Merged revisions 27044,27052-27116 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
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r27044 | bugman | 2014-12-09 14:59:51 +0100 (Tue, 09 Dec 2014) | 12 lines
Improvements for all of the tables of the relaxation dispersion chapter of the manual.
The captions are now the full width (or height for rotated tables) of the page in the PDF version of
the manual. The \latex{} command from the latex2html package has been used to improve the HTML
versions of the tables by deactivating the landscape environment, the cmidrule command, and the
caption width commands. This results in properly HTML formatted tables, rather than creating a PNG
image for the whole table. These should significantly improve the tables in the webpages
http://www.nmr-relax.com/manual/Comparison_of_dispersion_analysis_software.html,
http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis.html, and
http://www.nmr-relax.com/manual/Dispersion_model_summary.html.
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r27052 | bugman | 2014-12-10 13:58:30 +0100 (Wed, 10 Dec 2014) | 7 lines
Created the Structure.test_align_molecules system test.
This will be used to extend the functionality of the structure.align user function to be able to
align different molecules in the same data pipe, rather than requiring either models or identically
named structures in different data pipes.
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r27053 | bugman | 2014-12-10 14:05:33 +0100 (Wed, 10 Dec 2014) | 6 lines
Modified the Structure.test_align_molecules system test.
This now simultaneously checks both the pipes and molecules arguments to the structure.align user
function.
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r27054 | bugman | 2014-12-10 14:11:11 +0100 (Wed, 10 Dec 2014) | 3 lines
More changes for the new Structure.test_align_molecules system test.
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r27055 | bugman | 2014-12-10 14:12:18 +0100 (Wed, 10 Dec 2014) | 3 lines
Some more fixes for the Structure.test_align_molecules system test.
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r27056 | bugman | 2014-12-10 15:53:34 +0100 (Wed, 10 Dec 2014) | 7 lines
Change to the Structure.test_align system test.
The molecules argument for the structure.align user function has been changed to match the models
argument, in that it now needs to be a list of lists with the first dimension matching the pipes
argument. This change is to help with the implementation of the new structure.align functionality.
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r27057 | bugman | 2014-12-10 15:56:46 +0100 (Wed, 10 Dec 2014) | 9 lines
Implemented the new molecules argument for the structure.align user function.
In addition to accepting the new argument, the user function backend has been redesigned for
flexibility. The assembly of coordinates and final rotations and translations now consist of three
loops over desired data pipes, all models, and all molecules. If the models or molecules arguments
are supplied, then the models or molecules in the loop which do not match are skipped. This logic
simplifies and cleans up the backend.
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r27058 | bugman | 2014-12-10 16:37:18 +0100 (Wed, 10 Dec 2014) | 6 lines
Created the Structure.test_rmsd_molecules system test.
This will be used to implement a new molecules argument for the structure.rmsd user function so that
the RMSD between different molecules rather than different models can be calculated.
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r27059 | bugman | 2014-12-10 17:03:24 +0100 (Wed, 10 Dec 2014) | 6 lines
Implemented the new molecules argument for the structure.rmsd user function.
This allows the RMSD between different molecules rather than different models to be calculated,
extending the functionality of this user function.
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r27060 | bugman | 2014-12-10 17:07:08 +0100 (Wed, 10 Dec 2014) | 3 lines
Removed some temporary printouts from the structure.align user function.
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r27061 | bugman | 2014-12-10 17:20:19 +0100 (Wed, 10 Dec 2014) | 6 lines
Created the Structure.test_displacement_molecules system test.
This will be used to implement the new molecules argument for the structure.displacement user
function.
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r27062 | bugman | 2014-12-10 17:34:55 +0100 (Wed, 10 Dec 2014) | 7 lines
Implemented the molecules argument for the structure.displacement user function.
This allows the displacements (translations and rotations) to be calculated between different
molecules rather than different models. This information is stored in the dictionaries of the
cdp.structure.displacement object with the keys set to the molecule list indices.
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r27063 | bugman | 2014-12-10 18:53:48 +0100 (Wed, 10 Dec 2014) | 6 lines
Created the Structure.test_find_pivot system test.
This is to check the structure.find_pivot user function as this algorithm is currently not being
checked in the test suite.
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r27064 | bugman | 2014-12-10 18:57:14 +0100 (Wed, 10 Dec 2014) | 6 lines
Created the Structure.test_find_pivot_molecules system test.
