svn+ssh://bugman@.../svn/relax/branches/rdc_analysis
........
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.
........
r6656 | bugman | 2008-07-04 14:19:47 +0200 (Fri, 04 Jul 2008) | 3 lines
Renamed a run to a pipe in a comment.
........
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.
........
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.
........
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.
........
r6660 | bugman | 2008-07-04 14:47:33 +0200 (Fri, 04 Jul 2008) | 3 lines
Removed a broken and useless test.
........
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.
........
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.
........
r6663 | bugman | 2008-07-04 15:02:42 +0200 (Fri, 04 Jul 2008) | 3 lines
Fixes for the test_load_pdb() unit test.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r6684 | bugman | 2008-07-04 19:09:02 +0200 (Fri, 04 Jul 2008) | 3 lines
Fixes for the __atom_index() method.
........
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.
........
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().
........
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.
........
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.
........
r6698 | bugman | 2008-07-05 00:06:57 +0200 (Sat, 05 Jul 2008) | 3 lines
Created the user function interface for structure.write_pdb().
........
r6699 | bugman | 2008-07-05 00:21:37 +0200 (Sat, 05 Jul 2008) | 3 lines
Created the write_pdb() function.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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'.
........
r6711 | bugman | 2008-07-05 01:05:10 +0200 (Sat, 05 Jul 2008) | 3 lines
Fixed the creation of the FORMUL record.
........
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!
........
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.
........
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.
........
r6715 | bugman | 2008-07-05 01:24:13 +0200 (Sat, 05 Jul 2008) | 3 lines
Fixed the creation of the CONECT records.
........
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.
........
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!
........
r6718 | bugman | 2008-07-05 02:01:44 +0200 (Sat, 05 Jul 2008) | 3 lines
Fixed the creation of the MASTER record.
........
r6719 | bugman | 2008-07-05 02:34:48 +0200 (Sat, 05 Jul 2008) | 3 lines
Added a few initial remarks to the PDB file.
........
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.
........
r6721 | bugman | 2008-07-05 03:06:45 +0200 (Sat, 05 Jul 2008) | 3 lines
Improvements for the counts for the MASTER record.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r6727 | bugman | 2008-07-05 04:24:28 +0200 (Sat, 05 Jul 2008) | 3 lines
Improvements to the print outs during PDB creation.
........
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.
........
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.
........
r6730 | bugman | 2008-07-05 11:49:46 +0200 (Sat, 05 Jul 2008) | 3 lines
Removed TER from the add_atom() docstring.
........
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.
........
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().
........
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().
........
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.
........
