ZINC ideas: Difference between revisions
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(Created page with "<pre> Materialized view for Bioactivity Materialized view for all bioactivity allows for the tables to still remain separate, but the data to be queryable from a single sour...") |
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Latest revision as of 17:02, 18 March 2014
Materialized view for Bioactivity Materialized view for all bioactivity allows for the tables to still remain separate, but the data to be queryable from a single source. However, this cannot be fast on commit, so DBMS_MVIEW needs to be called manually – via a trigger (on update of any of the 4 tables) or on a cron. CREATE MATERIALIZED VIEW "CHEMAXON"."BIOACTIVITY” BUILD IMMEDIATE USING INDEX REFRESH ON DEMAND FORCE WITH PRIMARY KEY DISABLE QUERY REWRITE AS SELECT BIO_NUMBERS.ID_STRUC_FK, TARGET.TARGET_NAME, BIO_NUMBERS.IC50, BIO_NUMBERS.CHEMBL_ID, BIOACTIVITY_TYPE.ACTIVITY_DESC, TARGET_SRC.SOURCE, TARGET_SRC.FREE_FLAG, TARGET.SWISSPROT, TARGET.CHEMBL, TARGET.UNIPROT, TARGET.TARGET_SRC_FK FROM BIO_NUMBERS INNER JOIN TARGET ON BIO_NUMBERS.TARGET_FK = TARGET.TARGET_ID INNER JOIN BIOACTIVITY_TYPE ON TARGET.ACTIVITY_TYPE = BIOACTIVITY_TYPE.BIOACT_TYPE_ID INNER JOIN TARGET_SRC ON TARGET.TARGET_SRC_FK = TARGET_SRC.TARGET_SRC_ID; Protomer Table population Program written in Groovy and implemented via IJC because it was easier. In production this will be done via PL/SQL. Basic program: For molecule in Structures table: Calculate all pKas between 4.5 and 9 Insert original structure into Protomer table, with PH_REF=1 If pKa exists between 4.5 and 9 then Sort pKas in order. Determine halfway point between 4.5, pKa1, pKa2....pKan, 9. For each halfway point, calculate the major microspecies [check that microspecies is not the same as the original] Toggle PH_HI/MID/LO=1 for each range halfway point falls in Put pH of halfway point into PH_MAX_OCCUPANCY column Insert microspecies and relevant data into Protomer table The code is protomer_population.txt in the ZINC dropbox. Things to include in ZINC13 Common name searching (captopril, viagra, etc)