This will be used to implement support for a molecules argument in the structure.find_pivot user
function so that different molecules rather than different models can be used in the analysis.
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r27065 | bugman | 2014-12-11 08:37:45 +0100 (Thu, 11 Dec 2014) | 3 lines
Increased the precision of pivot optimisation in the Structure.test_find_pivot_molecules system test.
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r27066 | bugman | 2014-12-11 08:41:07 +0100 (Thu, 11 Dec 2014) | 6 lines
Implemented the molecules argument for the structure.find_pivot user function.
This allows the motional pivot optimisation between different molecules rather than different
models.
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r27067 | bugman | 2014-12-11 08:58:36 +0100 (Thu, 11 Dec 2014) | 8 lines
Shifted the atomic assembly code from the structure.align user function into its own function.
The new function assemble_coordinates() of the pipe_control.structure.main module will be used to
standardise the process of assembling atomic coordinates for all of the structure user functions.
This will improve the support for comparing different molecules rather than different models as
missing atoms or divergent primary sequence are properly handled, and it has multi-pipe support.
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r27068 | bugman | 2014-12-11 09:04:35 +0100 (Thu, 11 Dec 2014) | 5 lines
Changed the argument order for the structure.align user function.
The standardised order will now be pipes, models, molecules, atom_id, etc.
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r27069 | bugman | 2014-12-11 09:25:06 +0100 (Thu, 11 Dec 2014) | 12 lines
Converted the structure.find_pivot user function to the new pipes/models/molecules/atom_id design.
This allows the motional pivot algorithm to work on atomic coordinates from different data pipes,
different structural models, and different molecules. The change allows the
Structure.test_find_pivot_molecules system test to now pass, as missing atomic data is now correctly
handled. The user function backend uses the new pipe_control.structure.main.assemble_coordinates()
function.
The Structure.test_find_pivot and Structure.test_find_pivot_molecules system tests have been updated
for the user function argument changes.
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r27070 | bugman | 2014-12-11 09:44:53 +0100 (Thu, 11 Dec 2014) | 12 lines
Shift of the atomic coordinate assembly code into the relax library.
Most of the pipe_control.structure.main.assemble_coordinates() function has been shifted into the
assemble_coord_array() function of the new lib.structure.internal.coordinates module. The
pipe_control function now only checks the arguments and assembles the structural objects from the
relax data store, and then calls assemble_coord_array() to do all of the work.
This code abstraction increases the usefulness of the atomic coordinate assembly and allows it to be
significantly expanded in the future, for example by being able to take sequence alignments into
consideration.
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r27071 | bugman | 2014-12-11 09:49:08 +0100 (Thu, 11 Dec 2014) | 3 lines
Tooltip standardisation for the structure.align and structure.find_pivot user functions.
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r27072 | bugman | 2014-12-11 10:02:23 +0100 (Thu, 11 Dec 2014) | 3 lines
Comment fix.
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r27073 | bugman | 2014-12-11 10:20:56 +0100 (Thu, 11 Dec 2014) | 5 lines
The coordinate assembly function now returns list of unique IDs.
This is for each structural object, model and molecule.
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r27074 | bugman | 2014-12-11 10:33:05 +0100 (Thu, 11 Dec 2014) | 6 lines
Changed the structure ID strings returned by the assemble_coord_array() function.
This is from the lib.structure.internal.coordinates module. The structural object name is only
included if more than one structural object has been supplied.
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r27075 | bugman | 2014-12-11 10:38:43 +0100 (Thu, 11 Dec 2014) | 3 lines
More improvements for the structure ID strings returned by the assemble_coord_array() function.
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r27076 | bugman | 2014-12-11 10:43:48 +0100 (Thu, 11 Dec 2014) | 3 lines
More improvements for the structure ID strings returned by the assemble_coord_array() function.
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r27077 | bugman | 2014-12-11 10:48:26 +0100 (Thu, 11 Dec 2014) | 6 lines
Converted the internal structural displacement object to use unique IDs rather than model numbers.
This allows the object to be much more flexible in what types of structures it can handle. This is
in preparation for a change in the structure.displacement user function.
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r27078 | bugman | 2014-12-11 10:50:16 +0100 (Thu, 11 Dec 2014) | 9 lines
Converted the structure.displacement user function to the new pipes/models/molecules/atom_id design.
