FastROCS TK 1.8.2

New features

• Alternative starting points in FastROCS TK have been extended to now include OEFastROCSOrientation.AsIs and OEFastROCSOrientation.InertialAtColorAtoms.

  • OEFastROCSOrientation.AsIs presumes that the query and the database molecules are already correctly aligned in space (perhaps through docking), so a single optimization per query-database molecule pair is carried out.

  • OEFastROCSOrientation.InertialAtColorAtoms translates each database molecule to each color atom of the query molecule and optimizes for 4 inertial poses at each translation. This method can be used with both shape-only searches and combo searches. The only requirement is that the query molecule must have color atoms; otherwise, the search will throw a warning and default to inertial starts.

  See OEFastROCSOrientation and OEShapeDatabaseOptions.SetInitialOrientation for more information.

• The following new getter methods have been added to OEShapeDatabaseOptions for retrieving the number of starts for the relevant method:

  • OEShapeDatabaseOptions.GetNumUserStarts

  • OEShapeDatabaseOptions.GetNumColorAtomStarts

  • OEShapeDatabaseOptions.GetNumHeavyAtomStarts

  • OEShapeDatabaseOptions.GetNumStarts

  OEShapeDatabaseOptions.GetNumStarts has also been overloaded for each alternative start option.

• A new argument has been added to OEShapeDatabase.Open to ensure that conformers are correctly handled when using OEFastROCSOrientation.AsIs.

  When using the new OEFastROCSOrientation.AsIs feature, the shape database must be opened with the additional argument set to OEFastROCSOrientation.AsIs.

  There is no need to alter existing scripts if the OEFastROCSOrientation.AsIs alternative starts feature is not being used since the default argument results in the correct execution path for all other use cases.

  See OEShapeDatabase.Open and OEFastROCSOrientation.AsIs for more information.

• A new argument has been added to OEShapeDatabaseScore.Constructors to correctly transform conformers to their resultant position when using OEFastROCSOrientation.AsIs.

  Generally, the constructor is not used in most scripts as the OEShapeDatabaseScore object is constructed internally when calling OEShapeDatabase.GetScores or OEShapeDatabase.GetSortedScores. Therefore, most users will not be affected by this change.

  If the OEShapeDatabaseScore constructor is used and OEFastROCSOrientation.AsIs is set, the constructor can be modified with the additional argument set to OEFastROCSOrientation.AsIs.

  The default value for the additional argument satisfies all other use cases, so no action is required.

  See OEShapeDatabaseScore.Constructors for more information.

Major bug fixes

• Previously, GPU memory limits were being reached for routine searches when using OEFastROCSOrientation.InertialAtHeavyAtoms, causing searches to default to OEFastROCSOrientation.Inertial. The improved alternative starts algorithm handles any number of starts without reaching GPU memory limits.

  Warning

  Performance will be affected by using large numbers of alternative starts.

• OEShapeDatabaseOptions.SetMaxOverlays now sets the number of overlay results to return per conformer. Previously, this was broken and was restricting the number of overlays to 1 per conformer regardless of its setting. OEShapeDatabaseOptions.SetMaxOverlays is now fixed and works correctly with OEShapeDatabaseOptions.SetMaxConfs, OEShapeDatabaseOptions.SetNumInertialStarts and alternative starts for both OEShapeDatabase.GetScores and OEShapeDatabase.GetSortedScores.

• Tversky calculations no longer overestimate the score of caged systems or conformer pairs where one conformer is much larger than the other.

Minor bug fixes

• A warning is now thrown if OEFastROCSOrientation.UserInertialStarts is set with OEShapeDatabaseOptions.SetInitialOrientation and OEShapeDatabase.GetScores or if OEShapeDatabase.GetSortedScores is called before OEShapeDatabaseOptions.SetUserStarts.

Documentation changes

• A tutorials page has been created that walks through features of FastROCS TK and gives detailed examples. The first tutorial gives step-by-step instructions on how to use alternative starts.

  If you have a specific feature that you would like in a tutorial, please contact support at support@eyesopen.com with the subject header FastROCS TK Tutorial Request.