r2402 - in /1.2/prompt: diffusion_tensor.py model_free.py
Author: bugman
Date: Fri Mar 24 02:49:35 2006
New Revision: 2402
URL: http://svn.gna.org/viewcvs/relax?rev=2402view=rev
Log:
Set notation fix: Changed the square and round brackets to curly brackets and
replaced ':' with '='.
Modified:
1.2/prompt/diffusion_tensor.py
1.2/prompt/model_free.py
Modified: 1.2/prompt/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/diffusion_tensor.py?rev=2402r1=2401r2=2402view=diff
==
--- 1.2/prompt/diffusion_tensor.py (original)
+++ 1.2/prompt/diffusion_tensor.py Fri Mar 24 02:49:35 2006
@@ -181,8 +181,8 @@
To specify the time in nanoseconds, set the 'time_scale' argument to
1e-9. Alternative
parameters can be used by changing the 'param_types' flag to the
following integers
-0: tm (Default),
-1: Diso,
+0: {tm} (Default),
+1: {Diso},
where
@@ -226,11 +226,11 @@
round brackets, the elements of which are separated by commas.
Alternative sets of
parameters, 'param_types', are
-0: (tm, Da, theta, phi) (Default),
-1: (Diso, Da, theta, phi),
-2: (tm, Dratio, theta, phi),
-3: (Dpar, Dper, theta, phi),
-4: (Diso, Dratio, theta, phi),
+0: {tm, Da, theta, phi} (Default),
+1: {Diso, Da, theta, phi},
+2: {tm, Dratio, theta, phi},
+3: {Dpar, Dper, theta, phi},
+4: {Diso, Dratio, theta, phi},
where
@@ -310,9 +310,9 @@
six. A tuple is a type of data structure enclosed in round brackets,
the elements of which
are separated by commas. Alternative sets of parameters,
'param_types', are
-0: (tm, Da, Dr, alpha, beta, gamma) (Default),
-1: (Diso, Da, Dr, alpha, beta, gamma),
-2: (Dx, Dy, Dz, alpha, beta, gamma),
+0: {tm, Da, Dr, alpha, beta, gamma} (Default),
+1: {Diso, Da, Dr, alpha, beta, gamma},
+2: {Dx, Dy, Dz, alpha, beta, gamma},
where
Modified: 1.2/prompt/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/prompt/model_free.py?rev=2402r1=2401r2=2402view=diff
==
--- 1.2/prompt/model_free.py (original)
+++ 1.2/prompt/model_free.py Fri Mar 24 02:49:35 2006
@@ -305,52 +305,52 @@
~
The standard preset model-free models are
-'m0': [],
-'m1': [S2],
-'m2': [S2, te],
-'m3': [S2, Rex],
-'m4': [S2, te, Rex],
-'m5': [S2f, S2, ts],
-'m6': [S2f, tf, S2, ts],
-'m7': [S2f, S2, ts, Rex],
-'m8': [S2f, tf, S2, ts, Rex],
-'m9': [Rex].
+'m0' = {},
+'m1' = {S2},
+'m2' = {S2, te},
+'m3' = {S2, Rex},
+'m4' = {S2, te, Rex},
+'m5' = {S2f, S2, ts},
+'m6' = {S2f, tf, S2, ts},
+'m7' = {S2f, S2, ts, Rex},
+'m8' = {S2f, tf, S2, ts, Rex},
+'m9' = {Rex}.
The preset model-free models with optimisation of the CSA value are
-'m10': [CSA],
-'m11': [CSA, S2],
-'m12': [CSA, S2, te],
-'m13': [CSA, S2, Rex],
-'m14': [CSA, S2, te, Rex],
-'m15': [CSA, S2f, S2, ts],
-'m16': [CSA, S2f, tf, S2, ts],
-'m17': [CSA, S2f, S2, ts, Rex],
-'m18': [CSA, S2f, tf, S2, ts, Rex],
-'m19': [CSA, Rex].
+'m10' = {CSA},
+'m11' = {CSA, S2},
+'m12' = {CSA, S2, te},
+'m13' = {CSA, S2, Rex},
+'m14' = {CSA, S2, te, Rex},
+'m15' = {CSA, S2f, S2, ts},
+'m16' = {CSA, S2f, tf, S2, ts},
+'m17' = {CSA, S2f, S2, ts, Rex},
+'m18' = {CSA, S2f, tf, S2, ts, Rex},
+'m19' = {CSA, Rex}.
The preset model-free models with optimisation of the bond length are
-'m20': [r],
-'m21': [r, S2],
-'m22': [r, S2, te],
-'m23': [r, S2, Rex],
-'m24': [r, S2, te, Rex],
-'m25': [r, S2f, S2, ts],
-'m26': [r, S2f, tf, S2, ts],
-'m27': [r, S2f, S2, ts, Rex],
-'m28': [r, S2f, tf, S2, ts, Rex],
-'m29': [r, CSA, Rex].
+'m20' = {r},
+'m21' = {r, S2},
+'m22' = {r, S2, te},
+'m23' = {r, S2, Rex},
+'m24' = {r, S2, te, Rex},
+'m25' = {r, S2f, S2, ts},
+'m26' = {r, S2f, tf, S2, ts},
+'m27' = {r, S2f, S2, ts, Rex},
+'m28' = {r, S2f, tf, S2, ts, Rex},
+'m29' = {r, CSA, Rex}.
The preset model-free models with both optimisation of the bond
r2403 - in /1.2: relax test_suite/ testing/
Author: bugman Date: Fri Mar 24 03:17:11 2006 New Revision: 2403 URL: http://svn.gna.org/viewcvs/relax?rev=2403view=rev Log: Shifted the test suite from the directory 'testing' to 'test_suite'. Added: 1.2/test_suite/ - copied from r2399, 1.2/testing/ Removed: 1.2/testing/ Modified: 1.2/relax Modified: 1.2/relax URL: http://svn.gna.org/viewcvs/relax/1.2/relax?rev=2403r1=2402r2=2403view=diff == --- 1.2/relax (original) +++ 1.2/relax Fri Mar 24 03:17:11 2006 @@ -72,7 +72,7 @@ from prompt.interpreter import Interpreter from specific_fns.main import Specific from specific_fns.specific_setup import Specific_setup -from testing.test import Testing +from test_suite.test_suite import Test_suite from thread_classes import Threading, ThreadData import version @@ -173,7 +173,7 @@ self.interpreter._on() # Run the tests. -Testing(self) +Test_suite(self) # Test mode. elif mode == 'test': ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2410 - in /1.2/docs: latex/web.tex relax.pdf
Author: bugman
Date: Mon Mar 27 08:27:40 2006
New Revision: 2410
URL: http://svn.gna.org/viewcvs/relax?rev=2410view=rev
Log:
Created the web site, mailing list, and bug report sections of the web chapter
of the manual.
Modified:
1.2/docs/latex/web.tex
1.2/docs/relax.pdf
Modified: 1.2/docs/latex/web.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/web.tex?rev=2410r1=2409r2=2410view=diff
==
--- 1.2/docs/latex/web.tex (original)
+++ 1.2/docs/latex/web.tex Mon Mar 27 08:27:40 2006
@@ -4,26 +4,50 @@
\chapter{The web}
-% The web sites.
-%~~~
-\section{The web sites}
+% The relax web sites.
+%~
-\href{http://nmr-relax.com}{http://nmr-relax.com}
+\section{The relax web sites}
+
+The main web site for relax is
\href{http://nmr-relax.com}{http://nmr-relax.com}. From these pages, general
information about the program, links to the latest documentation, links to the
most current software releases, and information about the mailing lists are
availible. There are also search capabilities built into the pages for
searching both the HTML version of the manual and the archives of the mailing
lists.
+
+The relax website is hosted by Gna! project
\href{https://gna.org/}{https://gna.org/} which is described as ``a central
point for development, distribution and maintenance of Libre Software (Free
Software) projects''. relax is a registered Gna! project and its primary Gna!
webpage, which contains many more technical detailed than the main web site, is
\href{https://gna.org/projects/relax}{https://gna.org/projects/relax}.
+
% The mailing lists.
%~~~
\section{The mailing lists}
-\index{mailing list!textbf}
+\index{mailing list}
+
+A number of mailing lists have been created covering different aspects of
relax. These include the announcement list, the relax users list, the relax
development list, and the relax committers list.
+
+The relax announcement list, relax-announce at gna.org is reserved for
important announcements about the program. All new program versions will be
announced on this list. The amount of traffic on this list is relatively low,
so if you would like to receive information about relax you can subscribe to
the list by vising the information page at
\href{https://mail.gna.org/listinfo/relax-announce/}{https://mail.gna.org/listinfo/relax-announce/}.
Previous announcements can be viewed at
\href{https://mail.gna.org/public/relax-announce/}{https://mail.gna.org/public/relax-announce/}.
+
+If you would like to ask questions about relax, discuss certain features,
receive help, or to communicate on any other subject related to relax, the
mailing list relax-users at gna.org is the place to post your message. To
subscribe to the list, go to the relax-users information page at
\href{https://mail.gna.org/listinfo/relax-users/}{https://mail.gna.org/listinfo/relax-users/}.
You can also browse the mailing list archives at
\href{https://mail.gna.org/public/relax-users/}{https://mail.gna.org/public/relax-users/}.
+
+A second mailing list exists for posts relating to the development of relax.
The list is relax-devel at gna.org and to subscribe, go to the relax-devel
information page at
\href{https://mail.gna.org/listinfo/relax-devel/}{https://mail.gna.org/listinfo/relax-devel/}.
Feature requests, program design, or any other posts relating to relax's
structure or code should be sent to this list instead. The mailing list
archives can be browsed at
\href{https://mail.gna.org/public/relax-devel/}{https://mail.gna.org/public/relax-devel/}.
+
+When replying to a message on these lists, remember to hit 'respond to all' so
that the mailing list is included in the CC field. Otherwise your message will
only be sent to the original poster and not back to the list.
+
+One last mailing list is the relax commits list. This list is reserved for
automatically generated posts created by the version control software which
looks after the relax source code and these web pages. If you would like to
become a developer, you can subscribe to the list at relax-commits information
page
\href{https://mail.gna.org/listinfo/relax-commits/}{https://mail.gna.org/listinfo/relax-commits/}.
The list can also be browsed at
\href{https://mail.gna.org/public/relax-commits/}{https://mail.gna.org/public/relax-commits/}.
+
% Reporting bugs.
%
\section{Reporting bugs}
-\index{bugs!textbf}
+\index{bugs}
+
+One of the philosophies in the construction of relax is that if there is
something which is not immediately obvious, then that is considered a design
bug. If any flaws in relax are uncovered, including general design flaws, bugs
in the code, or documentation issues, these can be reported within relax's bug
tracker system. The link to submit a bug is
r2429 - in /1.2/docs: latex/develop.tex relax.pdf
commit access. If a number of developers agree while no one says no,
then commit access will be offered.
+
+One area where coding ability can be demonstrated is within the relax test
suite. The addition of tests, especially those where the relax internal data
structures of \texttt{self.relax.data} are scrutinised, can be a good starting
point for learning the structure of relax. The beauty of the tests is that the
introduction of bugs has no effect on normal program execution. The relax test
suite is an ideal proving ground.
+
+If skills in only certain areas of relax development, for example in creation
of the documentation, an understanding of C but not python, an understanding of
solely the code of the user interface, or an understanding of the code specific
to a certain type of data analysis methodology, then partial commit access may
be granted. Although you will have the ability to make modifications to any
part of the repository, please make modifications only those areas for which
you have permission.
% Format of the commit logs.
\subsection{Format of the commit logs}\label{commit log format}
+If you are a relax developer and you have commit access to the repository, the
following conventions should be followed.
+
The length of all lines in the commit log should never exceed 100 characters.
This is so that the log message viewed in either emails or by the command
prompt command \mbox{\texttt{svn log}} is legible. The first line of the
commit log should be a short description or synopsis of the changes. The
second line should be blank.
If the commit is a bug fix reported by someone else or if the commit
originates from a patch posted by someone else, the next lines should be
reserved for crediting. The name of the person and their obfuscated email
address (for example edward at nmr-relax.com) should be included in the message.
@@ -109,55 +156,6 @@
If the commit relates to an entry in the bug tracker or to a discussion on the
mailing lists, then the web address of either the bug report or the mailing
list archive message should be cited in the next section (separated from the
synopsis or credit section by a blank line). All relevant links should be
included to allow easy navigation between the repository, mailing lists, bug
tracker, etc. An example is bug \#5559 which is located at
\href{https://gna.org/bugs/?func=detailitem\item\_id=5559}{https://gna.org/bugs/?func=detailitem\item\_id=5559}
and the post to ``relax-devel at gna.org'' describing the fix to that bug
which is located at
\href{https://mail.gna.org/public/relax-devel/2006-03/msg00013.html}{https://mail.gna.org/public/relax-devel/2006-03/msg00013.html}.
A full description containing all the details can follow. This description
should follow a blank line, can itself be sectioned using blank lines, and
finally the log is terminated by one blank line at the end of the message.
-
-
-
-
-% Submitting changes to the relax project.
-%~
-
-\section{Submitting changes to the relax project}
-
-
-% Submitting changes as a patch.
-\subsection{Submitting changes as a patch}
-
-The preferred method for submitting fixes and improvements to the relax source
code is by the creation of a patch. If your changes are a fix, make sure you
have submitted a bug report to the bug tracker located at
\href{https://gna.org/bugs/?group=relax}{https://gna.org/bugs/?group=relax}
first. See section~\ref{reporting bugs} on page~\pageref{reporting bugs} for
more details. Two methods can be used to generate the patch, either using the
Unix command \texttt{diff} or using the Subversion program. The resultant file
\texttt{patch} of either the \texttt{diff} or \texttt{svn} command described
below can be posted to the ``relax-devel at gna.org'' mailing list. Please
label within your post which version of relax you modified or which revision
the patch is for. Also try to create a commit log message according to the
format described in section~\ref{commit log format} on page~\pageref{commit log
format} for one of the relax committers to use as a template for committing the
change.
-
-
-% Modifications of official releases -- creating patchs with diff.
-\subsection{Modifications of the latest sources -- creating patchs with diff}
-
-If your modifications have been made to the source code of one of the official
relax releases (for example 1.2.2), then the Unix command \texttt{diff} can be
used to create a patch. A patch file is simply the output of the diff command
used recursively and presented in the `unified' format. Therefore two
directories need to be compared. If the original sources are located in the
directory \texttt{relax\_orig} and the modified sources in \texttt{relax\_mod},
then the patch can be created by typing
-
-\example{\$ diff -ur relax\_orig relax\_mod patch}
-
-
-% Modifications of the latest sources -- creating patchs with Subversion
r2434 - in /1.2/docs: latex/relax.tex relax.pdf
Author: bugman
Date: Thu Mar 30 03:28:38 2006
New Revision: 2434
URL: http://svn.gna.org/viewcvs/relax?rev=2434view=rev
Log:
Removed the acknowledgment section of the manual.
Modified:
1.2/docs/latex/relax.tex
1.2/docs/relax.pdf
Modified: 1.2/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/relax.tex?rev=2434r1=2433r2=2434view=diff
==
--- 1.2/docs/latex/relax.tex (original)
+++ 1.2/docs/latex/relax.tex Thu Mar 30 03:28:38 2006
@@ -99,19 +99,6 @@
\end{center}
\end{titlepage}
-
-
-% Acknowledgements.
-%%%
-
-\chapter*{Acknowledgements}
-
-Firstly, I am grateful and would like to thank Paul Gooley for giving me the
opportunity to create this program as part of my PhD. The duration of
development has been considerable and I thank Paul for allowing me the time to
learn Python and to implement many data analysis concepts into relax.
-
-I would also like to thank Andrew James Perry for innumerable, thoughtful
discussions on both the science and programming aspects behind relax. Many of
the important design features of relax originated as ideas of his and much of
the usability and core layout came from these discussions. Examples include
the prompt based interface with the help system and tab completion, the
automatic generation of the documentation on the user functions by parsing
their docstrings, details of the interaction with and control of other
programs, and the powerful Python scripting. Without Andrew, this program
would not be what it is today.
-
-Finally I would like to thank Haydyn D.T. Mertens and James D. Swarbrick for
many discussions and feedback.
-
% Table of Contents.
Modified: 1.2/docs/relax.pdf
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/relax.pdf?rev=2434r1=2433r2=2434view=diff
==
Binary files - no diff available.
___
relax (http://nmr-relax.com)
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relax-commits@gna.org
To unsubscribe from this list, get a password
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visit the list information page at
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r2435 - /1.2/COMMITTERS
Author: bugman Date: Thu Mar 30 08:09:25 2006 New Revision: 2435 URL: http://svn.gna.org/viewcvs/relax?rev=2435view=rev Log: Completely reformatted the COMMITTERS file and added Andrew Perry to the list. Modified: 1.2/COMMITTERS Modified: 1.2/COMMITTERS URL: http://svn.gna.org/viewcvs/relax/1.2/COMMITTERS?rev=2435r1=2434r2=2435view=diff == --- 1.2/COMMITTERS (original) +++ 1.2/COMMITTERS Thu Mar 30 08:09:25 2006 @@ -1,4 +1,19 @@ -Full access committers: +Project Administrator +~ -Edward d'Auvergne edward at nmr-relax.com -Chris MacRaild c.a.macraild at leeds.ac.uk +d'Auvergne, Edward J. ... edward at nmr-relax.com + + + +Full access committers +~~ + +MacRaild, Chris A. .. c.a.macraild at leeds.ac.uk +Perry, Andrew J. ... pansapiens at pansapiens.com + + + +Partial access committers +~ + +N/A ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2441 - in /1.2/test_suite: __init__.py generic.py test_suite.py
Author: bugman
Date: Wed Apr 5 05:05:21 2006
New Revision: 2441
URL: http://svn.gna.org/viewcvs/relax?rev=2441view=rev
Log:
Addition of a new test to the relax test suite.
The test creates three runs, two of which have S2 values set to 0.9 and 0.7.
The difference is
calculated and assigned to the third run. If the S2 value of the third run is
not ~0.2, then the
test fails.
Added:
1.2/test_suite/generic.py
Modified:
1.2/test_suite/__init__.py
1.2/test_suite/test_suite.py
Modified: 1.2/test_suite/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/__init__.py?rev=2441r1=2440r2=2441view=diff
==
--- 1.2/test_suite/__init__.py (original)
+++ 1.2/test_suite/__init__.py Wed Apr 5 05:05:21 2006
@@ -21,5 +21,10 @@
###
-__all__ = ['test',
- 'run_create']
+__all__ = ['test_suite',
+ 'diffusion_tensor',
+ 'generic.py',
+ 'model_free',
+ 'relax_fit',
+ 'run_create',
+ 'sequence']
Added: 1.2/test_suite/generic.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/generic.py?rev=2441view=auto
==
--- 1.2/test_suite/generic.py (added)
+++ 1.2/test_suite/generic.py Wed Apr 5 05:05:21 2006
@@ -1,0 +1,78 @@
+###
+# #
+# Copyright (C) 2006 Edward d'Auvergne#
+# #
+# This file is part of the program relax. #
+# #
+# relax is free software; you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published by#
+# the Free Software Foundation; either version 2 of the License, or #
+# (at your option) any later version. #
+# #
+# relax is distributed in the hope that it will be useful,#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details.#
+# #
+# You should have received a copy of the GNU General Public License #
+# along with relax; if not, write to the Free Software#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA #
+# #
+###
+
+import sys
+
+
+class Generic:
+def __init__(self, relax, test_name):
+Class for testing various aspects specific to relaxation
curve-fitting.
+
+self.relax = relax
+
+# Value difference test.
+if test_name == 'value_diff':
+# The name of the test.
+self.name = S2 difference stored in a new run.
+
+# The test.
+self.test = self.value_diff
+
+
+def value_diff(self, run):
+The test of storing an S2 difference in a new run.
+
+# Arguments.
+self.run = run
+
+# Create three runs.
+self.relax.interpreter._Run.create('orig1', mf)
+self.relax.interpreter._Run.create('orig2', mf)
+self.relax.interpreter._Run.create('new', mf)
+
+# Load the Lupin Ap4Aase sequence.
+self.relax.interpreter._Sequence.read('orig1', file=Ap4Aase.seq,
dir=sys.path[-1] + /test_suite/data)
+self.relax.interpreter._Sequence.read('orig2', file=Ap4Aase.seq,
dir=sys.path[-1] + /test_suite/data)
+self.relax.interpreter._Sequence.read('new', file=Ap4Aase.seq,
dir=sys.path[-1] + /test_suite/data)
+
+# Only select residue 8.
+self.relax.interpreter._Select.res('orig1', num=8, change_all=1)
+self.relax.interpreter._Select.res('orig2', num=8, change_all=1)
+self.relax.interpreter._Select.res('new', num=8, change_all=1)
+
+# Set two order parameter values.
+self.relax.interpreter._Value.set('orig1', 0.9, 'S2', res_num=8)
+self.relax.interpreter._Value.set('orig2', 0.7, 'S2', res_num=8)
+
+# Calculate the difference and assign it to residue 8 (located in
position 7).
+diff = self.relax.data.res['orig1'][7].s2 -
self.relax.data.res['orig2'][7].s2
+self.relax.interpreter._Value.set('new', diff, 'S2
r2443 - in /1.2/specific_fns: base_class.py model_free.py
Author: bugman Date: Wed Apr 5 06:57:46 2006 New Revision: 2443 URL: http://svn.gna.org/viewcvs/relax?rev=2443view=rev Log: Fix to bug #5660. The bug report is located at https://gna.org/bugs/?func=detailitemitem_id=5660. To fix the bug, a function in the base class of the specific functions has been added called 'self.has_error()'. This function checks the diffusion tensor data structures and the residue specific data structures for error objects by looping over all objects 'object_name' and seeing if there is a corresponding object called 'object_name' + '_err'. The model-free results writing function now checks the 'self.has_error()' result and if successful, then the error section is executed. The simulation section has also been modified to improve flexibility. Modified: 1.2/specific_fns/base_class.py 1.2/specific_fns/model_free.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: 1.2/specific_fns/base_class.py URL: http://svn.gna.org/viewcvs/relax/1.2/specific_fns/base_class.py?rev=2443r1=2442r2=2443view=diff Modified: 1.2/specific_fns/model_free.py URL: http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2443r1=2442r2=2443view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2446 - /1.2/data.py
Author: bugman
Date: Wed Apr 5 09:45:10 2006
New Revision: 2446
URL: http://svn.gna.org/viewcvs/relax?rev=2446view=rev
Log:
Stored the runs which form the hybrid in self.relax.data.hybrid_runs[].
This code is for task #3122 located at
https://gna.org/task/?func=detailitemitem_id=3122.
Modified:
1.2/data.py
Modified: 1.2/data.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/data.py?rev=2446r1=2445r2=2446view=diff
==
--- 1.2/data.py (original)
+++ 1.2/data.py Wed Apr 5 09:45:10 2006
@@ -53,6 +53,9 @@
# The type of the runs.
self.run_types = []
+
+# Hybrid models.
+self.hybrid_runs = []
# Global minimisation statistics.
self.chi2 = {}
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r2452 - in /1.2/specific_fns: hybrid.py model_free.py
Author: bugman
Date: Fri Apr 7 04:26:16 2006
New Revision: 2452
URL: http://svn.gna.org/viewcvs/relax?rev=2452view=rev
Log:
The run type 'hybrid' model-statistic returning function now handles numerous
instances.
Modified:
1.2/specific_fns/hybrid.py
1.2/specific_fns/model_free.py
Modified: 1.2/specific_fns/hybrid.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/hybrid.py?rev=2452r1=2451r2=2452view=diff
==
--- 1.2/specific_fns/hybrid.py (original)
+++ 1.2/specific_fns/hybrid.py Fri Apr 7 04:26:16 2006
@@ -110,16 +110,26 @@
# Function type.
function_type =
self.relax.data.run_types[self.relax.data.run_names.index(run)]
-# Specific model statistics functions.
+# Specific model statistics and number of instances functions.
model_statistics = self.relax.specific_setup.setup('model_stats',
function_type)
+num_instances = self.relax.specific_setup.setup('num_instances',
function_type)
-# Get the statistics.
-k, n, chi2 = model_statistics(run, instance=0, min_instances=1)
+# Number of instances.
+num = num_instances(run)
-# Sum the stats.
-k_total = k_total + k
-n_total = n_total + n
-chi2_total = chi2_total + chi2
+# Loop over the instances.
+for i in xrange(num):
+# Get the statistics.
+k, n, chi2 = model_statistics(run, instance=i,
num_instances=num)
+
+# Bad stats.
+if k == None or n == None or chi2 == None:
+continue
+
+# Sum the stats.
+k_total = k_total + k
+n_total = n_total + n
+chi2_total = chi2_total + chi2
# Return the totals.
return k_total, n_total, chi2_total
Modified: 1.2/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2452r1=2451r2=2452view=diff
==
--- 1.2/specific_fns/model_free.py (original)
+++ 1.2/specific_fns/model_free.py Fri Apr 7 04:26:16 2006
@@ -2513,6 +2513,10 @@
# Sequence specific data.
# Statistics for a single residue.
if not global_stats and not combine:
+# Skip unselected residues.
+if not self.relax.data.res[self.run][instance].select:
+return None, None, None
+
# Missing data sets.
if not hasattr(self.relax.data.res[self.run][instance],
'relax_data'):
return None, None, None
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r2453 - /1.2/COMMITTERS
Author: bugman Date: Fri Apr 7 06:15:19 2006 New Revision: 2453 URL: http://svn.gna.org/viewcvs/relax?rev=2453view=rev Log: Added Gary Thompson to the list of full access committers. Modified: 1.2/COMMITTERS Modified: 1.2/COMMITTERS URL: http://svn.gna.org/viewcvs/relax/1.2/COMMITTERS?rev=2453r1=2452r2=2453view=diff == --- 1.2/COMMITTERS (original) +++ 1.2/COMMITTERS Fri Apr 7 06:15:19 2006 @@ -10,6 +10,7 @@ MacRaild, Chris A. .. c.a.macraild at leeds.ac.uk Perry, Andrew J. ... pansapiens at pansapiens.com +Thompson, Gary S. .. garyt at bmb.leeds.ac.uk ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2496 - in /1.2/docs: ./ latex/
Author: bugman Date: Sat May 6 13:06:40 2006 New Revision: 2496 URL: http://svn.gna.org/viewcvs/relax?rev=2496view=rev Log: Editing of all chapters of the manual and a few large changes. The data analysis chapter has been split into four. The new chapters include the NOE chapter, the relaxation curve-fitting chapter, the model-free chapter, and the reduced spectral density mapping chapter. The start of the 'Value, gradient, and Hessian' chapter has been moved into the new model-free chapter under the section 'Theory'. The material moved includes the chi-squared equation, the relaxation equations, the transformed relaxation equations, the model-free spectral density functions, and the Brownian rotational diffusion equations. Many more places in the text have been indexed. The text of all chapters has been proofed. Added: 1.2/docs/latex/curvefit.tex - copied, changed from r2495, 1.2/docs/latex/data_analysis.tex 1.2/docs/latex/jw_mapping.tex - copied, changed from r2495, 1.2/docs/latex/data_analysis.tex 1.2/docs/latex/model-free.tex - copied, changed from r2495, 1.2/docs/latex/data_analysis.tex 1.2/docs/latex/noe.tex - copied, changed from r2495, 1.2/docs/latex/data_analysis.tex Modified: 1.2/docs/latex/bibliography.bib 1.2/docs/latex/data_analysis.tex 1.2/docs/latex/develop.tex 1.2/docs/latex/docstring.tex 1.2/docs/latex/functions.tex 1.2/docs/latex/infrastruct.tex 1.2/docs/latex/install.tex 1.2/docs/latex/intro.tex 1.2/docs/latex/licence.tex 1.2/docs/latex/maths.tex 1.2/docs/latex/relax.tex 1.2/docs/relax.pdf [This mail would be too long, it was shortened to contain the URLs only.] Modified: 1.2/docs/latex/bibliography.bib URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/bibliography.bib?rev=2496r1=2495r2=2496view=diff Copied: 1.2/docs/latex/curvefit.tex (from r2495, 1.2/docs/latex/data_analysis.tex) URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/curvefit.tex?p2=1.2/docs/latex/curvefit.texp1=1.2/docs/latex/data_analysis.texr1=2495r2=2496rev=2496view=diff Modified: 1.2/docs/latex/data_analysis.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/data_analysis.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/latex/develop.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/develop.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/latex/docstring.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/docstring.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/latex/functions.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/functions.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/latex/infrastruct.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/infrastruct.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/latex/install.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/install.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/latex/intro.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/intro.tex?rev=2496r1=2495r2=2496view=diff Copied: 1.2/docs/latex/jw_mapping.tex (from r2495, 1.2/docs/latex/data_analysis.tex) URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/jw_mapping.tex?p2=1.2/docs/latex/jw_mapping.texp1=1.2/docs/latex/data_analysis.texr1=2495r2=2496rev=2496view=diff Modified: 1.2/docs/latex/licence.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/licence.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/latex/maths.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/maths.tex?rev=2496r1=2495r2=2496view=diff Copied: 1.2/docs/latex/model-free.tex (from r2495, 1.2/docs/latex/data_analysis.tex) URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/model-free.tex?p2=1.2/docs/latex/model-free.texp1=1.2/docs/latex/data_analysis.texr1=2495r2=2496rev=2496view=diff Copied: 1.2/docs/latex/noe.tex (from r2495, 1.2/docs/latex/data_analysis.tex) URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/noe.tex?p2=1.2/docs/latex/noe.texp1=1.2/docs/latex/data_analysis.texr1=2495r2=2496rev=2496view=diff Modified: 1.2/docs/latex/relax.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/relax.tex?rev=2496r1=2495r2=2496view=diff Modified: 1.2/docs/relax.pdf URL: http://svn.gna.org/viewcvs/relax/1.2/docs/relax.pdf?rev=2496r1=2495r2=2496view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2497 - in /1.2/sample_scripts: mf_multimodel.py modsel.py
Author: bugman
Date: Sat May 6 13:20:21 2006
New Revision: 2497
URL: http://svn.gna.org/viewcvs/relax?rev=2497view=rev
Log:
Added the model m0 to the sample scripts.
