The 2017.Oct release introduces Shape TK version 2.0.0, which is completely redesigned with a new API that is more flexible and easily extended with new functionality. Shape TK version 2.0.0 is now thread-safe and is able to:
Preliminary testing of functionality from Shape TK version 2.0.0 indicates that overlay optimization is up to 10% faster than the 2017.Jun version.
A new torsion library has been added to Omega TK based on a probabilistic analysis of torsion angles in the Cambridge Structural Database (CSD) by Guba et al. [Guba-2016] This torsion library, which contains more than 500 entries, complements the existing torsion library, which is based mainly on analysis of structures found in the Protein Data Bank (PDB). Replacement of the existing library with the new library has four important effects on OMEGA’s performance:
The 2017.Oct release expands these toolkits’ ability to assemble sets of graphical objects in SVG images.
Images can present great deal of information very quickly, but those that try to convey too much information at once can look convoluted. The solution lies in generating interactive images that on the surface are simple but that can reveal extra information on request. This release allows users to mouse over simple images to view additional embedded information.
In the example below, the sequence-level depiction of a peptide is easily comprehensible due to its simplicity (see image below). The more detailed atomic-level representation of the amino acid components of the peptide can be revealed on mouse-over without cluttering the simplified view.
|Hover the mouse over any peptide circle||Hover the mouse over any residue circle or “Legend” label|
|cyclic trypsin inhibitor (PDB: 1JBL)||protein-ligand visualization (PDB: 3EQB)|
For more information, see the Generating Interactive SVG Images chapter of the OEDepict TK documentation.
The standard InChI format includes chemical normalization activity that results in round-trip structure alterations to a very high percentage of structures when unnormalized or when arbitrary input chemistry is used. Even the output of OEMolToInChI, which generates a nonstandard InChI and attempts to minimize structure normalizations, results in many changes to input chemical structures.
The following API has been added to increase the reporting capabilities of OEDepict TK:
The following API has been added to render labels associated with certain parts of the depicted molecule:
A new function, OEDrawText, has been added.
The constructor of the OEHighlightByLasso class now takes a parameter that determines the width of the “lasso” used for highlighting. The corresponding GetLineWidthScale and SetLineWidthScale methods have been added.
A new constructor has been added to the OEImageFrame class that generates a new image with equal padding around it.
A new function, OEWriteReportPageByPage, has been added.
A new constructor has been added to the OE2DPath class that copies and rotates an already existing path.
Objects that have been drawn in hidden SVG groups are no longer visible in other image file formats. For example, when adding hover text to atoms (using the OEDrawSVGHoverText function), the text will only be visible in SVG images when the mouse is moved over a displayed atom. If the image is written into any other image file format, the hover text is no longer visible.
The following example scripts have been reworked to enable access to additional features of FastROCS TK:
Tversky sampling, shape-only searches, and basic alternative starting points can be accessed via the client without having to rerun or modify the server/proxy scripts. Users can submit a query as usual from the client adding the relevant flags. The new flags are:
- --alternativeStarts [inertialAtHeavyAtoms|inertialAtColorAtoms|subrocs|random [N]]
These scripts are not backwards compatible. The behavior of running server/proxy/client scripts with mismatched versions is undefined. In order to use the new client flags, ensure that the server and proxy scripts are also updated to this version.
Warnings that are thrown for Tversky and Tanimoto scores greater than 1.0 have been simplified. Messages showing the actual Tversky/Tanimoto calculation are now Debug-level messages.
The following new API has been added to customize peptide depiction:
The main feature is that OEDrawPeptide now can generate interactive SVG images where the amino acid components of the compact peptide representation are depicted on mouse-over.
Hover over any circle below
Example of interactive SVG image generated by OEDrawPeptide
The following new API has been added to customize active site depiction:
These new options allow users to generate interactive SVG images when calling the OERenderActiveSite function.
Hover over the legend label or any circle representing a residue
Example of interactive SVG image generated by OERenderActiveSite
The performance of the OEGetFPCoverage function has been improved.
The following functions have been added to help generate consistent command line interfaces for 2D molecule similarity examples and utilities:
Generated interfaces include correspondence between each command line option and its related entry point in OEGraphSim TK.
The change in the serialized data format requires that any existing saved matched pair analyzer index files be regenerated if they were created using a previous OpenEye Toolkit version. Indices serialized from this version cannot be read by older versions.
A set of classes that were previously derived from OEMolFunc1 are now derived from OEMolFunc2. With this change, all of these classes now provide analytical Hessians and can be optimized with OENewtonOpt. The list of classes is as follows:
Two of the OEForceField methods, OEMolPotential::OEForceField::Add and OEMolPotential::OEForceField::Remove, have been deprecated and replaced by more user-friendly methods in the derived classes OEGenericFF and OEGenericFF2.
The following table shows the older, deprecated functions and their replacements:
A new method, OEGenericFF::GetComponents, has been added that gives access to the function components of the force field.
The Shape TK has been completely redesigned to make the library thread-safe, to make the library more flexible to use, and to allow the API to be easily extended with additional functionality.
A new class, OEShapeGridOptions, has been added to define options related to grid-based method evaluations.
A new class, OEAnalyticOptions, has been added to define options related to analytic method evaluations.
A new class, OEOverlapPrep, has been added that can be used to prepare molecules for shape and/or color calculations.
A new class, OEOverlayOptions, has been added that sets all options for overlay optimization using OEOverlay. OEOverlayOptions provides flexibility to optimize based on shape or color or both, to choose any method for shape or color calculation, and to optimize overlap or Tanimoto individually for shape and color.
A new class, OEROCS, has been added that can be used to generate hits from a database on a reference system that can be a molecule, grid, or shape query. OEROCS provides top hits based on flexible scoring criterion.
Three overloads of a new function, OEROCSOverlay, have been added to provide the best hit between a pair of molecules.
New unary predicates have been added to terminate a hit search calculation using OEROCS:
With the introduction of the new API classes in Shape TK, several previously existing classes have been deprecated. The following table shows the deprecated classes and their replacements:
|Deprecated Class||New Class|
|OEShape::OEOverlap||OEExactShapeFunc OEGridShapeFunc OEAnalyticShapeFunc|
|OEShape::OEColorOverlap||OEExactColorFunc OEGridColorFunc OEAnalyticColorFunc|
With the introduction of the new API, several obsolete functionalities have been removed. These functionalities were added in the early development days of Shape TK and are no longer deemed useful. Methods related to such functionality, contained within the deprecated classes, are now ignored. The list of methods that fall into this category, with their current behavior, is as follows: