generateTPsBioTransformer | R Documentation |
Uses BioTransformer to predict TPs
generateTPsBioTransformer(
parents,
type = "env",
generations = 2,
maxExpGenerations = generations + 2,
extraOpts = NULL,
skipInvalid = TRUE,
prefCalcChemProps = TRUE,
neutralChemProps = FALSE,
neutralizeTPs = TRUE,
calcSims = FALSE,
fpType = "extended",
fpSimMethod = "tanimoto",
MP = FALSE
)
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
|
type |
The type of prediction. Valid values are: |
generations |
The number of generations (steps) for the predictions. Sets the |
maxExpGenerations |
The maximum number of generations during hierarchy expansion, see below. |
extraOpts |
A |
skipInvalid |
If set to |
prefCalcChemProps |
If |
neutralChemProps |
If |
neutralizeTPs |
If |
calcSims |
If set to |
fpType |
The type of structural fingerprint that should be calculated. See the |
fpSimMethod |
The method for calculating similarities (i.e. not dissimilarity!). See the |
MP |
If |
This function uses BioTransformer to obtain transformation products. This function is called when calling generateTPs
with
algorithm="biotransformer"
.
In order to use this function the ‘.jar’ command line utility should be installed and specified in the
patRoon.path.BioTransformer
option. The ‘.jar’ file can be obtained via
https://bitbucket.org/djoumbou/biotransformer/src/master. Alternatively, the patRoonExt package can be
installed to automatically install/configure the necessary files.
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.
The TPs are stored in an object derived from the transformationProductsStructure
class.
BioTransformer
only reports the direct parent for a TP, not
the complete pathway. For instance, consider the following results:
parent –> TP1
parent –> TP2
TP1 –> TP2
TP2 –> TP3
In this case, TP3 may be formed either as:
parent –> TP1 –> TP2 –> TP3
parent –> TP2 –> TP3
For this reason, patRoon simply expands the hierarchy and assumes that all routes are possible. For instance,
Parent
/- -\
/- -\
- -
TP1 TP2
| |
| |
TP2 TP3
|
|
TP3
Note that this may result in pathways with more generations than defined by the generations
argument. Thus,
the maxExpGenerations
argument is used to avoid excessive expansions.
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.
generateTPsBioTransformer
uses multiprocessing to parallelize
computations. Please see the parallelization section in the handbook for
more details and patRoon options for configuration
options.
When the parents
argument is a compounds
object, the candidate library identifier
is used in case the candidate has no defined compoundName
.
rcdk1
\insertRefOBoyle2011patRoon
\insertRefDjoumbouFeunang2019patRoon
\insertRefWicker2015patRoon
generateTPs
for more details and other algorithms.
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