Modified:
1.2/sample_scripts/mf_multimodel.py
1.2/sample_scripts/modsel.py
Modified: 1.2/sample_scripts/mf_multimodel.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/sample_scripts/mf_multimodel.py?rev=2497r1=2496r2=2497view=diff
==
--- 1.2/sample_scripts/mf_multimodel.py (original)
+++ 1.2/sample_scripts/mf_multimodel.py Sat May 6 13:20:21 2006
@@ -1,8 +1,8 @@
# Script for model-free analysis.
# Set the run names (also the names of preset model-free models).
-#runs = ['tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
-runs = ['m1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
+#runs = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
+runs = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
# Nuclei type
nuclei('N')
@@ -31,16 +31,9 @@
#diffusion_tensor.init(name, (1e-8, 1.0, 60, 290), param_types=0,
spheroid_type='oblate', fixed=0)
value.set(name, 1.02 * 1e-10, 'bond_length')
value.set(name, -160 * 1e-6, 'csa')
-#value.set(name, 0.970, 's2')
-#value.set(name, 1.0, 's2f')
-#value.set(name, 2048e-12, 'te')
-#value.set(name, 2048e-12, 'tf')
-#value.set(name, 2048e-12, 'ts')
-#value.set(name, 0.149/(2*pi*600e6)**2, 'rex')
# Select the model-free model.
model_free.select_model(run=name, model=name)
-#fix(name, 'all_res')
# Minimise.
grid_search(name, inc=11)
Modified: 1.2/sample_scripts/modsel.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/sample_scripts/modsel.py?rev=2497r1=2496r2=2497view=diff
==
--- 1.2/sample_scripts/modsel.py (original)
+++ 1.2/sample_scripts/modsel.py Sat May 6 13:20:21 2006
@@ -4,7 +4,7 @@
nuclei('N')
# Set the run names.
-runs = ['m1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
+runs = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
# Loop over the run names.
for name in runs:
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r2507 - in /1.2/docs: latex/develop.tex relax.pdf
Author: bugman
Date: Wed Jul 19 05:19:59 2006
New Revision: 2507
URL: http://svn.gna.org/viewcvs/relax?rev=2507view=rev
Log:
Spell check of the development chapter of the relax manual.
Modified:
1.2/docs/latex/develop.tex
1.2/docs/relax.pdf
Modified: 1.2/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/develop.tex?rev=2507r1=2506r2=2507view=diff
==
--- 1.2/docs/latex/develop.tex (original)
+++ 1.2/docs/latex/develop.tex Wed Jul 19 05:19:59 2006
@@ -375,7 +375,7 @@
\item[Prompt:] The main user interface consisting of a Python\index{Python}
prompt\index{prompt|textbf}. The namespace of the interpreter contains the
various user functions which are front ends to the generic code. The user
functions are simply Python functions which test the supplied arguments to make
sure they are of the correct type (string\index{string},
integer\index{integer}, list\index{list}, or any other type) before sending the
values to the generic code. The code for the prompt is located in the
directory \texttt{prompt/}.
-\item[Script:] If a script\index{script|textbf} is supplied on the command
line or executed within another user interface it will be run in the same
namespace as that of the prompt. Hence the script has access to all the user
functions availible at the relax prompt. This allows commands which are typed
at the prompt to be pasted directly and unmodified into a text file to be run
as a script.
+\item[Script:] If a script\index{script|textbf} is supplied on the command
line or executed within another user interface it will be run in the same
namespace as that of the prompt. Hence the script has access to all the user
functions available at the relax prompt. This allows commands which are typed
at the prompt to be pasted directly and unmodified into a text file to be run
as a script.
\item[GUI:] The graphical user interface\index{GUI|textbf}. Although not
coded the most mature and least destabilising widget set to use would be
QT\index{QT}. The GUI should be relatively easy to tie into relax. The design
is such that the GUI can be dropped straight into relax without effecting the
normal prompt and script based operation of the program.
@@ -383,7 +383,7 @@
\item[Generic code:] This code includes classes and functions which are
independent of the UI and not specific to a certain run type, for example not
being involved in model-free analysis, relaxation curve-fitting, the NOE
calculation, and reduced spectral density mapping. All this code is located in
the directory \texttt{generic\_fns/}.
-\item[Specific setup:] This code implements the internal interface between
the generic and specific code. The generic code calls the specific setup
asking for a specific function for the given run type. For example by asking
for the minimise function when the run type is model-free analysis the function
\texttt{self.rel\-ax.spec\-if\-ic.mod\-el\_free.min\-im\-ise()} is returned.
Althought the generic code accesses the specific code solely through this
interface the specific code can access the generic code directly. The code is
located in the file \texttt{specific\_fns/specific\_setup.py}.
+\item[Specific setup:] This code implements the internal interface between
the generic and specific code. The generic code calls the specific setup
asking for a specific function for the given run type. For example by asking
for the minimise function when the run type is model-free analysis the function
\texttt{self.rel\-ax.spec\-if\-ic.mod\-el\_free.min\-im\-ise()} is returned.
Although the generic code accesses the specific code solely through this
interface the specific code can access the generic code directly. The code is
located in the file \texttt{specific\_fns/specific\_setup.py}.
\item[Specific code:] This is the code which is specific to the run type --
model-free analysis, relaxation curve-fitting, reduced spectral density
mapping, and the NOE calculation. Each type is located in a separate file in
the directory \texttt{specific\_fns/}.
Modified: 1.2/docs/relax.pdf
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/relax.pdf?rev=2507r1=2506r2=2507view=diff
==
Binary files - no diff available.
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r2508 - /1.2/specific_fns/base_class.py
Author: bugman Date: Wed Jul 19 05:48:19 2006 New Revision: 2508 URL: http://svn.gna.org/viewcvs/relax?rev=2508view=rev Log: Fix to bug #6288. The report is located at https://gna.org/bugs/?func=detailitemitem_id=6288. The fix was to catch the value of None and hence not preform the 'float()' operation on it. Modified: 1.2/specific_fns/base_class.py Modified: 1.2/specific_fns/base_class.py URL: http://svn.gna.org/viewcvs/relax/1.2/specific_fns/base_class.py?rev=2508r1=2507r2=2508view=diff == --- 1.2/specific_fns/base_class.py (original) +++ 1.2/specific_fns/base_class.py Wed Jul 19 05:48:19 2006 @@ -161,7 +161,10 @@ self.data_init(self.relax.data.res[self.run][index]) # Set the value. -setattr(self.relax.data.res[self.run][index], object_name, float(value[i]) * scaling) +if value[i] == None: +setattr(self.relax.data.res[self.run][index], object_name, None) +else: +setattr(self.relax.data.res[self.run][index], object_name, float(value[i]) * scaling) # Individual data type. @@ -182,7 +185,10 @@ value = self.default_value(object_name) # Set the value. -setattr(self.relax.data.res[self.run][index], object_name, float(value) * scaling) +if value == None: +setattr(self.relax.data.res[self.run][index], object_name, None) +else: +setattr(self.relax.data.res[self.run][index], object_name, float(value) * scaling) # Set the error. if error != None: ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2511 - /1.2/specific_fns/model_free.py
Author: bugman Date: Wed Jul 19 07:13:44 2006 New Revision: 2511 URL: http://svn.gna.org/viewcvs/relax?rev=2511view=rev Log: Fix to bug #5806. The bug is located at https://gna.org/bugs/?func=detailitemitem_id=5806. To remove the bug, tests for the presence of relaxation data have been added to the model_statistics() functions. This may cause future bugs! Modified: 1.2/specific_fns/model_free.py Modified: 1.2/specific_fns/model_free.py URL: http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2511r1=2510r2=2511view=diff == --- 1.2/specific_fns/model_free.py (original) +++ 1.2/specific_fns/model_free.py Wed Jul 19 07:13:44 2006 @@ -2547,6 +2547,10 @@ if not self.relax.data.res[self.run][i].select: continue +# Skip residues with no relaxation data. +if not hasattr(self.relax.data.res[self.run][i], 'relax_data') or not len(self.relax.data.res[self.run][i].relax_data): +continue + # Count the number of parameters. self.param_vector = self.assemble_param_vector(index=i) k = k + len(self.param_vector) @@ -2568,6 +2572,10 @@ for i in xrange(len(self.relax.data.res[self.run])): # Skip unselected residues. if not self.relax.data.res[self.run][i].select: +continue + +# Skip residues with no relaxation data. +if not hasattr(self.relax.data.res[self.run][i], 'relax_data') or not len(self.relax.data.res[self.run][i].relax_data): continue n = n + len(self.relax.data.res[self.run][i].relax_data) ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2519 - /tags/1.2.5/
Author: bugman Date: Thu Jul 20 07:03:38 2006 New Revision: 2519 URL: http://svn.gna.org/viewcvs/relax?rev=2519view=rev Log: relax version 1.2.5. This is mainly a bugfix release. A large number of bugs have been eliminated including bug #5977, bug #6288, bug #6383, bug #5806, bug #6384, bug #6388, bug #6389, and bug #5746. These are described in more detail below. To fix a few of these bugs large disruptive changes were required. This included the change of the local tm parameter name from 'tm' to 'local_tm' and the simplification of the model-free model_statistics() function and modification of the model-free calculate() function. Therefore regressions and new bugs may appear in this release, most likely when the local tm parameter is encountered or during model selection. The full list of changes is: Features: * The data analysis chapter has been split into four: The NOE, relaxation curve-fitting, model-free, and reduced spectral density mapping chapters. * A section called the 'The core design of relax' has been added to the the development chapter of the manual. * The 'Values, gradients, and Hessians' chapter of the manual is now complete. These are all the equations used during optimisation. * The Hessian kite diagram and the gradient construction diagram have been added to the 'Values, gradients, and Hessians' chapter of the manual. Changes: * The distribution archives now unpack to the directory 'relax-x.x.x' rather than just' 'relax', where x.x.x is the version number. * All chapters of the manual have been edited and proofed. * The Sparky and XEasy peak intensity reading functions have been split to allow the easy addition of new peak intensity file types. * Test of AIC model selection between diffusion tensors added to the test suite. (To catch bug #5746) * Changing of the local tm parameter name of 'tm' to 'local_tm' to distinguish it from the global tumbling time 'tm'. (Preparation for fixing bug #6384) Bugfixes: * Fix of bug where self.relax.data.select_sim was treated as a list. (bug #5977) * The value.copy() function now handles the value of None. (bug #6288) * The global flag is now set by the relax_data.delete() function. (bug #6383) * The model-free model_statistics() function now tests for the presence of relaxation data. (bug #5806) * Sorting of global from local parameters in 'generic_fns/value.py' simplified and fixed by changing the parameter name 'tm' to 'local_tm'. (bug #6384) * Model-free parameters now set in the OpenDX mapping test of the test-suite. (bug #6388) * Failure of model elimination because of a 'local_tm' and 'tm' mix up. (bug #6389) * Modification of the model-free calculate() function and elimination of the 'combined' flag from the self.model_statistics() function. (bug #5746) Added: tags/1.2.5/ - copied from r2518, 1.2/ ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2521 - in /1.2/docs: Release_Checklist latex/docstring.tex latex/model-free.tex relax.pdf
Author: bugman
Date: Thu Jul 20 09:08:09 2006
New Revision: 2521
URL: http://svn.gna.org/viewcvs/relax?rev=2521view=rev
Log:
Fixed the Clore 1990 reference in the manual, changed the rsync command in the
release checklist,
and updated the manual.
Modified:
1.2/docs/Release_Checklist
1.2/docs/latex/docstring.tex
1.2/docs/latex/model-free.tex
1.2/docs/relax.pdf
Modified: 1.2/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/Release_Checklist?rev=2521r1=2520r2=2521view=diff
==
--- 1.2/docs/Release_Checklist (original)
+++ 1.2/docs/Release_Checklist Thu Jul 20 09:08:09 2006
@@ -33,7 +33,7 @@
* Move the distribution files and their signatures, as well as the PDF manual,
to the mirror directory for the relax download site. This directory should
contain all the files and directories accessible from
'http://download.gna.org/relax/'. Rsync the entire directory contents to
download.gna.org/upload/relax/ using the command
-$ rsync --delete -avr --rsh=ssh * [EMAIL PROTECTED]:/upload/relax/
+$ rsync --delete -av --rsh=ssh . [EMAIL PROTECTED]:/upload/relax/
Modified: 1.2/docs/latex/docstring.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/docstring.tex?rev=2521r1=2520r2=2521view=diff
==
--- 1.2/docs/latex/docstring.tex (original)
+++ 1.2/docs/latex/docstring.tex Thu Jul 20 09:08:09 2006
@@ -789,7 +789,7 @@
\toprule
Data type Object name Patterns \\
\midrule
- Local $\tau_m$ \quotecmd{tm} \quotecmd{\^{}tm\$} or \quotecmd{local\_tm}
\\
+ Local $\tau_m$ \quotecmd{local\_tm} \quotecmd{[Ll]ocal[ -\_]tm} \\
\\
Order\index{order parameter} parameter $S^2$ \quotecmd{s2}
\quotecmd{\^{}[Ss]2\$} \\
\\
@@ -1132,7 +1132,7 @@
\toprule
Data type Object name Patterns \\
\midrule
- Local $\tau_m$ \quotecmd{tm} \quotecmd{\^{}tm\$} or \quotecmd{local\_tm}
\\
+ Local $\tau_m$ \quotecmd{local\_tm} \quotecmd{[Ll]ocal[ -\_]tm} \\
\\
Order\index{order parameter} parameter $S^2$ \quotecmd{s2}
\quotecmd{\^{}[Ss]2\$} \\
\\
@@ -5727,7 +5727,7 @@
\toprule
Data type Object name Patterns \\
\midrule
- Local $\tau_m$ \quotecmd{tm} \quotecmd{\^{}tm\$} or \quotecmd{local\_tm}
\\
+ Local $\tau_m$ \quotecmd{local\_tm} \quotecmd{[Ll]ocal[ -\_]tm} \\
\\
Order\index{order parameter} parameter $S^2$ \quotecmd{s2}
\quotecmd{\^{}[Ss]2\$} \\
\\
@@ -5873,7 +5873,7 @@
\toprule
Data type Object name Patterns \\
\midrule
- Local $\tau_m$ \quotecmd{tm} \quotecmd{\^{}tm\$} or \quotecmd{local\_tm}
\\
+ Local $\tau_m$ \quotecmd{local\_tm} \quotecmd{[Ll]ocal[ -\_]tm} \\
\\
Order\index{order parameter} parameter $S^2$ \quotecmd{s2}
\quotecmd{\^{}[Ss]2\$} \\
\\
@@ -6054,7 +6054,7 @@
\toprule
Data type Object name Patterns \\
\midrule
- Local $\tau_m$ \quotecmd{tm} \quotecmd{\^{}tm\$} or \quotecmd{local\_tm}
\\
+ Local $\tau_m$ \quotecmd{local\_tm} \quotecmd{[Ll]ocal[ -\_]tm} \\
\\
Order\index{order parameter} parameter $S^2$ \quotecmd{s2}
\quotecmd{\^{}[Ss]2\$} \\
\\
@@ -6320,7 +6320,7 @@
\toprule
Data type Object name Patterns \\
\midrule
- Local $\tau_m$ \quotecmd{tm} \quotecmd{\^{}tm\$} or \quotecmd{local\_tm}
\\
+ Local $\tau_m$ \quotecmd{local\_tm} \quotecmd{[Ll]ocal[ -\_]tm} \\
\\
Order\index{order parameter} parameter $S^2$ \quotecmd{s2}
\quotecmd{\^{}[Ss]2\$} \\
\\
@@ -6352,7 +6352,7 @@
\toprule
Data type Object name Value \\
\midrule
- Local $\tau_m$ \quotecmd{tm} 10 * 1e-9 \\
+ Local $\tau_m$ \quotecmd{local\_tm} 10 * 1e-9 \\
\\
Order\index{order parameter} parameters $S^2$, $S^2_f$, and $S^2_s$
\quotecmd{s2}, \quotecmd{s2f}, \quotecmd{s2s} 0.8 \\
\\
@@ -6694,7 +6694,7 @@
\toprule
Data type Object name Patterns \\
\midrule
- Local $\tau_m$ \quotecmd{tm} \quotecmd{\^{}tm\$} or \quotecmd{local\_tm}
\\
+ Local $\tau_m$ \quotecmd{local\_tm} \quotecmd{[Ll]ocal[ -\_]tm} \\
\\
Order\index{order parameter} parameter $S^2$ \quotecmd{s2}
\quotecmd{\^{}[Ss]2\$} \\
\\
Modified: 1.2/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/model-free.tex?rev=2521r1=2520r2=2521view=diff
==
--- 1.2/docs/latex/model-free.tex (original)
+++ 1.2/docs/latex/model-free.tex Thu Jul 20 09:08:09 2006
@@ -81,7 +81,7 @@
\Bigg),
\end{equation}
-\noindent where $S^2$ is the square of the Lipari and Szabo generalised order
parameter and $\tau_e$ is the effective correlation time. The order parameter
reflects the amplitude of the motion and the correlation time in an indication
of the time scale
r2524 - /1.2/docs/CHANGES
Author: bugman Date: Fri Jul 21 05:09:18 2006 New Revision: 2524 URL: http://svn.gna.org/viewcvs/relax?rev=2524view=rev Log: Updated the CHANGES file for relax version 1.2.6, the fatal devnull import failure fix. Modified: 1.2/docs/CHANGES Modified: 1.2/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/1.2/docs/CHANGES?rev=2524r1=2523r2=2524view=diff == --- 1.2/docs/CHANGES (original) +++ 1.2/docs/CHANGES Fri Jul 21 05:09:18 2006 @@ -1,3 +1,19 @@ +Version 1.2.6 +(21 July 2006, from /1.2) +http://svn.gna.org/svn/relax/tags/1.2.6 + +Features: +N/A + +Changes: +N/A + +Bugfixes: +* Added the missing PDB file used by one of the OpenDX tests of the relax test-suite. (bug #6404) +* Fixed the fatal devnull import failure for Python versions 2.4. (bug #6403) + + + Version 1.2.5 (20 July 2006, from /1.2) http://svn.gna.org/svn/relax/tags/1.2.5 ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2528 - /branches/nan_catch_test/
Author: bugman Date: Wed Aug 9 07:28:47 2006 New Revision: 2528 URL: http://svn.gna.org/viewcvs/relax?rev=2528view=rev Log: Made a private branch of the 1.2 line to test proposed NaN catching code. Added: branches/nan_catch_test/ - copied from r2527, 1.2/ ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2530 - /branches/nan_catch_test/specific_fns/model_free.py
Author: bugman
Date: Wed Aug 9 07:48:36 2006
New Revision: 2530
URL: http://svn.gna.org/viewcvs/relax?rev=2530view=rev
Log:
Fix for the RelaxInfError and RelaxNaNError.
Modified:
branches/nan_catch_test/specific_fns/model_free.py
Modified: branches/nan_catch_test/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nan_catch_test/specific_fns/model_free.py?rev=2530r1=2529r2=2530view=diff
==
--- branches/nan_catch_test/specific_fns/model_free.py (original)
+++ branches/nan_catch_test/specific_fns/model_free.py Wed Aug 9 07:48:36 2006
@@ -2376,11 +2376,11 @@
# Catch infinite chi-squared values.
if self.func == float('inf'):
-raise RelaxInfError
+raise RelaxInfError, 'chi-squared'
# Catch chi-squared values of NaN.
if isnan(self.func):
-raise RelaxNaNError
+raise RelaxNaNError, 'chi-squared'
# Scaling.
if scaling:
___
relax (http://nmr-relax.com)
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r2532 - in /branches/nan_catch_test: errors.py generic_fns/pdb.py prompt/interpreter.py relax
Author: bugman
Date: Thu Aug 10 12:15:24 2006
New Revision: 2532
URL: http://svn.gna.org/viewcvs/relax?rev=2532view=rev
Log:
Created the RelaxWarning subsystem. The standard 'RelaxWarning' and the
'RelaxZeroVectorWarning'
warning classes have been created.
Modified:
branches/nan_catch_test/errors.py
branches/nan_catch_test/generic_fns/pdb.py
branches/nan_catch_test/prompt/interpreter.py
branches/nan_catch_test/relax
Modified: branches/nan_catch_test/errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nan_catch_test/errors.py?rev=2532r1=2531r2=2532view=diff
==
--- branches/nan_catch_test/errors.py (original)
+++ branches/nan_catch_test/errors.py Thu Aug 10 12:15:24 2006
@@ -23,7 +23,11 @@
import __builtin__
from re import match
from types import ClassType
-
+import warnings
+
+
+# Error objects.
+
class RelaxErrors:
def __init__(self):
@@ -476,3 +480,68 @@
class RelaxNaNError(BaseError):
def __init__(self, name):
self.text = The invalid + name + floating point value of NaN
(Not a Number) has occurred.
+
+
+
+# Warning objects.
+##
+
+class RelaxWarnings:
+def __init__(self):
+Class for placing all the warnings below into __builtin__
+
+# Loop over all objects in 'self'.
+for name in dir(self):
+# Get the object.
+object = getattr(self, name)
+
+# Skip over all non-warning class objects.
+if type(object) != ClassType or not match('Relax', name):
+continue
+
+# Place the warnings into __builtin__
+__builtin__.__setattr__(name, object)
+
+# Tuple of all the warnings.
+if hasattr(__builtin__, 'AllRelaxWarnings'):
+__builtin__.AllRelaxWarnings = __builtin__.AllRelaxWarnings,
object
+else:
+__builtin__.AllRelaxWarnings = object,
+
+# Change the formatting of the warning message.
+warnings.formatwarning = self.format
+
+
+def format(self, message, category, filename, lineno):
+Change the warning message formatting.
+
+# The RelaxWarning string.
+string = RelaxWarning: %s\n % message
+
+return string
+
+
+# Base class for all warnings.
+
+
+class BaseWarning(Warning):
+def __str__(self):
+return (self.text + \n)
+
+
+# Standard warnings.
+
+
+class RelaxWarning(BaseWarning):
+def __init__(self, text):
+self.text = text
+
+
+# Zero length vector.
+#
+
+class RelaxZeroVectorWarning(BaseWarning):
+def __init__(self, res):
+self.text = The XH bond vector for residue + `res` + is of
zero length.
+
+
Modified: branches/nan_catch_test/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nan_catch_test/generic_fns/pdb.py?rev=2532r1=2531r2=2532view=diff
==
--- branches/nan_catch_test/generic_fns/pdb.py (original)
+++ branches/nan_catch_test/generic_fns/pdb.py Thu Aug 10 12:15:24 2006
@@ -268,8 +268,10 @@
# Test for zero length.
if norm_factor == 0.0:
-if self.print_flag:
-print The XH bond vector for residue +
`self.relax.data.res[self.run][j].num` + is of zero length.
+# Warning.
+
warn(RelaxZeroVector(self.relax.data.res[self.run][j].num))
+
+# Set the vector to None.
self.relax.data.res[self.run][j].xh_vect.append(None)
# Calculate the normalised vector.
Modified: branches/nan_catch_test/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nan_catch_test/prompt/interpreter.py?rev=2532r1=2531r2=2532view=diff
==
--- branches/nan_catch_test/prompt/interpreter.py (original)
+++ branches/nan_catch_test/prompt/interpreter.py Thu Aug 10 12:15:24 2006
@@ -301,7 +301,10 @@
else:
more = self.push(line)
except KeyboardInterrupt:
-self.write(\nKeyboardInterrupt\n)
+if Debug:
+self.showtraceback()
+else:
+self.write(\nKeyboardInterrupt\n)
self.resetbuffer()
more = 0
@@ -345,6 +348,11 @@
self.showtraceback()
else:
sys.stderr.write(instance.__str__())
+except AllRelaxWarnings, instance:
+if Debug:
+self.showtraceback()
+else:
+sys.stderr.write(instance.__str__())
except:
raise
Modified: branches/nan_catch_test/relax
URL:
r2536 - /1.2/errors.py
Author: bugman
Date: Sat Aug 12 07:51:03 2006
New Revision: 2536
URL: http://svn.gna.org/viewcvs/relax?rev=2536view=rev
Log:
Significant improvements to the new error/warning system.
The idea of this system was suggested in two threads which commence at:
https://mail.gna.org/public/relax-devel/2006-08/msg00052.html
https://mail.gna.org/public/relax-devel/2006-08/msg00053.html
The improvements includes the addition of the printing of the traceback, the
option of saving the
program state (self.relax.data pickling), a new way of calling the RelaxErrors
or RelaxWarnings
(for example RelaxBadError('Hello')), addition of the warning functions, and a
number of other small
changes.
Modified:
1.2/errors.py
Modified: 1.2/errors.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/errors.py?rev=2536r1=2535r2=2536view=diff
==
--- 1.2/errors.py (original)
+++ 1.2/errors.py Sat Aug 12 07:51:03 2006
@@ -22,6 +22,7 @@
import __builtin__
from re import match, search
+from traceback import extract_stack, format_list
from types import ClassType
import time
import sys
@@ -43,16 +44,37 @@
self.initialise_errors()
-def error(self, message):
-Default error function - traceback, error message, then
sys.exit().
+def error(self, message, traceback=0, save=0):
+Default error function - traceback (Debug), error message, then
sys.exit().
+
+# Save the program state.
+if save:
+self.save_state()
# Write the traceback to stderr.
+if traceback and not self.UI_mode == 'prompt':
+self.traceback()
# Write the error message to stderr.
sys.stderr.write(RelaxError: + message + \n)
# Hard exit!
sys.exit()
+
+
+def error_no_exit(self, message, traceback=0, save=0):
+Error function without exit - print traceback (Debug) and error
message but don't exit.
+
+# Save the program state.
+if save:
+self.save_state()
+
+# Write the traceback to stderr.
+if traceback and not self.UI_mode == 'prompt':
+self.traceback()
+
+# Write the error message to stderr.
+sys.stderr.write(RelaxError: + message + \n\n\n)
def initialise_errors(self):
@@ -67,41 +89,159 @@
if type(object) != ClassType or not search('^Relax', name):
continue
-# Add the top level relax class.
-setattr(object, 'relax', self.relax)
+# Instantiate the object.
+instance = object()
+
+
+# Place data structures and functions into the RelaxError and
RelaxWarning instances.
+
#
+
+# Place the relax data structure into the instance.
+instance.relax = self.relax
+
+# Place the save state function into the instance.
+#instance.save_state = self.save_state
# Set up the RelaxError handling functions.
if search('Error$', name):
-object.exception = self.error
+# Default error.
+instance.exception = self.error
+
+# Don't exit the program in prompt mode when an error occurs.
+if self.UI_mode == 'prompt':
+instance.exception = self.error_no_exit
# Set up the RelaxWarning handling functions.
if search('Warning$', name):
-object.exception = self.warning
+# Default warning.
+instance.exception = self.warning
# Place the errors into __builtin__
-__builtin__.__setattr__(name, object)
+__builtin__.__setattr__(name, instance)
# Tuple of all the errors.
if hasattr(__builtin__, 'AllRelaxErrors'):
-__builtin__.AllRelaxErrors = __builtin__.AllRelaxErrors, object
+__builtin__.AllRelaxErrors = __builtin__.AllRelaxErrors,
instance
else:
-__builtin__.AllRelaxErrors = object,
-
-
+__builtin__.AllRelaxErrors = instance,
+
+
+def save_state(self):
+Function for saving the program state (self.relax.data) into a
temporary file.
+
+# Get the current time.
+now = time.localtime()
+
+# Format the file name.
+file_name = relax_state_%i%02i%02i_%02i%02i%02i % (now[0], now[2],
now[1], now[3], now[4], now[5])
+
+# Save the program state.
+self.relax.interpreter._State.save(file_name)
+
+
+def traceback(self):
+Function for formatting and printing out the traceback.
+
+# Get the stack.
+stack = extract_stack()
+
+# Initialise the trimmed stack and stack start flag.
