Metabolomics benchmarks update

benchmarks.R

# install.packages("microbenchmark")
# install.packages("plyr")
# 
# install.packages("rcdk")
# install.packages("OrgMassSpecR")
# install.packages("CHNOSZ")
# 
# BiocManager::install("Rdisop")
# BiocManager::install("MetaboCoreUtils")
# 
# BiocManager::install("ChemmineR")
# BiocManager::install("ChemmineOB")
# 
# BiocManager::install("enviPat")


## These require loading the packages explicitly
library(plyr)

library(CHNOSZ)
library(enviPat)
library(MetaboCoreUtils)
library(rcdk)
library(ChemmineR)
#library(ChemmineOB)
library(OrgMassSpecR)
library(Rdisop)

data(isotopes)




# original
# https://github.com/CDK-R/cdkr/blob/master/rcdk/R/formula.R
# get.formula <- function(mf, charge=0) {
#   
#   manipulator <- get("mfManipulator", envir = .rcdk.GlobalEnv)
#   if(!is.character(mf)) {
#     stop("Must supply a Formula string");
#   }else{
#     dcob <- .cdkFormula.createChemObject()
#     molecularformula <- .cdkFormula.createFormulaObject()
#     molecularFormula <- .jcall(manipulator,
#                                "Lorg/openscience/cdk/interfaces/IMolecularFormula;",
#                                "getMolecularFormula",
#                                mf,
#                                .jcast(molecularformula,.IMolecularFormula),
#                                TRUE);
#   }
#   
#   D <- new(J("java/lang/Integer"), as.integer(charge))
#   .jcall(molecularFormula,"V","setCharge",D);
#   object <- .cdkFormula.createObject(.jcast(molecularFormula,.IMolecularFormula));
#   return(object);
# }


mfManipulator    <- J("org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator")
silentchemobject <- J("org.openscience.cdk.silent.SilentChemObjectBuilder")


#' Rewrite the formual object and directly access Java
#'
get.formula2 <- function(mf) {
  
  formula <- mfManipulator$getMolecularFormula(
    "C2H3", 
    silentchemobject$getInstance())
  
  mfManipulator$getMass(formula)
  
}

#' Add type hints
#'
get.formula3 <- function(mf) {
  builderinstance <- .jcall(silentchemobject,
                           "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;",
                           "getInstance")
                           
  formula  <- .jcall(mfManipulator,
         "Lorg/openscience/cdk/interfaces/IMolecularFormula;",
         "getMolecularFormula",
         mf,
         builderinstance);
  
  mfManipulator$getMass(formula)
  
}


#' Add type hints
#'
get.formula4 <- function(mf) {
  builderinstance <- .jcall(silentchemobject,
                            "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;",
                            "getInstance")
  
  formula  <- .jcall(mfManipulator,
                     "Lorg/openscience/cdk/interfaces/IMolecularFormula;",
                     "getMolecularFormula",
                     mf,
                     builderinstance);
  
  .jcall(mfManipulator,
         "D",
        "getMass",
        formula)
}



benchmark <- microbenchmark::microbenchmark(
  MetaboCoreUtils = MetaboCoreUtils::calculateMass("C2H6O"),
  rcdk = rcdk::get.formula("C2H6O", charge = 0)@mass,
  rcdk2 = get.formula2("C2H6O"),
  rcdk3 = get.formula3("C2H6O"),
  rcdk4 = get.formula4("C2H6O"),
  Rdisop = Rdisop::getMolecule("C2H6O")$exactmass,
  ChemmineR = ChemmineR::exactMassOB(ChemmineR::smiles2sdf("CCO")),
  OrgMassSpecR = OrgMassSpecR::MonoisotopicMass(formula = OrgMassSpecR::ListFormula("C2H6O)"), charge = 0),
  
  CHNOSZ = CHNOSZ::mass("C2H6O"),
  enviPat = enviPat::isopattern(isotopes, "C2H6O", charge=FALSE, verbose=FALSE)[[1]][1,1]
  , times=1000L)


masses <- c(
  MetaboCoreUtils=MetaboCoreUtils::calculateMass("C2H6O"),
  rcdk=rcdk::get.formula("C2H6O", charge = 0)@mass,
  Rdisop=Rdisop::getMolecule("C2H6O")$exactmass,
  #ChemmineR=ChemmineR::exactMassOB(ChemmineR::smiles2sdf("CCO")),
  OrgMassSpecR=OrgMassSpecR::MonoisotopicMass(formula = OrgMassSpecR::ListFormula("C2H6O)"), charge = 0),
  CHNOSZ=CHNOSZ::mass("C2H6O"),
  enviPat=enviPat::isopattern(isotopes, "C2H6O", charge=FALSE, verbose=FALSE)[[1]][1,1]
)



options(digits=10)

t(t(sort(masses)))


summary(benchmark)[order(summary(benchmark)[,"median"]) , ]


clipr::write_clip(as.data.frame(summary(benchmark)[order(summary(benchmark)[,"median"]) , ] ))

results.txt

              expr       min         lq         mean     median         uq
1  MetaboCoreUtils    69.479   122.8465   154.049427   139.6495   156.2700
10         enviPat    83.250   143.0935   170.429197   160.5360   179.6570
5            rcdk4   175.889   228.8605   324.182735   271.2955   327.7135
8     OrgMassSpecR   249.287   333.3135   392.479869   357.6665   401.5585
6           Rdisop   382.417   459.8790   538.068697   490.1505   557.9975
9           CHNOSZ   355.145   510.2910   588.186951   555.9165   632.2060
4            rcdk3   781.987  1004.7160  1294.507318  1133.3415  1339.4695
3            rcdk2  2078.465  2392.4950  2920.601088  2612.8025  2931.5465
7        ChemmineR  3227.320  3790.0455  4808.783873  4044.1410  4465.1000
2             rcdk 14823.815 16456.7715 19088.569430 17485.0800 19468.7195

@sneumann its not that simple. the formula object that is built might be used for other things. A straight substitution is not backwards compatible.