GraphSim TK 2.0.0

New features

• Adding two new fingerprint types:

  • The OEFPType::Circular fingerprint is generated by exhaustively enumerating all circular fragments grown radially from each heavy atom of the input molecule up to the given radius. (See more details in Circular Fingerprint section and OEMakeCircularFP function)

  • The OEFPType::Tree fingerprint is generated by exhaustively enumerating all unique trees of a molecular graph. (See more details in Tree Fingerprint section and OEMakeTreeFP function)

• Adding the OEGetFPCoverage function that allows access to the patterns that are encoded into a fingerprint. (See example in Fingerprint Coverage chapter)

• Adding the OEGetFPOverlap function that returns the common patterns of two molecules based on their fingerprint. (See example in Fingerprint Overlap chapter)

• Adding version numbers for fingerprints that prevents the comparison of fingerprints that are generated by different versions of the algorithm. (See more details in Fingerprint version number section and OEGetFingerPrintVersion and OEGetFingerPrintVersionString functions)

• Adding three more atom typing options that can be used when generating path, circular or tree fingerprints:

  • OEFPAtomType::HCount

  • OEFPAtomType::EqHBondAcceptor

  • OEFPAtomType::EqHBondDonor

• Adding the OEGetFPType function that generates a fingerprint type from a valid string representation.

• Adding the OEFPTypeParams that allow to extract the parameters of the fingerprint types from their string representation:

• Adding 9 code examples in four different languages (C++, Python, Java, C#) that demonstrate the usage of fingerprints and functionalities.

Documentation changes

• Adding figures to the Fingerprint chapter that demonstrate how the OEFPType::Circular, OEFPType::Path and OEFPType::Tree fingerprints are generated.

• Adding a new chapter Fingerprint Types, that gives more details about fingerprint types.

• Adding two new examples to the Storage and Retrieval chapter that demonstrate how to store and retrieve fingerprints in SDF files.

• Rewriting part of the User-defined Fingerprint chapter, since the two new fingerprint types can also be customized.

• Adding two new chapters:

  • Fingerprint Coverage chapter

  • Fingerprint Overlap chapter