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[WIP] Fragdb proposal #39

Merged
merged 14 commits into from
Dec 20, 2023
Merged

[WIP] Fragdb proposal #39

merged 14 commits into from
Dec 20, 2023

Commits on Oct 12, 2021

  1. initial version of a fragment database. This uses unnormalized fragme… 

    …nt SMILES strings.
    @adalke
    adalke committed Oct 12, 2021
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  2. schema for the unnormalized fragdb

    @adalke
    adalke committed Oct 12, 2021
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Commits on Oct 13, 2021

  1. added comment about things to try for better performance

    @adalke
    adalke committed Oct 13, 2021
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  2. remove "fraginfo" output, use "input.fragdb" if no filename given, su… 

    …pport using a fragdb to index, fix fragment schema bugs
    @adalke
    adalke committed Oct 13, 2021
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Commits on Oct 15, 2021

  1. updated the schema based on the one generated by SQLAlchemy through S… 

    …QLite
    @adalke
    adalke committed Oct 15, 2021
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  2. switched to use dataclasses for the fragment_types, and cleaned-up an… 

    …d somewhat automated the SQL calls for fragdb
    @adalke
    adalke committed Oct 15, 2021
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  3. added comment about the location of three different fragment data con… 

    …figuration places
    @adalke
    adalke committed Oct 15, 2021
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  4. compatibility with Python 3.7

    @adalke
    adalke committed Oct 15, 2021
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  5. updated smifrag to work with record.fragmentations instead of record.… 

    …fragments
    @adalke
    adalke committed Oct 15, 2021
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Commits on Oct 26, 2021

  1. removed support for the old 'fragments' format. If "fragment" doesn't… 

    … have a "-o" then create a name based on the input.
    @adalke
    adalke committed Oct 26, 2021
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  2. report when using a default output filename

    @adalke
    adalke committed Oct 26, 2021
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  3. updated comments

    @adalke
    adalke committed Oct 26, 2021
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  4. renamed fragment_io to fragment_db

    @adalke
    adalke committed Oct 26, 2021
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  5. moved 'relabel' from fragment_db (nee fragment_io) to index_algorithm… 

    …, which is where it's actually used.
    @adalke
    adalke committed Oct 26, 2021
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