Please note that the changes I have made here may not yet be the final
form. It could be unstable until I have something fully functional
implemented. The creation of a mapping between the structural code
(PDB readers, etc.) and the relax data store is still very much up in
the air. I would like to have this evolve into a stable API in which
the two talk to each other independent of their implementation
details, so that other PDB or other structural file readers can be
added without needing to modify any other parts of relax.
Regards,
Edward
On Mon, Mar 31, 2008 at 8:36 PM, <sebastien.morin.1@xxxxxxxxx> wrote:
Author: semor
Date: Mon Mar 31 20:36:12 2008
New Revision: 5242
URL: http://svn.gna.org/viewcvs/relax?rev=5242&view=rev
Log:
Changes to the consistency tests code to reflect the model-free changes of
r5220.
These changes are similar to those made to the J(w) mapping code in r5223.
Modified:
branches/consistency_tests_1.3/specific_fns/consistency_tests.py
Modified: branches/consistency_tests_1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/consistency_tests.py?rev=5242&r1=5241&r2=5242&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/consistency_tests.py
(original)
+++ branches/consistency_tests_1.3/specific_fns/consistency_tests.py Mon
Mar 31 20:36:12 2008
@@ -221,21 +221,23 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
These default values are found in the file 'physical_constants.py'.
-
________________________________________________________________________________________
- | | |
|
- | Data type | Object name | Value
|
-
|_______________________________________|_______________|______________________________|
- | | |
|
- | Bond length | 'r' | 1.02 *
1e-10 |
- | | |
|
- | CSA | 'csa' | -172 *
1e-6 |
- | | |
|
- | Heteronucleus type | 'nucleus' | 'N'
|
- | | |
|
- | Angle Theta | 'orientation' | 15.7
|
- | | |
|
- | Correlation time | 'tc' | 13 *
1e-9 |
-
|_______________________________________|_______________|______________________________|
+
______________________________________________________________________________________
+ | | |
|
+ | Data type | Object name |
Value |
+
|_______________________________________|____________________|_________________________|
+ | | |
|
+ | Bond length | 'r' |
1.02 * 1e-10 |
+ | | |
|
+ | CSA | 'csa' |
-172 * 1e-6 |
+ | | |
|
+ | Heteronucleus type | 'heteronuc_type' |
'15N' |
+ | | |
|
+ | Proton type | 'proton_type' |
'1H' |
+ | | |
|
+ | Angle Theta | 'orientation' |
15.7 |
+ | | |
|
+ | Correlation time | 'tc' | 13
* 1e-9 |
+
|_______________________________________|____________________|_________________________|
"""
__docformat__ = "plaintext"
@@ -249,8 +251,12 @@
return N15_CSA
# Heteronucleus type.
- elif param == 'nucleus':
- return 'N'
+ elif param == 'heteronuc_type':
+ return '15N'
+
+ # Proton type.
+ elif param == 'proton_type':
+ return '1H'
# Angle Theta (default value)
elif param == 'orientation':
@@ -287,27 +293,29 @@
Consistency testing data type string matching patterns
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
____________________________________________________________________________________________
- | | |
|
- | Data type | Object name | Patterns
|
-
|_______________________|_______________|__________________________________________________|
- | | |
|
- | J(0) | 'j0' | '^[Jj]0$' or
'[Jj]\(0\)' |
- | | |
|
- | F_eta | 'f_eta' | '^[Ff]_[Ee][Tt][Aa]$'
|
- | | |
|
- | F_R2 | 'f_r2' | '^[Ff]_[Rr]2$'
|
- | | |
|
- | Bond length | 'r' | '^r$' or '[Bb]ond[
-_][Ll]ength' |
- | | |
|
- | CSA | 'csa' | '^[Cc][Ss][Aa]$'
|
- | | |
|
- | Heteronucleus type | 'nucleus' | '^[Nn]ucleus$'
|
- | | |
|
- | Angle Theta | 'orientation' |
'^[Oo][Rr][Ii][Ee][Nn][Tt][Aa][Tt][Ii][Oo][Nn]$' |
- | | |
|
- | Correlation time | 'tc' | '^[Tt]c$'
|
-
|_______________________|_______________|__________________________________________________|
+
__________________________________________________________________________________________
+ | | |
|
+ | Data type | Object name | Patterns
|
+
|_______________________|__________________|_______________________________________________|
+ | | |
|
+ | J(0) | 'j0' | '^[Jj]0$' or
'[Jj]\(0\)' |
+ | | |
|
+ | F_eta | 'f_eta' |
'^[Ff]_[Ee][Tt][Aa]$' |
+ | | |
|
+ | F_R2 | 'f_r2' | '^[Ff]_[Rr]2$'
|
+ | | |
|
+ | Bond length | 'r' | '^r$' or '[Bb]ond[
-_][Ll]ength' |
+ | | |
|
+ | CSA | 'csa' | '^[Cc][Ss][Aa]$'
|
+ | | |
|
+ | Heteronucleus type | 'heteronuc_type' | '^[Hh]eteronucleus$'
|
+ | | |
|
+ | Proton type | 'proton_type' | '^[Pp]roton$'
|
+ | | |
|
+ | Angle Theta | 'orientation' | '^[Oo]rientation$'
|
+ | | |
|
+ | Correlation time | 'tc' | '^[Tt]c$'
|
+
|_______________________|__________________|_______________________________________________|
"""
__docformat__ = "plaintext"
@@ -332,11 +340,15 @@
return 'csa'
# Heteronucleus type.
- if search('^[Nn]ucleus$', name):
- return 'nucleus'
+ if search('^[Hh]eteronucleus$', name):
+ return 'heteronuc_type'
+
+ # Proton type.
+ if search('^[Pp]roton$', name):
+ return 'proton_type'
# Angle Theta
- if search('^[Oo][Rr][Ii][Ee][Nn][Tt][Aa][Tt][Ii][Oo][Nn]$', name):
+ if search('^[Oo]rientation]$', name):
return 'orientation'
# Correlation time
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Re: r5242 - /branches/consistency_tests_1.3/specific_fns/consistency_tests.py