relax SVN archive

Expanded the OMP model-free optimisation system test.

The initial round of spherical diffusion optimisation (removal of tm and diffusion tensor opt) is
now tested. The first round of normal optimisation is also implemented with the optimisation of the
model-free models and model selection.

Module docsting updates in the generic_fns package.

All missing module docstrings were created, the current ones modified, and the copyright notices
updated.

Initialized merge tracking via "svnmerge" with revisions "1-6739" from
svn+ssh://bugman@.../svn/relax/1.3

Recreated the rdc_analysis branch.

The original branch ended up being a branch for PDB development. This was hence merged into 1.3 and
then deleted.

Deleted this branch as it ended up being used for PDB reading and writing development.

It will be recreated anew for its original purpose.

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/rdc_analysis

Merged revisions 6652,6654,6656-6733,6735-6736 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/rdc_analysis

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r6652 | bugman | 2008-07-04 11:43:17 +0200 (Fri, 04 Jul 2008) | 3 lines

Created a development branch for implementing some basic RDC and PCS dynamics analyses.
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r6656 | bugman | 2008-07-04 14:19:47 +0200 (Fri, 04 Jul 2008) | 3 lines

Renamed a run to a pipe in a comment.
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r6657 | bugman | 2008-07-04 14:24:00 +0200 (Fri, 04 Jul 2008) | 3 lines

Bug fix for the internal PDB reader, the HETATM records are now recognised.
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r6658 | bugman | 2008-07-04 14:37:18 +0200 (Fri, 04 Jul 2008) | 5 lines

Fixes for the internal PDB reader.

Non ATOM or HETATM records, after these records (i.e. CONECT) no longer cause the reader to fail.
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r6659 | bugman | 2008-07-04 14:45:23 +0200 (Fri, 04 Jul 2008) | 5 lines

Converted the file_name structural object variable into a list.

This will allow multiple files to be opened within one data pipe.
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r6660 | bugman | 2008-07-04 14:47:33 +0200 (Fri, 04 Jul 2008) | 3 lines

Removed a broken and useless test.
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r6661 | bugman | 2008-07-04 14:51:31 +0200 (Fri, 04 Jul 2008) | 3 lines

Added a check for the consistency of the PDB parser.
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r6662 | bugman | 2008-07-04 14:53:27 +0200 (Fri, 04 Jul 2008) | 6 lines

Bug fix for the read_pdb() method.

The structural object is only created if it does not yet exist. This bug was causing the loss of
previously loaded files.
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r6663 | bugman | 2008-07-04 15:02:42 +0200 (Fri, 04 Jul 2008) | 3 lines

Fixes for the test_load_pdb() unit test.
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r6666 | bugman | 2008-07-04 15:53:26 +0200 (Fri, 04 Jul 2008) | 3 lines

Added the ability to select the structure to load the spins from in the load_spins() main method.
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r6667 | bugman | 2008-07-04 15:58:28 +0200 (Fri, 04 Jul 2008) | 3 lines

Added the str_id arg to the atom_loop() structural API method.
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r6668 | bugman | 2008-07-04 15:59:52 +0200 (Fri, 04 Jul 2008) | 3 lines

Docstring modification for the atom_loop() internal PDB object method.
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r6669 | bugman | 2008-07-04 16:06:02 +0200 (Fri, 04 Jul 2008) | 3 lines

Added the ave arg to all atom_loop() methods to allow just the average properties to be returned.
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r6670 | bugman | 2008-07-04 16:09:11 +0200 (Fri, 04 Jul 2008) | 3 lines

Added the str_id arg to the Scientific PDB object atom_loop() method.
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r6671 | bugman | 2008-07-04 16:14:32 +0200 (Fri, 04 Jul 2008) | 3 lines

The internal PDB object atom_loop() method now recognises the ave arg, but does nothing when True.
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r6672 | bugman | 2008-07-04 16:35:43 +0200 (Fri, 04 Jul 2008) | 3 lines

The internal PDB object atom_loop() method now can return the average atom properties, if asked.
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r6674 | bugman | 2008-07-04 16:40:14 +0200 (Fri, 04 Jul 2008) | 5 lines

Bug fix for the load_spins() function.

