http://wiki.docking.org/index.php?action=history&feed=atom&title=Oracle_scraps 2026-04-07T04:42:07Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Oracle_scraps&diff=7260&oldid=prev 2014-03-18T17:01:49Z

<p>Created page with &quot;= Trigger for calculating fields upon structure insert = &lt;pre&gt; Basic BIOACTIVITY call based on current ZINC infrastructure (example): select ID_STRUC_FK from BIOACTIVITY whe...&quot;</p> <p><b>New page</b></p><div>= Trigger for calculating fields upon structure insert =<br /> &lt;pre&gt;<br /> <br /> Basic BIOACTIVITY call based on current ZINC infrastructure (example):<br /> select ID_STRUC_FK from BIOACTIVITY where TARGET_NAME=’Anandamide amidohydrolase’ AND ACTIVITY_DESC=’Binding, 1uM’;<br /> *Free flag as well?*<br /> AND FREE_FLAG=1<br /> <br /> Populating PROTOMER with chemical terms:<br /> <br /> ZINC descriptors as Oracle calls. Putting all these on PROTOMER for searching (also on STRUCTURES, but for benchmarking, pull from PROTOMER);<br /> update PROTOMER<br /> MW:<br /> LogP<br /> Net Charge<br /> Rotatable bonds<br /> PSA<br /> H Donors<br /> H Acceptors<br /> PolDesolv<br /> ApolarDesolv<br /> <br /> <br /> PL/SQL calls for various Oracle/Cartridge components based on current ZINC architecture:<br /> <br /> Structure searching - feed in SMILES<br /> select STRUCTURES_ID from STRUCTURES/PROTOMER where [call] =1<br /> jc_compare(STRUCTURE, ‘smiles’, options) Options separated by space<br /> Similarity<br /> ‘t:i simThreshold:0.9’ (or dissimilarityThreshold)<br /> Similarity metric<br /> dissimilarity<br /> Query by ‘t:t dissimilarityThreshold:0.6 dissimilarityMetric:tversky;0.3,0.7’<br /> duplicate/identity (flag stereo matching)<br /> ‘t:d’ duplicate<br /> index only (fingerprint, no atom matching) Speed difference?<br /> ‘t:na’<br /> substructure<br /> ‘t:s’ (substructure search is default, doesn’t need to be specified)<br /> superstructure<br /> ‘t:u’<br /> fragment (query and target must have same heavy atom network for matching, all features otherwise treated as substructure).<br /> ‘t:f’ <br /> toggle options to consider: <br /> max hit count<br /> maxHitCount:x<br /> max time <br /> maxTime:x (x in milliseconds, default is unlimited)<br /> early results (returned block size, provides fast results as first 100 returned for page, then can continue searching while visualization calls present the webpage)<br /> fingerprint type ‘descriptorName’ - requires additional structure index fields<br /> Different fingerprints can be generated through the addMd ALTER INDEX parameter and can be selected for use with descriptorName option<br /> alter index jcxnci parameters(&#039;addDfltMdConf=ECFP&#039;) [added]<br /> CF (default?), PF, BCUT, ECFP<br /> absolute or exact stereo, stereo ignored, required, etc.<br /> absoluteStereo:x<br /> radicals, isotopes, charges (ignored, exact, default)<br /> double bond stereo<br /> doubltBondStereo:A<br /> matching of implicit H<br /> polymer options (if Marvin applet input provided)<br /> tautomer searching: table level? Ability to specify yes or no?<br /> To be used together with duplicate search (t:d). For jchem index operations, tdf:y option has to be set for the jchem index or the underlying JChem table.<br /> If y, generic tautomer of query and target used in search.<br /> chemical terms filter with substructure to apply things like MW, donorcount, ring count, and of the bajillion chemical terms offered.<br /> Comparison: chemical terms as part of search, or part of INTERSECT from another table?<br /> Combine with filterquery to limit number of compounds searched? Compare<br /> R-atoms/homology groups if Marvin applets used to input structure<br /> Bioactivity: Materialized view of biological activity. Relevant columns for searching:<br /> ID_STRUC_FK: (Structure IDs)<br /> TARGET_NAME<br /> IC50<br /> CHEMBL_ID<br /> ACTIVITY_DESC: binding, etc<br /> SOURCE<br /> FREE_FLAG: 1/0<br /> SWISSPROT<br /> CHEMBL<br /> UNIPROT<br /> PH ranges of protomers<br /> All 1/null flags on relevant columns: PH_HI/MID/LO. Original structure is PH_REF. If the compound is a protomer, the pH of max occupancy will be in PH_MAX_OCCUPANCY.<br /> ZINC ID<br /> Vendor<br /> CATALOG_REF: VENDOR_NAME for CAT_REF_ID<br /> CATALOG: (has items) CAT_REF_ID_FK to link vendors, ID_STRUC_FK to link to structures.<br /> <br /> Oracle set operators read left to right unless parentheses say otherwise. INTERSECT ideal call vs. constructing AND sets. Oracle evaluates expressions inside parentheses before evaluating those outside.<br /> - put all other conditions in paranthesis, then structure search based on that returned set.<br /> <br /> Precedence using filterquery!<br /> <br /> SELECT count(*) FROM nci_10m WHERE jc_compare(structure, &#039;c1ccccc1&#039;, &#039;sep=! t:s!filterQuery:select rowid from nci_10m where projid = 502&#039;) = 1<br /> <br /> Build into filterquery all other statements, using INTERSECT<br /> <br /> Evaluating compounds using chemical terms<br /> select jc_evaluate_x(‘input’, ‘chemTerms:tautomers() outFormat:smiles’) from TABLE<br /> useful for structure check before search?<br /> <br /> <br /> Overall Call Structure<br /> <br /> Substructure only search:<br /> select STRUCTURES_ID from STRUCTURES where jc_compare(STRUCTURE, ‘query’, ‘t:s’)=1<br /> <br /> Addition of filterquery utility (5.8):<br /> select STRUCTURES_ID from STRUCTURES where jc_compare(STRUCTURE, ‘query’, ‘sel=! t:s!filterQuery:select logic’)=1<br /> <br /> <br /> Thoughts<br /> Family clustering on results page. eg instead of showing 25 stereoisomers, show a non-stereo compound and give it a ‘stack’ image with text saying “25 Stereoisomes”. Hover over and pop-up shows the isomers, then functions as normal. <br /> Subset definitions<br /> Purchasability definitions (popup over label?)<br /> <br /> &lt;/pre&gt;</div>

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