc) ** 2)) * (d + c/3.0))
+
# Return the three values.
- return j0, jwx, jwh
+ return j0, f_eta, f_r2
class Data:
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