Author: bugman
Date: Sat Jul 5 12:24:08 2008
New Revision: 6737
URL: http://svn.gna.org/viewcvs/relax?rev=6737&view=rev
Log:
Merged revisions 6652,6654,6656-6733,6735-6736 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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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Modified:
1.3/ (props changed)
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/geometric.py
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.py
1.3/generic_fns/structure/scientific.py
1.3/prompt/structure.py
1.3/specific_fns/n_state_model.py
1.3/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.3/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=6737&r1=6736&r2=6737&view=diff
Modified: 1.3/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=6737&r1=6736&r2=6737&view=diff
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=6737&r1=6736&r2=6737&view=diff
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=6737&r1=6736&r2=6737&view=diff
Modified: 1.3/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=6737&r1=6736&r2=6737&view=diff
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=6737&r1=6736&r2=6737&view=diff
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=6737&r1=6736&r2=6737&view=diff
Modified: 1.3/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_generic_fns/_structure/test_internal.py?rev=6737&r1=6736&r2=6737&view=diff
r6737 - in /1.3: ./ generic_fns/structure/ prompt/ specific_fns/ test_suite/unit_tests/_generic_fns/_structure/