BROOD 4.2.0

New Features

• BROOD has been rewritten to take advantage of newly released API and functionality in Bioisostere TK. This ensures that the results from the BROOD application are consistent with those from Bioisostere TK.

• Some flags have been modified for more consistency with the toolkit and other applications. Old flags continue to be functional unless they are REMOVED. A complete list of added and REMOVED flags can be found in the following table. The list of all existing flags could be looked up by running brood –help all in BROOD CLI app.

OLD BROOD	NEW BROOD
-qMol, -queryMol	-in
-queryFrag	REMOVED
-prot, -select	REMOVED
-noqueryprot	-ignoreProtein
-noqueryselectprot	-ignoreSelectionProtein
-csv	REMOVED
-maxFrag	REMOVED
-hitlistProt	REMOVED
-info	REMOVED
-format	-out
-dots	REMOVED
-quickLook (bool)	-quickLook (int) - Old Flag REMOVED
-ET, -linkonly	-scoreType rocs/et/linkonly - Old Flags REMOVED
-sdTag	REMOVED
-interval , -hitinterval	REMOVED
-ringOnly (string->true, none, false,[1,12])	-ringOnly (int [-2,12]) - true -> (-2), none -> (-1), false -> (0)
-attachColor	REMOVED
-attachFrag	REMOVED
-maxHit	-maxHits
-attachmentCutoff	-attachCutoff
-forcefield	REMOVED
-	-buildType (2d, noopt3d, optimized)
-attachmentScale	-attachScale
-title	REMOVED
-fromCT	REMOVED
-fileChrg (bool)	-chargeType (mmff94, fileChrg) - Old Flag REMOVED
-	-deltaLocalStrain

• vBROOD has been updated to work with OEDesignUnit contained in .oedu files for both active site and selectivity proteins. Molecule file formats, such as .oeb files, for proteins are no longer supported.

• Two new parameters have been added to both BROOD and vBROOD:

  • -quickLook: Has been changed from being a boolean to an integer option, enabling users to perform timed searches.

  • -deltaLocalStrain: Enables filtering based on relative local strain, instead of absolute local strain.

• The naming pattern of output files has been changed. The following files are now created as a result of a BROOD run:

  1. brood_log.txt: the log file

  2. brood_parm.txt: the param file

  3. brood_hitlist_rpt.csv: the hitlist report file

  4. brood_removed_rpt.csv: the removed hits report file

  5. brood_hitlist.oeb.gz: the hitlist

  6. brood_removed.oeb.gz: the removed hitlist

  In addition, the following two files are generated when the run is initiated from vBROOD:

  • brood_info.txt: the info file

  • brood_query.oeb.gz: a copy of the ran query

Related Toolkit Information

Bioisostere TK 4.2.0

New Features

• The new class OECPDDatabase has been added as a preliminary API, which can be used to perform 2D similarity comparisons between a Brood hit list and an external compound database.

• Eight new overloads have been added to the existing OECreateBroodQuery function. The new overloads extend the API for query generation in the presence of an active site protein and/or a selectivity protein. Additionally, there are new overloads to create a bridging query between two molecules.

• The following new methods have been added to OEHitlistBuilder:

  • GetRemovedHits

  • GetFailedCount

  • TrimHitlist

  • GetTrimmedCount

• The Build method in the OEHitlistBuilder has been expanded to accept an OETracerBase as an optional argument.

• The following new methods have been added to OEBroodHit:

  • GetBuildStatus

  • GetDeltaLocalStrain

Minor Bug Fixes

• Some memory management issues have been fixed in AddScores of the OEHitlistBuilder class.

• The OEBroodScore returned from the Overlay calculation now always contains the fragment, irrespective of whether the overlay was a success.

• The GetFrags method in the OEBroodDBPacket now properly returns an empty iterator if there are no fragments in a packet.

• The SetupRef method in OEFragOverlay is now substantially faster for subsequently initializing it with new reference fragments.

• The Init method in OEDBReader is now returning an unsigned int (instead of bool), reflecting the OEBioisostere OEBroodStatusCode Success or other error codes for database initialization.