This allows the displacements to be calculated between atomic coordinates from different data pipes,
different structural models, and different molecules. The user function backend has been hugely
simplified as it now uses the new pipe_control.structure.main.assemble_coordinates() function.
The Structure.test_displacement system test has been updated for the user function argument changes.
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r27079 | bugman | 2014-12-11 10:55:24 +0100 (Thu, 11 Dec 2014) | 3 lines
Another refinement for the structure ID strings returned by the assemble_coord_array() function.
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r27080 | bugman | 2014-12-11 10:55:53 +0100 (Thu, 11 Dec 2014) | 5 lines
Updated the Structure.test_displacement_molecules system test.
This is for the changes to the structure.displacement user function.
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r27081 | bugman | 2014-12-11 11:03:54 +0100 (Thu, 11 Dec 2014) | 3 lines
Docstring spelling fixes for the steady-state NOE and relaxation curve-fitting auto-analyses.
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r27082 | bugman | 2014-12-11 11:20:03 +0100 (Thu, 11 Dec 2014) | 10 lines
Converted the structure.rmsd user function to the new pipes/models/molecules/atom_id design.
This allows the RMSD calculation to work on atomic coordinates from different data pipes, different
structural models, and different molecules. The user function backend uses the new
pipe_control.structure.main.assemble_coordinates() function.
The Structure.test_rmsd_molecules system test has been updated for the user function argument
changes.
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r27083 | bugman | 2014-12-11 11:34:24 +0100 (Thu, 11 Dec 2014) | 5 lines
Created the internal structural object model_list() method.
This is to simplify the assembly of a list of all current models in the structural object.
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r27084 | bugman | 2014-12-11 11:37:33 +0100 (Thu, 11 Dec 2014) | 8 lines
Converted the structure.superimpose user function to the new pipes/models/molecules/atom_id design.
The user function arguments have not changed, however the backend now uses the new
pipe_control.structure.main.assemble_coordinates() function. This is to simply decrease the number
of failure points possible in the structure user functions. The change has no effect on the user
function use or results.
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r27085 | bugman | 2014-12-11 11:42:40 +0100 (Thu, 11 Dec 2014) | 6 lines
Documentation fix for the assemble_coord_array() function.
The return values for lib.structure.internal.coordinates.assemble_coord_array() were incorrectly
documented.
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r27086 | bugman | 2014-12-11 11:46:04 +0100 (Thu, 11 Dec 2014) | 6 lines
Modified the Structure.test_bug_22070_structure_superimpose_after_deletion system test.
This now calls the structure.align user function after calling the structure.superimpose user
function to better test a condition that can trigger bugs.
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r27087 | bugman | 2014-12-11 11:49:26 +0100 (Thu, 11 Dec 2014) | 6 lines
Fixes for the structure.superimpose and structure.align user functions.
The fit_to_mean() and fit_to_first() functions of lib.structure.superimpose where being incorrectly
called, in that they expect a list of elements and not lists of lists.
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r27088 | bugman | 2014-12-11 12:25:03 +0100 (Thu, 11 Dec 2014) | 9 lines
Code refactorisation for the structure.align user function backend.
The looping over data pipes, model numbers, and molecule names, skipping those that don't match the
function arguments, has been shifted into the new structure_loop() generator function of the
pipe_control.structure.main module. This function assembles the data from the data store and then
calls the new loop_coord_structures() generator function of the lib.structure.internal.coordinates
module which does all of the work.
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r27089 | bugman | 2014-12-11 13:13:19 +0100 (Thu, 11 Dec 2014) | 3 lines
Some docstring expansions for the pipe_control.structure.main module functions.
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r27090 | bugman | 2014-12-11 13:40:41 +0100 (Thu, 11 Dec 2014) | 9 lines
Refactored the descriptions of a number of structure user functions.
This includes the structure.align, structure.displacement, structure.find_pivot, structure.rmsd and
structure.superimpose user functions. The paragraph_multi_struct and paragraph_atom_id module
strings have been created and are shared as two paragraphs for each of these user function
descriptions. This standardises the pipe/model/molecule/atom_id descriptions. The user function
wizard page sizes have been updated for these changes.