+trimmed_stack = []
+start = 0
+
+# Trim the stack (script
r2537 - /1.2/errors.py
Author: bugman Date: Tue Aug 15 07:12:05 2006 New Revision: 2537 URL: http://svn.gna.org/viewcvs/relax?rev=2537view=rev Log: Modified the sys.exit() statements to return 1 to the shell to indicate failure. Modified: 1.2/errors.py Modified: 1.2/errors.py URL: http://svn.gna.org/viewcvs/relax/1.2/errors.py?rev=2537r1=2536r2=2537view=diff == --- 1.2/errors.py (original) +++ 1.2/errors.py Tue Aug 15 07:12:05 2006 @@ -58,8 +58,8 @@ # Write the error message to stderr. sys.stderr.write(RelaxError: + message + \n) -# Hard exit! -sys.exit() +# Hard exit (and return 1 to indicate failure)! +sys.exit(1) def error_no_exit(self, message, traceback=0, save=0): @@ -203,8 +203,8 @@ # Write the warning message to stderr. sys.stderr.write(RelaxWarning: + message + \n) -# Hard exit! -sys.exit() +# Hard exit (and return 1 to indicate failure)! +sys.exit(1) ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2548 - /1.2/sconstruct
Author: bugman Date: Fri Sep 1 13:50:52 2006 New Revision: 2548 URL: http://svn.gna.org/viewcvs/relax?rev=2548view=rev Log: Added a try statement to catch the ImportError failure of the 'lstat' and 'symlink' functions of the 'os' module within the 'sconstruct' script. This is a fix for bug #6841 (https://gna.org/bugs/?func=detailitemitem_id=6841) which was reported by Daniel Perez in the post at https://mail.gna.org/public/relax-users/2006-09/msg0.html (Message-id: [EMAIL PROTECTED]). The sconstruct function problems were identified by Chris MacRaild at https://mail.gna.org/public/relax-users/2006-09/msg3.html (Message-id: [EMAIL PROTECTED]). This import statement fails under MS Windows as the symlink 'os' functions are UNIX only. Modified: 1.2/sconstruct Modified: 1.2/sconstruct URL: http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2548r1=2547r2=2548view=diff == --- 1.2/sconstruct (original) +++ 1.2/sconstruct Fri Sep 1 13:50:52 2006 @@ -28,13 +28,20 @@ # Import statements. from glob import glob import platform -from os import F_OK, access, chdir, getcwd, lstat, path, remove, rmdir, sep, symlink, system, walk +from os import F_OK, access, chdir, getcwd, path, remove, rmdir, sep, system, walk from re import search from shutil import copytree, move import sys from tarfile import TarFile from version import version + +# UNIX only functions from the os module. +try: +from os import lstat, symlink +except ImportError: +pass + class Main: ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2551 - /branches/nan_catch_test/specific_fns/model_free.py
Author: bugman Date: Sun Sep 3 08:48:21 2006 New Revision: 2551 URL: http://svn.gna.org/viewcvs/relax?rev=2551view=rev Log: Commented out the calls to 'isnan()' and 'isinf()' in the model-free code. Modified: branches/nan_catch_test/specific_fns/model_free.py Modified: branches/nan_catch_test/specific_fns/model_free.py URL: http://svn.gna.org/viewcvs/relax/branches/nan_catch_test/specific_fns/model_free.py?rev=2551r1=2550r2=2551view=diff == --- branches/nan_catch_test/specific_fns/model_free.py (original) +++ branches/nan_catch_test/specific_fns/model_free.py Sun Sep 3 08:48:21 2006 @@ -2375,12 +2375,12 @@ self.h_count = self.h_count + hc # Catch infinite chi-squared values. -if self.relax.float.isinf(self.func): -raise RelaxInfError, 'chi-squared' +#if self.relax.float.isinf(self.func): +#raise RelaxInfError, 'chi-squared' # Catch chi-squared values of NaN. -if self.relax.float.isnan(self.func): -raise RelaxNaNError, 'chi-squared' +#if self.relax.float.isnan(self.func): +#raise RelaxNaNError, 'chi-squared' # Scaling. if scaling: ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2553 - in /1.2: errors.py float.py generic_fns/pdb.py minimise/line_search/backtrack.py relax specific_fns/model_free.py
Author: bugman Date: Sun Sep 3 10:28:49 2006 New Revision: 2553 URL: http://svn.gna.org/viewcvs/relax?rev=2553view=rev Log: Merged the 'nan_catch_test' branch (r2552) into the 1.2 line (r2552). The command used was: svn merge svn+ssh://[EMAIL PROTECTED]/svn/relax/[EMAIL PROTECTED] svn+ssh://[EMAIL PROTECTED]/svn/relax/branches/[EMAIL PROTECTED] This branch was created as a branch off the 1.2 line at r2528. It was in response to bug #6503 (https://gna.org/bugs/?func=detailitemitem_id=6503) and the subsequent discussions in the threads starting at https://mail.gna.org/public/relax-devel/2006-08/msg0.html (Message-id: [EMAIL PROTECTED]) and https://mail.gna.org/public/relax-devel/2006-08/msg00029.html (Message-id: [EMAIL PROTECTED]). The two functions 'isnan()' and 'isinf()' have been created to fix the bug. These are however not currently functional. In addition bug #6510 (https://gna.org/bugs/?func=detailitemitem_id=6510) has been fixed. Added: 1.2/float.py - copied unchanged from r2552, branches/nan_catch_test/float.py Modified: 1.2/errors.py 1.2/generic_fns/pdb.py 1.2/minimise/line_search/backtrack.py 1.2/relax 1.2/specific_fns/model_free.py Modified: 1.2/errors.py URL: http://svn.gna.org/viewcvs/relax/1.2/errors.py?rev=2553r1=2552r2=2553view=diff == --- 1.2/errors.py (original) +++ 1.2/errors.py Sun Sep 3 10:28:49 2006 @@ -597,4 +597,21 @@ self.text = The colour + `colour` + is invalid. if Debug: self.save_state() - + + +# Value errors. +### + +# Infinity. +class RelaxInfError(BaseError): +def __init__(self, name): +self.text = The invalid + name + floating point value of infinity has occurred. +if Debug: +self.save_state() + +# NaN (Not a Number). +class RelaxNaNError(BaseError): +def __init__(self, name): +self.text = The invalid + name + floating point value of NaN (Not a Number) has occurred. +if Debug: +self.save_state() Modified: 1.2/generic_fns/pdb.py URL: http://svn.gna.org/viewcvs/relax/1.2/generic_fns/pdb.py?rev=2553r1=2552r2=2553view=diff == --- 1.2/generic_fns/pdb.py (original) +++ 1.2/generic_fns/pdb.py Sun Sep 3 10:28:49 2006 @@ -156,6 +156,10 @@ print The PDB file + `self.file_path` + cannot be found, no structures will be loaded. return +# Test that the nuclei have been correctly set. +if self.heteronuc == self.proton: +raise RelaxError, The proton and heteronucleus are set to the same atom. + # Data creation. @@ -256,9 +260,21 @@ # Get the heteronucleus position. posX = pdb_res.atoms[self.heteronuc].position.array +# Calculate the XH bond vector. +vector = posH - posX + +# Normalisation factor. +norm_factor = sqrt(dot(vector, vector)) + +# Test for zero length. +if norm_factor == 0.0: +if self.print_flag: +print The XH bond vector for residue + `self.relax.data.res[self.run][j].num` + is of zero length. +self.relax.data.res[self.run][j].xh_vect.append(None) + # Calculate the normalised vector. -vector = posH - posX -self.relax.data.res[self.run][j].xh_vect.append(vector / sqrt(dot(vector, vector))) +else: +self.relax.data.res[self.run][j].xh_vect.append(vector / norm_factor) # Print out. if self.print_flag: Modified: 1.2/minimise/line_search/backtrack.py URL: http://svn.gna.org/viewcvs/relax/1.2/minimise/line_search/backtrack.py?rev=2553r1=2552r2=2553view=diff == --- 1.2/minimise/line_search/backtrack.py (original) +++ 1.2/minimise/line_search/backtrack.py Sun Sep 3 10:28:49 2006 @@ -23,7 +23,7 @@ from Numeric import dot -def backtrack(func, args, x, f, g, p, a_init=1.0, rho=0.5, c=1e-4): +def backtrack(func, args, x, f, g, p, a_init=1.0, rho=0.5, c=1e-4, max_iter=500): Backtracking line search. Procedure 3.1, page 41, from 'Numerical Optimization' by Jorge Nocedal and Stephen J. Wright, @@ -63,8 +63,9 @@ # Initialise values. a = a_init f_count = 0 +i = 0 -while 1: +while i = max_iter: fk = apply(func, (x + a*p,)+args) f_count = f_count + 1 @@ -73,3 +74,6 @@ return a, f_count else: a = rho*a + +#
r2554 - in /1.2: generic_fns/minimise.py thread_classes.py
Author: bugman Date: Mon Sep 4 09:23:26 2006 New Revision: 2554 URL: http://svn.gna.org/viewcvs/relax?rev=2554view=rev Log: Removed the 'Popen3' class, UNIX only dependency from relax by commenting out two import statements. This was in response to Daniel Perez's post at https://mail.gna.org/public/relax-users/2006-09/msg6.html (Message-id: [EMAIL PROTECTED]). The changes were discussed in my response to the post at https://mail.gna.org/public/relax-users/2006-09/msg7.html (Message-id: [EMAIL PROTECTED]). The Popen3 dependance prevents relax from running under MS Windows and hence has been removed. Although previously broken, the threading code is now definitely non-functional. This will have to be addressed in the future when someone works on the threading code. I've created task #3629 (https://gna.org/task/?func=detailitemitem_id=3629) for this. Modified: 1.2/generic_fns/minimise.py 1.2/thread_classes.py Modified: 1.2/generic_fns/minimise.py URL: http://svn.gna.org/viewcvs/relax/1.2/generic_fns/minimise.py?rev=2554r1=2553r2=2554view=diff == --- 1.2/generic_fns/minimise.py (original) +++ 1.2/generic_fns/minimise.py Mon Sep 4 09:23:26 2006 @@ -24,7 +24,7 @@ from Queue import Queue from re import search -from processes import RelaxPopen3 +#from processes import RelaxPopen3 from thread_classes import RelaxParentThread, RelaxThread Modified: 1.2/thread_classes.py URL: http://svn.gna.org/viewcvs/relax/1.2/thread_classes.py?rev=2554r1=2553r2=2554view=diff == --- 1.2/thread_classes.py (original) +++ 1.2/thread_classes.py Mon Sep 4 09:23:26 2006 @@ -31,7 +31,7 @@ from threading import Lock, Thread from data import Element -from processes import RelaxPopen3 +#from processes import RelaxPopen3 # Class for setting up threading. ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2556 - /1.2/relax
Author: bugman Date: Sun Sep 10 14:10:11 2006 New Revision: 2556 URL: http://svn.gna.org/viewcvs/relax?rev=2556view=rev Log: Changed the introduction string width to be 80 characters wide under MS Windows (the width of cmd.exe). Modified: 1.2/relax Modified: 1.2/relax URL: http://svn.gna.org/viewcvs/relax/1.2/relax?rev=2556r1=2555r2=2556view=diff == --- 1.2/relax (original) +++ 1.2/relax Sun Sep 10 14:10:11 2006 @@ -36,6 +36,7 @@ # Python modules. import __builtin__ from os import F_OK, access, getpid, putenv +import platform import profile import pstats from re import match @@ -93,6 +94,9 @@ # Get and store the PID of this process. self.pid = getpid() +# Store the operating system name. +self.platform = platform.uname()[0] + # Set up the program internal errors. RelaxErrors(self) @@ -346,33 +350,48 @@ def set_intro_string(self): Create the program introduction. +# The width of the printout. +if self.platform == 'Windows': +width = 80 +else: +width = 100 + # Some new lines. self.intro_string = '\n\n\n' # Program name and version. string = relax + self.version -self.intro_string = self.intro_string + self.spacing(string) + '\n\n' +self.intro_string = self.intro_string + self.spacing(string, width) + '\n\n' # Program description. string = Protein dynamics by NMR relaxation data analysis -self.intro_string = self.intro_string + self.spacing(string) + '\n\n' +self.intro_string = self.intro_string + self.spacing(string, width) + '\n\n' # Copyright printout. string = Copyright (C) 2001-2006 Edward d'Auvergne -self.intro_string = self.intro_string + self.spacing(string) + '\n\n' - -# Program licence and help. -self.intro_string = self.intro_string + This is free software which you are welcome to modify and redistribute under the conditions of the\n -self.intro_string = self.intro_string + GNU General Public License (GPL). This program, including all modules, is licensed under the GPL\n -self.intro_string = self.intro_string + and comes with absolutely no warranty. For details type 'GPL'. Assistance in using this program\n -self.intro_string = self.intro_string + can be accessed by typing 'help'.\n - - -def spacing(self, string): +self.intro_string = self.intro_string + self.spacing(string, width) + '\n\n' + +# Program licence and help (80 characters wide). +if width == 80: +self.intro_string = self.intro_string + This is free software which you are welcome to modify and redistribute under\n +self.intro_string = self.intro_string + the conditions of the GNU General Public License (GPL). This program,\n +self.intro_string = self.intro_string + including all modules, is licensed under the GPL and comes with absolutely no\n +self.intro_string = self.intro_string + warranty. For details type 'GPL'. Assistance in using this program can be\n +self.intro_string = self.intro_string + accessed by typing 'help'.\n + +# Program licence and help (100 characters wide). +else: +self.intro_string = self.intro_string + This is free software which you are welcome to modify and redistribute under the conditions of the\n +self.intro_string = self.intro_string + GNU General Public License (GPL). This program, including all modules, is licensed under the GPL\n +self.intro_string = self.intro_string + and comes with absolutely no warranty. For details type 'GPL'. Assistance in using this program\n +self.intro_string = self.intro_string + can be accessed by typing 'help'.\n + + +def spacing(self, string, width=100): Function for formatting the string to be centered to 100 spaces. # Calculate the number of spaces needed. -spaces = (100 - len(string)) / 2 +spaces = (width - len(string)) / 2 # The new string. string = spaces * ' ' + string ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2557 - /branches/warning/errors.py
Author: bugman Date: Wed Sep 13 12:44:23 2006 New Revision: 2557 URL: http://svn.gna.org/viewcvs/relax?rev=2557view=rev Log: A number of cosmetic changes to the 'error.py' file (addition of comments and removal of spaces). I mentioned these changes within the post located at https://mail.gna.org/public/relax-devel/2006-08/msg00082.html (Message-id: [EMAIL PROTECTED]). I've added a number of comments to both the RelaxError and RelaxWarning systems. There were also a large number of empty lines with trailing white-space that I've cleaned up as well. This may make the merging process a little more difficult. Modified: branches/warning/errors.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/warning/errors.py URL: http://svn.gna.org/viewcvs/relax/branches/warning/errors.py?rev=2557r1=2556r2=2557view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2560 - /1.2/relax.bat
Author: bugman Date: Thu Sep 14 08:25:40 2006 New Revision: 2560 URL: http://svn.gna.org/viewcvs/relax?rev=2560view=rev Log: Added a few comments to the Windows batch file and added the clear screen command 'cls'. Modified: 1.2/relax.bat Modified: 1.2/relax.bat URL: http://svn.gna.org/viewcvs/relax/1.2/relax.bat?rev=2560r1=2559r2=2560view=diff == --- 1.2/relax.bat (original) +++ 1.2/relax.bat Thu Sep 14 08:25:40 2006 @@ -8,4 +8,13 @@ REM variable and add the text ;C:\Program Files\Python24;C:\relax to the end REM of variable value field (modify the text to point to the correct location). -python %~dp0%0 %* +REM Catch [Ctrl-C] and exit without asking Terminate batch job (Y/N)?. +REM on break quit + +REM Clear the screen. +cls + +REM Run relax using python. %~dp0 will expand to the path where relax is found +REM and %0 is simply 'relax'. %* will send all the remaining arguments to +REM relax. +python %~dp0%0 %* ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2564 - /1.2/sconstruct
Author: bugman
Date: Fri Sep 15 06:58:28 2006
New Revision: 2564
URL: http://svn.gna.org/viewcvs/relax?rev=2564view=rev
Log:
Modified the LaTeX manual compilation section of the sconstruct script so that
scons does not fail
when the PS or PDF files are missing.
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2564r1=2563r2=2564view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Fri Sep 15 06:58:28 2006
@@ -787,8 +787,10 @@
system('ps2pdf -dAutoFilterColorImages=false
-dAutoFilterGrayImages=false -dColorImageFilter=/FlateEncode
-dColorImageFilter=/FlateEncode -dGrayImageFilter=/FlateEncode
-dMonoImageFilter=/FlateEncode -dPDFSETTINGS=/prepress relax.ps')
print \n\n\n Removing the PS file and shifting the PDF down a
directory \n\n\n
-remove('relax.ps')
-move('relax.pdf', '..')
+if access('relax.ps', F_OK):
+remove('relax.ps')
+if access('relax.pdf', F_OK):
+move('relax.pdf', '..')
# Return to the base directory.
chdir(base_dir)
___
relax (http://nmr-relax.com)
This is the relax-commits mailing list
relax-commits@gna.org
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
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r2566 - /1.2/docs/CHANGES
Author: bugman Date: Mon Sep 18 07:53:37 2006 New Revision: 2566 URL: http://svn.gna.org/viewcvs/relax?rev=2566view=rev Log: Updated the CHANGES file for relax version 1.2.7, the MS Windows release. Modified: 1.2/docs/CHANGES Modified: 1.2/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/1.2/docs/CHANGES?rev=2566r1=2565r2=2566view=diff == --- 1.2/docs/CHANGES (original) +++ 1.2/docs/CHANGES Mon Sep 18 07:53:37 2006 @@ -1,3 +1,27 @@ +Version 1.2.7 +(18 September 2006, from /1.2) +http://svn.gna.org/svn/relax/tags/1.2.7 + +Features: +* The C modules now compile without problem on MS Windows. +* The MS Windows binary distribution packages are now successfully built using the SCons build system. +* The batch file 'relax.bat' has been created for running relax from the MS Windows command prompt. +* The program introduction width is now 80 characters in MS Windows for proper display from the command prompt. + +Changes: +* The program state is saved when a RelaxError occurs in debugging mode. +* KeyboardInterupt during script execution in debugging mode will print the Python traceback. + +Bugfixes: +* The sconstruct script no longer fails in MS Windows. (bug #6980) +* Model selection is now functional on all operating systems. (bug #6873). +* The use of the Unix only class 'Popen3' has been removed to allow relax to function on all non-Unix operating systems. (bug #6841) +* If the XH bond vector length is 0, the vector is set to None rather than raising a RelaxError. (partial fix to bug #6503) +* Fix for the sconstruct script failure on MS Windows due to ImportErrors caused by importing Unix specific code. (bug #6841) +* Fix for ImportErrors in MS Windows preventing relax from running. (bug #6841) + + + Version 1.2.6 (21 July 2006, from /1.2) http://svn.gna.org/svn/relax/tags/1.2.6 ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2567 - /tags/1.2.7/
Author: bugman Date: Mon Sep 18 09:00:43 2006 New Revision: 2567 URL: http://svn.gna.org/viewcvs/relax?rev=2567view=rev Log: relax version 1.2.7. This is the MS Windows compatibility release. To allow relax to function properly on MS Windows a number of changes were necessary. This includes a number of bug fixes, the creation of the 'relax.bat' batch file, and modifications to allow the C modules to be compiled. Pre-compiled Windows zip files will now be available for download from the relax download page (http://www.nmr-relax.com/download.html). The full list of changes is: Features: * The C modules now compile without problem on MS Windows. * The MS Windows binary distribution packages are now successfully built using the SCons build system. * The batch file 'relax.bat' has been created for running relax from the MS Windows command prompt. * The program introduction width is now 80 characters in MS Windows for proper display from the command prompt. Changes: * The program state is saved when a RelaxError occurs in debugging mode. * KeyboardInterupt during script execution in debugging mode will print the Python traceback. Bugfixes: * The sconstruct script no longer fails in MS Windows. (bug #6980) * Model selection is now functional on all operating systems. (bug #6873) * The use of the Unix only class 'Popen3' has been removed to allow relax to function on all non-Unix operating systems. (bug #6841) * If the XH bond vector length is 0, the vector is set to None rather than raising a RelaxError. (partial fix to bug #6503) * Fix for the sconstruct script failure on MS Windows due to ImportErrors caused by importing Unix specific code. (bug #6841) * Fix for ImportErrors in MS Windows preventing relax from running. (bug #6841) Added: tags/1.2.7/ - copied from r2566, 1.2/ ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2568 - in /1.2/docs: latex/install.tex relax.pdf
Author: bugman
Date: Mon Sep 18 10:58:39 2006
New Revision: 2568
URL: http://svn.gna.org/viewcvs/relax?rev=2568view=rev
Log:
Added MS Windows installation instructions to the manual.
Modified:
1.2/docs/latex/install.tex
1.2/docs/relax.pdf
Modified: 1.2/docs/latex/install.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/install.tex?rev=2568r1=2567r2=2568view=diff
==
--- 1.2/docs/latex/install.tex (original)
+++ 1.2/docs/latex/install.tex Mon Sep 18 10:58:39 2006
@@ -12,10 +12,10 @@
The following packages need to be installed before using relax:
\begin{description}
-\item[Python:] Version 2.4 or higher\index{Python} (although any 2.x version
may work).
-\item[Numeric:] Version 21 or higher\index{Numeric}.
-\item[ScientificPython:] Version 2.2 or higher\index{ScientificPython}.
-\item[Optik:] Version 1.4 or higher. This is only needed if running python
= 2.2\index{Optik}.
+\item[\href{http://python.org/}{Python}\index{Python}:] Version 2.4 or higher
(although any 2.x version may work).
+\item[\href{http://numpy.scipy.org/}{Numeric}\index{Numeric}:] Version 21 or
higher.
+\item[\href{http://starship.python.net/~hinsen/ScientificPython/}{ScientificPython}\index{ScientificPython}:]
Version 2.2 or higher.
+\item[Optik\index{Optik}:] Version 1.4 or higher. This is only needed if
running python $=$ 2.2.
\end{description}
Older versions of these packages may work, use them at your own risk. If, for
older dependency versions, errors do occur please submit a bug report to the
bug tracker\index{bug tracker} at
\href{https://gna.org/bugs/?group=relax}{https://gna.org/bugs/?group=relax}.
That way a solution may be created for the next relax release.
@@ -68,17 +68,27 @@
+% Installation on MS Windows.
+\subsection{Installation on MS Windows}
+\index{MS Windows|textbf}
+
+In addition to the above dependencies, running relax on MS Windows requires a
number of additional programs. These include:
+
+\begin{description}
+\item[\href{http://projects.scipy.org/ipython/ipython/wiki/PyReadline/Intro}{pyreadline}\index{pyreadline}:]
Version 1.3 or higher
(\href{http://ipython.scipy.org/dist/pyreadline-1.3.win32.exe}{download}).
+\item[\href{http://starship.python.net/crew/theller/ctypes/}{ctypes}\index{ctypes}:]
The pyreadline package requires ctypes
(\href{http://prdownloads.sourceforge.net/ctypes/ctypes-1.0.0.win32-py2.4.exe?download}{download}).
+\end{description}
+
+To install, simply download the pre-compiled binary distribution
\texttt{relax-x.x.x.Win32.zip} or the source distribution
\texttt{relax-x.x.x.src.zip} and extract the files to
\texttt{C:$\backslash$Program Files$\backslash$relax-x.x.x}. Then add this
directory to the system environment path (in Windows XP, right click on `My
Computer', go to `Properties', click on the `Advanced' tab, and click on the
`Envirnment Variables' button. Then double click on the `Path' system variable
and add the text ``;C:$\backslash$Program Files$\backslash$relax-x.x.x'' to the
end of variable value field. The Python installation must also be located on
the path (add the text ``;C:$\backslash$Program Files$\backslash$Python24'',
changing the text to point to the correct directory, to the field). To run the
program from any directory inside the Windows command prompt (or dos prompt)
type:
+
+\example{C:$\backslash$ relax}
+
+
+
+
% Installation on Mac OS X.
\subsection{Installation on Mac OS X}
\index{Mac OS X|textbf}
-
-Please write me if you know how to do this!
-
-
-
-% Installation on MS Windows.
-\subsection{Installation on MS Windows}
-\index{MS Windows|textbf}
Please write me if you know how to do this!
@@ -94,9 +104,7 @@
% Running a non-compiled version.
\subsection{Running a non-compiled version}
-Compilation of the C code is not essential for running relax. However certain
features of the program will be disabled. One example is relaxation
curve-fitting. This approach may be necessary for systems, such as MS Windows,
where C compilers are not readily available (although the cygwin environment
may provide the tools required for compilation).
-
-To run relax without compilation install the dependencies detailed above,
download the source distribution which should be named
\texttt{relax-x.x.x.src.tar.bz2}, extract the files, and then run the file
called \texttt{relax} in the base directory.
+Compilation of the C code is not essential for running relax, however certain
features of the program will be disabled. Currently only the exponential
curve-fitting for determining the $\Rone$ and $\Rtwo$ relaxation rates requires
compilation. To run relax without compilation install the dependencies
detailed above, download the source distribution which should be named
\texttt{relax-x.x.x.src.tar.bz2}, extract the files, and then run the file
called \texttt{relax} in the base directory.
Modified:
r2569 - in /tags/1.2.7/docs: latex/install.tex relax.pdf
Author: bugman
Date: Mon Sep 18 11:02:38 2006
New Revision: 2569
URL: http://svn.gna.org/viewcvs/relax?rev=2569view=rev
Log:
Merged in the MS Windows installation instructions from the 1.2 line.
The command used was 'svn merge -r2567:2568 svn+ssh://[EMAIL
PROTECTED]/svn/relax/1.2'.
Modified:
tags/1.2.7/docs/latex/install.tex
tags/1.2.7/docs/relax.pdf
Modified: tags/1.2.7/docs/latex/install.tex
URL:
http://svn.gna.org/viewcvs/relax/tags/1.2.7/docs/latex/install.tex?rev=2569r1=2568r2=2569view=diff
==
--- tags/1.2.7/docs/latex/install.tex (original)
+++ tags/1.2.7/docs/latex/install.tex Mon Sep 18 11:02:38 2006
@@ -12,10 +12,10 @@
The following packages need to be installed before using relax:
\begin{description}
-\item[Python:] Version 2.4 or higher\index{Python} (although any 2.x version
may work).
-\item[Numeric:] Version 21 or higher\index{Numeric}.
-\item[ScientificPython:] Version 2.2 or higher\index{ScientificPython}.
-\item[Optik:] Version 1.4 or higher. This is only needed if running python
= 2.2\index{Optik}.
+\item[\href{http://python.org/}{Python}\index{Python}:] Version 2.4 or higher
(although any 2.x version may work).
+\item[\href{http://numpy.scipy.org/}{Numeric}\index{Numeric}:] Version 21 or
higher.
+\item[\href{http://starship.python.net/~hinsen/ScientificPython/}{ScientificPython}\index{ScientificPython}:]
Version 2.2 or higher.
+\item[Optik\index{Optik}:] Version 1.4 or higher. This is only needed if
running python $=$ 2.2.
\end{description}
Older versions of these packages may work, use them at your own risk. If, for
older dependency versions, errors do occur please submit a bug report to the
bug tracker\index{bug tracker} at
\href{https://gna.org/bugs/?group=relax}{https://gna.org/bugs/?group=relax}.
That way a solution may be created for the next relax release.
@@ -68,17 +68,27 @@
+% Installation on MS Windows.
+\subsection{Installation on MS Windows}
+\index{MS Windows|textbf}
+
+In addition to the above dependencies, running relax on MS Windows requires a
number of additional programs. These include:
+
+\begin{description}
+\item[\href{http://projects.scipy.org/ipython/ipython/wiki/PyReadline/Intro}{pyreadline}\index{pyreadline}:]
Version 1.3 or higher
(\href{http://ipython.scipy.org/dist/pyreadline-1.3.win32.exe}{download}).
+\item[\href{http://starship.python.net/crew/theller/ctypes/}{ctypes}\index{ctypes}:]
The pyreadline package requires ctypes
(\href{http://prdownloads.sourceforge.net/ctypes/ctypes-1.0.0.win32-py2.4.exe?download}{download}).
+\end{description}
+
+To install, simply download the pre-compiled binary distribution
\texttt{relax-x.x.x.Win32.zip} or the source distribution
\texttt{relax-x.x.x.src.zip} and extract the files to
\texttt{C:$\backslash$Program Files$\backslash$relax-x.x.x}. Then add this
directory to the system environment path (in Windows XP, right click on `My
Computer', go to `Properties', click on the `Advanced' tab, and click on the
`Envirnment Variables' button. Then double click on the `Path' system variable
and add the text ``;C:$\backslash$Program Files$\backslash$relax-x.x.x'' to the
end of variable value field. The Python installation must also be located on
the path (add the text ``;C:$\backslash$Program Files$\backslash$Python24'',
changing the text to point to the correct directory, to the field). To run the
program from any directory inside the Windows command prompt (or dos prompt)
type:
+
+\example{C:$\backslash$ relax}
+
+
+
+
% Installation on Mac OS X.
