tests/testthat/test_create_reaction.R
In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam
## function .create_reaction
test_that(".create_reaction works", {
## acyldhap_to_alkyldhap
acyldhap <- "DHAP(18:0)"
fao <- "FAO(16:0)"
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36171")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) = H+ + FA(18:0) + DHAP(O-16:0)")
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36172")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) => H+ + FA(18:0) + DHAP(O-16:0)")
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36173")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) <= H+ + FA(18:0) + DHAP(O-16:0)")
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36174")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) <=> H+ + FA(18:0) + DHAP(O-16:0)")
## alkyldhap_to_lpao
alkyldhap <- "DHAP(O-18:0)"
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36175")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) = PA(O-18:0/0:0) + NADP+")
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36176")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) => PA(O-18:0/0:0) + NADP+")
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36177")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) <= PA(O-18:0/0:0) + NADP+")
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36178")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) <=> PA(O-18:0/0:0) + NADP+")
## cerp_to_cer
cerp <- "CerP(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(CerP = cerp),
template = NULL, reaction = "cerp_to_cer")
expect_equal(reaction_l[[1]]$Cer, "Cer(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CerP(16:0(3OH,4OH,15Me)/18:0) <=> Pi + Cer(16:0(3OH,4OH,15Me)/18:0)")
## cdpdg_to_pgp
cdpdg <- "CDP-DG(12:0(11Me)/14:0)"
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12593")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) = H+ + CMP + PGP(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12594")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) => H+ + CMP + PGP(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12595")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) <= H+ + CMP + PGP(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12596")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) <=> H+ + CMP + PGP(12:0(11Me)/14:0)")
## cdpdg_to_pi
cdgdg <- "CDP-DG(12:0(11Me)/14:0)"
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11580")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) = H+ + CMP + PI(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11581")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) => H+ + CMP + PI(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11582")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) <= H+ + CMP + PI(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11583")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) <=> H+ + CMP + PI(12:0(11Me)/14:0)")
## cer_to_cerp
cer <- "Cer(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(Cer = cer),
template = NULL, reaction = "RHEA:17929")
expect_equal(reaction_l[[1]]$CerP, "CerP(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + Cer(16:0(3OH,4OH,15Me)/18:0) <=> H+ + ADP + CerP(16:0(3OH,4OH,15Me)/18:0)")
## cer_to_glccer
cer <- "Cer(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(Cer = cer),
template = NULL, reaction = "RHEA:12088")
expect_equal(reaction_l[[1]]$GlcCer, "GlcCer(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"UDP-Glucose + Cer(16:0(3OH,4OH,15Me)/18:0) <=> H+ + UDP + GlcCer(16:0(3OH,4OH,15Me)/18:0)")
## cer_to_sm
cer <- "Cer(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(Cer = cer),
template = NULL, reaction = "RHEA:18765")
expect_equal(reaction_l[[1]]$SM, "SM(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC + Cer(16:0(3OH,4OH,15Me)/18:0) <=> DG + SM(16:0(3OH,4OH,15Me)/18:0)")
## cl_to_lcl
cl <- "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])"
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32935")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) = CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32936")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) => CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32937")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) <= CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32938")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) <=> CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
## coa_to_acyldhap
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17657")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) = CoA + DHAP(18:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17658")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) => CoA + DHAP(18:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17659")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) <= CoA + DHAP(18:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17660")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) <=> CoA + DHAP(18:0)")
## coa_to_fao
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52716")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ = FAO(18:0) + 2 NADP+ + CoA")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52717")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ => FAO(18:0) + 2 NADP+ + CoA")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52718")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ <= FAO(18:0) + 2 NADP+ + CoA")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52719")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ <=> FAO(18:0) + 2 NADP+ + CoA")
## coa_to_lpa
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15325")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) = CoA + PA(18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15326")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) => CoA + PA(18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15327")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) <= CoA + PA(18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15328")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) <=> CoA + PA(18:0/0:0)")
## dg_to_sn1mg
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44712")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) = H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35663")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) = H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44713")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) => H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35664")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) => H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44714")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <= H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35665")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <= H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44715")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <=> H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35666")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <=> H+ + MG(18:0/0:0/0:0) + FA(16:0)")
## dg_to_sn2mg
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33275")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) = H+ + MG(0:0/16:0/0:0) + FA(18:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33276")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) => H+ + MG(0:0/16:0/0:0) + FA(18:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33277")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <= H+ + MG(0:0/16:0/0:0) + FA(18:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33278")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <=> H+ + MG(0:0/16:0/0:0) + FA(18:0)")