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r27091 | bugman | 2014-12-11 16:00:21 +0100 (Thu, 11 Dec 2014) | 10 lines
Changed the design of the lib.structure.internal.coordinates.assemble_coord_array() function.
The elements_flag argument has been renamed to seq_info_flag. If this is set, then in addition to
the atomic elements, the molecule name, residue name, residue number, and atom name is now assembled
and returned. This information is now the common information between the structures, hence the
return values for the elements are a list of str rather than list of lists.
All of the code in pipe_control.structure.main has been updated for the change.
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r27092 | bugman | 2014-12-11 16:03:42 +0100 (Thu, 11 Dec 2014) | 6 lines
Fix for the structure.align user function if no data pipes are supplied.
The pipes list was no longer being created as it was shifted to the assemble_coordinates() function,
however it is required for the translation and rotation function calls.
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r27093 | bugman | 2014-12-11 16:23:46 +0100 (Thu, 11 Dec 2014) | 7 lines
Bug fix for the lib.arg_check.is_int_list() function for checking a list of lists.
This is used to check user function arguments, but was causing a RelaxError to be raised for all
integer list of lists user function arguments when a valid value is supplied. The function has been
updated to match the is_str_list() function which does not suffer from this bug.
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r27094 | bugman | 2014-12-11 17:13:55 +0100 (Thu, 11 Dec 2014) | 17 lines
Converted the structure.web_of_motion user function to the new pipe/model/molecule/atom_id design.
This allows the web of motion representation to work on atomic coordinates from different data
pipes, different structural models, and different molecules. The user function backend uses the new
pipe_control.structure.main.assemble_coordinates() function to assemble the common atom coordinates,
molecule names, residue names, residue numbers, atom names and elements. All this information is
then used to construct the new web of motion PDB file. Therefore the entire backend has been
rewritten.
The Structure.test_web_of_motion_12, Structure.test_web_of_motion_13, and
Structure.test_web_of_motion_all system tests have all been updated for the changed
structure.web_of_motion user function arguments. In addition, the system tests
Structure.test_web_of_motion_12_molecules, Structure.test_web_of_motion_13_molecules and
Structure.test_web_of_motion_all_molecules have been created as a copy of the other tests but with
the 3 structures loaded as different molecules.
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r27095 | bugman | 2014-12-11 17:27:20 +0100 (Thu, 11 Dec 2014) | 7 lines
Fix for the IDs returned by lib.structure.internal.coordinates.assemble_coord_array().
The list of unique structure IDs was being incorrectly constructed if multiple molecules are present
but the molecules argument was not supplied. It would be of a different size to the coordinate data
structure.
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r27096 | bugman | 2014-12-11 17:27:46 +0100 (Thu, 11 Dec 2014) | 3 lines
Fix for the Structure.test_displacement system test for the assemble_coord_array() function bugfix.
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r27097 | bugman | 2014-12-11 17:28:11 +0100 (Thu, 11 Dec 2014) | 3 lines
Removed a debugging printout.
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r27098 | bugman | 2014-12-11 18:55:25 +0100 (Thu, 11 Dec 2014) | 6 lines
Modified the Structure.test_align system test to show a failure of the structure.align user function.
The alignment causes all atoms in the structural object to be translated and rotated, whereas it
should only operate on the atoms of the atom_id argument.
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r27099 | bugman | 2014-12-11 19:01:54 +0100 (Thu, 11 Dec 2014) | 7 lines
Modified the Structure.test_superimpose_fit_to_mean system test.
This is also to demonstrate a bug, this time in the structure.superimpose user function, in which
the algorithm causes a translation and rotation of all atoms rather than just those selected by the
atom_id argument.
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r27100 | bugman | 2014-12-11 19:10:37 +0100 (Thu, 11 Dec 2014) | 8 lines
Modified some system tests of the structure.align and structure.superimpose user functions.
The displace_id argument has been introduced for both of these user functions for finer control over
which atoms are translated and rotated by the algorithm. This allows, for example, to align
structures based on a set of backbone heavy atoms while the protons and side chains are displaced by
default. Or if a domain is aligned, then just that domain can be displaced.
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r27101 | bugman | 2014-12-11 19:37:46 +0100 (Thu, 11 Dec 2014) | 8 lines
Added the displace_id argument to the structure.align and structure.superimpose user functions.