\subsection{Installation on Mac OS X}
\index{Mac OS X|textbf}
-
-Please write me if you know how to do this!
-
-
-
-% Installation on MS Windows.
-\subsection{Installation on MS Windows}
-\index{MS Windows|textbf}
Please write me if you know how to do this!
@@ -94,9 +104,7 @@
% Running a non-compiled version.
\subsection{Running a non-compiled version}
-Compilation of the C code is not essential for running relax. However certain
features of the program will be disabled. One example is relaxation
curve-fitting. This approach may be necessary for systems, such as MS Windows,
where C compilers are not readily available (although the cygwin environment
may provide the tools required for compilation).
-
-To run relax without compilation install the dependencies detailed above,
download the source distribution which should be named
\texttt{relax-x.x.x.src.tar.bz2}, extract the files, and then run the file
called \texttt{relax} in the base directory.
+Compilation of the C code is not essential for running relax, however certain
features of the program will be disabled. Currently only the exponential
curve-fitting for determining the $\Rone$ and $\Rtwo$ relaxation rates requires
compilation. To run relax without compilation install the dependencies
detailed above, download the source distribution which should be named
r2570 - in /tags/1.2.7: docs/latex/relax_version.tex docs/relax.pdf version.py
Author: bugman Date: Tue Sep 19 05:39:43 2006 New Revision: 2570 URL: http://svn.gna.org/viewcvs/relax?rev=2570view=rev Log: Updated the manual and changed the version number to 1.2.7. Modified: tags/1.2.7/docs/latex/relax_version.tex tags/1.2.7/docs/relax.pdf tags/1.2.7/version.py Modified: tags/1.2.7/docs/latex/relax_version.tex URL: http://svn.gna.org/viewcvs/relax/tags/1.2.7/docs/latex/relax_version.tex?rev=2570r1=2569r2=2570view=diff == --- tags/1.2.7/docs/latex/relax_version.tex (original) +++ tags/1.2.7/docs/latex/relax_version.tex Tue Sep 19 05:39:43 2006 @@ -1,1 +1,1 @@ -Version repository checkout +Version 1.2.7 Modified: tags/1.2.7/docs/relax.pdf URL: http://svn.gna.org/viewcvs/relax/tags/1.2.7/docs/relax.pdf?rev=2570r1=2569r2=2570view=diff == Binary files - no diff available. Modified: tags/1.2.7/version.py URL: http://svn.gna.org/viewcvs/relax/tags/1.2.7/version.py?rev=2570r1=2569r2=2570view=diff == --- tags/1.2.7/version.py (original) +++ tags/1.2.7/version.py Tue Sep 19 05:39:43 2006 @@ -1,1 +1,1 @@ -version = repository checkout +version = 1.2.7 ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2571 - /1.2/sconstruct
Author: bugman Date: Tue Sep 19 10:30:20 2006 New Revision: 2571 URL: http://svn.gna.org/viewcvs/relax?rev=2571view=rev Log: Readded the machine name to the GNU/Linux binary distribution package which was accidentally lost. Modified: 1.2/sconstruct Modified: 1.2/sconstruct URL: http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2571r1=2570r2=2571view=diff == --- 1.2/sconstruct (original) +++ 1.2/sconstruct Tue Sep 19 10:30:20 2006 @@ -449,7 +449,7 @@ self.SRC_FILE = 'relax-' + version + '.src.zip' self.DIST_TYPE = 'zip' else: -self.BIN_FILE = 'relax-' + version + '.' + self.SYS + '.tar.bz2' +self.BIN_FILE = 'relax-' + version + '.' + self.SYS + '.' + self.MACH + '.tar.bz2' self.SRC_FILE = 'relax-' + version + '.src.tar.bz2' self.DIST_TYPE = 'tar' ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2580 - /1.2/sconstruct
Author: bugman Date: Wed Sep 20 10:25:54 2006 New Revision: 2580 URL: http://svn.gna.org/viewcvs/relax?rev=2580view=rev Log: Removed a few lines of sconstruct code which had been commented out and are no longer used. Modified: 1.2/sconstruct Modified: 1.2/sconstruct URL: http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2580r1=2579r2=2580view=diff == --- 1.2/sconstruct (original) +++ 1.2/sconstruct Wed Sep 20 10:25:54 2006 @@ -511,18 +511,6 @@ if self.DIST_TYPE == 'tar': archive.add(name=name, arcname=arcname) -# Open the file. -#file = open(path.join(root, files[i])) - -# Tar information. -#tarinfo = archive.gettarinfo(name, arcname) - -# Add the file. -#archive.addfile(tarinfo, file) - -# Close the file. -#file.close() - # Close the archive. archive.close() ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2583 - in /1.2/docs: latex/intro.tex relax.pdf
Author: bugman
Date: Sat Sep 30 07:40:48 2006
New Revision: 2583
URL: http://svn.gna.org/viewcvs/relax?rev=2583view=rev
Log:
Changes to Chapter 2 of the manual (sample scripts and the test suite).
These changes complete task #3781 (https://gna.org/task/?3781).
The sample script section has been modified and a section for the relax test
suite has been added.
Modified:
1.2/docs/latex/intro.tex
1.2/docs/relax.pdf
Modified: 1.2/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/intro.tex?rev=2583r1=2582r2=2583view=diff
==
--- 1.2/docs/latex/intro.tex (original)
+++ 1.2/docs/latex/intro.tex Sat Sep 30 07:40:48 2006
@@ -237,7 +237,17 @@
\section{Sample scripts}
\index{scripting!sample scripts}
-A few sample scripts have been provided in the directory `sample\_scripts'.
These can be used as a good starting point for using relax.
+A few sample scripts have been provided in the directory `sample\_scripts'.
These can be copied and modified for different types of data analysis.
+
+
+
+% The test suite.
+%
+
+\section{The test suite}
+\index{test suite}
+
+To test that the program functions correctly, relax possesses an inbuilt test
suite. The suite is a collection of simple tests which execute or probe
different parts of the program checking that the software runs without problem.
The test suite is executed by running relax using the command \texttt{`relax
--test-suite'}.
Modified: 1.2/docs/relax.pdf
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/relax.pdf?rev=2583r1=2582r2=2583view=diff
==
Binary files - no diff available.
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r2587 - /1.2/generic_fns/angles.py
Author: bugman Date: Sat Sep 30 10:50:54 2006 New Revision: 2587 URL: http://svn.gna.org/viewcvs/relax?rev=2587view=rev Log: Fix for bug #7224 (https://gna.org/bugs/?7224). The problem was simply that the run name was being replaced by None. Modified: 1.2/generic_fns/angles.py Modified: 1.2/generic_fns/angles.py URL: http://svn.gna.org/viewcvs/relax/1.2/generic_fns/angles.py?rev=2587r1=2586r2=2587view=diff == --- 1.2/generic_fns/angles.py (original) +++ 1.2/generic_fns/angles.py Sat Sep 30 10:50:54 2006 @@ -66,11 +66,8 @@ raise RelaxError, No coded yet. -def ellipsoid_frame(self, run=None): +def ellipsoid_frame(self): Function for calculating the spherical angles of the XH vector in the ellipsoid frame. - -# Arguments. -self.run = run # Get the unit vectors Dx, Dy, and Dz of the diffusion tensor axes. Dx, Dy, Dz = self.relax.generic.diffusion_tensor.unit_axes() @@ -93,11 +90,8 @@ self.relax.data.res[self.run][i].phi = acos(dx / sin(self.relax.data.res[self.run][i].theta)) -def spheroid_frame(self, run=None): +def spheroid_frame(self): Function for calculating the angle alpha of the XH vector within the spheroid frame. - -# Arguments. -self.run = run # Get the unit vector Dpar of the diffusion tensor axis. Dpar = self.relax.generic.diffusion_tensor.unit_axes() ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2588 - /1.2/generic_fns/palmer.py
Author: bugman
Date: Sat Sep 30 15:20:34 2006
New Revision: 2588
URL: http://svn.gna.org/viewcvs/relax?rev=2588view=rev
Log:
Modified the Modelfree4 execution code to test the return status when a PDB
file is used.
Modified:
1.2/generic_fns/palmer.py
Modified: 1.2/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/palmer.py?rev=2588r1=2587r2=2588view=diff
==
--- 1.2/generic_fns/palmer.py (original)
+++ 1.2/generic_fns/palmer.py Sat Sep 30 15:20:34 2006
@@ -456,12 +456,17 @@
if search('out$', file) or search('rotate$', file):
remove(file)
-# Execute Modelfree4.
+# Execute Modelfree4 (inputting a PDB file).
if pdb:
-spawnlp(P_WAIT, self.binary, self.binary, '-i', 'mfin', '-d',
'mfdata', '-p', 'mfpar', '-m', 'mfmodel', '-o', 'mfout', '-e', 'out', '-s', pdb)
+status = spawnlp(P_WAIT, self.binary, self.binary, '-i',
'mfin', '-d', 'mfdata', '-p', 'mfpar', '-m', 'mfmodel', '-o', 'mfout', '-e',
'out', '-s', pdb)
+if status:
+raise RelaxProgFailError, 'Modelfree4'
+
+
+# Execute Modelfree4 (without a PDB file).
else:
-test = spawnlp(P_WAIT, self.binary, self.binary, '-i', 'mfin',
'-d', 'mfdata', '-p', 'mfpar', '-m', 'mfmodel', '-o', 'mfout', '-e', 'out')
-if test:
+status = spawnlp(P_WAIT, self.binary, self.binary, '-i',
'mfin', '-d', 'mfdata', '-p', 'mfpar', '-m', 'mfmodel', '-o', 'mfout', '-e',
'out')
+if status:
raise RelaxProgFailError, 'Modelfree4'
# Failure.
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r2589 - in /1.2: errors.py generic_fns/palmer.py io.py
Author: bugman
Date: Sat Sep 30 15:35:17 2006
New Revision: 2589
URL: http://svn.gna.org/viewcvs/relax?rev=2589view=rev
Log:
Fix to bug #7225.
This bug was reported by Alex Hansen at https://gna.org/bugs/index.php?7225.
To enable comprehensible error messages when attempting to execute Modelfree4,
the function
'self.test_binary()' was added to the file 'io.py'. This was described in the
post located at
https://mail.gna.org/public/relax-devel/2006-09/msg00034.html (Message-id:
[EMAIL PROTECTED]). The implementation is slightly
different to the post though. Firstly the supplied string corresponding to the
binary is tested to
see if the full path has been supplied. If so then the string is tested to see
if the file exists
and if the file is executable. Otherwise the file is searched for in the PATH
environmental
variable. Point 5 of the post at
https://mail.gna.org/public/relax-devel/2006-09/msg00034.html,
testing that the binary is in the current directory was not implemented. The
reason is because I
was unable to successfully modify the PATH variable.
Three new RelaxErrors have been created to print out comprehensible messages:
RelaxMissingBinaryError, RelaxNonExecError, and RelaxNoInPathError.
Modified:
1.2/errors.py
1.2/generic_fns/palmer.py
1.2/io.py
Modified: 1.2/errors.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/errors.py?rev=2589r1=2588r2=2589view=diff
==
--- 1.2/errors.py (original)
+++ 1.2/errors.py Sat Sep 30 15:35:17 2006
@@ -103,6 +103,31 @@
if Debug:
self.save_state()
+
+# The binary executable file does not exist (full path has been given!).
+class RelaxMissingBinaryError(BaseError):
+def __init__(self, name):
+self.text = The binary executable file + `name` + does not
exist.
+if Debug:
+self.save_state()
+
+
+# The binary executable file is not executable.
+class RelaxNonExecError(BaseError):
+def __init__(self, name):
+self.text = The binary executable file + `name` + is not
executable.
+if Debug:
+self.save_state()
+
+
+# The binary executable file is not located within the system path.
+class RelaxNoInPathError(BaseError):
+def __init__(self, name):
+self.text = The binary executable file + `name` + is not
located within the system path.
+if Debug:
+self.save_state()
+
+
# Program execution failure.
class RelaxProgFailError(BaseError):
def __init__(self, name):
Modified: 1.2/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/palmer.py?rev=2589r1=2588r2=2589view=diff
==
--- 1.2/generic_fns/palmer.py (original)
+++ 1.2/generic_fns/palmer.py Sat Sep 30 15:35:17 2006
@@ -456,6 +456,9 @@
if search('out$', file) or search('rotate$', file):
remove(file)
+# Test the binary file string corresponds to a valid executable.
+self.relax.IO.test_binary(self.binary)
+
# Execute Modelfree4 (inputting a PDB file).
if pdb:
status = spawnlp(P_WAIT, self.binary, self.binary, '-i',
'mfin', '-d', 'mfdata', '-p', 'mfpar', '-m', 'mfmodel', '-o', 'mfout', '-e',
'out', '-s', pdb)
Modified: 1.2/io.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/io.py?rev=2589r1=2588r2=2589view=diff
==
--- 1.2/io.py (original)
+++ 1.2/io.py Sat Sep 30 15:35:17 2006
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2003-2005 Edward d'Auvergne #
+# Copyright (C) 2003-2006 Edward d'Auvergne #
# #
# This file is part of the program relax. #
# #
@@ -41,7 +41,7 @@
__builtin__.devnull_import = 0
__builtin__.devnull_import_message = message.args[0]
-from os import F_OK, access, makedirs, remove, stat
+from os import F_OK, X_OK, access, altsep, getenv, makedirs, pathsep, remove,
sep, stat
from os.path import expanduser
from re import match, search
from string import split
@@ -363,6 +363,41 @@
sys.stderr = self.tee_stderr
+def test_binary(self, binary):
+Function for testing that the binary string corresponds to a valid
executable file.
+
+# Path separator RE string.
+if altsep:
+path_sep = '[' + sep + altsep + ']'
+else:
+path_sep = sep
r2590 - in /1.2: dx/opendx.py generic_fns/dasha.py generic_fns/grace.py generic_fns/molmol.py
Author: bugman
Date: Sat Sep 30 16:07:51 2006
New Revision: 2590
URL: http://svn.gna.org/viewcvs/relax?rev=2590view=rev
Log:
Added tests for the Dasha, Molmol, Grace, and OpenDX executables.
This is an extension of the ideas introduced to fix bug #7225
(https://gna.org/bugs/?7225). This
change was discussed at
https://mail.gna.org/public/relax-devel/2006-09/msg00034.html (Message-id:
[EMAIL PROTECTED]).
Modified:
1.2/dx/opendx.py
1.2/generic_fns/dasha.py
1.2/generic_fns/grace.py
1.2/generic_fns/molmol.py
Modified: 1.2/dx/opendx.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/dx/opendx.py?rev=2590r1=2589r2=2590view=diff
==
--- 1.2/dx/opendx.py (original)
+++ 1.2/dx/opendx.py Sat Sep 30 16:07:51 2006
@@ -74,5 +74,8 @@
if vp_exec:
execute_text = -execute
+# Test the binary file string corresponds to a valid executable.
+self.relax.IO.test_binary(dx_exe)
+
# Run OpenDX.
system(dx_exe + dir_text + -program + file + .net + execute_text
+ )
Modified: 1.2/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/dasha.py?rev=2590r1=2589r2=2590view=diff
==
--- 1.2/generic_fns/dasha.py (original)
+++ 1.2/generic_fns/dasha.py Sat Sep 30 16:07:51 2006
@@ -338,6 +338,9 @@
self.force = force
self.binary = binary
+# Test the binary file string corresponds to a valid executable.
+self.relax.IO.test_binary(self.binary)
+
# The current directory.
orig_dir = getcwd()
Modified: 1.2/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/grace.py?rev=2590r1=2589r2=2590view=diff
==
--- 1.2/generic_fns/grace.py (original)
+++ 1.2/generic_fns/grace.py Sat Sep 30 16:07:51 2006
@@ -161,6 +161,9 @@
def view(self, file=None, dir=None, grace_exe='xmgrace'):
Function for running Grace.
+# Test the binary file string corresponds to a valid executable.
+self.relax.IO.test_binary(grace_exe)
+
# File path.
self.file_path = self.relax.IO.file_path(file, dir)
Modified: 1.2/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/molmol.py?rev=2590r1=2589r2=2590view=diff
==
--- 1.2/generic_fns/molmol.py (original)
+++ 1.2/generic_fns/molmol.py Sat Sep 30 16:07:51 2006
@@ -100,6 +100,9 @@
def pipe_open(self):
Function for opening a Molmol pipe.
+# Test that the Molmol binary exists.
+self.relax.IO.test_binary('molmol')
+
# Open the Molmol pipe.
self.relax.data.molmol = popen(molmol -f -, 'w', 0)
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r2591 - in /1.2: errors.py generic_fns/pdb.py
Author: bugman Date: Sat Sep 30 16:51:33 2006 New Revision: 2591 URL: http://svn.gna.org/viewcvs/relax?rev=2591view=rev Log: An attempt at fixing bug #7241 (https://gna.org/bugs/?7241). The algorithm I've implemented is to first check for and use peptide chains, then check for and use nucleotide chains. If neither are present a new error RelaxNoPdbChainError is raised. Modified: 1.2/errors.py 1.2/generic_fns/pdb.py Modified: 1.2/errors.py URL: http://svn.gna.org/viewcvs/relax/1.2/errors.py?rev=2591r1=2590r2=2591view=diff == --- 1.2/errors.py (original) +++ 1.2/errors.py Sat Sep 30 16:51:33 2006 @@ -135,6 +135,7 @@ if Debug: self.save_state() + # PDB errors. # @@ -155,7 +156,7 @@ # Loading error. class RelaxPdbLoadError(BaseError): def __init__(self, name): -self.text = The PDB file + `name` + could not be loaded properly, no proteins could be extracted. +self.text = The PDB file + `name` + could not be loaded properly, no molecular chains could be extracted. if Debug: self.save_state() @@ -165,6 +166,14 @@ self.text = The unit XH bond vectors for the run + `run` + have not been calculated. if Debug: self.save_state() + +# PDB data corresponding to the run already exists. +class RelaxNoPdbChainError(BaseError): +def __init__(self): +self.text = No peptide or nucleotide chains can be found within the PDB file. +if Debug: +self.save_state() + # Nuclear errors. # Modified: 1.2/generic_fns/pdb.py URL: http://svn.gna.org/viewcvs/relax/1.2/generic_fns/pdb.py?rev=2591r1=2590r2=2591view=diff == --- 1.2/generic_fns/pdb.py (original) +++ 1.2/generic_fns/pdb.py Sat Sep 30 16:51:33 2006 @@ -225,8 +225,13 @@ if self.print_flag: print \nStructure + `i + 1` + \n -# Reassign the first peptide chain of the first structure. -pdb_residues = self.relax.data.pdb[self.run].structures[i].peptide_chains[0].residues +# Reassign the first peptide or nucleotide chain of the first structure. +if hasattr(self.relax.data.pdb[self.run].structures[i], 'peptide_chains'): +pdb_residues = self.relax.data.pdb[self.run].structures[i].peptide_chains[0].residues +elif hasattr(self.relax.data.pdb[self.run].structures[i], 'nucleotide_chains'): +pdb_residues = self.relax.data.pdb[self.run].structures[i].nucleotide_chains[0].residues +else: +raise RelaxNoPdbChainError # Loop over the sequence. for j in xrange(len(self.relax.data.res[self.run])): ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2592 - /1.2/specific_fns/model_free.py
Author: bugman Date: Sun Oct 1 05:54:27 2006 New Revision: 2592 URL: http://svn.gna.org/viewcvs/relax?rev=2592view=rev Log: Fix for bug #7226 (https://gna.org/bugs/?7226). This bug was reported by Alex Hansen. The problem was caused by the model-free results file reading function, specifically for model m0. The parameter array for this model is the empty array '[]'. However the test for setting up the model-free models was being bypassed because the empty array evaluates to False. By removing the test for the parameter array and only checking for the model name and equation type, the bug is removed. Modified: 1.2/specific_fns/model_free.py Modified: 1.2/specific_fns/model_free.py URL: http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2592r1=2591r2=2592view=diff == --- 1.2/specific_fns/model_free.py (original) +++ 1.2/specific_fns/model_free.py Sun Oct 1 05:54:27 2006 @@ -2927,7 +2927,7 @@ model = self.file_line[self.col['model']] equation = self.file_line[self.col['eqi']] params = eval(self.file_line[self.col['params']]) -if model and equation and params: +if model and equation: self.model_setup(self.run, model=model, equation=equation, params=params, res_num=self.res_num) # Values. ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2599 - in /1.2/docs/latex: develop.tex infrastruct.tex
Author: bugman
Date: Wed Oct 4 07:11:26 2006
New Revision: 2599
URL: http://svn.gna.org/viewcvs/relax?rev=2599view=rev
Log:
Changed all references to Sconstruct in the manual to SCons. The program is
really called SCons!
Modified:
1.2/docs/latex/develop.tex
1.2/docs/latex/infrastruct.tex
Modified: 1.2/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/develop.tex?rev=2599r1=2598r2=2599view=diff
==
--- 1.2/docs/latex/develop.tex (original)
+++ 1.2/docs/latex/develop.tex Wed Oct 4 07:11:26 2006
@@ -244,20 +244,20 @@
-% The Sconstruct build system.
+% The SCons build system.
%~
-\section{The Sconstruct build system}
-
-\index{Sconstruct|textbf}
-The Sconstruct build system was chosen over other build systems including
\texttt{`make'}\index{make} as it is a cross-platform build system which can be
used in Unix\index{Unix}, GNU/Linux\index{GNU/Linux}, Mac OS X\index{Mac OS X},
and even MS Windows\index{MS Windows} (the correct compilers are nevertheless
required). Various components of the program relax can be created using the
Sconstruct utility. This includes C module compilation, manual creation,
distribution creation, and cleaning up and removing certain files. The file
`sconstruct' in the base relax directory, which consists of python code,
directs the operation of Sconstruct for the various functions.
+\section{The SCons build system}
+
+\index{SCons|textbf}
+The SCons build system was chosen over other build systems including
\texttt{`make'}\index{make} as it is a cross-platform build system which can be
used in Unix\index{Unix}, GNU/Linux\index{GNU/Linux}, Mac OS X\index{Mac OS X},
and even MS Windows\index{MS Windows} (the correct compilers are nevertheless
required). Various components of the program relax can be created using the
SCons utility. This includes C module compilation, manual creation,
distribution creation, and cleaning up and removing certain files. The file
`sconstruct' in the base relax directory, which consists of python code,
directs the operation of SCons for the various functions.
% C module compilation.
\subsection{C module compilation}
\index{C module compilation|textbf}
-\index{Sconstruct!C module compilation|textbf}
+\index{SCons!C module compilation|textbf}
As described in the installation chapter typing \texttt{`scons'} in the base
directory will create the shared objects which are imported into Python as
modules.
@@ -270,9 +270,9 @@
To create the PDF version of the relax manual type
\example{\$ scons manual}
-\index{Sconstruct!PDF manual|textbf}
-
-in the base directory. Sconstruct will then run a series of shell commands to
create the manual from the \LaTeX\ sources located in the \texttt{`docs/latex'}
directory. This is dependent on the programs \texttt{`latex'},
\texttt{`makeindex'}, \texttt{`dvips'}, and \texttt{`ps2pdf'} being located
within the environment's path.
+\index{SCons!PDF manual|textbf}
+
+in the base directory. SCons will then run a series of shell commands to
create the manual from the \LaTeX\ sources located in the \texttt{`docs/latex'}
directory. This is dependent on the programs \texttt{`latex'},
\texttt{`makeindex'}, \texttt{`dvips'}, and \texttt{`ps2pdf'} being located
within the environment's path.
@@ -283,7 +283,7 @@
The HTML version of the relax manual is made by typing
\example{\$ scons manual\_html}
-\index{Sconstruct!HTML manual|textbf}
+\index{SCons!HTML manual|textbf}
in the base directory. One command calling the program \texttt{`latex2html'}
will be executed which will create HTML pages from the \LaTeX\ sources.
@@ -296,12 +296,12 @@
Two types of distribution archive can be created from the currently checked
out sources -- the source and binary distributions. To create the source
distribution type
\example{\$ scons source\_dist}
-\index{Sconstruct!source distribution|textbf}
+\index{SCons!source distribution|textbf}
whereas to create the binary distribution, whereby the C modules are compiled
and the resultant shared objects are included in the bzipped tar file, type
\example{\$ scons binary\_dist}
-\index{Sconstruct!binary distribution|textbf}
+\index{SCons!binary distribution|textbf}
If a binary distribution does not exist for your architecture feel free to
create it yourself and contribute the archive to be included on the download
pages. To do this you will need to check out the appropriate tagged branch
from the relax subversion repository. If the current stable release is called
1.2.3 check out that branch by typing
@@ -324,7 +324,7 @@
If the command
\example{\$ scons clean}
-\index{Sconstruct!clean up|textbf}
+\index{SCons!clean up|textbf}
is run in the base directory all Python byte compiled files \texttt{`*.pyc'},
all C object files \texttt{`*.o'} and \texttt{`*.os'}, all C
r2600 - /1.2/generic_fns/diffusion_tensor.py
Author: bugman Date: Wed Oct 4 07:36:41 2006 New Revision: 2600 URL: http://svn.gna.org/viewcvs/relax?rev=2600view=rev Log: Fix for bug #7297 (https://gna.org/bugs/index.php?7297). This bug was reported by Alex Hansen. The problem was that relax was being too strict with the checking of the Da and Dr diffusion tensor parameters. I have added a margin of error to these checks to allow machine precision errors and optimisation precision issues (for the Method of Multipliers constraint algorithm which allows the parameters outside of the limits). Modified: 1.2/generic_fns/diffusion_tensor.py Modified: 1.2/generic_fns/diffusion_tensor.py URL: http://svn.gna.org/viewcvs/relax/1.2/generic_fns/diffusion_tensor.py?rev=2600r1=2599r2=2600view=diff == --- 1.2/generic_fns/diffusion_tensor.py (original) +++ 1.2/generic_fns/diffusion_tensor.py Wed Oct 4 07:36:41 2006 @@ -1336,6 +1336,9 @@ def test_params(self, num_params): Function for testing the validity of the input parameters. +# An allowable error to account for machine precision, optimisation quality, etc. +error = 1e-4 + # tm. tm = self.relax.data.diff[self.run].tm if tm = 0.0 or tm 1e-6: @@ -1348,7 +1351,7 @@ Da = self.relax.data.diff[self.run].Da # Da. -if Da -1.5*Diso or Da 3.0*Diso: +if Da (-1.5*Diso - error*Diso) or Da (3.0*Diso + error*Diso): raise RelaxError, The Da value of + `Da` + should be between -3/2 * Diso and 3Diso. # Ellipsoid. @@ -1359,11 +1362,11 @@ Dr = self.relax.data.diff[self.run].Dr # Da. -if Da 0.0 or Da 3.0*Diso: +if Da (0.0 - error*Diso) or Da (3.0*Diso + error*Diso): raise RelaxError, The Da value of + `Da` + should be between zero and 3Diso. # Dr. -if Dr 0.0 or Dr 1.0: +if Dr (0.0 - error) or Dr (1.0 + error): raise RelaxError, The Dr value of + `Dr` + should be between zero and one. ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2601 - in /1.3: generic_fns/pdb.py prompt/interpreter.py prompt/pdb.py
: 1.3/prompt/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/pdb.py?rev=2601r1=2600r2=2601view=diff
==
--- 1.3/prompt/pdb.py (original)
+++ 1.3/prompt/pdb.py Fri Oct 6 08:55:01 2006
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2003, 2004 Edward d'Auvergne #
+# Copyright (C) 2003, 2004, 2006 Edward d'Auvergne#
# #
# This file is part of the program relax. #
# #
@@ -22,15 +22,23 @@
import sys
+import help
+
class PDB:
def __init__(self, relax):
-Class containing the function for loading a pdb file.
-
-self.relax = relax
-
-
-def pdb(self, run=None, file=None, dir=None, model=None, heteronuc='N',
proton='H', load_seq=1):
+# Help.
+self.__relax_help__ = \
+Class containing the PDB related functions.
+
+# Add the generic help string.
+self.__relax_help__ = self.__relax_help__ + \n +
help.relax_class_help
+
+# Place relax in the class namespace.
+self.__relax__ = relax
+
+
+def read(self, run=None, file=None, dir=None, model=None, heteronuc='N',
proton='H', load_seq=1):
The pdb loading function.
Keyword Arguments
@@ -43,10 +51,6 @@
dir: The directory where the file is located.
model: The PDB model number.
-
-heteronuc: The name of the heteronucleus as specified in the PDB file.
-
-proton: The name of the proton as specified in the PDB file.
load_seq: A flag specifying whether the sequence should be loaded
from the PDB file.
@@ -61,39 +65,31 @@
To load the sequence from the PDB file, set the 'load_seq' flag to 1.
If the sequence has
previously been loaded, then this flag will be ignored.