## dg_to_pa
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10272")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) = H+ + ADP + PA(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10273")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) => H+ + ADP + PA(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10274")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) <= H+ + ADP + PA(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10275")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) <=> H+ + ADP + PA(18:0/16:0)")
## dg_to_pc
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32939")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) = H+ + CMP + PC(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32940")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) => H+ + CMP + PC(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32941")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) <= H+ + CMP + PC(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32942")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) <=> H+ + CMP + PC(18:0/16:0)")
## dg_to_pe
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32943")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) = H+ + CMP + PE(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32944")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) => H+ + CMP + PE(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32945")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) <= H+ + CMP + PE(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32946")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) <=> H+ + CMP + PE(18:0/16:0)")
## dg_to_tg
dg <- "DG(18:0/16:0/0:0)"
acylcoa <- "CoA(14:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10868")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) = CoA + TG(18:0/16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10869")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) => CoA + TG(18:0/16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10870")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) <= CoA + TG(18:0/16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10871")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) <=> CoA + TG(18:0/16:0/14:0)")
## dgo_to_pco
dgo <- "DG(O-18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36179")
expect_equal(reaction_l[[1]]$PCO, "PC(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(O-18:0/16:0/0:0) <=> H+ + CMP + PC(O-18:0/16:0)")
## dgo_to_peo
dgo <- "DG(O-18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36187")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) = H+ + CMP + PE(O-18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36188")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) => H+ + CMP + PE(O-18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36189")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) <= H+ + CMP + PE(O-18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36190")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) <=> H+ + CMP + PE(O-18:0/16:0)")
## dhcer_to_cer
dhcer <- "Cer(d16:0(3OH,4OH)(15Me)/12:0)" ###################################################
reaction_l <- .create_reaction(substrates = list(DhCer = dhcer),
template = NULL, reaction = "dhcer_to_cer")
expect_equal(reaction_l[[1]]$Cer, "Cer(d16:0(3OH,4OH)(15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADH + O2 + Cer(d16:0(3OH,4OH)(15Me)/12:0) <=> 2 H2O + NAD+ + Cer(d16:0(3OH,4OH)(15Me)/12:0)")
## dhcer_to_dhsm
dhcer <- "Cer(16:1(3OH,4OH,15Me)/12:0)" ###################################################
reaction_l <- .create_reaction(substrates = list(DhCer = dhcer),
template = NULL, reaction = "RHEA:44620")
expect_equal(reaction_l[[1]]$DhSM, "SM(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC + Cer(16:1(3OH,4OH,15Me)/12:0) <=> DG + SM(16:1(3OH,4OH,15Me)/12:0)")
## dhsm_to_dhcer
dhsm <- "SM(16:1(3OH,4OH,15Me)/12:0)" ###################################################
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45300")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) = Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45301")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) => Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45302")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) <= Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45303")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) <=> Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
## fa_to_coa
fa <- "FA(18:0)"
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15421")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) = PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38883")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) = PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15422")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) => PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38884")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) => PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15423")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <= PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38885")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <= PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15424")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <=> PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38886")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <=> PPi + AMP + CoA(18:0)")
## lcl_to_cl
lcl <- "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])"
acylcoa <- "CoA(18:4(6Z,9Z,12Z,15Z))"
reaction_l <- .create_reaction(
substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35839")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) = CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
reaction_l <- .create_reaction(substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35840")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) => CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
reaction_l <- .create_reaction(substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35841")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) <= CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
reaction_l <- .create_reaction(substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35842")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) <=> CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
## lnape_to_gpnae
lnape <- "NAPE(14:0/0:0/0:0)"
reaction_l <- .create_reaction(substrates = list(LNAPE = lnape),
template = NULL, reaction = "RHEA:45420")
expect_equal(reaction_l[[1]]$GPNAE, "GPNAE(0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/0:0/0:0) + H2O <=> GPNAE(0:0) + FA(14:0)")
## lpa_to_pa
lpa <- "PA(18:0/0:0)"
acylcoa <- "CoA(14:0)"
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19709")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) = CoA + PA(18:0/14:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19710")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) => CoA + PA(18:0/14:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19711")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) <= CoA + PA(18:0/14:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19712")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) <=> CoA + PA(18:0/14:0)")
## lpao_to_pao
lpao <- "PA(O-18:0/0:0)"