Molecule, residue, and spin information can be missing and the function still work.
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r6678 | bugman | 2008-07-04 17:58:14 +0200 (Fri, 04 Jul 2008) | 7 lines

Bug fix for the loading of multiple files.

Each time a new file was loaded, all its atoms would be appended to all other presently loaded
structures. This would cause large slow downs of the atom_loop() function, and a few other
problems. Now structures are referenced by structure index rather than model number.
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r6680 | bugman | 2008-07-04 18:43:32 +0200 (Fri, 04 Jul 2008) | 3 lines

Added code to connect atoms via CONECT records in the internal PDB reader.
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r6682 | bugman | 2008-07-04 18:51:35 +0200 (Fri, 04 Jul 2008) | 3 lines

Modified the __parse_pdb_record() method to parse CONECT records.
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r6683 | bugman | 2008-07-04 19:03:49 +0200 (Fri, 04 Jul 2008) | 3 lines

Created the __atom_index() method to find the atom index corresponding to an atom number.
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r6684 | bugman | 2008-07-04 19:09:02 +0200 (Fri, 04 Jul 2008) | 3 lines

Fixes for the __atom_index() method.
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r6694 | bugman | 2008-07-04 20:48:24 +0200 (Fri, 04 Jul 2008) | 3 lines

Updated the atom_connect() method to use the structural index rather than model number.
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r6695 | bugman | 2008-07-04 23:33:04 +0200 (Fri, 04 Jul 2008) | 3 lines

Added a catch for empty atom columns in the CONECT record within __fill_object_from_pdb().
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r6696 | bugman | 2008-07-04 23:37:51 +0200 (Fri, 04 Jul 2008) | 3 lines

Added a RelaxWarning for when a CONECT atom is not in the HETATM or ATOM records.
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r6697 | bugman | 2008-07-04 23:41:16 +0200 (Fri, 04 Jul 2008) | 5 lines

Fix for the CONECT processing part of __parse_pdb_record().

The last CONECT atom was not being converted into an int.
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r6698 | bugman | 2008-07-05 00:06:57 +0200 (Sat, 05 Jul 2008) | 3 lines

Created the user function interface for structure.write_pdb().
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r6699 | bugman | 2008-07-05 00:21:37 +0200 (Sat, 05 Jul 2008) | 3 lines

Created the write_pdb() function.
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r6700 | bugman | 2008-07-05 00:24:06 +0200 (Sat, 05 Jul 2008) | 3 lines

Added the force arg to the structure.write_pdb() user function.
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r6701 | bugman | 2008-07-05 00:25:55 +0200 (Sat, 05 Jul 2008) | 3 lines

The struct_index is now passed into the write_pdb() method.
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r6702 | bugman | 2008-07-05 00:30:36 +0200 (Sat, 05 Jul 2008) | 3 lines

Converted the write_pdb() function to loop over all structures.
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r6703 | bugman | 2008-07-05 00:33:37 +0200 (Sat, 05 Jul 2008) | 5 lines

Updated the __validate_data_arrays() method to handle multiple structures.

The structure_container instance is now passed into the method.
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r6704 | bugman | 2008-07-05 00:35:54 +0200 (Sat, 05 Jul 2008) | 3 lines

Fixes for the write_pdb() method for handling multiple structures better.
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r6705 | bugman | 2008-07-05 00:46:18 +0200 (Sat, 05 Jul 2008) | 3 lines

Modified how non-standard residue information is collected and stored for future writing.
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r6706 | bugman | 2008-07-05 00:47:40 +0200 (Sat, 05 Jul 2008) | 5 lines

Fix for the main write_pdb() method.