-Once the PDB structures are loaded, unit XH bond vectors will be
calculated. The vectors
-are calculated using the atomic coordinates of the atoms specified by
the arguments
-heteronuc and proton. If more than one model structure is loaded, the
unit XH vectors for
-each model will be calculated and the final unit XH vector will be
taken as the average.
-
Example
~~~
To load all structures from the PDB file 'test.pdb' in the directory
'~/pdb' for use in the
-model-free analysis run 'm8' where the heteronucleus in the PDB file
is 'N' and the proton
-is 'H', type:
-
-relax pdb('m8', 'test.pdb', '~/pdb', 1, 'N', 'H')
-relax pdb(run='m8', file='test.pdb', dir='pdb', model=1,
heteronuc='N', proton='H')
+model-free analysis run 'm8', type:
+
+relax pdb.read('m8', 'test.pdb', '~/pdb', 1)
+relax pdb.read(run='m8', file='test.pdb', dir='pdb', model=1)
To load the 10th model from the file 'test.pdb', use:
-relax pdb('m1', 'test.pdb', model=10)
-relax pdb(run='m1', file='test.pdb', model=10)
+relax pdb.read('m1', 'test.pdb', model=10)
+relax pdb.read(run='m1', file='test.pdb', model=10)
# Function intro text.
if self.relax.interpreter.intro:
-text = sys.ps3 + pdb(
+text = sys.ps3 + pdb.read(
text = text + run= + `run`
text = text + , file= + `file`
text = text + , dir= + `dir`
text = text + , model= + `model`
-text = text + , heteronuc= + `heteronuc`
-text = text + , proton= + `proton`
text = text + , load_seq= + `load_seq` + )
print text
@@ -113,6 +109,79 @@
if model != None and type(model) != int:
raise RelaxIntError, ('model', model)
+# The load sequence argument.
+if type(load_seq) != int or (load_seq != 0 and load_seq != 1):
+raise RelaxBinError, ('load sequence flag', load_seq)
+
+# Execute the functional code.
+self.__relax__.generic.pdb.read(run=run, file=file, dir=dir,
model=model, load_seq=load_seq)
+
+
+def vectors(self, run=None, heteronuc='N', proton='H', res_num=None,
res_name=None):
+Function for calculating/extracting XH vectors from the structure.
+
+Keyword arguments
+~
+
+run: The run to assign the vectors to.
+
+heteronuc: The heteronucleus name as specified in the PDB file.
+
+proton: The name of the proton as specified in the PDB file.
+
+res_num: The residue number.
+
+res_name: The name of the residue.
+
+
+Description
+~~~
+
+Once
r2602 - in /1.3/docs/latex: develop.tex infrastruct.tex
Author: bugman
Date: Sat Oct 7 10:49:58 2006
New Revision: 2602
URL: http://svn.gna.org/viewcvs/relax?rev=2602view=rev
Log:
Ported r2599 from the 1.2 line.
The command used was:
$ svn merge -r2598:2599 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2
This changes 'Sconstruct' to 'SCons' in the relax manual.
Modified:
1.3/docs/latex/develop.tex
1.3/docs/latex/infrastruct.tex
Modified: 1.3/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/develop.tex?rev=2602r1=2601r2=2602view=diff
==
--- 1.3/docs/latex/develop.tex (original)
+++ 1.3/docs/latex/develop.tex Sat Oct 7 10:49:58 2006
@@ -244,20 +244,20 @@
-% The Sconstruct build system.
+% The SCons build system.
%~
-\section{The Sconstruct build system}
-
-\index{Sconstruct|textbf}
-The Sconstruct build system was chosen over other build systems including
\texttt{`make'}\index{make} as it is a cross-platform build system which can be
used in Unix\index{Unix}, GNU/Linux\index{GNU/Linux}, Mac OS X\index{Mac OS X},
and even MS Windows\index{MS Windows} (the correct compilers are nevertheless
required). Various components of the program relax can be created using the
Sconstruct utility. This includes C module compilation, manual creation,
distribution creation, and cleaning up and removing certain files. The file
`sconstruct' in the base relax directory, which consists of python code,
directs the operation of Sconstruct for the various functions.
+\section{The SCons build system}
+
+\index{SCons|textbf}
+The SCons build system was chosen over other build systems including
\texttt{`make'}\index{make} as it is a cross-platform build system which can be
used in Unix\index{Unix}, GNU/Linux\index{GNU/Linux}, Mac OS X\index{Mac OS X},
and even MS Windows\index{MS Windows} (the correct compilers are nevertheless
required). Various components of the program relax can be created using the
SCons utility. This includes C module compilation, manual creation,
distribution creation, and cleaning up and removing certain files. The file
`sconstruct' in the base relax directory, which consists of python code,
directs the operation of SCons for the various functions.
% C module compilation.
\subsection{C module compilation}
\index{C module compilation|textbf}
-\index{Sconstruct!C module compilation|textbf}
+\index{SCons!C module compilation|textbf}
As described in the installation chapter typing \texttt{`scons'} in the base
directory will create the shared objects which are imported into Python as
modules.
@@ -270,9 +270,9 @@
To create the PDF version of the relax manual type
\example{\$ scons manual}
-\index{Sconstruct!PDF manual|textbf}
-
-in the base directory. Sconstruct will then run a series of shell commands to
create the manual from the \LaTeX\ sources located in the \texttt{`docs/latex'}
directory. This is dependent on the programs \texttt{`latex'},
\texttt{`makeindex'}, \texttt{`dvips'}, and \texttt{`ps2pdf'} being located
within the environment's path.
+\index{SCons!PDF manual|textbf}
+
+in the base directory. SCons will then run a series of shell commands to
create the manual from the \LaTeX\ sources located in the \texttt{`docs/latex'}
directory. This is dependent on the programs \texttt{`latex'},
\texttt{`makeindex'}, \texttt{`dvips'}, and \texttt{`ps2pdf'} being located
within the environment's path.
@@ -283,7 +283,7 @@
The HTML version of the relax manual is made by typing
\example{\$ scons manual\_html}
-\index{Sconstruct!HTML manual|textbf}
+\index{SCons!HTML manual|textbf}
in the base directory. One command calling the program \texttt{`latex2html'}
will be executed which will create HTML pages from the \LaTeX\ sources.
@@ -296,12 +296,12 @@
Two types of distribution archive can be created from the currently checked
out sources -- the source and binary distributions. To create the source
distribution type
\example{\$ scons source\_dist}
-\index{Sconstruct!source distribution|textbf}
+\index{SCons!source distribution|textbf}
whereas to create the binary distribution, whereby the C modules are compiled
and the resultant shared objects are included in the bzipped tar file, type
\example{\$ scons binary\_dist}
-\index{Sconstruct!binary distribution|textbf}
+\index{SCons!binary distribution|textbf}
If a binary distribution does not exist for your architecture feel free to
create it yourself and contribute the archive to be included on the download
pages. To do this you will need to check out the appropriate tagged branch
from the relax subversion repository. If the current stable release is called
1.2.3 check out that branch by typing
@@ -324,7 +324,7 @@
If the command
\example{\$ scons clean}
-\index{Sconstruct!clean up|textbf}
+\index{SCons!clean up|textbf}
is run in the base directory all Python byte compiled files
r2603 - /1.3/generic_fns/diffusion_tensor.py
Author: bugman Date: Sat Oct 7 10:52:57 2006 New Revision: 2603 URL: http://svn.gna.org/viewcvs/relax?rev=2603view=rev Log: Ported r2600 from the 1.2 line. The command used was: svn merge -r2599:2600 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 This fixes bug #7297 (https://gna.org/bugs/index.php?7297). Modified: 1.3/generic_fns/diffusion_tensor.py Modified: 1.3/generic_fns/diffusion_tensor.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/diffusion_tensor.py?rev=2603r1=2602r2=2603view=diff == --- 1.3/generic_fns/diffusion_tensor.py (original) +++ 1.3/generic_fns/diffusion_tensor.py Sat Oct 7 10:52:57 2006 @@ -1336,6 +1336,9 @@ def test_params(self, num_params): Function for testing the validity of the input parameters. +# An allowable error to account for machine precision, optimisation quality, etc. +error = 1e-4 + # tm. tm = self.relax.data.diff[self.run].tm if tm = 0.0 or tm 1e-6: @@ -1348,7 +1351,7 @@ Da = self.relax.data.diff[self.run].Da # Da. -if Da -1.5*Diso or Da 3.0*Diso: +if Da (-1.5*Diso - error*Diso) or Da (3.0*Diso + error*Diso): raise RelaxError, The Da value of + `Da` + should be between -3/2 * Diso and 3Diso. # Ellipsoid. @@ -1359,11 +1362,11 @@ Dr = self.relax.data.diff[self.run].Dr # Da. -if Da 0.0 or Da 3.0*Diso: +if Da (0.0 - error*Diso) or Da (3.0*Diso + error*Diso): raise RelaxError, The Da value of + `Da` + should be between zero and 3Diso. # Dr. -if Dr 0.0 or Dr 1.0: +if Dr (0.0 - error) or Dr (1.0 + error): raise RelaxError, The Dr value of + `Dr` + should be between zero and one. ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2604 - /1.3/docs/JOBS
Author: bugman Date: Sat Oct 7 13:28:39 2006 New Revision: 2604 URL: http://svn.gna.org/viewcvs/relax?rev=2604view=rev Log: Created the JOBS file. This file describes the roles of the relax manager positions. Added: 1.3/docs/JOBS Added: 1.3/docs/JOBS URL: http://svn.gna.org/viewcvs/relax/1.3/docs/JOBS?rev=2604view=auto == --- 1.3/docs/JOBS (added) +++ 1.3/docs/JOBS Sat Oct 7 13:28:39 2006 @@ -1,0 +1,90 @@ +The relax managers. + +This file presents the details of the tasks preformed by the relax managers. The day-to-day activities which keep the relax project running are documented. + + +Index: +1. All managers +1.1 Documentation +1.2 Transitions +2. The mailing list manager +2.1 Tasks +2.1.1 Configuration +2.1.2 Spam +2.1.3 Rejection +2.1.4 Acceptance +2.1.5 Redirection +2.1.6 Invitation +2.1.7 Sharing the job +2.1.6 Invitation +2.2 Email addresses +2.3 Administrative passwords + + + + + +1. All managers + +The following are tasks common to all the manager positions. + + +1.1 Documentation + +An important part of the job of the relax managers is to document all the actions performed as the manager and to keep the job descriptions below up to date. This file will constantly evolve as the manager positions are refined. There may also be tasks or details missing from the descriptions. This is an important task as it allows the next volunteer to easily take over when a transition occurs. + + +1.2 Transitions + +The management position can be passed on by request at any time. This may be because you would like to move onto another job, if job becomes too demanding, or if you do not currently have the time to contribute to the project. + + + + + +2. The mailing list manager + +This position is currently held by Chris MacRaild (c.a.macraild at leeds.ac.uk). + + +2.1 Tasks + +2.1.1 Configuration + +Part of the job is to change the mailing list settings as necessary. This is a relatively infrequent task. The changes should be discussed on the relax-devel mailing list first so that subscribers are aware that a change may soon occur. Changes to relax-users and relax-devel should also be announced prior to the event. + +2.1.2 Spam + +All four mailing lists (relax-announce, relax-users, relax-devel, and relax-commits) are moderated - only members can post to the lists. Posts by non-subscribers are first sent to the Mailing List Manager for approval, denial, rejection, etc. The number of spam messages are low because all posts must first pass through Gna's blacklists and SpamAssassin (https://gna.org/cookbook/?func=detailitemitem_id=112). + +2.1.3 Rejection + +All posts to relax-announce and relax-commits are to be rejected. The exceptions are posts to relax-announce by the Project Administrator and posts to relax-commits by the subversion and CVS relax repositories (https://gna.org/svn/?group=relax and https://gna.org/cvs/?group=relax). The repository commit messages are currently automatically accepted. + +2.1.4 Acceptance + +Non-member posts to relax-users or relax-devel should be quickly accepted if they are legitimate. The poster will receive an automatic email saying that the list is for members only and that the email is awaiting approval. Even if the poster subsequently subscribes to the list, their post should nevertheless be accepted by the manager as it will still be waiting for approval. + +2.1.5 Redirection + +If people have sent the message to the wrong forum (a post talking about source code modifications is sent to relax-user, somebody accidentally sending a message to relax-announce or relax-commits when it should be sent to one of the other lists, or program usage questions which are sent to relax-users, etc.) then redirection is necessary. To do this, the person should be politely asked to repost the message to the relevant forum. This should be done publicly as a reply to their original post unless the message was sent to relax-announce or relax-commits. + +If somebody reports a bug on one of the mailing lists, then the Mailing List Manager should politely ask the person if they would like to create a bug report (pointing them to the bug tracker at https://gna.org/bugs/?group=relax or the bug submission page https://gna.org/bugs/?func=additemgroup=relax). In the post the person should be directed to the relevant section of the manual describing how to submit a bug report (both the PDF and HTML versions). It is quite likely that the poster won't take the time to create the report. If that is the case then the Mailing List Manager should create a report pointing to the original post. An example of this is bug #6873 (https://gna.org/bugs/?6873). Redirection is not an exclusive job, anyone can request redirection, however if no one responds then
r2605 - /1.2/generic_fns/palmer.py
Author: bugman Date: Sat Oct 7 17:32:17 2006 New Revision: 2605 URL: http://svn.gna.org/viewcvs/relax?rev=2605view=rev Log: Fix for bug #7277 (https://gna.org/bugs/?7277). This bug was reported by Alex Hansen. The problem was that the 'self.relax.generic_fns.palmer.create()' function was skipping spins when no relaxation data was present whereas the complementary funtion 'self.relax.generic_fns.palmer.extract()' was not skipping these spins. Hence the second of these functions was expecting more spins than were in the modelfree4 generated 'mfout' file. Modified: 1.2/generic_fns/palmer.py Modified: 1.2/generic_fns/palmer.py URL: http://svn.gna.org/viewcvs/relax/1.2/generic_fns/palmer.py?rev=2605r1=2604r2=2605view=diff == --- 1.2/generic_fns/palmer.py (original) +++ 1.2/generic_fns/palmer.py Sat Oct 7 17:32:17 2006 @@ -534,6 +534,10 @@ if not hasattr(data, 'model'): continue +# No relaxation data. +if not hasattr(data, 'num_frq'): +continue + # Get the S2 data. if 'S2' in data.params: data.s2, data.s2_err = self.get_mf_data(self.mfout_S2_pos + pos) ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2606 - /1.3/generic_fns/palmer.py
Author: bugman Date: Sat Oct 7 17:35:24 2006 New Revision: 2606 URL: http://svn.gna.org/viewcvs/relax?rev=2606view=rev Log: Ported r2605 from the 1.2 line. The command used was: $ svn merge -r2604:2605 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 This fixes bug #7277 (https://gna.org/bugs/?7277). Modified: 1.3/generic_fns/palmer.py Modified: 1.3/generic_fns/palmer.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/palmer.py?rev=2606r1=2605r2=2606view=diff == --- 1.3/generic_fns/palmer.py (original) +++ 1.3/generic_fns/palmer.py Sat Oct 7 17:35:24 2006 @@ -534,6 +534,10 @@ if not hasattr(data, 'model'): continue +# No relaxation data. +if not hasattr(data, 'num_frq'): +continue + # Get the S2 data. if 'S2' in data.params: data.s2, data.s2_err = self.get_mf_data(self.mfout_S2_pos + pos) ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2607 - in /1.3/test_suite: angles.py model_free.py sequence.py
Author: bugman Date: Sat Oct 7 19:13:42 2006 New Revision: 2607 URL: http://svn.gna.org/viewcvs/relax?rev=2607view=rev Log: Fix for bug #7333 (https://gna.org/bugs/index.php?7333). The three tests of the test-suite have been modified to use the correct PDB functions. A few calls to the user function 'pdb.vectors()' needed to be added and the 'heteronuc' and 'proton' argments to the 'pdb.read()' funtion had to be removed. Modified: 1.3/test_suite/angles.py 1.3/test_suite/model_free.py 1.3/test_suite/sequence.py Modified: 1.3/test_suite/angles.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/angles.py?rev=2607r1=2606r2=2607view=diff == --- 1.3/test_suite/angles.py (original) +++ 1.3/test_suite/angles.py Sat Oct 7 19:13:42 2006 @@ -40,7 +40,10 @@ self.relax.interpreter._Run.create(run, 'mf') # Read a PDB file. -self.relax.interpreter._PDB.pdb(run, file='test.pdb', dir=sys.path[-1] + '/test_suite/data', model=1, heteronuc='N', proton='H') +self.relax.interpreter._PDB.read(run, file='test.pdb', dir=sys.path[-1] + '/test_suite/data', model=1) + +# Set the NH vector. +self.relax.interpreter._PDB.vectors(run, heteronuc='N', proton='H') # Initialise a diffusion tensor. self.relax.interpreter._Diffusion_tensor.init(run, (1.698e7, 1.417e7, 67.174, -83.718), param_types=3) Modified: 1.3/test_suite/model_free.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/model_free.py?rev=2607r1=2606r2=2607view=diff == --- 1.3/test_suite/model_free.py (original) +++ 1.3/test_suite/model_free.py Sat Oct 7 19:13:42 2006 @@ -199,8 +199,9 @@ # Read the sequence. self.relax.interpreter._Sequence.read(self.run, file='noe.500.out', dir=path) -# Read the PDF file. -self.relax.interpreter._PDB.pdb(run, file='pdb', dir=path, model=1, heteronuc='N', proton='H', load_seq=0) +# Read the PDF file and set the vectors. +self.relax.interpreter._PDB.read(run, file='pdb', dir=path, model=1, load_seq=0) +self.relax.interpreter._PDB.vectors(run, heteronuc='N', proton='H') # Read the relaxation data. self.relax.interpreter._Relax_data.read(self.run, 'R1', '600', 600.0 * 1e6, 'r1.600.out', dir=path) Modified: 1.3/test_suite/sequence.py URL: http://svn.gna.org/viewcvs/relax/1.3/test_suite/sequence.py?rev=2607r1=2606r2=2607view=diff == --- 1.3/test_suite/sequence.py (original) +++ 1.3/test_suite/sequence.py Sat Oct 7 19:13:42 2006 @@ -53,7 +53,7 @@ self.relax.generic.runs.create(run, 'mf') # Read the sequence. -self.relax.interpreter._PDB.pdb(run, file='test.pdb', dir=sys.path[-1] + '/test_suite/data', model=1, heteronuc='N', proton='H', load_seq=1) +self.relax.interpreter._PDB.read(run, file='test.pdb', dir=sys.path[-1] + '/test_suite/data', model=1, load_seq=1) # Success. return 1 ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2609 - /1.3/generic_fns/pdb.py
Author: bugman
Date: Sat Oct 7 19:37:56 2006
New Revision: 2609
URL: http://svn.gna.org/viewcvs/relax?rev=2609view=rev
Log:
Fix for bug #7335 (https://gna.org/bugs/index.php?7335).
The code which tests that the proton and heteronucleus have not been set to the
same atom name has
been moved from the 'self.read()' function to the 'self.vectors()' function.
Two more lines of
code, which were placing the atom names into the 'self.relax.data.pdb' data
structure were also
identified to cause similar problems and were shifted from the read to the
vectors function.
Modified:
1.3/generic_fns/pdb.py
Modified: 1.3/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pdb.py?rev=2609r1=2608r2=2609view=diff
==
--- 1.3/generic_fns/pdb.py (original)
+++ 1.3/generic_fns/pdb.py Sat Oct 7 19:37:56 2006
@@ -152,10 +152,6 @@
warn(RelaxNoPDBFileWarning(self.file_path))
return
-# Test that the nuclei have been correctly set.
-if self.heteronuc == self.proton:
-raise RelaxError, The proton and heteronucleus are set to the
same atom.
-
# Data creation.
@@ -168,10 +164,6 @@
# Model.
self.relax.data.pdb[self.run].model = model
-
-# Nuclei.
-self.relax.data.pdb[self.run].proton = proton
-self.relax.data.pdb[self.run].heteronuc = heteronuc
# Load the structures.
@@ -227,9 +219,17 @@
except:
raise RelaxRegExpError, ('residue name', name)
+# Test that the nuclei have been correctly set.
+if self.heteronuc == self.proton:
+raise RelaxError, The proton and heteronucleus are set to the
same atom.
+
# Print out.
if self.print_flag:
print \nCalculating unit XH vectors.\n
+
+# Nuclei.
+self.relax.data.pdb[self.run].proton = proton
+self.relax.data.pdb[self.run].heteronuc = heteronuc
# Number of structures.
num_str = len(self.relax.data.pdb[self.run].structures)
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r2611 - /1.2/scons/
Author: bugman Date: Wed Oct 11 12:08:35 2006 New Revision: 2611 URL: http://svn.gna.org/viewcvs/relax?rev=2611view=rev Log: Created the directory 'scons' for splitting up the 'sconstruct' script into multiple Python modules. Added: 1.2/scons/ ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2613 - /1.3/scons/
Author: bugman Date: Thu Oct 12 05:20:26 2006 New Revision: 2613 URL: http://svn.gna.org/viewcvs/relax?rev=2613view=rev Log: Ported r2611 from the 1.2 line. The command used was: $ svn merge -r2610:2611 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 This adds the directory for Scons Python modules for the Builder functions. Added: 1.3/scons/ - copied from r2611, 1.2/scons/ ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2614 - /1.3/generic_fns/sequence.py
Author: bugman Date: Thu Oct 12 05:23:22 2006 New Revision: 2614 URL: http://svn.gna.org/viewcvs/relax?rev=2614view=rev Log: Ported r2612 from the 1.2 line. The command used was: $ svn merge -r2611:2612 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 This completes the fixing of bug #7241 (https://gna.org/bugs/?7241). Modified: 1.3/generic_fns/sequence.py Modified: 1.3/generic_fns/sequence.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=2614r1=2613r2=2614view=diff == --- 1.3/generic_fns/sequence.py (original) +++ 1.3/generic_fns/sequence.py Thu Oct 12 05:23:22 2006 @@ -143,7 +143,12 @@ print \nLoading the sequence from the PDB file.\n # Reassign the sequence of the first structure. -res = self.relax.data.pdb[run].structures[0].peptide_chains[0].residues +if self.relax.data.pdb[run].structures[0].peptide_chains: +res = self.relax.data.pdb[run].structures[0].peptide_chains[0].residues +elif self.relax.data.pdb[run].structures[0].nucleotide_chains: +res = self.relax.data.pdb[run].structures[0].nucleotide_chains[0].residues +else: +raise RelaxNoPdbChainError # Add the run to 'self.relax.data.res'. self.relax.data.res.add_list(run) ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2616 - /1.2/maths_fns/test.c_chi.py
Author: bugman Date: Thu Oct 12 05:43:31 2006 New Revision: 2616 URL: http://svn.gna.org/viewcvs/relax?rev=2616view=rev Log: Deletion of the file 'maths_fns/test.c_chi.py'. This file is an ancient file last touched in 2004. It serves no purpose so has been removed. Removed: 1.2/maths_fns/test.c_chi.py ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2617 - /1.3/maths_fns/test.c_chi.py
Author: bugman Date: Thu Oct 12 05:46:16 2006 New Revision: 2617 URL: http://svn.gna.org/viewcvs/relax?rev=2617view=rev Log: Ported r2616 from the 1.2 line. The command used was: $ svn merge -r2615:2616 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 This removes the ancient unused file 'maths_fns/test.c_chi.py'. Removed: 1.3/maths_fns/test.c_chi.py ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2618 - in /1.2: scons/__init__.py scons/manuals.py sconstruct
Author: bugman Date: Thu Oct 12 06:02:01 2006 New Revision: 2618 URL: http://svn.gna.org/viewcvs/relax?rev=2618view=rev Log: A number of large changes to the Scons system. The package initialisation file '__init__.py' has been added to the 'scons' directory. The 'sconstruct' script has been split in half. The script was copied to 'scons/manuals.py' and only the manual compilation functions remain in this file. The class structure has been eliminated from 'scons/manuals.py' so 'sconstruct' now imports each function from this module. This means that 4 spaces have been removed from the indentation. All the manual compilation Environment setups, custom BUILDERS actions, and Depends statements have been shifted to the 'self.__init__()' function of the 'sconstruct' script. The default values of None for the target functions have been removed as they are always passed to the functions. For example def dummy(self, target=None, source=None, env=None): has been changed to def dummy(self, target, source, env): Environmental variables such as LATEX_DIR, SYSTEM, BIN_PATH, etc. (all the variables created in 'self.paths()') are now placed in the Scons Build Environments. The Environment is passed into each function as 'env' so the variables are accessed by typing, for example, env['LATEX_DIR']. The variable 'self.system' has been renamed to 'self.SYSTEM'. The 'self.gpg_bin_sign()' and 'self.gpg_src_sign()' target functions have been merged into the single function 'self.gpg_sign()'. Added: 1.2/scons/__init__.py - copied, changed from r2610, 1.2/docs/__init__.py 1.2/scons/manuals.py - copied, changed from r2610, 1.2/sconstruct Modified: 1.2/sconstruct [This mail would be too long, it was shortened to contain the URLs only.] Copied: 1.2/scons/__init__.py (from r2610, 1.2/docs/__init__.py) URL: http://svn.gna.org/viewcvs/relax/1.2/scons/__init__.py?p2=1.2/scons/__init__.pyp1=1.2/docs/__init__.pyr1=2610r2=2618rev=2618view=diff Copied: 1.2/scons/manuals.py (from r2610, 1.2/sconstruct) URL: http://svn.gna.org/viewcvs/relax/1.2/scons/manuals.py?p2=1.2/scons/manuals.pyp1=1.2/sconstructr1=2610r2=2618rev=2618view=diff Modified: 1.2/sconstruct URL: http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2618r1=2617r2=2618view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2619 - /1.2/sconstruct
Author: bugman
Date: Thu Oct 12 06:32:18 2006
New Revision: 2619
URL: http://svn.gna.org/viewcvs/relax?rev=2619view=rev
Log:
Fixed a bug in the 'self.package()' target function.
The variable 'file_name' was being accessed when the variable should have been
called
env['DIST_FILE'].
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2619r1=2618r2=2619view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 06:32:18 2006
@@ -533,7 +533,7 @@
print ###
print # Packaging the files #
print ###\n\n
-print Creating the package distribution + `file_name` + .\n
+print Creating the package distribution + `env['DIST_FILE']` + .\n
# Open the Zip distribution file.
if self.DIST_TYPE == 'zip':
@@ -541,9 +541,9 @@
# Open the Tar distribution file.
elif self.DIST_TYPE == 'tar':
-if search('.bz2$', file_name):
+if search('.bz2$', env['DIST_FILE']):
archive = TarFile.bz2open(path.pardir + path.sep +
env['DIST_FILE'], 'w')
-elif search('.gz$', file_name):
+elif search('.gz$', env['DIST_FILE']):
archive = TarFile.gzopen(path.pardir + path.sep +
env['DIST_FILE'], 'w')
else:
archive = TarFile.open(path.pardir + path.sep +
env['DIST_FILE'], 'w')
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r2621 - in /1.2: scons/manuals.py sconstruct
Author: bugman
Date: Thu Oct 12 07:08:18 2006
New Revision: 2621
URL: http://svn.gna.org/viewcvs/relax?rev=2621view=rev
Log:
Complete overhaul of the relax manual targets.
The relax manual is now referred to as the user manaul (to allow a developers
manual in the future).
The functions for compiling the manual have been renamed:
'user_manual_html()' to 'compile_user_manual_html()'.
'user_manual_pdf()' to 'compile_user_manual_pdf()'.
The header printed when compiling from the LaTeX sources has been updated.
Many target names have changes:
'manual_dist' to 'user_manual_pdf_dist'.
'manual' to 'user_manual_pdf'.
'manual_nofetch' to 'user_manual_pdf_nofetch'.
'manual_dist' to 'user_manual_pdf_dist'.
'user_manual_pdf' to 'compile_user_manual_pdf'.
'user_manual_html' to 'compile_user_manual_html'.
The HTML target has been split in two.
Modified:
1.2/scons/manuals.py
1.2/sconstruct
Modified: 1.2/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/scons/manuals.py?rev=2621r1=2620r2=2621view=diff
==
--- 1.2/scons/manuals.py (original)
+++ 1.2/scons/manuals.py Thu Oct 12 07:08:18 2006
@@ -94,34 +94,14 @@
print \n\n\n
-def fetch_docstrings(target, source, env):
-Builder action for fetching the relax user function docstrings.
-
-# Print out.
-print
-print ###
-print # Fetching the relax user function docstrings #
-print ###\n\n
-
-# Import the fetch_docstrings module (needs to be done here so that
Sconstruct doesn't need to load the entire program each time).
-sys.path.append(getcwd())
-from docs.latex.fetch_docstrings import Fetch_docstrings
-
-# Get the docstrings.
-Fetch_docstrings(env['LATEX_DIR'] + sep + 'docstring.tex')
-
-# Final print out.
-print \n\n\n
-
-
-def user_manual_html(target, source, env):
-Builder action for creating the HTML manual.
-
-# Print out.
