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.