generateTPsLibrary: Obtain transformation products (TPs) from a library

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Obtain transformation products (TPs) from a library

Description

Automatically obtains transformation products from a library.

Usage

generateTPsLibrary(
  parents = NULL,
  TPLibrary = NULL,
  generations = 1,
  skipInvalid = TRUE,
  prefCalcChemProps = TRUE,
  neutralChemProps = FALSE,
  neutralizeTPs = FALSE,
  matchParentsBy = "InChIKey",
  matchGenerationsBy = "InChIKey",
  calcSims = FALSE,
  fpType = "extended",
  fpSimMethod = "tanimoto"
)

Arguments

parents	The parents for which transformation products should be obtained. This can be (1) a suspect list (see suspect screening for more information), (2) the resulting output of screenSuspects or (3) a compounds annotation object. In the former two cases, the suspect (hits) are used as parents, whereas in the latter case all candidates are used as parents. If NULL then TPs for all parents in the library are obtained.
TPLibrary	If NULL, a default PubChem based library is used. Otherwise, TPLibrary should be a data.frame. See the details below.
generations	An integer that specifies the number of transformation generations. TPs for subsequent iterations obtained by repeating the library search where the TPs from the previous generation are considered parents.
skipInvalid	If set to TRUE then the parents will be skipped (with a warning) for which insufficient information (e.g. SMILES) is available.
prefCalcChemProps	If TRUE then calculated chemical properties such as the formula and InChIKey are preferred over what is already present in the parent suspect list. For efficiency reasons it is recommended to set this to TRUE. See the ⁠Validating and calculating chemical properties⁠ section for more details.
neutralChemProps	If TRUE then the neutral form of the molecule is considered to calculate SMILES, formulae etc. Enabling this may improve feature matching when considering common adducts (e.g. [M+H]+, [M-H]-). See the ⁠Validating and calculating chemical properties⁠ section for more details.
neutralizeTPs	If TRUE then all resulting TP structure information is neutralized. This argument has a similar meaning as neutralChemProps. This is defaulted to TRUE for prediction algorithms, as these may output charged molecules. NOTE: if neutrlization results in duplicate TPs, i.e. when the neutral form of the TP was also generated by the algorithm, then the neutralized TP will be removed.
matchParentsBy	A character that specifies how the input parents are matched with the data from the TP library. Valid options are: "InChIKey", "InChIKey1", "InChI", "SMILES", "formula", "name". If the parent from the TP library is matched with multiple input parents then only the first is considered.
matchGenerationsBy	Similar to matchParentsBy, but specifies how parents/TPs are matched when generations>1.
calcSims	If set to TRUE then structural similarities between the parent and its TPs are calculated. A minimum similarity can be obtained by using the filter method. 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.

Details

This function uses a library to obtain transformation products. This function is called when calling generateTPs with algorithm="library".

By default, a library is used that is based on data from PubChem. However, it also possible to use your own library.

An important advantage of this algorithm is that it provides structural information for generated TPs. However, this also means that if the input is from a parent suspect list or screening then either SMILES or InChI information must be available for the parents.

Value

The TPs are stored in an object derived from the transformationProductsStructure class.

TP libraries

The TPLibrary argument is used to specify a custom TP library. This should be a data.frame where each row specifies a TP for a parent, with the following columns:

• parent_name and TP_name: The name of the parent/TP.

• parent_SMILES and TP_SMILES The SMILES of the parent/TP structure.

• retDir The retention direction of the TP compared to its parent: ‘⁠-1⁠’ (elutes before), ‘⁠1⁠’ (elutes after) or ‘⁠0⁠’ (elutes similarly or unknown). If not specified then the log P values below may be used to calculate retention time directions. (optional)

• parent_LogP and TP_LogP The log P values for the parent/TP. (optional)

• LogPDiff The difference between parent and TP Log P values. Ignored if both parent_LogP and TP_LogP are specified. (optional)

Other columns are allowed, and will be included in the final object. Multiple TPs for a single parent are specified by repeating the value within parent_ columns.

Validating and calculating chemical properties

Chemical properties such as SMILES, InChIKey and formula in the parent suspect list are automatically validated and calculated if missing/invalid.

The internal validation/calculation process performs the following steps:

• Validation of SMILES, InChI, InChIKey and formula data (if present). Invalid entries will be set to NA.

• If neutralChemProps=TRUE then chemical data (SMILES, formulae etc.) is neutralized by (de-)protonation (using the --neutralized option of OpenBabel). An additional column molNeutralized is added to mark those molecules that were neutralized. Note that neutralization requires either SMILES or InChI data to be available.

• The SMILES and InChI data are used to calculate missing or invalid SMILES, InChI, InChIKey and formula data. If prefCalcChemProps=TRUE then existing InChIKey and formula data is overwritten by calculated values whenever possible.

• The chemical formulae which were not calculated are verified and normalized. This process may be time consuming, and is potentially largely avoided by setting prefCalcChemProps=TRUE.

• Neutral masses are calculated for missing values (prefCalcChemProps=FALSE) or whenever possible (prefCalcChemProps=TRUE).

Note that calculation of formulae for molecules that are isotopically labelled is currently only supported for deuterium (2H) elements.

This functionality relies heavily on OpenBabel, please make sure it is installed.

Note

When the parents argument is a compounds object, the candidate library identifier is used in case the candidate has no defined compoundName.

References

\addCitations

rcdk1

\insertRef

OBoyle2011patRoon

See Also

generateTPs for more details and other algorithms.

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.