Significantly sped up filtering and minor bug fixes #51
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… functionality added back
maylinnp
requested review from
diogomart,
nbruciaferri and
althea-hansel
and removed request for
nbruciaferri
diogomart
approved these changes
Oct 9, 2024
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Main change:
Cleaned up the method (
_generate_result_filtering_query) that writes the database filtering query, and restructured it completely. Previously when filtering for interactions, the query would do multiple complete scans of the interactions/interaction_bitvector table. This is why filtering took even longer in 2.0.0 once it used the "long-skinny" Interactions table, as this table is significantly longer than the interaction_bitvector table. Instead it now uses CASE statements to evaluate interaction combinations, and scans the Interactions table only once.The queries for all the different filters were fully or partially re-written to support the new format. A few methods were added to support this new query style such as pre-formatting filters so they are easily concatenated into a query string. A lot of specialized functionality was also taken out of the main filtering method and made into separate methods, including ligand clustering, and complex methods related to filtering for the chemical composition of the ligand.
A few extra indices were added to the interactions and results table.
Minor changes:
The documentation was updated to reflect the new changes, as well as fixing some bugs in the presentation of the readthedocs (needed to mock a module to display the full RingtailCore contents including objects and methods). I also updated the installation and testing instructions to include conda-forge (new), and made it more clear the differences between pip, conda-forge, and source code installation.
There was a bug in the API method
drop_bookmarkwhich would make Ringtail freeze, this was fixed.The last big bug fix was how ligand filter values are handled when using the Ringtail CLI. If the ligand filters were supplied with more than one value, it would not append them to a list but instead use the last written value. This was fixed, as well as the format for
ligand_substruct_poswas changed to support multiple filter values.