relax SVN archive

Merged revisions 7942-7948,7952,7961-7963,7965-7968 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r7942 | bugman | 2008-10-23 16:44:53 +0200 (Thu, 23 Oct 2008) | 6 lines

Fix for the relax IO logging with the -l command line argument.

This is a partial fix for bug #12489 (https://gna.org/bugs/?12489). The teeing problem still has
to be fixed.
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r7943 | bugman | 2008-10-23 16:54:43 +0200 (Thu, 23 Oct 2008) | 3 lines

Converted the tee class method into a module function.
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r7944 | bugman | 2008-10-23 16:56:12 +0200 (Thu, 23 Oct 2008) | 3 lines

Epydoc'd the tee function docstring.
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r7945 | bugman | 2008-10-23 16:57:45 +0200 (Thu, 23 Oct 2008) | 3 lines

Docstring improvements for the log() function.
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r7946 | bugman | 2008-10-23 16:58:04 +0200 (Thu, 23 Oct 2008) | 3 lines

Removed a line of redundant code.
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r7947 | bugman | 2008-10-23 16:58:56 +0200 (Thu, 23 Oct 2008) | 3 lines

Added the missing import of relax_io.tee.
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r7948 | bugman | 2008-10-23 17:01:18 +0200 (Thu, 23 Oct 2008) | 5 lines

Final fixes for bug #12489 (https://gna.org/bugs/?12489).

The log() and tee() functions are now operational.
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r7952 | bugman | 2008-10-23 17:39:25 +0200 (Thu, 23 Oct 2008) | 9 lines

Fix for bug #12487 (https://gna.org/bugs/index.php?12487).

This bug was reported by Tyler Reddy (TREDDY at dal dot ca).

The problem was that missing XH bond vector data was being manifested as the spin.xh_vect object
being set to None. The overfit_deselect() function which is responsible for deselecting unsuitable
spins prior to optimisation was only checking if the object existed, not if it was None!
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r7961 | bugman | 2008-10-24 13:44:28 +0200 (Fri, 24 Oct 2008) | 3 lines

Added a check to the atom_loop() to make sure structural data is loaded.
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r7962 | bugman | 2008-10-24 13:56:38 +0200 (Fri, 24 Oct 2008) | 3 lines

Added a check for empty PDB files in the internal structural object.
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r7963 | bugman | 2008-10-24 14:22:44 +0200 (Fri, 24 Oct 2008) | 3 lines

Added another spin to try to catch a program bug (unsuccessfully).
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r7965 | semor | 2008-10-24 15:41:46 +0200 (Fri, 24 Oct 2008) | 5 lines

Introduced verifications for the '-t' and '-l' options not to erase the python script used.

This should fix bug 12498 (http://gna.org/bugs/?12498).
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r7966 | bugman | 2008-10-24 16:14:19 +0200 (Fri, 24 Oct 2008) | 3 lines

Created a system test using Tyler Reddy's bug report - bug #12487 (https://gna.org/bugs/?12487).
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r7967 | semor | 2008-10-24 16:19:17 +0200 (Fri, 24 Oct 2008) | 7 lines

Modified the '-l' and '-t' options so they check for an existing file and don't overwrite it.

This was proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00087.html
(Message ID: 7f080ed10810240648p19b83da1x4c8990acf1834c5b@...)
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r7968 | semor | 2008-10-24 17:55:21 +0200 (Fri, 24 Oct 2008) | 7 lines

Still improved the detection of existing files not to be overwritten when logging or teeing.

This follows a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-10/msg00091.html
(Message ID: 7f080ed10810240816o30acc1ddlbaa131bc5a9ea1ff@...)
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Merged revisions 7952,7961-7963,7965-7968 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r7952 | bugman | 2008-10-23 17:39:25 +0200 (Thu, 23 Oct 2008) | 9 lines

Fix for bug #12487 (https://gna.org/bugs/index.php?12487).

This bug was reported by Tyler Reddy (TREDDY at dal dot ca).

The problem was that missing XH bond vector data was being manifested as the spin.xh_vect object
being set to None. The overfit_deselect() function which is responsible for deselecting unsuitable
spins prior to optimisation was only checking if the object existed, not if it was None!
........
r7961 | bugman | 2008-10-24 13:44:28 +0200 (Fri, 24 Oct 2008) | 3 lines

Added a check to the atom_loop() to make sure structural data is loaded.
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r7962 | bugman | 2008-10-24 13:56:38 +0200 (Fri, 24 Oct 2008) | 3 lines

Added a check for empty PDB files in the internal structural object.
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r7963 | bugman | 2008-10-24 14:22:44 +0200 (Fri, 24 Oct 2008) | 3 lines

Added another spin to try to catch a program bug (unsuccessfully).
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r7965 | semor | 2008-10-24 15:41:46 +0200 (Fri, 24 Oct 2008) | 5 lines

Introduced verifications for the '-t' and '-l' options not to erase the python script used.

This should fix bug 12498 (http://gna.org/bugs/?12498).
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r7966 | bugman | 2008-10-24 16:14:19 +0200 (Fri, 24 Oct 2008) | 3 lines

Created a system test using Tyler Reddy's bug report - bug #12487 (https://gna.org/bugs/?12487).
........
r7967 | semor | 2008-10-24 16:19:17 +0200 (Fri, 24 Oct 2008) | 7 lines

Modified the '-l' and '-t' options so they check for an existing file and don't overwrite it.

This was proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00087.html
(Message ID: 7f080ed10810240648p19b83da1x4c8990acf1834c5b@...)
........
r7968 | semor | 2008-10-24 17:55:21 +0200 (Fri, 24 Oct 2008) | 7 lines

Still improved the detection of existing files not to be overwritten when logging or teeing.

This follows a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-10/msg00091.html
(Message ID: 7f080ed10810240816o30acc1ddlbaa131bc5a9ea1ff@...)
........

Still improved the detection of existing files not to be overwritten when logging or teeing.

This follows a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-10/msg00091.html
(Message ID: 7f080ed10810240816o30acc1ddlbaa131bc5a9ea1ff@...)

Modified the '-l' and '-t' options so they check for an existing file and don't overwrite it.

This was proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00087.html
(Message ID: 7f080ed10810240648p19b83da1x4c8990acf1834c5b@...)

Created a system test using Tyler Reddy's bug report - bug #12487 (https://gna.org/bugs/?12487).

Introduced verifications for the '-t' and '-l' options not to erase the python script used.

This should fix bug 12498 (http://gna.org/bugs/?12498).

Renamed and converted the read() method to relax_time().

The method now simply creates a structure in the relax data store matching cdp.spectrum_ids and
storing the associated relaxation time periods.

Added another spin to try to catch a program bug (unsuccessfully).

Added a check for empty PDB files in the internal structural object.

Added a check to the atom_loop() to make sure structural data is loaded.