acylcoa <- "CoA(14:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36235")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) = PA(O-18:0/14:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36236")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) => PA(O-18:0/14:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36237")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) <= PA(O-18:0/14:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36238")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) <=> PA(O-18:0/14:0) + CoA")
## sn1lpc_to_fa
sn1lpc <- "PC(14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15177")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) = Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15178")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) => Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15179")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) <= Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15180")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) <=> Glycerophosphocholine + H+ + FA(14:0)")
## sn2lpc_to_fa
sn2lpc <- "PC(0:0/14:0)"
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44696")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) = Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44697")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) => Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44698")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) <= Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44699")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) <=> Glycerophosphocholine + H+ + FA(14:0)")
## sn1lpc_to_pc
sn1lpc <- "PC(14:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12937")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) = PC(14:0/18:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12938")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) => PC(14:0/18:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12939")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) <= PC(14:0/18:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12940")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) <=> PC(14:0/18:0) + CoA")
## sn1lpe_to_fa
pe <- "PE(14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32967")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) = H+ + FA(14:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32968")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) => H+ + FA(14:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32969")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) <= H+ + FA(14:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32970")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) <=> H+ + FA(14:0) + Glycerophosphoethanolamine")
## sn2lpe_to_fa
sn2lpe <- "PE(0:0/14:0)"
reaction_l <- .create_reaction(substrates = list(sn2LPE = sn2lpe),
template = NULL, reaction = "sn2lpe_to_fa")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(0:0/14:0) <=> H+ + FA(14:0) + Glycerophosphoethanolamine")
## sn1lpe_to_pe
sn1lpe <- "PE(14:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32995")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) = CoA + PE(14:0/18:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32996")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) => CoA + PE(14:0/18:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32997")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) <= CoA + PE(14:0/18:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32998")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) <=> CoA + PE(14:0/18:0)")
## sn1lpi_to_pi
sn1lpi <- "PI(16:0/0:0)"
acylcoa <- "CoA(18:1(9Z))"
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33195")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) = PI(16:0/18:1(9Z)) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33196")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) => PI(16:0/18:1(9Z)) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33197")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) <= PI(16:0/18:1(9Z)) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33198")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) <=> PI(16:0/18:1(9Z)) + CoA")
## lpeo_to_peo
lpeo <- "PE(O-16:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(
substrates = list(sn1LPEO = lpeo, AcylCoA = acylcoa),
template = NULL, reaction = "lpeo_to_peo")
expect_equal(reaction_l[[1]]$PEO, "PE(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(O-16:0/0:0) <=> CoA + PE(O-16:0/18:0)")
## lpep_to_pep
lpep <- "PE(P-16:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16245")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16246")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16247")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16248")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
## sn1mg_to_dg
sn1mg <- "MG(14:0/0:0/0:0)"
acylcoa <- "CoA(16:0)"
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38463")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) = CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39943")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) = CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38464")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) => CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39944")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) => CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38465")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <= CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39945")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <= CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38466")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <=> CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39946")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <=> CoA + DG(14:0/16:0/0:0)")
## sn2mg_to_dg
sn2mg <- "MG(0:0/14:0/0:0)"
acylcoa <- "CoA(16:0)"
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32947")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) = CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16741")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) = CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32948")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) => CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16742")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) => CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32949")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <= CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16743")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <= CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32950")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <=> CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16744")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <=> CoA + DG(16:0/14:0/0:0)")
## sn1mg_to_fa
sn1mg <- "MG(14:0/0:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34019")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) = Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34020")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) => Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34021")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) <= Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34022")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) <=> Glycerol + H+ + FA(14:0)")
