Author: bugman
Date: Thu Dec 11 18:21:45 2008
New Revision: 8195
URL: http://svn.gna.org/viewcvs/relax?rev=8195&view=rev
Log:
Merged revisions 8160,8180,8183,8186-8189,8191-8193 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8160 | bugman | 2008-12-08 14:47:42 +0100 (Mon, 08 Dec 2008) | 3 lines
Renamed the noe.read() user function to noe.read_constraints().
........
r8180 | bugman | 2008-12-10 14:15:47 +0100 (Wed, 10 Dec 2008) | 6 lines
Bug fix for the vector_dist() function.
The PyMOL structure loading command should not use the file root but the
full file name!!! A few
unused 'id' file root variables were also deleted.
........
r8183 | bugman | 2008-12-10 18:35:05 +0100 (Wed, 10 Dec 2008) | 3 lines
Added a print out for the loading of PDB models.
........
r8186 | bugman | 2008-12-10 18:46:37 +0100 (Wed, 10 Dec 2008) | 3 lines
Added tests of structure.load_spins() to all the structure system tests.
........
r8187 | bugman | 2008-12-11 10:33:32 +0100 (Thu, 11 Dec 2008) | 10 lines
Partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).
The problem fixed here is that of the missing molecule container. This was
caused by the weirdness
of the Scientific python PDB reader splitting one modified lactose molecule
into 2 molecules. The
lactose part was unnamed, while the modifier was named after the residues
'UNK'. The
generic_fns.mol_res_spin.return_molecule() function was having problems
with this concept of the
first molecule unnamed and the second named. This is now fixed and the
unnamed molecule can be
retrieved.
........
r8188 | bugman | 2008-12-11 10:53:22 +0100 (Thu, 11 Dec 2008) | 8 lines
Another partial fix for bug #12735 (https://gna.org/bugs/index.php?12735).
This problem was trigged by the internal reader (where the problem lies)
together with the
gromacs_phthalic_acid.pdb file. The issue was that the
__fill_object_from_pdb() was operating on
all structures currently loaded into relax. Hence with the 2 models of
this PDB file, the first
molecule had all the atoms of the first and second PDB models combined.
........
r8189 | bugman | 2008-12-11 11:14:00 +0100 (Thu, 11 Dec 2008) | 9 lines
Final fixes for bug #12735 (https://gna.org/bugs/index.php?12735).
The last problem was again triggered by the Scientific python PDB reader
weirdness. Residues ending
in '+' were being treated by the PDB reader as a different molecule. But
then the molecule names
LYS+, ARG+, etc. were causing problems as '+' was being treated as regular
expression when matching
molecule names. Therefore the '+' character has been stripped from all
molecule, residue, and atom
names.
........
r8191 | bugman | 2008-12-11 17:24:46 +0100 (Thu, 11 Dec 2008) | 8 lines
Fixes for bug #12573 (https://gna.org/bugs/index.php?12573).
This bug was reported by Jack Howarth (https://gna.org/users/jhowarth).
The problem was simply that the optimisation checks are exact and had to be
slightly modified for
the Darwin kernel on 32 bit PowerPC.
........
r8192 | bugman | 2008-12-11 17:48:43 +0100 (Thu, 11 Dec 2008) | 11 lines
Fixes for the 2 test_atom_loop_spin_selection2() unit tests.
This problem was reported by Jack Howarth (https://gna.org/users/jhowarth)
in the post at
https://mail.gna.org/public/relax-users/2008-10/msg00089.html (Message-id:
<20081024141150.GA879@xxxxxxxxxxxxxxxxx>).
The problem was with the position array comparison as this was being
converted to a string and then
compared. The string representations of the numpy arrays is obviously
different on the intel vs.
powerpc chips.
........
r8193 | bugman | 2008-12-11 18:09:51 +0100 (Thu, 11 Dec 2008) | 10 lines
Another PowerPC system test bug fix.
This problem was reported by Jack Howarth (https://gna.org/users/jhowarth)
in the post at
https://mail.gna.org/public/relax-users/2008-10/msg00089.html (Message-id:
<20081024141150.GA879@xxxxxxxxxxxxxxxxx>).
The string.fromstring() function appears to be useless when switching
between big and little endian
machines.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/generic_fns/mol_res_spin.py
branches/bmrb/generic_fns/pymol.py
branches/bmrb/generic_fns/structure/internal.py
branches/bmrb/generic_fns/structure/main.py
branches/bmrb/prompt/noe.py
branches/bmrb/test_suite/system_tests/angles.py
branches/bmrb/test_suite/system_tests/model_free.py
branches/bmrb/test_suite/system_tests/structure.py
branches/bmrb/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
branches/bmrb/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bmrb/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/mol_res_spin.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/generic_fns/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/pymol.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/internal.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/main.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/noe.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/angles.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/model_free.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/structure.py?rev=8195&r1=8194&r2=8195&view=diff
Modified:
branches/bmrb/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_generic_fns/_structure/test_internal.py?rev=8195&r1=8194&r2=8195&view=diff
Modified:
branches/bmrb/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py?rev=8195&r1=8194&r2=8195&view=diff
Modified: branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py?rev=8195&r1=8194&r2=8195&view=diff
r8195 - in /branches/bmrb: ./ generic_fns/ generic_fns/structure/ prompt/ test_suite/system_tests/ test_suite/unit_tests/_ge...