relax SVN archive

Merged revisions 8160,8180,8183,8186-8189,8191-8193 via svnmerge from
svn+ssh://bugman@.../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.
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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@...>).

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@...>).

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

Merged revisions 8191-8193 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
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@...>).

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@...>).

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

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.

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.

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.

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.
........

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.

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.

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.

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