## sn2mg_to_fa
sn2mg <- "MG(0:0/14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32871")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) = Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32872")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) => Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32873")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) <= Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32874")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) <=> Glycerol + H+ + FA(14:0)")
## sn1mg_to_lpa
sn1mg <- "MG(14:0/0:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33747")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) = H+ + ADP + PA(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33748")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) => H+ + ADP + PA(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33749")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) <= H+ + ADP + PA(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33750")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) <=> H+ + ADP + PA(14:0/0:0)")
## sn2mg_to_sn1mg
sn2mg <- "MG(0:0/14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "sn2mg_to_sn1mg")
expect_equal(reaction_l[[1]]$sn1MG, "MG(14:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(0:0/14:0/0:0) <=> MG(14:0/0:0/0:0)")
## nae_to_fa
nae <- "NAE(18:0)"
reaction_l <- .create_reaction(substrates = list(NAE = nae),
template = NULL, reaction = "nae_to_fa")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + NAE(18:0) <=> Ethanolamine + H+ + FA(18:0)")
## nape_to_lnape
nape <- "NAPE(14:0/16:0/18:0)"
reaction_l <- .create_reaction(substrates = list(NAPE = nape),
template = NULL, reaction = "nape_to_lnape")
expect_equal(reaction_l[[1]]$LNAPE, "NAPE(14:0/0:0/18:0)")
expect_equal(reaction_l[[1]]$FA, "FA(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/16:0/18:0) + H2O <=> NAPE(14:0/0:0/18:0) + FA(16:0)")
## nape_to_nae
nape <- "NAPE(14:0/16:0/18:0)"
reaction_l <- .create_reaction(substrates = list(NAPE = nape),
template = NULL, reaction = "nape_to_nae")
expect_equal(reaction_l[[1]]$NAE, "NAE(18:0)")
expect_equal(reaction_l[[1]]$PA, "PA(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/16:0/18:0) + H2O <=> NAE(18:0) + PA(14:0/16:0)")
## nape_to_pnae
nape <- "NAPE(14:0/16:0/18:0)"
reaction_l <- .create_reaction(substrates = list(NAPE = nape),
template = NULL, reaction = "nape_to_pnae")
expect_equal(reaction_l[[1]]$PNAE, "PNAE(18:0)")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/16:0/18:0) + H2O <=> PNAE(18:0) + DG(14:0/16:0/0:0)")
## napeo_to_nae
napeo <- "NAPE(O-18:0/16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(NAPEO = napeo),
template = NULL, reaction = "napeo_to_nae")
expect_equal(reaction_l[[1]]$NAE, "NAE(14:0)")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(O-18:0/16:0/14:0) + H2O <=> NAE(14:0) + PA(O-18:0/16:0)")
## pa_to_cdpdg
pa <- "PA(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16229")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) = PPi + CDP-DG(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16230")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) => PPi + CDP-DG(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16231")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) <= PPi + CDP-DG(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16232")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) <=> PPi + CDP-DG(14:0/16:0)")
## pa_to_dg
pa <- "PA(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27429")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) = Pi + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27430")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) => Pi + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27431")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) <= Pi + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27432")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) <=> Pi + DG(14:0/16:0/0:0)")
## pao_to_dgo
pao <- "PA(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36239")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) = Pi + DG(O-16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36240")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) => Pi + DG(O-16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36241")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) <= Pi + DG(O-16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36242")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) <=> Pi + DG(O-16:0/14:0/0:0)")
## pc_to_dg
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10604")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) = Phosphocholine + DG(20:0/18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10605")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) => Phosphocholine + DG(20:0/18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10606")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) <= Phosphocholine + DG(20:0/18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10607")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) <=> Phosphocholine + DG(20:0/18:0/0:0)")
## pc_to_sn1lpc
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15801")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) = PC(16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15802")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) => PC(16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15803")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <= PC(16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15804")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <=> PC(16:0/0:0) + FA(14:0)")
## pc_to_sn2lpc
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18689")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) = PC(0:0/14:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18690")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) => PC(0:0/14:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18691")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <= PC(0:0/14:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18692")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <=> PC(0:0/14:0) + FA(16:0)")
## pc_to_pa
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14445")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) = Choline + PA(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14446")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) => Choline + PA(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14447")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <= Choline + PA(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14448")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <=> Choline + PA(16:0/14:0)")
## pc_to_ps
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45088")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) = Choline + PS(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45089")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) => Choline + PS(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45090")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) <= Choline + PS(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45091")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) <=> Choline + PS(16:0/14:0)")
## pco_to_lpco
pco <- "PC(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36231")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) = H+ + PC(O-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36232")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) => H+ + PC(O-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36233")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) <= H+ + PC(O-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36234")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) <=> H+ + PC(O-16:0/0:0) + FA(14:0)")