Now the file object is sent into the specific write_pdb() method rather than the file path string.
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r6707 | bugman | 2008-07-05 00:53:42 +0200 (Sat, 05 Jul 2008) | 3 lines

HETATM records with no residue info are now skipped in the HET record construction.
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r6708 | bugman | 2008-07-05 00:57:11 +0200 (Sat, 05 Jul 2008) | 3 lines

Missing chain_ids are now caught and replaced by empty strings.
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r6709 | bugman | 2008-07-05 00:59:20 +0200 (Sat, 05 Jul 2008) | 3 lines

Modified the __get_chemical_name() to handle unidentifiable residue names.
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r6710 | bugman | 2008-07-05 01:02:39 +0200 (Sat, 05 Jul 2008) | 3 lines

Fix for the creation of the HETNAM record. The None description value is replaced by 'Unknown'.
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r6711 | bugman | 2008-07-05 01:05:10 +0200 (Sat, 05 Jul 2008) | 3 lines

Fixed the creation of the FORMUL record.
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r6712 | bugman | 2008-07-05 01:10:15 +0200 (Sat, 05 Jul 2008) | 5 lines

Fix for the creation of the het_atom data structure.

The index i was being overwritten!
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r6713 | bugman | 2008-07-05 01:11:06 +0200 (Sat, 05 Jul 2008) | 3 lines

The index i was being overwritten in another place as well.
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r6714 | bugman | 2008-07-05 01:21:12 +0200 (Sat, 05 Jul 2008) | 3 lines

Fixed the creation of the ATOM, HETATM, and TER records.
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r6715 | bugman | 2008-07-05 01:24:13 +0200 (Sat, 05 Jul 2008) | 3 lines

Fixed the creation of the CONECT records.
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r6716 | bugman | 2008-07-05 01:48:08 +0200 (Sat, 05 Jul 2008) | 6 lines

Fix for the atom_connect() method and the creation of the CONECT record.

The atom_connect() method was modified to only append the atom index if it wasn't already in the
bonded list. The CONECT record now uses the atom numbers and not atom indecies.
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r6717 | bugman | 2008-07-05 01:57:38 +0200 (Sat, 05 Jul 2008) | 3 lines

Fixed the creation of the CONECT record, really this time!
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r6718 | bugman | 2008-07-05 02:01:44 +0200 (Sat, 05 Jul 2008) | 3 lines

Fixed the creation of the MASTER record.
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r6719 | bugman | 2008-07-05 02:34:48 +0200 (Sat, 05 Jul 2008) | 3 lines

Added a few initial remarks to the PDB file.
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r6720 | bugman | 2008-07-05 02:59:19 +0200 (Sat, 05 Jul 2008) | 3 lines

Shifted the MASTER record to the very end of the PDB.
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r6721 | bugman | 2008-07-05 03:06:45 +0200 (Sat, 05 Jul 2008) | 3 lines

Improvements for the counts for the MASTER record.
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r6722 | bugman | 2008-07-05 03:26:27 +0200 (Sat, 05 Jul 2008) | 3 lines

Updated the base API write_pdb() docstring to the 3.1 PDB format and added the MODEL record desc.
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r6723 | bugman | 2008-07-05 03:35:15 +0200 (Sat, 05 Jul 2008) | 3 lines

The MODEL and ENDMDL records are now created, if multiple structures exist.
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r6724 | bugman | 2008-07-05 03:38:39 +0200 (Sat, 05 Jul 2008) | 3 lines

Split the PDB creation code into the hetrogen and coordinate sections.
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r6725 | bugman | 2008-07-05 04:19:04 +0200 (Sat, 05 Jul 2008) | 5 lines

Fixes for the hetrogen section.

These records are now correctly created, independent of the number of loaded structures.
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r6726 | bugman | 2008-07-05 04:20:52 +0200 (Sat, 05 Jul 2008) | 3 lines

Shifted the ENDMDL record to be before the CONECT records.
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r6727 | bugman | 2008-07-05 04:24:28 +0200 (Sat, 05 Jul 2008) | 3 lines

Improvements to the print outs during PDB creation.
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r6728 | bugman | 2008-07-05 11:29:08 +0200 (Sat, 05 Jul 2008) | 3 lines

Fix for the number of hetrogens in the MASTER record.
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r6729 | bugman | 2008-07-05 11:48:58 +0200 (Sat, 05 Jul 2008) | 3 lines

The TER record is now automatically created after any ATOM or HETATM stretch.
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r6730 | bugman | 2008-07-05 11:49:46 +0200 (Sat, 05 Jul 2008) | 3 lines

Removed TER from the add_atom() docstring.
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r6731 | bugman | 2008-07-05 11:54:54 +0200 (Sat, 05 Jul 2008) | 5 lines

Deleted all the PDB terminate() function calls and methods.

