relax SVN archive

Fix for the sequence.read user function for a problem with r17028.

The sequence.generate() function was not returning the correct result as it didn't take into account
the renaming and renumbering of empty spin containers. Now sequence.read will always print out the
generated sequence and not result in a RelaxError for most of the system tests.

Merged revisions 17028 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17028 | bugman | 2012-06-22 15:15:56 +0200 (Fri, 22 Jun 2012) | 5 lines

The sequence.read user function now fails with a RelaxError if no sequence data was loaded.

This is for better user feedback.
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The sequence.read user function now fails with a RelaxError if no sequence data was loaded.

This is for better user feedback.

Fix for the relax_data module pack_data() function for the trunk changes of r17021.

For the relax_data.read user function spin_id argument to be respected, the
return_spin_from_selection() function needs to be used to return multiple matching spins.

Eliminated all of the bond length and heteronucleus type value.set units tests.

These are no longer specific analysis parameters.

Removed all of the unit tests of the deleted structure.vectors user function.

Missing import.

Updated the generic_fns package __all__ list.

Merged revisions 17017-17021 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines

The spin ID lookup table has been made private so that it is not included in the save files.
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r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines

Fix for reading of BMRB CSA saveframe data - spin IDs generated from the data now have molecule info.

This is problematic only in certain edge cases, for example a multi-molecule entry.
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r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines

Removal of a hack from the generic_fns.bmrb.generate_sequence() function.

This hack was for naming unnamed spins. But this is not needed as the
generic_fns.mol_res_spin.create_spin() function already does this but with many more safety checks.
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r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines

Removed a hack from the generic_fns.relax_data.pack_data() function for the BMRB support.

This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB code paths access the
pack_data() function, this is a nasty hack which would have caused problems in the future.
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r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines

Creation of a fast molecule, residue and spin data lookup framework using private metadata.

This consists of two elements: The already existing private lookup table now at
cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a list of molecule, residue
and spin indices as values; and a set of private variables within the molecule, residue and spin
containers which identify the parent container names, numbers and indices. As all data is private,
it will not be visible to the user or be saved in the XML results and save files and should be
considered volatile.

All this private metadata is kept up to date via the two new generic_fns.mol_res_spin functions
metadata_prune() and metadata_update(). For fast operation, these methods can update specific
container subsets via the mol_index, res_index and spin_index arguments. All parts of relax which
modify the data pipe's molecule, residue and spin data structure (the generic_fns.mol_res_spin
functions and test suite) call these two functions as needed. Two auxiliary functions
spin_id_variants() and spin_id_variants_elim() have been added to create all possible matching spin
ID strings for a given spin (the second created IDs strings which should no longer exist).

The speed ups from this change are significant. On one system, the system and unit tests decrease
from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from 330.7s/17.4s to 258.9s/15.4s.

In addition, the pipe argument has been added to the generic_fns.mol_res_spin functions
create_molecule(), create_residue(), create_pseudo_spin() and create_spin(). Also, the molecule
name will now always be a string! Previously this was allowed to be an integer. This is needed for
the private metadata functions to operate correctly. A number of unit tests have been updated for
the changes.
........

Creation of a fast molecule, residue and spin data lookup framework using private metadata.

This consists of two elements: The already existing private lookup table now at
cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a list of molecule, residue
and spin indices as values; and a set of private variables within the molecule, residue and spin
containers which identify the parent container names, numbers and indices. As all data is private,
it will not be visible to the user or be saved in the XML results and save files and should be
considered volatile.

All this private metadata is kept up to date via the two new generic_fns.mol_res_spin functions
metadata_prune() and metadata_update(). For fast operation, these methods can update specific
container subsets via the mol_index, res_index and spin_index arguments. All parts of relax which
modify the data pipe's molecule, residue and spin data structure (the generic_fns.mol_res_spin
functions and test suite) call these two functions as needed. Two auxiliary functions
spin_id_variants() and spin_id_variants_elim() have been added to create all possible matching spin
ID strings for a given spin (the second created IDs strings which should no longer exist).

The speed ups from this change are significant. On one system, the system and unit tests decrease
from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from 330.7s/17.4s to 258.9s/15.4s.

In addition, the pipe argument has been added to the generic_fns.mol_res_spin functions
create_molecule(), create_residue(), create_pseudo_spin() and create_spin(). Also, the molecule
name will now always be a string! Previously this was allowed to be an integer. This is needed for
the private metadata functions to operate correctly. A number of unit tests have been updated for
the changes.