## lpco_to_lpao
sn1lpco <- "PC(O-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39927")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) = PA(O-16:0/0:0) + H+ + Choline")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39928")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) => PA(O-16:0/0:0) + H+ + Choline")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39929")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <= PA(O-16:0/0:0) + H+ + Choline")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39930")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <=> PA(O-16:0/0:0) + H+ + Choline")
## lpco_to_mgo
sn1lpco <- "PC(O-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36083")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) = H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36084")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) => H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36085")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <= H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36086")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <=> H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
## lpco_to_pco
sn1lpco <- "PC(O-16:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23992")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) = PC(O-16:0/18:0) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23993")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) => PC(O-16:0/18:0) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23994")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) <= PC(O-16:0/18:0) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23995")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) <=> PC(O-16:0/18:0) + CoA")
## pe_to_dg
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "pe_to_dg")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> P-Ethanolamine + DG(14:0/16:0/0:0)")
## pe_to_sn1lpe
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44604")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) = H+ + FA(16:0) + PE(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44605")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) => H+ + FA(16:0) + PE(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44606")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <= H+ + FA(16:0) + PE(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44607")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> H+ + FA(16:0) + PE(14:0/0:0)")
## pe_to_sn2lpe
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44408")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) = H+ + FA(16:0) + PE(0:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44409")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) => H+ + FA(16:0) + PE(0:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44410")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <= H+ + FA(16:0) + PE(0:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44411")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> H+ + FA(16:0) + PE(0:0/14:0)")
## pe_to_nape_sn1
pe <- "PE(14:0/16:0)"
pc <- "PC(18:0/20:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe, PC = pc),
template = NULL, reaction = "pe_to_nape_sn1")
expect_equal(reaction_l[[1]]$NAPE, "NAPE(14:0/16:0/18:0)")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/20:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(14:0/16:0) + PC(18:0/20:0) <=> NAPE(14:0/16:0/18:0) + PC(0:0/20:0)")
## pe_to_nape_sn2
pe <- "PE(14:0/16:0)"
pc <- "PC(18:0/20:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe, PC = pc),
template = NULL, reaction = "pe_to_nape_sn2")
expect_equal(reaction_l[[1]]$NAPE, "NAPE(14:0/16:0/20:0)")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(14:0/16:0) + PC(18:0/20:0) <=> NAPE(14:0/16:0/20:0) + PC(18:0/0:0)")
## pe_to_pa
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "pe_to_pa")
expect_equal(reaction_l[[1]]$PA, "PA(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> Ethanolamine + H+ + PA(14:0/16:0)")
## pe_to_ps
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27606")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) = Ethanolamine + PS(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27607")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) => Ethanolamine + PS(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27608")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) <= Ethanolamine + PS(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27609")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) <=> Ethanolamine + PS(14:0/16:0)")
## peo_to_lpeo
peo <- "PE(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "peo_to_lpeo")
expect_equal(reaction_l[[1]]$sn1LPEO, "PE(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(O-16:0/14:0) <=> H+ + PE(O-16:0/0:0) + FA(14:0)")
## peo_to_napeo_sn1
peo <- "PE(O-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo, PC = pc),
template = NULL, reaction = "peo_to_napeo_sn1") ################
expect_equal(reaction_l[[1]]$NAPEO, "NAPE(O-16:0/14:0/20:0)")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + PC(20:0/18:0) <=> NAPE(O-16:0/14:0/20:0) + PC(0:0/18:0)")
## peo_to_napeo_sn2
peo <- "PE(O-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo, PC = pc),
template = NULL, reaction = "peo_to_napeo_sn2")
expect_equal(reaction_l[[1]]$NAPEO, "NAPE(O-16:0/14:0/18:0)")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(20:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + PC(20:0/18:0) <=> NAPE(O-16:0/14:0/18:0) + PC(20:0/0:0)")
## peo_to_pep
peo <- "PE(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22956")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 = PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22957")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 => PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22958")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 <= PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22959")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 <=> PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
## pep_to_lpep
pep <- "PE(P-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36195")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) = H+ + PE(P-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36196")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) => H+ + PE(P-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36197")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) <= H+ + PE(P-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36198")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) <=> H+ + PE(P-16:0/0:0) + FA(14:0)")
## lpep_to_fal
sn1lpep <- "PE(P-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16905")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) = FAL(16:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16906")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) => FAL(16:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16907")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <= FAL(16:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16908")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <=> FAL(16:0) + Glycerophosphoethanolamine")
