Automatically obtains transformation products from a library.
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"
)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.
If NULL, a default PubChem based library is
used. Otherwise, TPLibrary should be a data.frame. See the details below.
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.
If set to TRUE then the parents will be skipped (with a warning) for which insufficient
information (e.g. SMILES) is available.
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.
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.
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.
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.
Similar to matchParentsBy, but specifies how parents/TPs are matched when
generations>1.
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).
The type of structural fingerprint that should be calculated. See the type argument of the
get.fingerprint function of rcdk.
The method for calculating similarities (i.e. not dissimilarity!). See the method argument
of the fp.sim.matrix function of the fingerprint package.
The TPs are stored in an object derived from the transformationProductsStructure class.
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.
When the parents argument is a compounds object, the candidate library identifier
is used in case the candidate has no defined compoundName.
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.
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.
rcdk1
OBoyle2011patRoon
generateTPs for more details and other algorithms.