These are not necessary as the TER record is now automatically generated.
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r6732 | bugman | 2008-07-05 12:15:51 +0200 (Sat, 05 Jul 2008) | 3 lines

Changed the model arg to struct_index in the structural object API method atom_add().
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r6733 | bugman | 2008-07-05 12:17:21 +0200 (Sat, 05 Jul 2008) | 3 lines

Changed the model arg to struct_index in the structural object API method atom_connect().
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r6735 | bugman | 2008-07-05 12:20:58 +0200 (Sat, 05 Jul 2008) | 3 lines

Added the struct_index keyword arg to the structural object API write_pdb() method.
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Initialized merge tracking via "svnmerge" with revisions "1-6651" from
svn+ssh://bugman@.../svn/relax/branches/rdc_analysis

Added the struct_index keyword arg to the structural object API write_pdb() method.

Merged revisions 6655-6733 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r6665 | semor | 2008-07-04 15:41:05 +0200 (Fri, 04 Jul 2008) | 6 lines

Corrected an error in the definition of eta.

This change had been made on the 1.2 line, but was also needed on the 1.3 line.
See r6611 (http://svn.gna.org/viewcvs/relax?rev=6611&view=rev) for details.
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r6673 | semor | 2008-07-04 16:37:40 +0200 (Fri, 04 Jul 2008) | 5 lines

Some changes towards the new design.

The script doesn't work yet and will be introduced into the test suite for further debugging.
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r6675 | semor | 2008-07-04 16:41:12 +0200 (Fri, 04 Jul 2008) | 7 lines

Changed the test suite reference value for eta so the test passes after the equation modification.

This change follows the one for r6665 (http://svn.gna.org/viewcvs/relax?rev=6665&view=rev) and had
already been made on the 1.2 line, but was also needed on the 1.3 line. See r6611
(http://svn.gna.org/viewcvs/relax?rev=6611&view=rev) for details.
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r6676 | semor | 2008-07-04 17:17:00 +0200 (Fri, 04 Jul 2008) | 3 lines

Added the use of a script for consistency_tests system testing.
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r6677 | semor | 2008-07-04 17:18:39 +0200 (Fri, 04 Jul 2008) | 6 lines

Added a script for consistency_tests system testing.

This one is, basically, a copy of the sample script. Changes are thus needed for it to work as a
system test script.
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r6679 | semor | 2008-07-04 18:38:34 +0200 (Fri, 04 Jul 2008) | 3 lines

Added a copyright to the consistency_tests script.
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r6681 | semor | 2008-07-04 18:45:50 +0200 (Fri, 04 Jul 2008) | 3 lines

Improved the consistency_tests system testing script.
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r6685 | semor | 2008-07-04 19:11:30 +0200 (Fri, 04 Jul 2008) | 3 lines

Converted the output file to 'devnull'.
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r6686 | semor | 2008-07-04 19:21:03 +0200 (Fri, 04 Jul 2008) | 3 lines

Converted the force flags to bools.
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r6687 | semor | 2008-07-04 19:22:02 +0200 (Fri, 04 Jul 2008) | 3 lines

Correcte the copyright.
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r6688 | semor | 2008-07-04 19:27:43 +0200 (Fri, 04 Jul 2008) | 3 lines

Converted more force flags to bools.
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r6689 | semor | 2008-07-04 19:29:20 +0200 (Fri, 04 Jul 2008) | 3 lines

Still more conversions of the force flags to bools.
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r6690 | semor | 2008-07-04 19:32:51 +0200 (Fri, 04 Jul 2008) | 3 lines

Conversion of force flags to bools.
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r6691 | semor | 2008-07-04 19:36:15 +0200 (Fri, 04 Jul 2008) | 3 lines

Corrected a typo.
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r6692 | semor | 2008-07-04 20:00:09 +0200 (Fri, 04 Jul 2008) | 3 lines

Conversion of force flags to bools.
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r6693 | semor | 2008-07-04 20:01:41 +0200 (Fri, 04 Jul 2008) | 3 lines

Conversion of force flags to bools.
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