-print
-print
-print # Creating the HTML manual #
-print \n\n
+def compile_user_manual_html(target, source, env):
+Builder action for compiling the HTML version of the user manual from
the LaTeX sources.
+
+# Print out.
+print
+print #
+print # Compiling the HTML version of the user manual #
+print #\n\n
# Go to the LaTeX directory.
base_dir = getcwd()
@@ -138,14 +118,14 @@
print \n\n\n
-def user_manual_pdf(target, source, env):
-Builder action for compiling the LaTeX manual into a PDF file.
-
-# Print out.
-print
-print ###
-print # LaTeX compilation of the manual #
-print ###\n\n
+def compile_user_manual_pdf(target, source, env):
+Builder action for compiling the PDF version of the user manual from
the LaTeX sources.
+
+# Print out.
+print
+print
+print # Compiling the PDF version of the user manual #
+print \n\n
# Go to the LaTeX directory.
base_dir = getcwd()
@@ -195,6 +175,26 @@
print \n\n\n
+def fetch_docstrings(target, source, env):
+Builder action for fetching the relax user function docstrings.
+
+# Print out.
+print
+print ###
+print # Fetching the relax user function docstrings #
+print ###\n\n
+
+# Import the fetch_docstrings module (needs to be done here so that
Sconstruct doesn't need to load the entire program each time).
+sys.path.append(getcwd())
+from docs.latex.fetch_docstrings import Fetch_docstrings
+
+# Get the docstrings.
+Fetch_docstrings(env['LATEX_DIR'] + sep + 'docstring.tex')
+
+# Final print out.
+print \n\n\n
+
+
def version_file(target, source, env):
Builder action for creating the LaTeX relax version file.
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2621r1=2620r2=2621view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 07:08:18 2006
@@ -42,7 +42,7 @@
# relax and Scons modules.
-from scons.manuals import acro, clean_manual_files, fetch_docstrings,
user_manual_html, user_manual_pdf, version_file
+from scons.manuals import acro, clean_manual_files, compile_user_manual_html,
compile_user_manual_pdf, fetch_docstrings, version_file
from version import version
@@ -100,7 +100,7 @@
binary_dist_env.dummy(target='binary_dist', source=None)
binary_dist_env.Depends('binary_dist', 'version_check') #
First
r2622 - /1.2/sconstruct
Author: bugman
Date: Thu Oct 12 07:13:24 2006
New Revision: 2622
URL: http://svn.gna.org/viewcvs/relax?rev=2622view=rev
Log:
Created a single custom builder (using the dummy function) for all the standard
manual targets.
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2622r1=2621r2=2622view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 07:13:24 2006
@@ -174,9 +174,12 @@
LATEX_DIR=self.LATEX_DIR,
SYSTEM=self.SYSTEM)
+
+# Set up the builder for the standard manual targets (using the
self.dummy function).
+manual_env.Append(BUILDERS={'Manual' : Builder(action=self.dummy)})
+
# Target for creating the PDF version of the user manual.
-manual_env.Append(BUILDERS={'UserManualPDF' :
Builder(action=self.dummy)})
-manual_env.UserManualPDF(target='user_manual_pdf', source=None)
+manual_env.Manual(target='user_manual_pdf', source=None)
manual_env.Depends('user_manual_pdf', 'manual_clean')
manual_env.Depends('user_manual_pdf', 'manual_version_file')
manual_env.Depends('user_manual_pdf', 'fetch_docstrings')
@@ -184,8 +187,7 @@
manual_env.Depends('user_manual_pdf', 'manual_acro')
# Target for creating the HTML version of the user manual.
-manual_env.Append(BUILDERS={'UserManualHTML' :
Builder(action=self.dummy)})
-manual_env.UserManualHTML(target='user_manual_html', source=None)
+manual_env.Manual(target='user_manual_html', source=None)
manual_env.Depends('user_manual_html', 'manual_clean')
manual_env.Depends('user_manual_html', 'manual_version_file')
manual_env.Depends('user_manual_html', 'fetch_docstrings')
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r2623 - /1.2/sconstruct
Author: bugman
Date: Thu Oct 12 07:18:12 2006
New Revision: 2623
URL: http://svn.gna.org/viewcvs/relax?rev=2623view=rev
Log:
Removed the Adobe Acrobat dependancy from the standard manual targets.
This allows for the removal of the target 'user_manual_pdf_dist' as the only
difference between that
target and 'user_manual_pdf' was the launching of Acroreader!
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2623r1=2622r2=2623view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 07:18:12 2006
@@ -100,7 +100,7 @@
binary_dist_env.dummy(target='binary_dist', source=None)
binary_dist_env.Depends('binary_dist', 'version_check') #
First check the program version number.
binary_dist_env.Depends('binary_dist', self.relax_fit_object) #
Compile the C code.
-binary_dist_env.Depends('binary_dist', 'user_manual_pdf_dist')#
Compile the PDF version of the user manual.
+binary_dist_env.Depends('binary_dist', 'user_manual_pdf') #
Compile the PDF version of the user manual.
binary_dist_env.Depends('binary_dist', 'manual_clean_nodeps') #
Clean up the temporary manual files.
binary_dist_env.Depends('binary_dist', 'clean_temp') #
Then clean up all other temporary files.
binary_dist_env.Depends('binary_dist', 'package_bin') #
Package the binary distribution.
@@ -110,7 +110,7 @@
source_dist_env = Environment(BUILDERS={'dummy' :
Builder(action=self.dummy)})
source_dist_env.dummy(target='source_dist', source=None)
source_dist_env.Depends('source_dist', 'version_check') #
First check the program version number.
-source_dist_env.Depends('source_dist', 'user_manual_pdf_dist')#
Compile the PDF version of the user manual.
+source_dist_env.Depends('source_dist', 'user_manual_pdf') #
Compile the PDF version of the user manual.
source_dist_env.Depends('source_dist', 'manual_clean_nodeps') #
Clean up the temporary manual files.
source_dist_env.Depends('source_dist', 'clean') #
Then clean up the sources.
source_dist_env.Depends('source_dist', 'package_src') #
Package the source distribution.
@@ -184,7 +184,12 @@
manual_env.Depends('user_manual_pdf', 'manual_version_file')
manual_env.Depends('user_manual_pdf', 'fetch_docstrings')
manual_env.Depends('user_manual_pdf', 'compile_user_manual_pdf')
-manual_env.Depends('user_manual_pdf', 'manual_acro')
+
+# Target for creating the PDF version of the user manual (without
fetching the docstrings).
+manual_env.Manual(target='user_manual_pdf_nofetch', source=None)
+manual_env.Depends('user_manual_pdf_nofetch', 'manual_clean')
+manual_env.Depends('user_manual_pdf_nofetch', 'manual_version_file')
+manual_env.Depends('user_manual_pdf_nofetch',
'compile_user_manual_pdf')
# Target for creating the HTML version of the user manual.
manual_env.Manual(target='user_manual_html', source=None)
@@ -192,21 +197,6 @@
manual_env.Depends('user_manual_html', 'manual_version_file')
manual_env.Depends('user_manual_html', 'fetch_docstrings')
manual_env.Depends('user_manual_html', 'compile_user_manual_html')
-manual_env.Depends('user_manual_html', 'manual_acro')
-
-# Target for creating the PDF version of the user manual (without
fetching the docstrings).
-manual_env.Manual(target='user_manual_pdf_nofetch', source=None)
-manual_env.Depends('user_manual_pdf_nofetch', 'manual_clean')
-manual_env.Depends('user_manual_pdf_nofetch', 'manual_version_file')
-manual_env.Depends('user_manual_pdf_nofetch',
'compile_user_manual_pdf')
-manual_env.Depends('user_manual_pdf_nofetch', 'manual_acro')
-
-# Target for creating the PDF version of the user manual for
distribution.
-manual_env.Manual(target='user_manual_pdf_dist', source=None)
-manual_env.Depends('user_manual_pdf_dist', 'manual_clean')
-manual_env.Depends('user_manual_pdf_dist', 'manual_version_file')
-manual_env.Depends('user_manual_pdf_dist', 'fetch_docstrings')
-manual_env.Depends('user_manual_pdf_dist', 'compile_user_manual_pdf')
# Target for creating relax version number LaTeX file.
manual_env.Append(BUILDERS={'Version' : Builder(action=version_file)})
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r2624 - /1.2/sconstruct
Author: bugman
Date: Thu Oct 12 07:19:57 2006
New Revision: 2624
URL: http://svn.gna.org/viewcvs/relax?rev=2624view=rev
Log:
Created a new standard manual target called 'user_manual_html_nofetch'.
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2624r1=2623r2=2624view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 07:19:57 2006
@@ -42,7 +42,7 @@
# relax and Scons modules.
-from scons.manuals import acro, clean_manual_files, compile_user_manual_html,
compile_user_manual_pdf, fetch_docstrings, version_file
+from scons.manuals import clean_manual_files, compile_user_manual_html,
compile_user_manual_pdf, fetch_docstrings, version_file
from version import version
@@ -198,6 +198,13 @@
manual_env.Depends('user_manual_html', 'fetch_docstrings')
manual_env.Depends('user_manual_html', 'compile_user_manual_html')
+# Target for creating the HTML version of the user manual (without
fetching the docstrings).
+manual_env.Manual(target='user_manual_html_nofetch', source=None)
+manual_env.Depends('user_manual_html_nofetch', 'manual_clean')
+manual_env.Depends('user_manual_html_nofetch', 'manual_version_file')
+manual_env.Depends('user_manual_html_nofetch',
'compile_user_manual_html')
+
+
# Target for creating relax version number LaTeX file.
manual_env.Append(BUILDERS={'Version' : Builder(action=version_file)})
manual_env.Version(target='manual_version_file', source=None)
@@ -213,10 +220,6 @@
# Target for compiling the HTML version of the user manual from the
LaTeX sources.
manual_env.Append(BUILDERS={'CompileUserManualHTML' :
Builder(action=compile_user_manual_html)})
manual_env.CompileUserManualHTML(target='compile_user_manual_html',
source=None)
-
-# Target for launching Adobe Acrobat with the PDF version of the relax
manual.
-manual_env.Append(BUILDERS={'Acro' : Builder(action=acro)})
-manual_env.Acro(target='manual_acro', source=None)
# Clean target.
manual_env.Append(BUILDERS={'Clean' :
Builder(action=clean_manual_files)})
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r2625 - /1.2/scons/manuals.py
Author: bugman Date: Thu Oct 12 07:21:15 2006 New Revision: 2625 URL: http://svn.gna.org/viewcvs/relax?rev=2625view=rev Log: Removed all traces of Adobe Acrobat Reader (deleted the acro() function, etc.). Modified: 1.2/scons/manuals.py Modified: 1.2/scons/manuals.py URL: http://svn.gna.org/viewcvs/relax/1.2/scons/manuals.py?rev=2625r1=2624r2=2625view=diff == --- 1.2/scons/manuals.py (original) +++ 1.2/scons/manuals.py Thu Oct 12 07:21:15 2006 @@ -30,19 +30,6 @@ from version import version - - -def acro(target, source, env): -Builder action for executing Adobe Acrobat reader with the PDF manual. - -# Print out. -print -print ## -print # Viewing the PDF manual using Adobe Acrobat # -print ##\n\n - -print Running the command:\n$ acroread -openInNewWindow + env['DOCS_DIR'] + relax.pdf \n\n\n -system(acroread -openInNewWindow + env['DOCS_DIR'] + relax.pdf ) def clean_manual_files(target, source, env): ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2626 - in /1.2: scons/manuals.py sconstruct
Author: bugman Date: Thu Oct 12 08:33:45 2006 New Revision: 2626 URL: http://svn.gna.org/viewcvs/relax?rev=2626view=rev Log: Added the API documentation creation (using Epydoc) to the Scons scripts. The Scons target to create the HTML API documentation is called 'api_manual_html'. The documentation can be created by typing: $ scons api_manual_html The function 'compile_api_manual_html()' was added to the 'scons/manuals.py' file. This function runs the 'epydoc' command. All the Epydoc options are specified in that function. Modified: 1.2/scons/manuals.py 1.2/sconstruct Modified: 1.2/scons/manuals.py URL: http://svn.gna.org/viewcvs/relax/1.2/scons/manuals.py?rev=2626r1=2625r2=2626view=diff == --- 1.2/scons/manuals.py (original) +++ 1.2/scons/manuals.py Thu Oct 12 08:33:45 2006 @@ -81,6 +81,199 @@ print \n\n\n +def compile_api_manual_html(target, source, env): +Builder action for compiling the API documentation manual (HTML version) using Epydoc. + +# Print out. +print +print # +print # Compiling API documentation manual (HTML version) # +print #\n\n + + +# Set up the Epydoc configuration (adapted from http://epydoc.sourceforge.net/configfile.html). + ### + +# modules +# The list of objects to document. +modules = ['relax', + '*.py', + 'docs/*.py', + 'docs/latex/*.py', + 'dx/*.py', + 'generic_fns/*.py', + 'maths_fns/*.py', + 'prompt/*.py', + 'specific_fns/*.py', + 'test_suite/*.py', + 'sconstruct', + 'scons/*.py'] + +# output +# The type of output that should be generated. Should be one +# of: html, text, latex, dvi, ps, pdf. +output = 'html' + +# target +# The path to the output directory. May be relative or absolute. +target = 'docs/api' + +# docformat +# The default markup language for docstrings, for modules that do +# not define __docformat__. +docformat = 'epytext' + +# css +# The CSS stylesheet for HTML output. Can be the name of a builtin +# stylesheet, or the name of a file. +css = 'white' + +# name +# The documented project's name. +name = 'relax' + +# url +# The documented project's URL. +url = 'http://nmr-relax.com' + +# link +# HTML code for the project link in the navigation bar. If left +# unspecified, the project link will be generated based on the +# project's name and URL. +#link = 'a href=http://nmr-relax.com;relax/a' + +# top +# The top page for the documentation. Can be a URL, the name +# of a module or class, or one of the special names trees.html, +# indices.html, or help.html +# top = 'os.path' + +# help +# An alternative help file. The named file should contain the +# body of an HTML file; navigation bars will be added to it. +# help = 'my_helpfile.html' + +# frames +# Whether or not to include a frames-based table of contents. +frames = 1 + +# private +# Whether or not to inclue private variables. (Even if included, +# private variables will be hidden by default.) +private = 1 + +# imports +# Whether or not to list each module's imports. +imports = 1 + +# verbosity +# An integer indicating how verbose epydoc should be. The default +# value is 0; negative values will supress warnings and errors; +# positive values will give more verbose output. +verbosity = 1 + +# parse +# Whether or not parsing should be used to examine objects. +parse = 1 + +# introspect +# Whether or not introspection should be used to examine objects. +introspect = 1 + +# graph +# The list of graph types that should be automatically included +# in the output. Graphs are generated using the Graphviz dot +# executable. Graph types include: classtree, callgraph, +# umlclass. Use all to include all graph types +graph = 'all' + +# dotpath +# The path to the Graphviz dot executable, used to generate +# graphs. +#dotpath = '/usr/local/bin/dot' + +# sourcecode +# Whether or not to include syntax highlighted source code in +# the output (HTML only). +sourcecode = 1 + +# pstat +# The name of one or more pstat files (generated by the profile +# or hotshot module). These are used to generate call graphs. +#pstat = 'profile.out' + +# separate-classes +# Whether each class should be listed in its own section when +# generating LaTeX or PDF
r2627 - /1.2/scons/manuals.py
Author: bugman
Date: Thu Oct 12 08:58:43 2006
New Revision: 2627
URL: http://svn.gna.org/viewcvs/relax?rev=2627view=rev
Log:
Modification of the CSS file for the API documentation (HTML version).
The file 'docs/api/epydoc.css' is being modified so that the links are not
underlined, change colour
when the mouse is over them, are not in bold, and have the same colouring as
the standard
http://nmr-relax.com pages. This makes the API documentation pages fit better
with the style of
http://nmr-relax.com.
Modified:
1.2/scons/manuals.py
Modified: 1.2/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/scons/manuals.py?rev=2627r1=2626r2=2627view=diff
==
--- 1.2/scons/manuals.py (original)
+++ 1.2/scons/manuals.py Thu Oct 12 08:58:43 2006
@@ -270,6 +270,24 @@
# System call.
system(epydoc_cmd)
+
+
+# Modify the CSS file.
+##
+
+# Open the file.
+css_file = open(target + '/epydoc.css', 'a')
+
+# Header.
+css_file.write(\n\n\n\n/* Edward */\n\n)
+
+# Append the new link style to the end.
+css_file.write(a { text-decoration:none; color:#0017aa;
font-weight:normal; }\n)
+css_file.write(a:hover { color:#316fff; }\n)
+
+# Close the file.
+css_file.close()
+
# Final print out.
print \n\n\n
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r2628 - in /1.2: scons/manuals.py sconstruct
Author: bugman
Date: Thu Oct 12 09:05:36 2006
New Revision: 2628
URL: http://svn.gna.org/viewcvs/relax?rev=2628view=rev
Log:
Changed the comments and docstrings of the Scons manual targets.
The PDF or HMTL version is now in brackets after the 'user manual' and 'API
documentation manual'
parts.
Modified:
1.2/scons/manuals.py
1.2/sconstruct
Modified: 1.2/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/scons/manuals.py?rev=2628r1=2627r2=2628view=diff
==
--- 1.2/scons/manuals.py (original)
+++ 1.2/scons/manuals.py Thu Oct 12 09:05:36 2006
@@ -293,13 +293,13 @@
def compile_user_manual_html(target, source, env):
-Builder action for compiling the HTML version of the user manual from
the LaTeX sources.
-
-# Print out.
-print
-print #
-print # Compiling the HTML version of the user manual #
-print #\n\n
+Builder action for compiling the user manual (HTML version) from the
LaTeX sources.
+
+# Print out.
+print
+print
+print # Compiling the user manual (HTML version) #
+print \n\n
# Go to the LaTeX directory.
base_dir = getcwd()
@@ -317,13 +317,13 @@
def compile_user_manual_pdf(target, source, env):
-Builder action for compiling the PDF version of the user manual from
the LaTeX sources.
-
-# Print out.
-print
-print
-print # Compiling the PDF version of the user manual #
-print \n\n
+Builder action for compiling the user manual (PDF version) from the
LaTeX sources.
+
+# Print out.
+print
+print ###
+print # Compiling the user manual (PDF version) #
+print ###\n\n
# Go to the LaTeX directory.
base_dir = getcwd()
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2628r1=2627r2=2628view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 09:05:36 2006
@@ -178,33 +178,33 @@
# Set up the builder for the standard manual targets (using the
self.dummy function).
manual_env.Append(BUILDERS={'Manual' : Builder(action=self.dummy)})
-# Target for creating the PDF version of the user manual.
+# Target for creating the user manual (PDF version).
manual_env.Manual(target='user_manual_pdf', source=None)
manual_env.Depends('user_manual_pdf', 'manual_clean')
manual_env.Depends('user_manual_pdf', 'manual_version_file')
manual_env.Depends('user_manual_pdf', 'fetch_docstrings')
manual_env.Depends('user_manual_pdf', 'compile_user_manual_pdf')
-# Target for creating the PDF version of the user manual (without
fetching the docstrings).
+# Target for creating the user manual (PDF version, without fetching
the docstrings).
manual_env.Manual(target='user_manual_pdf_nofetch', source=None)
manual_env.Depends('user_manual_pdf_nofetch', 'manual_clean')
manual_env.Depends('user_manual_pdf_nofetch', 'manual_version_file')
manual_env.Depends('user_manual_pdf_nofetch',
'compile_user_manual_pdf')
-# Target for creating the HTML version of the user manual.
+# Target for creating the user manual (HTML version).
manual_env.Manual(target='user_manual_html', source=None)
manual_env.Depends('user_manual_html', 'manual_clean')
manual_env.Depends('user_manual_html', 'manual_version_file')
manual_env.Depends('user_manual_html', 'fetch_docstrings')
manual_env.Depends('user_manual_html', 'compile_user_manual_html')
-# Target for creating the HTML version of the user manual (without
fetching the docstrings).
+# Target for creating the user manual (HTML version, without fetching
the docstrings).
manual_env.Manual(target='user_manual_html_nofetch', source=None)
manual_env.Depends('user_manual_html_nofetch', 'manual_clean')
manual_env.Depends('user_manual_html_nofetch', 'manual_version_file')
manual_env.Depends('user_manual_html_nofetch',
'compile_user_manual_html')
-# Target for creating the HTML version of the API documentation manual.
+# Target for creating the API documentation manual (HTML version).
manual_env.Manual(target='api_manual_html', source=None)
manual_env.Depends('api_manual_html', 'manual_clean')
manual_env.Depends('api_manual_html', 'compile_api_manual_html')
___
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r2629 - /1.2/scons/manuals.py
Author: bugman Date: Thu Oct 12 09:07:31 2006 New Revision: 2629 URL: http://svn.gna.org/viewcvs/relax?rev=2629view=rev Log: Fixed an incorrect comment in the 'compile_user_manual_html()' Scons build target function. Modified: 1.2/scons/manuals.py Modified: 1.2/scons/manuals.py URL: http://svn.gna.org/viewcvs/relax/1.2/scons/manuals.py?rev=2629r1=2628r2=2629view=diff == --- 1.2/scons/manuals.py (original) +++ 1.2/scons/manuals.py Thu Oct 12 09:07:31 2006 @@ -305,7 +305,7 @@ base_dir = getcwd() chdir(env['LATEX_DIR']) -# Get the docstrings. +# Run the latex2html command. print Running the command:\n$ latex2html -split +3 -html_version 4.0 -dir + path.pardir + path.sep + html relax.tex\n\n\n system(latex2html -split +3 -html_version 4.0 -dir + path.pardir + path.sep + html relax.tex) ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2630 - /1.2/sconstruct
Author: bugman
Date: Thu Oct 12 09:33:35 2006
New Revision: 2630
URL: http://svn.gna.org/viewcvs/relax?rev=2630view=rev
Log:
A completely new Scons help message has been created.
The message (produced after typing 'scons --help') has been formatted to be in
the same style as the
relax help message ('relax --help'). A line describing the Scons usage has
been added. The result
of providing no target, C module compilation, has been added. Both the
'standard targets' and the
'specific targets' are now described. Every last Scons target is fully
described.
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2630r1=2629r2=2630view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 09:33:35 2006
@@ -218,7 +218,7 @@
manual_env.Append(BUILDERS={'Fetch' :
Builder(action=fetch_docstrings)})
manual_env.Fetch(target='fetch_docstrings', source=None)
-# Target for compiling the PDF version of the user manaul from the
LaTeX sources.
+# Target for compiling the PDF version of the user manual from the
LaTeX sources.
manual_env.Append(BUILDERS={'CompileUserManualPDF' :
Builder(action=compile_user_manual_pdf)})
manual_env.CompileUserManualPDF(target='compile_user_manual_pdf',
source=None)
@@ -321,11 +321,43 @@
The help message.
# Intro.
-string = '\nSconstruct help for relax.\n\n'
-
-# Main text.
-string = string + 'To build the C modules, type\n\n$ scons\n\n'
-string = string + 'To install the program, type\n\n$ scons install\n\n'
+string = '\nHelp for using Scons to build the various components of
relax.\n\n'
+
+# Usage message.
+string = string + 'usage: scons [target]\n'
+
+# No target.
+string = string + '\nNo target:\n'
+string = string + ' %-25s\n' % ('build the C modules')
+
+# Standard targets.
+string = string + '\nStandard targets:\n'
+string = string + ' %-25s%-40s\n' % ('install', 'install relax')
+string = string + ' %-25s%-40s\n' % ('uninstall', 'uninstall relax')
+string = string + ' %-25s%-40s\n' % ('binary_dist', 'create the
binary distribution packages')
+string = string + ' %-25s%-40s\n' % ('source_dist', 'create the
source distribution packages')
+string = string + ' %-25s%-40s\n' % ('clean', 'remove the compiled
and temporary files')
+string = string + ' %-25s%-40s\n' % ('user_manual_pdf', 'create the
user manual (PDF version)')
+string = string + ' %-25s%-40s\n' % ('user_manual_pdf_nofetch',
'create the user manual (PDF version, without fetching the docstrings)')
+string = string + ' %-25s%-40s\n' % ('user_manual_html', 'create the
user manual (HTML version)')
+string = string + ' %-25s%-40s\n' % ('user_manual_html_nofetch',
'create the user manual (HTML version, without fetching the docstrings)')
+string = string + ' %-25s%-40s\n' % ('api_manual_html', 'create the
API documentation manual (HTML version)')
+
+# Specific targets.
+string = string + '\nSpecific targets:\n'
+string = string + ' %-25s%-40s\n' % ('package_bin', 'package the
binary distribution')
+string = string + ' %-25s%-40s\n' % ('package_src', 'package the
source distribution')
+string = string + ' %-25s%-40s\n' % ('gpg_bin', 'GPG sign the binary
distribution file')
+string = string + ' %-25s%-40s\n' % ('gpg_src', 'GPG sign the source
distribution file')
+string = string + ' %-25s%-40s\n' % ('version_check', 'check the
relax version number')
+string = string + ' %-25s%-40s\n' % ('clean_temp', 'remove the
temporary files')
+string = string + ' %-25s%-40s\n' % ('manual_version_file', 'create
the relax version number LaTeX file')
+string = string + ' %-25s%-40s\n' % ('fetch_docstrings', 'fetch and
LaTeX format the docstrings')
+string = string + ' %-25s%-40s\n' % ('compile_user_manual_pdf',
'compile the PDF version of the user manual from the LaTeX sources')
+string = string + ' %-25s%-40s\n' % ('compile_user_manual_html',
'compile the HTML version of the user manual from the LaTeX sources')
+string = string + ' %-25s%-40s\n' % ('compile_api_manual_html',
'compile the HTML version of the API documentation manual using Epydoc')
+string = string + ' %-25s%-40s\n' % ('manual_clean', 'remove the
temporary manual files')
+string = string + ' %-25s%-40s\n' % ('manual_clean_nodeps', 'remove
the temporary manual files (with no manual environments dependent on it)')
# Set the help message.
Help(string)
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To
r2631 - /1.2/sconstruct
Author: bugman
Date: Thu Oct 12 09:34:28 2006
New Revision: 2631
URL: http://svn.gna.org/viewcvs/relax?rev=2631view=rev
Log:
Changed the C module compilation Scons help message.
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2631r1=2630r2=2631view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 09:34:28 2006
@@ -328,7 +328,7 @@
# No target.
string = string + '\nNo target:\n'
-string = string + ' %-25s\n' % ('build the C modules')
+string = string + ' %-25s\n' % ('compile the C modules')
# Standard targets.
string = string + '\nStandard targets:\n'
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r2632 - /1.2/sconstruct
Author: bugman
Date: Thu Oct 12 09:36:12 2006
New Revision: 2632
URL: http://svn.gna.org/viewcvs/relax?rev=2632view=rev
Log:
Fixed a very minor bug in the Scons source packaging target.
The relax version was not being checked because the Depends statement was using
'package_bin' rather
than 'package_src'.
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2632r1=2631r2=2632view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Thu Oct 12 09:36:12 2006
@@ -126,7 +126,7 @@
package_src_env = Environment(BUILDERS={'archive' :
Builder(action=self.package)},
DIST_FILE=self.SRC_FILE)
package_src_env.archive(target='package_src', source=None)
-package_src_env.Depends('package_bin', 'version_check') # Check
the program version number first.
+package_src_env.Depends('package_src', 'version_check') # Check
the program version number first.
