OEMedChem TK 1.0.0

Licensing changes

• In preparation for new licensing requirements for OEMedChem TK, license checks have been added to OEMatchedPairAnalyzer constructor. Visit https://www.eyesopen.com/contact if you need a license for matched pair activities.

OEMedChem functionalities

This is the first official release of OEMedChem functionalities, previously released in beta form. An overview of its capabilities is provided below.

Matched molecular pair analysis

A powerful analysis engine and functions support the identification of matched molecular pairs that differ by both heavy-atom and hydrogen-atom substitutions. Additionally, the analyzer supports the ability to be saved and restored to disk or stream. The analyzer includes the following functions:

• OEMatchedPairAnalyzer

• OEMatchedPairApplyTransforms

• OEReadMatchedPairAnalyzer

• OEWriteMatchedPairAnalyzer

• OEMatchedPairAnalyzerOptions

• OEConfigureMatchedPairIndexOptions

• OESetupMatchedPairIndexOptions

Functions and classes are provided to allow extraction and inspection of transformations based on matched molecular pairs found during structure indexing as well as the specific matched pairs and data associated with those transformations:

• OEMatchedPair

• OEMatchedPairTransform

• OEMatchedPairGetTransforms

ChEMBL18 solubility data has been indexed with the matched pair analyzer to modify input structures according to the solubility transforms and to annotate modified structures with the net change in solubility data from ChEMBL:

• OEApplyChEMBL18SolubilityTransforms

Fragmentation and perception capabilities

The following functions are provided to return perceived regions for fragmentation strategies:

• OEGetBemisMurcko

• OEGetFuncGroupFragments

• OEGetRegionTypeName

• OEGetRegionType

• OEGetRingChainFragments

• OEGetRingLinkerSideChainFragments

Belief theory

Functions are provided to return information for belief theory usage based on [Muchmore-2008]:

• OECalculateComboBelief

• OECalculateETComboBelief

Similarity

Functions are provided to return the graph-edit similarity used in clustering BROOD hitlists:

• OECreateIDString

• OECreateIDStrings

Complexity measures

Functions are provided to return individual terms that make up the molecular complexity as defined by [Bertz-1981]:

• OEDetermineConnectiveComplexity

• OEDetermineElementalComplexity

• OEDetermineMolecularComplexity

• OEDetermineSymmetryComplexity

• OENormalMolecularComplexity

Functions are provided to return a ring complexity measure similar to that defined by [Gasteiger-1979]:

• OEDetermineRingComplexity

• OEGetRingValue

Functions are provided to return a measure of stereo complexity as defined by [Boda-2007]:

• OEDetermineStereoComplexity

• OENormalStereoComplexity

A function is provided to return a measure of the total molecular complexity, which is a sum of the provided individual complexity measures:

• OETotalMolecularComplexity

Minor bug fixes

• As a result of a minor bug fix in OEChem TK, OEDetermineStereoComplexity, OENormalStereoComplexity, and OENormalStereoComplexity functions might return slightly different values for molecules containing transition metals, lanthanides, or actinides.

Documentation changes

• New documentation code snippets for C++, Java, and C# have been added to demonstrate matched pair index creation, serialization, and deserialization.

• Examples have been updated to allow explicit specification of the mmpMinPairThreshold arguments for OEMatchedPairApplyTransforms and OEApplyChEMBL18SolubilityTransforms.

• Several molecular complexity functions that were inadvertently removed from the documentation have been re-added.

• The Matched Pair analysis and transformations example has been modified to reduce the amount of output that is typical for a general indexing activity.