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Install and benchmark a number of
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| 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) | |
| ## enviPat | |
| data(isotopes) | |
| benchmark <- microbenchmark::microbenchmark( | |
| MetaboCoreUtils = MetaboCoreUtils::calculateMass("C2H6O"), | |
| rcdk = rcdk::get.formula("C2H6O", charge = 0)@mass, | |
| Rdisop = Rdisop::getMolecule("C2H6O")$exactmass, | |
| ChemmineR = ChemmineR::exactMassOB(ChemmineR::smiles2sdf("CCO")), | |
| OrgMassSpecR = OrgMassSpecR::MonoisotopicMass(formula = OrgMassSpecR::ListFormula("C2H6O)"), charge = 0), | |
| CHNOSZ = CHNOSZ::mass("C2H6O"), | |
| enviPat = enviPat::isopattern(isotopes, "C2H6O", charge=FALSE, verbose=FALSE)[[1]][1,1] | |
| , times=1000L) | |
| masses <- c( | |
| MetaboCoreUtils=MetaboCoreUtils::calculateMass("C2H6O"), | |
| rcdk=rcdk::get.formula("C2H6O", charge = 0)@mass, | |
| Rdisop=Rdisop::getMolecule("C2H6O")$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"]) , ] )) |
Updated code with some improvements to RCDK: https://gist.github.com/zachcp/ac410b900d67264ffb8061d2b8fa45bf
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Yeah. I think what this needs is some testing of what happens if you throw them odd things they might not be expecting like HCOOH, C3H2S0, Na+Cl-, H3O+, +H2O-, Fe4+, Cp3UCl, 2H2O (isotope notation I guess would vary), D2O.