# Target for creating a GPG signature of the binary distribution file.
gpg_bin_env = Environment(BUILDERS={'sign' :
Builder(action=self.gpg_sign)},
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r2633 - in /1.3: scons/__init__.py scons/manuals.py sconstruct
Author: bugman Date: Thu Oct 12 09:43:25 2006 New Revision: 2633 URL: http://svn.gna.org/viewcvs/relax?rev=2633view=rev Log: Ported r2618 to r2632 from the 1.2 line. The command used was: $ svn merge -r2617:2632 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 These changes all relate to the Scons system. The Scons scripts have been completely overhauled. Bugs have been removed. The help system has been redone. A target for creating the API documentation using Epydoc has been added. Added: 1.3/scons/__init__.py - copied unchanged from r2632, 1.2/scons/__init__.py 1.3/scons/manuals.py - copied unchanged from r2632, 1.2/scons/manuals.py Modified: 1.3/sconstruct [This mail would be too long, it was shortened to contain the URLs only.] Modified: 1.3/sconstruct URL: http://svn.gna.org/viewcvs/relax/1.3/sconstruct?rev=2633r1=2632r2=2633view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2635 - in /1.2: scons/distrib.py sconstruct
Author: bugman Date: Thu Oct 12 11:04:46 2006 New Revision: 2635 URL: http://svn.gna.org/viewcvs/relax?rev=2635view=rev Log: Shifted the Scons distribution target functions from 'sconstruct' to 'scons/distrib.py'. The functions 'self.package' and 'self.gpg_sign' have been shifted into their own file 'scons/distrib.py'. Added: 1.2/scons/distrib.py - copied, changed from r2632, 1.2/sconstruct Modified: 1.2/sconstruct [This mail would be too long, it was shortened to contain the URLs only.] Copied: 1.2/scons/distrib.py (from r2632, 1.2/sconstruct) URL: http://svn.gna.org/viewcvs/relax/1.2/scons/distrib.py?p2=1.2/scons/distrib.pyp1=1.2/sconstructr1=2632r2=2635rev=2635view=diff Modified: 1.2/sconstruct URL: http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2635r1=2634r2=2635view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2637 - /1.2/scons/distrib.py
Author: bugman Date: Fri Oct 13 07:33:29 2006 New Revision: 2637 URL: http://svn.gna.org/viewcvs/relax?rev=2637view=rev Log: Fixed a bug in the Scons distribution target functions. The relax version number variable 'version' which exists in the base 'sconstruct' module doesn't exist within the 'scons/distrib.py' module. It is now passed into the construction Environment as an environmental variable. Modified: 1.2/scons/distrib.py Modified: 1.2/scons/distrib.py URL: http://svn.gna.org/viewcvs/relax/1.2/scons/distrib.py?rev=2637r1=2636r2=2637view=diff == --- 1.2/scons/distrib.py (original) +++ 1.2/scons/distrib.py Fri Oct 13 07:33:29 2006 @@ -86,10 +86,10 @@ # Create the file name (without the base directory). name = path.join(root, files[i]) name = name[len(base):] -print 'relax-' + version + path.sep + name +print 'relax-' + env['RELAX_VERSION'] + path.sep + name # The archive file name. -arcname = 'relax-' + version + path.sep + name +arcname = 'relax-' + env['RELAX_VERSION'] + path.sep + name # Zip archives. if env['DIST_TYPE'] == 'zip': ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2638 - /1.2/scons/distrib.py
Author: bugman Date: Fri Oct 13 07:38:50 2006 New Revision: 2638 URL: http://svn.gna.org/viewcvs/relax?rev=2638view=rev Log: The fix of the previous revision has been redone. Rather than 'sconstruct' passing in the relax version number as an environmental variable, the file 'scons/distrib.py' now just imports the file 'version.py'. This is a much simpler solution! Modified: 1.2/scons/distrib.py Modified: 1.2/scons/distrib.py URL: http://svn.gna.org/viewcvs/relax/1.2/scons/distrib.py?rev=2638r1=2637r2=2638view=diff == --- 1.2/scons/distrib.py (original) +++ 1.2/scons/distrib.py Fri Oct 13 07:38:50 2006 @@ -26,6 +26,9 @@ from re import search from tarfile import TarFile from zipfile import ZipFile + +# relax version file. +from version import version @@ -86,10 +89,10 @@ # Create the file name (without the base directory). name = path.join(root, files[i]) name = name[len(base):] -print 'relax-' + env['RELAX_VERSION'] + path.sep + name +print 'relax-' + version + path.sep + name # The archive file name. -arcname = 'relax-' + env['RELAX_VERSION'] + path.sep + name +arcname = 'relax-' + version + path.sep + name # Zip archives. if env['DIST_TYPE'] == 'zip': ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2639 - /1.2/scons/install.py
Author: bugman Date: Fri Oct 13 07:40:19 2006 New Revision: 2639 URL: http://svn.gna.org/viewcvs/relax?rev=2639view=rev Log: Shifted the 'install' and 'uninstall' target functions into their own module in the 'scons' dir. Added: 1.2/scons/install.py - copied, changed from r2635, 1.2/sconstruct [This mail would be too long, it was shortened to contain the URLs only.] Copied: 1.2/scons/install.py (from r2635, 1.2/sconstruct) URL: http://svn.gna.org/viewcvs/relax/1.2/scons/install.py?p2=1.2/scons/install.pyp1=1.2/sconstructr1=2635r2=2639rev=2639view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2640 - /1.2/sconstruct
Author: bugman
Date: Fri Oct 13 07:43:59 2006
New Revision: 2640
URL: http://svn.gna.org/viewcvs/relax?rev=2640view=rev
Log:
Removal of the installation targets and changing of the initialisation of the
system path variables.
The installation target functions 'self.install()' and 'self.uninstall()' have
been deleted as they
are now located in the 'scons.install' module.
The 'self.paths()' function has been removed. All the paths, environmental
variables, etc. are now
initialised at the top of the 'sconstruct' file.
Modified:
1.2/sconstruct
Modified: 1.2/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.2/sconstruct?rev=2640r1=2639r2=2640view=diff
==
--- 1.2/sconstruct (original)
+++ 1.2/sconstruct Fri Oct 13 07:43:59 2006
@@ -27,24 +27,121 @@
# Import statements.
import platform
-from os import F_OK, access, getcwd, path, remove, rmdir, sep, system, walk
+from os import getcwd, path, remove, sep, walk
from re import search
-from shutil import copytree
import sys
-from tarfile import TarFile
-from zipfile import ZipFile
-
-# UNIX only functions from the os module.
-try:
-from os import lstat, symlink
-except ImportError:
-pass
-
-
-# relax and Scons modules.
+
+# Scons modules.
from scons.distrib import package, gpg_sign
+from scons.install import install, uninstall
from scons.manuals import clean_manual_files, compile_api_manual_html,
compile_user_manual_html, compile_user_manual_pdf, fetch_docstrings,
version_file
+
+# relax version file.
from version import version
+
+
+
+
+# Paths and file names #
+
+
+# The operating system.
+SYSTEM = platform.uname()[0]
+
+# The machine type.
+MACH = platform.uname()[4]
+
+# Symbolic link flag.
+SYMLINK_FLAG = 1
+
+# GNU/Linux.
+if SYSTEM == 'Linux':
+# System specific string.
+SYS = 'GNU-Linux'
+
+# Linux installation path.
+INSTALL_PATH = '/usr/local'
+
+
+# MS Windows.
+elif SYSTEM == 'Windows':
+# Architecture.
+arch = platform.architecture()[0]
+
+# 32 bit.
+if arch == '32bit':
+SYS = 'Win32'
+
+# 64 bit.
+elif arch == '64bit':
+SYS = 'Win64'
+
+# Unknown.
+else:
+SYS = 'Win'
+
+# Windows installation path.
+INSTALL_PATH = 'C:\\'
+
+# No symlinks!
+SYMLINK_FLAG = 0
+
+
+# Mac OS X.
+elif SYSTEM == 'Darwin':
+# System specific string.
+SYS = SYSTEM
+
+# Mac OS X installation path.
+INSTALL_PATH = sys.prefix + sep + 'local'
+
+
+# All other operating systems.
+else:
+# System specific string.
+SYS = SYSTEM
+
+# Installation path.
+INSTALL_PATH = sys.prefix + sep + 'local'
+
+
+
+# Installation.
+###
+
+# Relax installation directory.
+RELAX_PATH = INSTALL_PATH + sep + 'relax'
+
+# Installation path for binaries.
+BIN_PATH = INSTALL_PATH + sep + 'bin'
+
+# Symbolic link installation path.
+SYMLINK = BIN_PATH + sep + 'relax'
+
+
+
+# The distribution files.
+#
+
+if SYSTEM == 'Windows':
+BIN_FILE = 'relax-' + version + '.' + SYS + '.zip'
+SRC_FILE = 'relax-' + version + '.src.zip'
+DIST_TYPE = 'zip'
+else:
+BIN_FILE = 'relax-' + version + '.' + SYS + '.' + MACH + '.tar.bz2'
+SRC_FILE = 'relax-' + version + '.src.tar.bz2'
+DIST_TYPE = 'tar'
+
+
+# Documentation.
+
+
+# Documentation directory.
+DOCS_DIR = 'docs' + sep
+
+# LaTeX directory.
+LATEX_DIR = 'docs' + sep + 'latex' + sep
+
@@ -62,13 +159,6 @@
# Set the help message.
self.help()
-# The operating system.
-self.SYSTEM = platform.uname()[0]
-
-# Set up the paths and file names.
-self.set_paths()
-
-
# C module compilation.
###
@@ -83,12 +173,21 @@
###
# Install target.
-install_env = Environment(BUILDERS={'install' :
Builder(action=self.install)},
- RELAX_PATH=self.RELAX_PATH)
+install_env = Environment(BUILDERS={'install' :
Builder(action=install)},
+ BIN_PATH=BIN_PATH,
+ INSTALL_PATH=INSTALL_PATH,
+ RELAX_PATH=RELAX_PATH,
+ SYMLINK=SYMLINK,
+ SYMLINK_FLAG=SYMLINK_FLAG)
install_env.install(target='install', source=None)
# Uninstall target.
-uninstall_env = Environment(BUILDERS={'uninstall' :
Builder(action=self.uninstall)})
+uninstall_env = Environment(BUILDERS={'uninstall' :
Builder(action=uninstall)},
+ BIN_PATH=BIN_PATH,
+ INSTALL_PATH=INSTALL_PATH,
+ RELAX_PATH=RELAX_PATH,
+ SYMLINK=SYMLINK,
+
r2641 - /1.2/docs/latex/maths.tex
Author: bugman
Date: Fri Oct 13 07:59:18 2006
New Revision: 2641
URL: http://svn.gna.org/viewcvs/relax?rev=2641view=rev
Log:
Fix for the documentation bug #7402 (https://gna.org/bugs/?7402).
This fixes the sigma(NOE) equations in section 8.8.1 of the relax user manual.
Alex Hansen reported
that the equations incorrect as one of the spectral density terms were
multiplied by a factor of 6
when there should be nothing. This problem does not affect the code, the
equations there are
correct.
Modified:
1.2/docs/latex/maths.tex
Modified: 1.2/docs/latex/maths.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/maths.tex?rev=2641r1=2640r2=2641view=diff
==
--- 1.2/docs/latex/maths.tex (original)
+++ 1.2/docs/latex/maths.tex Fri Oct 13 07:59:18 2006
@@ -502,21 +502,21 @@
For the dipolar component of the $\crossrate$ equation~\eqref{eq: sigma_NOE}
on page~\pageref{eq: sigma_NOE} the spectral density terms are
\begin{equation}
-J_d^{\crossrate} = 6J(\omega_H + \omega_X) - 6J(\omega_H - \omega_X).
\label{eq: J terms: JsigmaNOEd}
+J_d^{\crossrate} = 6J(\omega_H + \omega_X) - J(\omega_H - \omega_X).
\label{eq: J terms: JsigmaNOEd}
\end{equation}
\noindent The partial derivative of these terms with respect to the spectral
density function parameter $\theta_j$ is
\begin{equation}
{J_d^{\crossrate}}' \equiv \frac{\partial J_d^{\crossrate}}{\partial
\theta_j}
= 6 \frac{\partial J(\omega_H + \omega_X)}{\partial \theta_j}
-- 6 \frac{\partial J(\omega_H - \omega_X)}{\partial \theta_j}.
\label{eq: J terms: JsigmaNOEd'}
+ - \frac{\partial J(\omega_H - \omega_X)}{\partial \theta_j}.
\label{eq: J terms: JsigmaNOEd'}
\end{equation}
\noindent The second partial derivative with respect to the spectral density
function parameters $\theta_j$ and $\theta_k$ is
\begin{equation}
{J_d^{\crossrate}}'' \equiv \frac{\partial^2 J_d^{\crossrate}}{\partial
\theta_j \cdot \partial \theta_k}
= 6 \frac{\partial^2 J(\omega_H + \omega_X)}{\partial \theta_j \cdot
\partial \theta_k}
-- 6 \frac{\partial^2 J(\omega_H - \omega_X)}{\partial \theta_j \cdot
\partial \theta_k}. \label{eq: J terms: JsigmaNOEd}
+ - \frac{\partial^2 J(\omega_H - \omega_X)}{\partial \theta_j \cdot
\partial \theta_k}. \label{eq: J terms: JsigmaNOEd}
\end{equation}
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r2642 - /1.2/docs/latex/infrastruct.tex
Author: bugman
Date: Mon Oct 16 10:02:49 2006
New Revision: 2642
URL: http://svn.gna.org/viewcvs/relax?rev=2642view=rev
Log:
Modified the infrastructure chapter of the user manual.
Each mailing list has been given their own subsections.
A warning about the thread breaking caused by changing the email subject when
using Gmail has been
added.
Modified:
1.2/docs/latex/infrastruct.tex
Modified: 1.2/docs/latex/infrastruct.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/infrastruct.tex?rev=2642r1=2641r2=2642view=diff
==
--- 1.2/docs/latex/infrastruct.tex (original)
+++ 1.2/docs/latex/infrastruct.tex Mon Oct 16 10:02:49 2006
@@ -25,15 +25,35 @@
A number of mailing lists have been created covering different aspects of
relax. These include the announcement list\index{mailing list!relax-announce},
the relax users list\index{mailing list!relax-users}, the relax development
list\index{mailing list!relax-devel}, and the relax committers
list\index{mailing list!relax-commits}.
+
+% relax-announce mailing list.
+\subsection{relax-announce}
+
The relax announcement list ``relax-announce at gna.org''\index{mailing
list!relax-announce} is reserved for important announcements about the program
including the release of new program versions. The amount of traffic on this
list is relatively low. If you would like to receive information about relax
you can subscribe to the list by vising the information page at
\href{https://mail.gna.org/listinfo/relax-announce/}{https://mail.gna.org/listinfo/relax-announce/}.
Previous announcements can be viewed at
\href{https://mail.gna.org/public/relax-announce/}{https://mail.gna.org/public/relax-announce/}\index{mailing
list!archives}.
+
+
+% relax-users mailing list.
+\subsection{relax-users}
If you would like to ask questions about relax, discuss certain features,
receive help, or to communicate on any other subject related to relax the
mailing list ``relax-users at gna.org''\index{mailing list!relax-users} is the
place to post your message. To subscribe to the list go to the relax-users
information page at
\href{https://mail.gna.org/listinfo/relax-users/}{https://mail.gna.org/listinfo/relax-users/}.
You can also browse the mailing list archives at
\href{https://mail.gna.org/public/relax-users/}{https://mail.gna.org/public/relax-users/}\index{mailing
list!archives}.
+
+% relax-devel mailing list.
+\subsection{relax-devel}
+
A second mailing list exists for posts relating to the development of relax.
The list is ``relax-devel at gna.org''\index{mailing list!relax-devel} and to
subscribe go to the relax-devel information page at
\href{https://mail.gna.org/listinfo/relax-devel/}{https://mail.gna.org/listinfo/relax-devel/}.
Feature requests, program design, or any other posts relating to relax's
structure or code should be sent to this list instead. The mailing list
archives can be browsed at
\href{https://mail.gna.org/public/relax-devel/}{https://mail.gna.org/public/relax-devel/}\index{mailing
list!archives}.
-When replying to a message on these lists remember to hit `respond to all' so
that the mailing list is included in the CC field. Otherwise your message will
only be sent to the original poster and not return back to the list.
-One last mailing list is the relax commits list\index{mailing
list!relax-commits}. This list is reserved for automatically generated posts
created by the version control software which looks after the relax source code
and these web pages. If you would like to become a developer you can subscribe
to the list at relax-commits information page
\href{https://mail.gna.org/listinfo/relax-commits/}{https://mail.gna.org/listinfo/relax-commits/}.
The list can also be browsed at
\href{https://mail.gna.org/public/relax-commits/}{https://mail.gna.org/public/relax-commits/}\index{mailing
list!archives}.
+% relax-commits mailing list.
+\subsection{relax-commits}
+
+One last mailing list is the relax commits list\index{mailing
list!relax-commits}. This list is reserved for automatically generated posts
created by the version control software which looks after the relax source code
and these web pages. If you would like to become a developer you can subscribe
to the list at relax-commits information page
\href{https://mail.gna.oactuallyrg/listinfo/relax-commits/}{https://mail.gna.org/listinfo/relax-commits/}.
The list can also be browsed at
\href{https://mail.gna.org/public/relax-commits/}{https://mail.gna.org/public/relax-commits/}\index{mailing
list!archives}.
+
+
+% Replying to a message.
+\subsection{Replying to a message}
+
+When replying to a message on these lists remember to hit `respond to all' so
that the mailing list is included in the CC field. Otherwise your message will
only be sent to the original poster and not return back to the list. Only
messages to relax-users and relax-devel will be
r2643 - /1.2/specific_fns/model_free.py
Author: bugman Date: Mon Oct 16 10:11:12 2006 New Revision: 2643 URL: http://svn.gna.org/viewcvs/relax?rev=2643view=rev Log: Two small formatting changes to the model-free file. Modified: 1.2/specific_fns/model_free.py Modified: 1.2/specific_fns/model_free.py URL: http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2643r1=2642r2=2643view=diff == --- 1.2/specific_fns/model_free.py (original) +++ 1.2/specific_fns/model_free.py Mon Oct 16 10:11:12 2006 @@ -309,7 +309,7 @@ # Initialise. if len(self.param_vector) == 0: -self.scaling_matrix = zeros((0,0), Float64) +self.scaling_matrix = zeros((0, 0), Float64) else: self.scaling_matrix = identity(len(self.param_vector), Float64) i = 0 @@ -2005,7 +2005,6 @@ 'mf' - Model-free parameters for single residues. 'diff' - Diffusion tensor parameters. 'all' - All model-free and all diffusion tensor parameters. - # Arguments. ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2644 - in /1.2/docs: latex/develop.tex relax.pdf
Author: bugman Date: Mon Oct 16 10:25:47 2006 New Revision: 2644 URL: http://svn.gna.org/viewcvs/relax?rev=2644view=rev Log: A large expansion of the relax development chapter. The title has been changed from 'Development of relax' to 'relax development'. Many sections have been edited/modified. The section on relax's coding conventions has been re-written. The docstring subsection has been itemized and examples added. Examples have been added to the 'Variable, function, and class names' subsection and a subsubsection titled 'Long names' has been added. A subsection called 'Whitespace' has been added with examples. And finally a subsection called 'Comments' has also been added. The commit log format section has been itemized and a number of examples given. The SCons help system which displays the target descriptions is now described. The subsection titled 'Compilation of the API documentation (HTML version)' has been added to the SCons section. Three completely new sections have been added to the end. These include 'The mailing lists', 'The bug, task, and support request trackers', and 'Links, links, and more links'. Modified: 1.2/docs/latex/develop.tex 1.2/docs/relax.pdf [This mail would be too long, it was shortened to contain the URLs only.] Modified: 1.2/docs/latex/develop.tex URL: http://svn.gna.org/viewcvs/relax/1.2/docs/latex/develop.tex?rev=2644r1=2643r2=2644view=diff Modified: 1.2/docs/relax.pdf URL: http://svn.gna.org/viewcvs/relax/1.2/docs/relax.pdf?rev=2644r1=2643r2=2644view=diff ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2646 - in /1.2/test_suite: model_free.py test_suite.py
Author: bugman
Date: Tue Oct 17 06:45:34 2006
New Revision: 2646
URL: http://svn.gna.org/viewcvs/relax?rev=2646view=rev
Log:
Added a number of model-free optimisation tests to the test-suite.
These tests use the synthetic data back calculated for the model-free parameter
values of {S2=0.970,
te=2048, Rex=0.149}.
The following optimisation techniques are currently tested:
Grid search.
Steepest descent, backtracking line search.
Steepest descent, More and Thuente line search.
Coordinate descent, backtracking line search.
Coordinate descent, More and Thuente line search.
BFGS, backtracking line search.
BFGS, More and Thuente line search.
Newton, GMW Hessian modification, backtracking line search.
Newton, GMW Hessian modification, More and Thuente line search.
Modified:
1.2/test_suite/model_free.py
1.2/test_suite/test_suite.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.2/test_suite/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/model_free.py?rev=2646r1=2645r2=2646view=diff
Modified: 1.2/test_suite/test_suite.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/test_suite.py?rev=2646r1=2645r2=2646view=diff
___
relax (http://nmr-relax.com)
This is the relax-commits mailing list
relax-commits@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-commits
r2649 - in /1.3: scons/distrib.py sconstruct
Author: bugman
Date: Tue Oct 17 07:09:57 2006
New Revision: 2649
URL: http://svn.gna.org/viewcvs/relax?rev=2649view=rev
Log:
Ported r2635 from the 1.2 line.
The command used was:
$ svn merge -r2634:2635 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2
This involves a few functions moving to the new Scons module file
'scons/distrib.py'.
Added:
1.3/scons/distrib.py
- copied unchanged from r2635, 1.2/scons/distrib.py
Modified:
1.3/sconstruct
Modified: 1.3/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.3/sconstruct?rev=2649r1=2648r2=2649view=diff
==
--- 1.3/sconstruct (original)
+++ 1.3/sconstruct Tue Oct 17 07:09:57 2006
@@ -42,6 +42,7 @@
# relax and Scons modules.
+from scons.distrib import package, gpg_sign
from scons.manuals import clean_manual_files, compile_api_manual_html,
compile_user_manual_html, compile_user_manual_pdf, fetch_docstrings,
version_file
from version import version
@@ -117,25 +118,27 @@
source_dist_env.Depends('source_dist', 'gpg_src') #
GPG sign the source distribution file.
# Target for packaging the binary distribution.
-package_bin_env = Environment(BUILDERS={'archive' :
Builder(action=self.package)},
- DIST_FILE=self.BIN_FILE)
+package_bin_env = Environment(BUILDERS={'archive' :
Builder(action=package)},
+ DIST_FILE=self.BIN_FILE,
+ DIST_TYPE=self.DIST_TYPE)
package_bin_env.archive(target='package_bin', source=None)
package_bin_env.Depends('package_bin', 'version_check') # Check
the program version number first.
# Target for packaging the source distribution.
-package_src_env = Environment(BUILDERS={'archive' :
Builder(action=self.package)},
- DIST_FILE=self.SRC_FILE)
+package_src_env = Environment(BUILDERS={'archive' :
Builder(action=package)},
+ DIST_FILE=self.SRC_FILE,
+ DIST_TYPE=self.DIST_TYPE)
package_src_env.archive(target='package_src', source=None)
package_src_env.Depends('package_src', 'version_check') # Check
the program version number first.
# Target for creating a GPG signature of the binary distribution file.
-gpg_bin_env = Environment(BUILDERS={'sign' :
Builder(action=self.gpg_sign)},
+gpg_bin_env = Environment(BUILDERS={'sign' : Builder(action=gpg_sign)},
DIST_FILE=self.BIN_FILE)
gpg_bin_env.sign(target='gpg_bin', source=None)
gpg_bin_env.Depends('gpg_bin', 'version_check') # Check the
program version number before signing.
# Target for creating a GPG signature of the source distribution file.
-gpg_src_env = Environment(BUILDERS={'sign' :
Builder(action=self.gpg_sign)},
+gpg_src_env = Environment(BUILDERS={'sign' : Builder(action=gpg_sign)},
DIST_FILE=self.SRC_FILE)
gpg_src_env.sign(target='gpg_src', source=None)
gpg_src_env.Depends('gpg_src', 'version_check') # Check the
program version number before signing.
@@ -299,22 +302,6 @@
Dummy function which returns zero.
return 0
-
-
-def gpg_sign(self, target, source, env):
-Builder action for creating a GPG signature of the binary
distribution file.
-
-# Print out.
-print
-print
-print # GPG signing the binary distribution file #
-print \n\n
-
-# Run the 'gpg' command.
-system(gpg --detach-sign --default-key relax + path.pardir +
path.sep + env['DIST_FILE'])
-
-# Final print out.
-print \n\n\n
def help(self):
@@ -593,68 +580,6 @@
self.LATEX_DIR = 'docs' + sep + 'latex' + sep
-
-def package(self, target, source, env):
-Builder action for packaging the distribution archives.
-
-# Print out.
-print
-print ###
-print # Packaging the files #
-print ###\n\n
-print Creating the package distribution + `env['DIST_FILE']` + .\n
-
-# Open the Zip distribution file.
-if self.DIST_TYPE == 'zip':
-archive = ZipFile(path.pardir + path.sep + env['DIST_FILE'], 'w',
compression=8)
-
-# Open the Tar distribution file.
-elif self.DIST_TYPE == 'tar':
-if search('.bz2$', env['DIST_FILE']):
-archive = TarFile.bz2open(path.pardir + path.sep +
env['DIST_FILE'], 'w')
-elif search('.gz$', env['DIST_FILE']):
-archive = TarFile.gzopen(path.pardir + path.sep +
env['DIST_FILE'], 'w')
-else:
-
r2650 - in /1.3: scons/distrib.py scons/install.py sconstruct
Author: bugman
Date: Tue Oct 17 07:13:09 2006
New Revision: 2650
URL: http://svn.gna.org/viewcvs/relax?rev=2650view=rev
Log:
Ported r2637 to r2640 from the 1.2 line.
The command used was:
$ svn merge -r2636:2640 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2
This includes a number of changes to the Scons system including fixes for the
distribution target
functions, the creation of the new module 'scons.install', and a restructure of
the base
'sconstruct' file.
Added:
1.3/scons/install.py
- copied unchanged from r2640, 1.2/scons/install.py
Modified:
1.3/scons/distrib.py
1.3/sconstruct
Modified: 1.3/scons/distrib.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/scons/distrib.py?rev=2650r1=2649r2=2650view=diff
==
--- 1.3/scons/distrib.py (original)
+++ 1.3/scons/distrib.py Tue Oct 17 07:13:09 2006
@@ -26,6 +26,9 @@
from re import search
from tarfile import TarFile
from zipfile import ZipFile
+
+# relax version file.
+from version import version
Modified: 1.3/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/1.3/sconstruct?rev=2650r1=2649r2=2650view=diff
==
--- 1.3/sconstruct (original)
+++ 1.3/sconstruct Tue Oct 17 07:13:09 2006
@@ -27,24 +27,121 @@
# Import statements.
import platform
-from os import F_OK, access, getcwd, path, remove, rmdir, sep, system, walk
+from os import getcwd, path, remove, sep, walk
from re import search
-from shutil import copytree
import sys
-from tarfile import TarFile
-from zipfile import ZipFile
-
-# UNIX only functions from the os module.
-try:
-from os import lstat, symlink
-except ImportError:
-pass
-
-
-# relax and Scons modules.
+
+# Scons modules.
from scons.distrib import package, gpg_sign
+from scons.install import install, uninstall
from scons.manuals import clean_manual_files, compile_api_manual_html,
compile_user_manual_html, compile_user_manual_pdf, fetch_docstrings,
version_file
+
+# relax version file.
from version import version
+
+
+
+
+# Paths and file names #
+
+
+# The operating system.
+SYSTEM = platform.uname()[0]
+
+# The machine type.
+MACH = platform.uname()[4]
+
+# Symbolic link flag.
+SYMLINK_FLAG = 1
+
+# GNU/Linux.
+if SYSTEM == 'Linux':
+# System specific string.
+SYS = 'GNU-Linux'
+
+# Linux installation path.
+INSTALL_PATH = '/usr/local'
+
+
+# MS Windows.
+elif SYSTEM == 'Windows':
+# Architecture.
+arch = platform.architecture()[0]
+
+# 32 bit.
+if arch == '32bit':
+SYS = 'Win32'
+
+# 64 bit.
+elif arch == '64bit':
+SYS = 'Win64'
+
+# Unknown.
+else:
+SYS = 'Win'
+
+# Windows installation path.
+INSTALL_PATH = 'C:\\'
+
+# No symlinks!
+SYMLINK_FLAG = 0
+
+
+# Mac OS X.
+elif SYSTEM == 'Darwin':
+# System specific string.
+SYS = SYSTEM
+
+# Mac OS X installation path.
+INSTALL_PATH = sys.prefix + sep + 'local'
+
+
+# All other operating systems.
+else:
+# System specific string.
+SYS = SYSTEM
+
+# Installation path.
+INSTALL_PATH = sys.prefix + sep + 'local'
+
+
+
+# Installation.
+###
+
+# Relax installation directory.
+RELAX_PATH = INSTALL_PATH + sep + 'relax'
+
+# Installation path for binaries.
+BIN_PATH = INSTALL_PATH + sep + 'bin'
+
+# Symbolic link installation path.
+SYMLINK = BIN_PATH + sep + 'relax'
+
+
+
+# The distribution files.
+#
+
+if SYSTEM == 'Windows':
+BIN_FILE = 'relax-' + version + '.' + SYS + '.zip'
+SRC_FILE = 'relax-' + version + '.src.zip'
+DIST_TYPE = 'zip'
+else:
+BIN_FILE = 'relax-' + version + '.' + SYS + '.' + MACH + '.tar.bz2'
+SRC_FILE = 'relax-' + version + '.src.tar.bz2'
+DIST_TYPE = 'tar'
+
+
+# Documentation.
+
+
+# Documentation directory.
+DOCS_DIR = 'docs' + sep
+
+# LaTeX directory.
+LATEX_DIR = 'docs' + sep + 'latex' + sep
+
@@ -62,13 +159,6 @@
# Set the help message.
self.help()
-# The operating system.
-self.SYSTEM = platform.uname()[0]
-
-# Set up the paths and file names.