This gives both of these user functions finer control over which atoms are translated and rotated by
the algorithm. This allows, for example, to align structures based on a set of backbone heavy atoms
while the protons and side chains are displaced by default. Or if a domain is aligned, then just
that domain can be displaced.
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r27102 | bugman | 2014-12-11 19:38:25 +0100 (Thu, 11 Dec 2014) | 3 lines
Fixes for the Structure.test_superimpose_fit_to_mean system test for the displace_id argument.
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r27103 | bugman | 2014-12-12 10:48:40 +0100 (Fri, 12 Dec 2014) | 6 lines
Modified the Structure.test_align_molecules system test to catch a bug.
This is the failure of the displace_id argument of the structure.align user function when the
molecules argument is supplied - all atoms are being displaced instead of a subset.
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r27104 | bugman | 2014-12-12 10:52:24 +0100 (Fri, 12 Dec 2014) | 6 lines
Fix for the displace_id and molecules arguments of the structure.align user function.
The atom ID used for the translations and rotations is now properly constructed from the molecule
names in the molecules list and the displace_id string.
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r27105 | bugman | 2014-12-12 11:41:11 +0100 (Fri, 12 Dec 2014) | 5 lines
Changes for water in the PDB file created by the structure.write_pdb user function.
The waters with the residue name 'HOH' are no longer output to HET records.
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r27106 | bugman | 2014-12-12 12:08:20 +0100 (Fri, 12 Dec 2014) | 6 lines
Improvement for the structure.read_pdb user function.
The helix and sheet secondary structure reading now takes the real_mol argument into account to
avoid reading in too much information.
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r27107 | bugman | 2014-12-12 12:22:03 +0100 (Fri, 12 Dec 2014) | 6 lines
Improvement for the merge argument of the structure.read_pdb user function.
This argument is now overridden if the molecule to merge to does not exist. This allows the merge
flag to be used together with read_mol and set_mol_name set to lists.
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r27108 | bugman | 2014-12-12 12:22:47 +0100 (Fri, 12 Dec 2014) | 5 lines
Fix for the selective secondary structure reading of the structure.read_pdb user function.
The molecule index needs to incremented by 1 to be the molecule number.
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r27109 | bugman | 2014-12-12 15:36:01 +0100 (Fri, 12 Dec 2014) | 9 lines
Large improvement for the PDB molecule identification code.
This affects the structure.read_pdb user function. Now the chain ID code, if present in the PDB
file, is being used to determine which ATOM and HETATM records belong to which molecule. All of the
records for each molecule are stored until the end, when they are all yielded. This allows for
discontinuous chain IDs throughout the PDB file, something which occurs often with the HETATM
records.
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r27110 | bugman | 2014-12-12 16:06:47 +0100 (Fri, 12 Dec 2014) | 6 lines
Expanded the displace_id argument for the structure.align user function.
This can now be a list of atom IDs, so that any atoms can be rotated together with the structure
being aligned. This is useful if the molecules argument is supplied.
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r27111 | bugman | 2014-12-12 21:48:16 +0100 (Fri, 12 Dec 2014) | 7 lines
Fix for the Noe.test_bug_21562_noe_replicate_fail system test.
This is for the changed behaviour of the structure.read_pdb user function. The problem is that the
PDB file read in this test has the chain ID set to X. This broken PDB causes molecule numbering
problems.
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r27112 | bugman | 2014-12-15 18:44:42 +0100 (Mon, 15 Dec 2014) | 3 lines
Expanded the description of the structure.rmsd user function.
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r27113 | bugman | 2014-12-16 09:10:28 +0100 (Tue, 16 Dec 2014) | 5 lines
Changed the paragraph ordering in the documentation of a number of the structure user functions.
This includes the structure.align, structure.displacement, and structure.find_pivot user functions.
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r27114 | bugman | 2014-12-16 09:11:58 +0100 (Tue, 16 Dec 2014) | 3 lines
Fix for the prompt examples documentation for the structure.align user function.
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r27115 | bugman | 2014-12-16 09:15:35 +0100 (Tue, 16 Dec 2014) | 3 lines
Improved the sizing layout of the structure.align user function GUI dialog.
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r27116 | bugman | 2014-12-16 09:19:19 +0100 (Tue, 16 Dec 2014) | 3 lines
Improved the sizing layout of the structure.superimpose user function GUI dialog.
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