Parameters to handle TP data with structural information

Source: R/utils-exported.R

Parameters used by generateTPs with algorithms that use structural information.

getDefTPStructParams(...)

Arguments

...

optional named arguments that override defaults.

Details

The following parameters can be configured:

  • calcLogP A character specifying whether log P values should be calculated with rcdk::get.xlogp (calcLogP="rcdk"), OpenBabel (calcLogP="obabel") or not at all (calcLogP="none"). The log P are values of parents and TPs are used for retention order calculation.

  • forceCalcLogP Force calculation of Log P values, even if already provided by the TP generation algorithm. This is primarily useful to obtain log P values that were consistently calculated with the same algorithm, as some algorithms may only partially output these values (e.g. not for parents).

  • forceCalcRetDir Force calculation of retention order directions, even if already provided by the TP generation algorithm. This is primarily intended for re-calculation of library TP data, which may have been calculated with different log P values.

  • minLogPDiff The minimum difference in log P values between a parent and its TPs to be considered eluting differently. This is used for retention order calculation.

  • calcSims If set to TRUE then structural similarities between the parent and its TPs are calculated. The filter method can be used to threshold structural similarities. This may be useful under the assumption that parents and TPs who have a high structural similarity, also likely have a high MS/MS spectral similarity (which can be evaluated after componentization with generateComponentsTPs).

  • fpType The type of structural fingerprint that should be calculated. See the type argument of the get.fingerprint function of rcdk.

  • fpSimMethod The method for calculating similarities (i.e. not dissimilarity!). See the method argument of the fp.sim.matrix function of the fingerprint package.

These parameters are passed as a named list as the TPStructParams argument to functions.

The getDefTPStructParams function generates such parameter list with defaults.

References

Guha R (2007). “Chemical Informatics Functionality in R.” Journal of Statistical Software, 18(6).

OBoyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011). “Open Babel: An open chemical toolbox.” Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-33 .