-self.set_paths()
-
-
# C module compilation.
###
@@ -83,12 +173,21 @@
###
# Install target.
-install_env = Environment(BUILDERS={'install' :
Builder(action=self.install)},
- RELAX_PATH=self.RELAX_PATH)
+install_env = Environment(BUILDERS={'install' :
Builder(action=install)},
+ BIN_PATH=BIN_PATH,
+ INSTALL_PATH=INSTALL_PATH,
+ RELAX_PATH=RELAX_PATH,
+ SYMLINK=SYMLINK,
+ SYMLINK_FLAG=SYMLINK_FLAG)
install_env.install(target='install',
r2653 - /1.3/specific_fns/model_free.py
Author: bugman Date: Tue Oct 17 07:22:34 2006 New Revision: 2653 URL: http://svn.gna.org/viewcvs/relax?rev=2653view=rev Log: Ported r2643 from the 1.2 line. The command used was: $ svn merge -r2642:2643 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 This includes a few small formatting changes to the model-free file. Modified: 1.3/specific_fns/model_free.py Modified: 1.3/specific_fns/model_free.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free.py?rev=2653r1=2652r2=2653view=diff == --- 1.3/specific_fns/model_free.py (original) +++ 1.3/specific_fns/model_free.py Tue Oct 17 07:22:34 2006 @@ -308,7 +308,7 @@ # Initialise. if len(self.param_vector) == 0: -self.scaling_matrix = zeros((0,0), Float64) +self.scaling_matrix = zeros((0, 0), Float64) else: self.scaling_matrix = identity(len(self.param_vector), Float64) i = 0 @@ -2004,7 +2004,6 @@ 'mf' - Model-free parameters for single residues. 'diff' - Diffusion tensor parameters. 'all' - All model-free and all diffusion tensor parameters. - # Arguments. ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2655 - /1.3/generic_fns/pdb.py
Author: bugman Date: Fri Oct 20 13:57:49 2006 New Revision: 2655 URL: http://svn.gna.org/viewcvs/relax?rev=2655view=rev Log: This fixes a bug in the compile re function. The bug was reported by Alex Hansen at https://mail.gna.org/public/relax-devel/2006-10/msg00112.html (Message-id: [EMAIL PROTECTED]). The simple fix is described at https://mail.gna.org/public/relax-devel/2006-10/msg00113.html (Message-id: [EMAIL PROTECTED]). Modified: 1.3/generic_fns/pdb.py Modified: 1.3/generic_fns/pdb.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pdb.py?rev=2655r1=2654r2=2655view=diff == --- 1.3/generic_fns/pdb.py (original) +++ 1.3/generic_fns/pdb.py Fri Oct 20 13:57:49 2006 @@ -23,6 +23,7 @@ from math import sqrt from Numeric import Float64, dot, zeros from os import F_OK, access +from re import compile import Scientific.IO.PDB ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2658 - in /1.2/specific_fns: jw_mapping.py specific_setup.py
Author: bugman
Date: Sun Oct 22 06:18:02 2006
New Revision: 2658
URL: http://svn.gna.org/viewcvs/relax?rev=2658view=rev
Log:
Completion of task #4002 (https://gna.org/task/index.php?4002).
This task was created in response to Daniel Perez's (daniel dot perez at mol
dot biol dot ethz dot
ch) post at https://mail.gna.org/public/relax-users/2006-10/msg00040.html
(Message-id:
[EMAIL PROTECTED]).
Three things were required:
1. The pre-existing function
self.relax.specific.jw_mapping.return_conversion_factor was added to
the specific setup interface in 'specific_fns/specific_setup.py'.
2. The string 'J(0)' was not being recognised by the function
'self.relax.specific.jw_mapping.return_data_name' as the round brackets needed
to be commented out
for the 'search' function to work.
3. The specific setup interface was returning the wrong 'return_grace_string'
function. The
problem was that the model-free version of the function was being returned
instead. The function
'return_units' was also that of model-free analysis instead of reduced spectral
density mapping.
Modified:
1.2/specific_fns/jw_mapping.py
1.2/specific_fns/specific_setup.py
Modified: 1.2/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/jw_mapping.py?rev=2658r1=2657r2=2658view=diff
==
--- 1.2/specific_fns/jw_mapping.py (original)
+++ 1.2/specific_fns/jw_mapping.py Sun Oct 22 06:18:02 2006
@@ -274,11 +274,11 @@
| Data type | Object name | Patterns
|
||__|__|
|| |
|
-| J(0) | 'j0' | '^[Jj]0$' or '[Jj](0)'
|
+| J(0) | 'j0' | '^[Jj]0$' or '[Jj]\(0\)'
|
|| |
|
-| J(wX) | 'jwx'| '^[Jj]w[Xx]$' or
'[Jj](w[Xx])' |
+| J(wX) | 'jwx'| '^[Jj]w[Xx]$' or
'[Jj]\(w[Xx]\)' |
|| |
|
-| J(wH) | 'jwh'| '^[Jj]w[Hh]$' or
'[Jj](w[Hh])' |
+| J(wH) | 'jwh'| '^[Jj]w[Hh]$' or
'[Jj]\(w[Hh]\)' |
|| |
|
| Bond length| 'r' | '^r$' or '[Bb]ond[
-_][Ll]ength' |
|| |
|
@@ -288,15 +288,15 @@
# J(0).
-if search('^[Jj]0$', name) or search('[Jj](0)', name):
+if search('^[Jj]0$', name) or search('[Jj]\(0\)', name):
return 'j0'
# J(wX).
-if search('^[Jj]w[Xx]$', name) or search('[Jj](w[Xx])', name):
+if search('^[Jj]w[Xx]$', name) or search('[Jj]\(w[Xx]\)', name):
return 'jwx'
# J(wH).
-if search('^[Jj]w[Hh]$', name) or search('[Jj](w[Hh])', name):
+if search('^[Jj]w[Hh]$', name) or search('[Jj]\(w[Hh]\)', name):
return 'jwh'
# Bond length.
Modified: 1.2/specific_fns/specific_setup.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/specific_setup.py?rev=2658r1=2657r2=2658view=diff
==
--- 1.2/specific_fns/specific_setup.py (original)
+++ 1.2/specific_fns/specific_setup.py Sun Oct 22 06:18:02 2006
@@ -162,13 +162,17 @@
if self.eqi == 'return_data_name':
return self.relax.specific.jw_mapping.return_data_name
+# Factor of conversion between different parameter units returning
function.
+if self.eqi == 'return_conversion_factor':
+return self.relax.specific.jw_mapping.return_conversion_factor
+
# Data error returning function.
if self.eqi == 'return_error':
return self.relax.specific.jw_mapping.return_error
# Grace string returning function.
if self.eqi == 'return_grace_string':
-return self.relax.specific.model_free.return_grace_string
+return self.relax.specific.jw_mapping.return_grace_string
# Simulation parameter array returning function.
if self.eqi == 'return_sim_param':
@@ -180,7 +184,7 @@
# String of the external parameter units returning function.
if self.eqi == 'return_units':
-return self.relax.specific.model_free.return_units
+return
r2659 - in /1.3/specific_fns: jw_mapping.py specific_setup.py
Author: bugman
Date: Sun Oct 22 11:51:57 2006
New Revision: 2659
URL: http://svn.gna.org/viewcvs/relax?rev=2659view=rev
Log:
Ported r2658 from the 1.2 line.
The command used was:
$ svn merge -r2657:2658 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2
These changes complete task #4002 (https://gna.org/task/index.php?4002), the
implementation of the
'grace.write()' user function for reduced spectral density mapping.
Modified:
1.3/specific_fns/jw_mapping.py
1.3/specific_fns/specific_setup.py
Modified: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=2659r1=2658r2=2659view=diff
==
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Sun Oct 22 11:51:57 2006
@@ -274,11 +274,11 @@
| Data type | Object name | Patterns
|
||__|__|
|| |
|
-| J(0) | 'j0' | '^[Jj]0$' or '[Jj](0)'
|
+| J(0) | 'j0' | '^[Jj]0$' or '[Jj]\(0\)'
|
|| |
|
-| J(wX) | 'jwx'| '^[Jj]w[Xx]$' or
'[Jj](w[Xx])' |
+| J(wX) | 'jwx'| '^[Jj]w[Xx]$' or
'[Jj]\(w[Xx]\)' |
|| |
|
-| J(wH) | 'jwh'| '^[Jj]w[Hh]$' or
'[Jj](w[Hh])' |
+| J(wH) | 'jwh'| '^[Jj]w[Hh]$' or
'[Jj]\(w[Hh]\)' |
|| |
|
| Bond length| 'r' | '^r$' or '[Bb]ond[
-_][Ll]ength' |
|| |
|
@@ -288,15 +288,15 @@
# J(0).
-if search('^[Jj]0$', name) or search('[Jj](0)', name):
+if search('^[Jj]0$', name) or search('[Jj]\(0\)', name):
return 'j0'
# J(wX).
-if search('^[Jj]w[Xx]$', name) or search('[Jj](w[Xx])', name):
+if search('^[Jj]w[Xx]$', name) or search('[Jj]\(w[Xx]\)', name):
return 'jwx'
# J(wH).
-if search('^[Jj]w[Hh]$', name) or search('[Jj](w[Hh])', name):
+if search('^[Jj]w[Hh]$', name) or search('[Jj]\(w[Hh]\)', name):
return 'jwh'
# Bond length.
Modified: 1.3/specific_fns/specific_setup.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/specific_setup.py?rev=2659r1=2658r2=2659view=diff
==
--- 1.3/specific_fns/specific_setup.py (original)
+++ 1.3/specific_fns/specific_setup.py Sun Oct 22 11:51:57 2006
@@ -162,13 +162,17 @@
if self.eqi == 'return_data_name':
return self.relax.specific.jw_mapping.return_data_name
+# Factor of conversion between different parameter units returning
function.
+if self.eqi == 'return_conversion_factor':
+return self.relax.specific.jw_mapping.return_conversion_factor
+
# Data error returning function.
if self.eqi == 'return_error':
return self.relax.specific.jw_mapping.return_error
# Grace string returning function.
if self.eqi == 'return_grace_string':
-return self.relax.specific.model_free.return_grace_string
+return self.relax.specific.jw_mapping.return_grace_string
# Simulation parameter array returning function.
if self.eqi == 'return_sim_param':
@@ -180,7 +184,7 @@
# String of the external parameter units returning function.
if self.eqi == 'return_units':
-return self.relax.specific.model_free.return_units
+return self.relax.specific.jw_mapping.return_units
# Value and error returning function.
if self.eqi == 'return_value':
___
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r2661 - /1.3/specific_fns/jw_mapping.py
Author: bugman Date: Mon Oct 23 10:28:26 2006 New Revision: 2661 URL: http://svn.gna.org/viewcvs/relax?rev=2661view=rev Log: Ported r2660 from the 1.2 line. The command used was: $ svn merge -r2659:2660 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.2 This fixes an error when trying to plot the MC simulation data in reduced spectral density mapping using the 'grace.write()' user function. Modified: 1.3/specific_fns/jw_mapping.py Modified: 1.3/specific_fns/jw_mapping.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=2661r1=2660r2=2661view=diff == --- 1.3/specific_fns/jw_mapping.py (original) +++ 1.3/specific_fns/jw_mapping.py Mon Oct 23 10:28:26 2006 @@ -355,35 +355,6 @@ return 'ppm' -def return_value(self, run, i, data_type): -Function for returning the value and error corresponding to 'data_type'. - -# Arguments. -self.run = run - -# Remap the data structure 'self.relax.data.res[run][i]'. -data = self.relax.data.res[run][i] - -# Get the object. -object_name = self.return_data_name(data_type) -if not object_name: -raise RelaxError, The reduced spectral density mapping data type + `data_type` + does not exist. -object_error = object_name + _err - -# Get the value. -value = None -if hasattr(data, object_name): -value = getattr(data, object_name) - -# Get the error. -error = None -if hasattr(data, object_error): -error = getattr(data, object_error) - -# Return the data. -return value, error - - def set(self, run=None, value=None, error=None, param=None, index=None): Reduced spectral density mapping set details ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2666 - /branches/tensor_pdb/generic_fns/pdb.py
Author: bugman Date: Thu Oct 26 07:50:36 2006 New Revision: 2666 URL: http://svn.gna.org/viewcvs/relax?rev=2666view=rev Log: Created functions for calculating the center of mass of the selected residues. The function 'self.center_of_mass()' in the file 'generic_fns/pdb.py' has been created to calculate the center of mass. All unselected residues are skipped to allow hybrid models, two fused runs of non-overlapping residues, to be handled. Hence the center of mass will be biased! The function 'self.atomic_mass()' has also been added to the file. This function returns the atomic mass corresponding to the supplied element string. Modified: branches/tensor_pdb/generic_fns/pdb.py Modified: branches/tensor_pdb/generic_fns/pdb.py URL: http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2666r1=2665r2=2666view=diff == --- branches/tensor_pdb/generic_fns/pdb.py (original) +++ branches/tensor_pdb/generic_fns/pdb.py Thu Oct 26 07:50:36 2006 @@ -37,6 +37,95 @@ self.print_flag = 1 +def atomic_mass(self, element=None): +Return the atomic mass of the given element. + +# Proton. +if element == 'H' or element == 'Q': +return 1.00794 + +# Carbon. +elif element == 'C': +return 12.0107 + +# Nitrogen. +elif element == 'N': +return 14.0067 + +# Oxygen. +elif element == 'O': +return 15.9994 + +# Sulphur. +elif element == 'S': +return 32.065 + +# Unknown. +else: +raise RelaxError, The mass of the element + `element` + has not yet been programmed into relax. + + +def center_of_mass(self): +Calculate and return the center of mass of the structure. + +# Print out. +print Calculating the center of mass. + +# Initialise the center of mass. +R = zeros(3, Float64) + +# Initialise the total mass. +M = 0.0 + +# Loop over the structures. +for struct in self.relax.data.pdb[self.run].structures: +# Protein. +if struct.peptide_chains: +chains = struct.peptide_chains + +# RNA/DNA. +elif struct.nucleotide_chains: +chains = struct.nucleotide_chains + +# Loop over the residues of the protein in the PDB file. +for res in chains[0].residues: +# Find the corresponding residue in 'self.relax.data'. +found = 0 +for res_data in self.relax.data.res[self.run]: +if res.number == res_data.num: +found = 1 +break + +# Doesn't exist. +if not found: +continue + +# Skip unselected residues. +if not res_data.select: +continue + +# Loop over the atoms of the residue. +for atom in res: +# Atomic mass. +mass = self.atomic_mass(atom.properties['element']) + +# Total mass. +M = M + mass + +# Sum of mass * position. +R = R + mass * atom.position.array + +# Normalise. +R = R / M + +# Final print out. +print Total mass: M = + `M` +print Center of mass: R = + `R` + +# Return the center of mass. +return R + + def create_tensor_pdb(self, run=None, file=None, dir=None, force=0): The pdb loading function. @@ -60,6 +149,9 @@ # Open the PDB file for writing. tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir, self.force) + +# Calculate the center of mass. +R = self.center_of_mass() # Close the PDB file. tensor_pdb_file.close() ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2667 - /branches/tensor_pdb/generic_fns/pdb.py
Author: bugman
Date: Thu Oct 26 08:08:47 2006
New Revision: 2667
URL: http://svn.gna.org/viewcvs/relax?rev=2667view=rev
Log:
Creation of a rudimentary PDB file for representing the diffusion tensor.
The new function 'self.write_pdb_file()' has been added which creates a
properly formatted PDB file.
It creates HET, HETNAM, and FORMUL records for the pseudo-residue 'TNS'. It
also adds HETATM
records for each atom, adds the TER record, and then connects the appropriate
atoms using CONECT
records. The file is terminated with the MASTER and END records. For a
description of this, see
the post at https://mail.gna.org/public/relax-devel/2006-10/msg00136.html
(Message-id:
[EMAIL PROTECTED]).
The function 'self.create_tensor_pdb()' has been modified to create the data
for the new
'self.write_pdb_file()' function.
Modified:
branches/tensor_pdb/generic_fns/pdb.py
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2667r1=2666r2=2667view=diff
==
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Thu Oct 26 08:08:47 2006
@@ -121,6 +121,7 @@
# Final print out.
print Total mass: M = + `M`
print Center of mass: R = + `R`
+print
# Return the center of mass.
return R
@@ -135,6 +136,9 @@
self.dir = dir
self.force = force
+# Tests.
+
+
# Test if the run exists.
if not run in self.relax.data.run_names:
raise RelaxNoRunError, run
@@ -147,13 +151,50 @@
if not self.load_seq and not len(self.relax.data.res[self.run]):
raise RelaxNoSequenceError, self.run
-# Open the PDB file for writing.
-tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir,
self.force)
+
+# Initialise the PDB data.
+##
+
+# PDB HETATM and CONECT data.
+hetatm = []
+conect = []
+
+# Chain ID, residue number, residue name.
+chain_id = 'A'
+res_num = 1
+res_name = 'TNS'
+chemical_name = 'Tensor'
+occupancy = 1.0
+element = 'C'
+
+
+# Center of mass.
+#
# Calculate the center of mass.
R = self.center_of_mass()
-# Close the PDB file.
+# Add the central atom.
+hetatm.append(R)
+
+
+# Connectivities.
+#
+
+#conect.append(['1', '2'])
+#conect.append(['2', '1'])
+
+
+# Create the PDB file.
+##
+
+# Open the PDB file for writing.
+tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir,
force=self.force)
+
+# Write the data.
+self.write_pdb_file(tensor_pdb_file, hetatm, conect, chain_id,
res_num, res_name, chemical_name, occupancy, element)
+
+# Close the file.
tensor_pdb_file.close()
@@ -485,3 +526,63 @@
# Replace the temporary vector list with the normalised average
vector.
data.xh_vect = ave_vector / sqrt(dot(ave_vector, ave_vector))
+
+
+def write_pdb_file(self, file, hetatm, conect, chain_id, res_num,
res_name, chemical_name, occupancy, element):
+Function for creating a PDB file from the given data.
+
+# The HET record.
+file.write(%-6s %3s %1s%4s%1s %5s %-40s\n % ('HET', res_name,
chain_id, res_num, '', len(hetatm), ''))
+
+# The HETNAM record.
+file.write(%-6s %2s %3s %-55s\n % ('HETNAM', '', res_name,
chemical_name))
+
+# The FORMUL record (chemical formula).
+file.write(%-6s %2s %3s %2s%1s%-51s\n % ('FORMUL', 1, res_name,
'', '', element+`len(hetatm)`))
+
+# Loop over the HETATMs.
+serial_num = 1
+for vector in hetatm:
+# Write the HETATM record.
+file.write(%-6s%5s %4s%1s%3s %1s%4s%1s
%8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s%2s\n % ('HETATM', serial_num,
element+`serial_num`, '', res_name, chain_id, res_num, '', vector[0],
vector[1], vector[2], occupancy, 0, '', element, ''))
+
+# Increment the atom number.
+serial_num = serial_num + 1
+
+# Terminate (TER record).
+file.write(%-6s%5s %3s %1s%4s%1s\n % ('TER', serial_num,
res_name, chain_id, '', ''))
+
+# Loop over the connections.
+for array in conect:
+# The atom.
+atom_serial_num = array[0]
+
+# First bonded atom.
+bonded1 = array[1]
+
+# Second bonded atom.
+if len(array) 2:
+bonded2 = array[2]
+else:
+bonded2 = ''
+
+# Third bonded atom.
+if len(array) 3:
+bonded3 = array[3]
+
r2668 - /1.3/generic_fns/pdb.py
Author: bugman Date: Thu Oct 26 09:52:51 2006 New Revision: 2668 URL: http://svn.gna.org/viewcvs/relax?rev=2668view=rev Log: Fixed a bug whereby the match re function had not been imported. Modified: 1.3/generic_fns/pdb.py Modified: 1.3/generic_fns/pdb.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pdb.py?rev=2668r1=2667r2=2668view=diff == --- 1.3/generic_fns/pdb.py (original) +++ 1.3/generic_fns/pdb.py Thu Oct 26 09:52:51 2006 @@ -23,7 +23,7 @@ from math import sqrt from Numeric import Float64, dot, zeros from os import F_OK, access -from re import compile +from re import compile, match import Scientific.IO.PDB ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2884 - /1.3/specific_fns/model_free.py
Author: bugman
Date: Sat Nov 25 03:49:40 2006
New Revision: 2884
URL: http://svn.gna.org/viewcvs/relax?rev=2884view=rev
Log:
Fix for bug #7845 (https://gna.org/bugs/?7845).
This bug was reported by Sébastien Morin (https://gna.org/users/semor).
The fix was to increase the precision of the chi-squared value in the
model-free results file.
Modified:
1.3/specific_fns/model_free.py
Modified: 1.3/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free.py?rev=2884r1=2883r2=2884view=diff
==
--- 1.3/specific_fns/model_free.py (original)
+++ 1.3/specific_fns/model_free.py Sat Nov 25 03:49:40 2006
@@ -4717,57 +4717,67 @@
s2 = None
if hasattr(data, 's2') and data.s2 != None:
s2 = data.s2 / self.return_conversion_factor('s2')
+s2 = `s2`
# S2f.
s2f = None
if hasattr(data, 's2f') and data.s2f != None:
s2f = data.s2f / self.return_conversion_factor('s2f')
+s2f = `s2f`
# S2s.
s2s = None
if hasattr(data, 's2s') and data.s2s != None:
s2s = data.s2s / self.return_conversion_factor('s2s')
+s2s = `s2s`
# Local tm.
local_tm = None
if hasattr(data, 'local_tm') and data.local_tm != None:
local_tm = data.local_tm /
self.return_conversion_factor('local_tm')
+local_tm = `local_tm`
# te.
te = None
if hasattr(data, 'te') and data.te != None:
te = data.te / self.return_conversion_factor('te')
+te = `te`
# tf.
tf = None
if hasattr(data, 'tf') and data.tf != None:
tf = data.tf / self.return_conversion_factor('tf')
+tf = `tf`
# ts.
ts = None
if hasattr(data, 'ts') and data.ts != None:
ts = data.ts / self.return_conversion_factor('ts')
+ts = `ts`
# Rex.
rex = None
if hasattr(data, 'rex') and data.rex != None:
rex = data.rex / self.return_conversion_factor('rex')
+rex = `rex`
# Bond length.
r = None
if hasattr(data, 'r') and data.r != None:
r = data.r / self.return_conversion_factor('r')
+r = `r`
# CSA.
csa = None
if hasattr(data, 'csa') and data.csa != None:
csa = data.csa / self.return_conversion_factor('csa')
+csa = `csa`
# Minimisation details.
try:
# Global minimisation results.
if self.param_set == 'diff' or self.param_set == 'all':
-chi2 = self.relax.data.chi2[self.run]
+chi2 = `self.relax.data.chi2[self.run]`
iter = self.relax.data.iter[self.run]
f = self.relax.data.f_count[self.run]
g = self.relax.data.g_count[self.run]
@@ -4779,7 +4789,7 @@
# Individual residue results.
else:
-chi2 = data.chi2
+chi2 = `data.chi2`
iter = data.iter
f = data.f_count
g = data.g_count
@@ -4825,7 +4835,7 @@
ri_error.append(None)
# Write the line.
-self.write_columnar_line(file=file, num=data.num, name=data.name,
select=data.select, data_set='value', nucleus=nucleus, model=model,
equation=equation, params=params, param_set=self.param_set, s2=`s2`, s2f=`s2f`,
s2s=`s2s`, local_tm=`local_tm`, te=`te`, tf=`tf`, ts=`ts`, rex=`rex`, r=`r`,
csa=`csa`, chi2=chi2, i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=data.heteronuc, pdb_proton=data.proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+self.write_columnar_line(file=file, num=data.num, name=data.name,
select=data.select, data_set='value', nucleus=nucleus, model=model,
equation=equation, params=params, param_set=self.param_set, s2=s2, s2f=s2f,
s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa,
chi2=chi2, i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=data.heteronuc, pdb_proton=data.proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
# Errors.
@@ -4889,51 +4899,61 @@
s2 = None
if hasattr(data, 's2_err') and data.s2_err != None:
s2 = data.s2_err /
r2885 - /1.2/specific_fns/model_free.py
Author: bugman
Date: Sat Nov 25 03:57:19 2006
New Revision: 2885
URL: http://svn.gna.org/viewcvs/relax?rev=2885view=rev
Log:
Ported r2884 from the 1.3 line to fix bug #7845 (https://gna.org/bugs/?7845).
The command used was:
svn merge -r2883:2884 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.3
This bug was reported by Sebastien Morin (https://gna.org/users/semor) and the
fix was to increase
the precision of the chi-squared value in the model-free results file.
Modified:
1.2/specific_fns/model_free.py
Modified: 1.2/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/specific_fns/model_free.py?rev=2885r1=2884r2=2885view=diff
==
--- 1.2/specific_fns/model_free.py (original)
+++ 1.2/specific_fns/model_free.py Sat Nov 25 03:57:19 2006
@@ -3439,6 +3439,9 @@
# Set up the simulations.
if len(sims):
+print sims: + `sims`
+print Select sim: + `select_sim`
+print len sim: + `len(select_sim)`
self.relax.generic.monte_carlo.setup(self.run,
select_sim=select_sim)
@@ -4729,57 +4732,67 @@
s2 = None
if hasattr(data, 's2') and data.s2 != None:
s2 = data.s2 / self.return_conversion_factor('s2')
+s2 = `s2`
# S2f.
s2f = None
if hasattr(data, 's2f') and data.s2f != None:
s2f = data.s2f / self.return_conversion_factor('s2f')
+s2f = `s2f`
# S2s.
s2s = None
if hasattr(data, 's2s') and data.s2s != None:
s2s = data.s2s / self.return_conversion_factor('s2s')
+s2s = `s2s`
# Local tm.
local_tm = None
if hasattr(data, 'local_tm') and data.local_tm != None:
local_tm = data.local_tm /
self.return_conversion_factor('local_tm')
+local_tm = `local_tm`
# te.
te = None
if hasattr(data, 'te') and data.te != None:
te = data.te / self.return_conversion_factor('te')
+te = `te`
# tf.
tf = None
if hasattr(data, 'tf') and data.tf != None:
tf = data.tf / self.return_conversion_factor('tf')
+tf = `tf`
# ts.
ts = None
if hasattr(data, 'ts') and data.ts != None:
ts = data.ts / self.return_conversion_factor('ts')
+ts = `ts`
# Rex.
rex = None
if hasattr(data, 'rex') and data.rex != None:
rex = data.rex / self.return_conversion_factor('rex')
+rex = `rex`
# Bond length.
r = None
if hasattr(data, 'r') and data.r != None:
r = data.r / self.return_conversion_factor('r')
+r = `r`
# CSA.
csa = None
if hasattr(data, 'csa') and data.csa != None:
csa = data.csa / self.return_conversion_factor('csa')
+csa = `csa`
# Minimisation details.
try:
# Global minimisation results.
if self.param_set == 'diff' or self.param_set == 'all':
-chi2 = self.relax.data.chi2[self.run]
+chi2 = `self.relax.data.chi2[self.run]`
iter = self.relax.data.iter[self.run]
f = self.relax.data.f_count[self.run]
g = self.relax.data.g_count[self.run]
@@ -4791,7 +4804,7 @@
# Individual residue results.
else:
-chi2 = data.chi2
+chi2 = `data.chi2`
iter = data.iter
f = data.f_count
g = data.g_count
@@ -4837,7 +4850,7 @@
ri_error.append(None)
# Write the line.
-self.write_columnar_line(file=file, num=data.num, name=data.name,
select=data.select, data_set='value', nucleus=nucleus, model=model,
equation=equation, params=params, param_set=self.param_set, s2=`s2`, s2f=`s2f`,
s2s=`s2s`, local_tm=`local_tm`, te=`te`, tf=`tf`, ts=`ts`, rex=`rex`, r=`r`,
csa=`csa`, chi2=chi2, i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=pdb_heteronuc, pdb_proton=pdb_proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+self.write_columnar_line(file=file, num=data.num, name=data.name,
select=data.select, data_set='value', nucleus=nucleus, model=model,
equation=equation, params=params, param_set=self.param_set, s2=s2, s2f=s2f,
s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa,
chi2=chi2, i=iter, f=f, g=g, h=h, warn=warn,
r2886 - /1.3/docs/relax.pdf
Author: bugman Date: Sat Nov 25 08:09:36 2006 New Revision: 2886 URL: http://svn.gna.org/viewcvs/relax?rev=2886view=rev Log: Removed the PDF user manual from the repository. As the file is a large (2.6 Mb) binary file and changes often, it has been removed from the repository. This should stop the relax Subversion repository getting too bign. The manual can easily be compiled from the sources using Scons. Removed: 1.3/docs/relax.pdf ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
r2887 - /1.2/docs/relax.pdf
Author: bugman Date: Sat Nov 25 08:14:34 2006 New Revision: 2887 URL: http://svn.gna.org/viewcvs/relax?rev=2887view=rev Log: Ported r2886 from the 1.3 line. The command used was: svn merge -r2885:2886 svn+ssh://[EMAIL PROTECTED]/svn/relax/1.3 This removes the PDF manual from the repository. Removed: 1.2/docs/relax.pdf ___ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@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-commits
