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Commits on Dec 20, 2023

• Merge pull request #53 from adalke/v3-dev

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Commits on Nov 28, 2023

• updated the version to 3.1

  adalke

  committed
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• updated for 3.1

  adalke

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• fixed drop index which was for the old schema; now uses the new schema

  adalke

  committed
  992d91a

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• added two indicies and a SQLite pragma; all of which Roche says helps with overall performance.

  adalke

  committed
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• fixed old code in propcat which still expected the argparse API instead of using click

  adalke

  committed
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• Added min_heavies_total_const_frag / --min-heavies-total-const-frag fragmentation option, and updated fragdb schema to v4

  adalke

  committed
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Commits on Nov 1, 2023

• In generate, added explanation for the search for a matching query/variable in the fragmentation of the input SMILES.

  adalke

  committed
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Commits on Oct 26, 2023

• In 'generate', updated the subquery generation code to also support 2- and 3-cut queries.

  adalke

  committed
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Commits on Oct 25, 2023

• Working on "generate" support when the query or constant has more than one attachment point. --subqueries still not working.

  adalke

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Commits on Sep 14, 2023

• first go at supporting multiple cuts during generate. Using it to bootstrap the full changes.

  adalke

  committed
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Commits on Sep 5, 2023

• removed debug code

  adalke

  committed
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Commits on May 31, 2023

• sticking a pin on the current code and calling it 3.0, without the b1.

  adalke

  committed
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Commits on Nov 11, 2022

• trying an improved generate query, along with some temporary debugging output.

  adalke

  committed
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Commits on Oct 18, 2022

• added 'random' option for --select-pair. Added 'better' as alias for 'quadratic', via a new SelectPairMethod() click type.

  adalke

  committed
  b3a947c

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• added --select-pair method to choose how to select a representative pair

  adalke

  committed
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• Also include the total execute time when reporting times. Improve timing print text.

  adalke

  committed
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• remove a lengthy query which is only used for user feedback and isn't part of the actual answer.

  adalke

  committed
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• (temporarily?) removing a sort when selecting a representative pair. Result is several times faster.

  adalke

  committed
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• simplified a SQL query by replacing an INNER JOIN with a more direct query

  adalke

  committed
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• removed debugging information about single/multi-threaded

  adalke

  committed
  11c8ee7

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• removed timing code

  adalke

  committed
  00574e4

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• added index 'pair_compound_ids' on pair (compound1_id, compound2_id) to improve 'generate' performance

  adalke

  committed
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• allow MMPDB_TIME_EXECUTE=1 to enable reporting+timing of SQL executes

  adalke

  committed
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• switch to approximate analyze before closing the merged database.

  adalke

  committed
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• disable sync and journaling during merge. Hope to get better performance.

  adalke

  committed
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• include the rule id in the rulecat output

  adalke

  committed
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Commits on Oct 8, 2022

• fix the SQL used to iterate over the rule environments. Had left out a WHERE clause so was getting a powerset

  adalke

  committed
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• get ruleenvcat --no-pairs to work, and add missing columns for SMARTS and pseudoSMILES

  adalke

  committed
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• updated 'fingerprint' references to SMARTS + pseudoSMILES

  adalke

  committed
  ea8fb3a

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• Updated 'transform --help' to reflect the change from an environment fingerprint to a SMARTS/pseudoSMILES

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• this is 3.0b1 (from 3.0a1).

  adalke

  committed
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• updated another use of old-style ".fragments" instead of 3.0-style ".fragdb"

  adalke

  committed
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• removed the apw mention in the README

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• updated --help to mmpdb 3.0

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