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[r8193] by bugman

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@...>).

The string.fromstring() function appears to be useless when switching between big and little endian
machines.

2008-12-11 17:09:51 Tree
[r8192] by bugman

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@...>).

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.

2008-12-11 16:48:43 Tree
[r8191] by bugman

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.

2008-12-11 16:24:46 Tree
[r8190] by bugman

Merged revisions 8186-8189 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
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.
........

2008-12-11 10:15:46 Tree
[r8189] by bugman

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.

2008-12-11 10:14:00 Tree
[r8188] by bugman

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.

2008-12-11 09:53:22 Tree
[r8187] by bugman

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.

2008-12-11 09:33:32 Tree
[r8186] by bugman

Added tests of structure.load_spins() to all the structure system tests.

2008-12-10 17:46:37 Tree
[r8185] by bugman

Merged revisions 8180,8183 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
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.
........

2008-12-10 17:37:41 Tree
[r8184] by bugman

Initialized merge tracking via "svnmerge" with revisions "1-8160" from
svn+ssh://bugman@.../svn/relax/1.3

2008-12-10 17:37:25 Tree
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