## lpep_to_lpap
sn1lpep <- "PE(P-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36203")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) = PA(P-16:0/0:0) + H+ + Ethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36204")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) => PA(P-16:0/0:0) + H+ + Ethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36205")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <= PA(P-16:0/0:0) + H+ + Ethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36206")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <=> PA(P-16:0/0:0) + H+ + Ethanolamine")
## lpep_to_mgp
sn1lpep <- "PE(P-18:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36199")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) = Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36200")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) => Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36201")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) <= Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36202")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) <=> Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
## pep_to_napep_sn1
pep <- "PE(P-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEP = pep, PC = pc),
template = NULL, reaction = "pep_to_napep_sn1")
expect_equal(reaction_l[[1]]$NAPEP, "NAPE(P-16:0/14:0/20:0)")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(P-16:0/14:0) + PC(20:0/18:0) <=> NAPE(P-16:0/14:0/20:0) + PC(0:0/18:0)")
## pep_to_napep_sn2
pep <- "PE(P-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEP = pep, PC = pc),
template = NULL, reaction = "pep_to_napep_sn2")
expect_equal(reaction_l[[1]]$NAPEP, "NAPE(P-16:0/14:0/18:0)")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(20:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(P-16:0/14:0) + PC(20:0/18:0) <=> NAPE(P-16:0/14:0/18:0) + PC(20:0/0:0)")
## pg_to_cl
pg <- "PG(18:4(6Z,9Z,12Z,15Z)/14:0)"
cdpdg <- "CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0)"
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32931")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) = H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32932")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) => H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32933")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) <= H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32934")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) <=> H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
## pgp_to_pg
pgp <- "PGP(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33751")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) = Pi + PG(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33752")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) => Pi + PG(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33753")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) <= Pi + PG(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33754")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) <=> Pi + PG(16:0/14:0)")
## pi_to_dg
pi <- "PI(16:0/18:1(9Z))"
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43484")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) = myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43485")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) => myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43486")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <= myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43487")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <=> myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
## pi_to_sn1lpi
pi <- "PI(16:0/18:1(9Z))"
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18001")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) = PI(16:0/0:0) + H+ + FA(18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18002")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) => PI(16:0/0:0) + H+ + FA(18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18003")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <= PI(16:0/0:0) + H+ + FA(18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18004")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <=> PI(16:0/0:0) + H+ + FA(18:1(9Z))")
## ps_to_pe
ps <- "PS(14:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20828")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) = CO2 + PE(14:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20829")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) => CO2 + PE(14:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20830")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) <= CO2 + PE(14:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20831")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) <=> CO2 + PE(14:0/14:0)")
## sm_to_cer
sm <- "SM(16:0(3OH,4OH,15Me)/12:0)"
reaction_l <- .create_reaction(substrates = list(SM = sm),
template = NULL, reaction = "sm_to_cer")
expect_equal(reaction_l[[1]]$Cer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:0(3OH,4OH,15Me)/12:0) <=> Phosphocholine + H+ + Cer(16:0(3OH,4OH,15Me)/12:0)")
## sphinga_to_dhcer
acylcoa <- "CoA(12:0)" ###############################################################
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53424")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) = CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53425")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) => CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53426")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) <= CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53427")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) <=> CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
## should be: "CoA(12:0) + SPH(16:0(1OH,3OH,15Me)) <=> CoA + Cer(16:0(3OH,4OH,15Me)/12:0)"
## tg_to_dg
tg <- "TG(18:0/16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33271")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44864")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33272")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44865")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33273")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44866")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33274")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44867")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(14:0) + DG(18:0/16:0/0:0)")
})
## function create_reactions
test_that("create_reactions works.", {
FA <- c("FA(16:0)", "FA(12:0)", "FA(14:0)")
## create data.frame with reactions and reaction order
reactions <- rbind(
c(1, "RHEA:15421", "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA", FALSE),
c(2, "RHEA:15325", "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA", FALSE),
c(3, "RHEA:19709", "M_LPA + M_AcylCoA = M_CoA + M_PA", FALSE),
c(4, "RHEA:27429", "M_H2O + M_PA = M_Pi + M_1,2-DG", FALSE))
reactions <- data.frame(order = reactions[, 1], RHEA = reactions[, 2],
reactions = reactions[, 3], directed = reactions[, 4])
reactions$order <- as.numeric(reactions$order)
reactions$directed <- as.logical(reactions$directed)
## run the function
reactions_l <- create_reactions(substrates = list(FA = FA),
reactions = reactions)
expect_equal(length(reactions_l), 4)
## first entry
expect_equal(names(reactions_l[[1]][[1]]), c("FA", "AcylCoA"))
expect_equal(reactions_l[[1]][[1]]$FA,
c("FA(16:0)", "FA(12:0)", "FA(14:0)"))
expect_equal(reactions_l[[1]][[1]]$AcylCoA,
c("CoA(16:0)", "CoA(12:0)", "CoA(14:0)"))
expect_equal(colnames(reactions_l[[1]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[1]][[2]]), 3)
expect_equal(reactions_l[[1]][[2]]$reaction_formula[1:3],
c("ATP + CoA + FA(16:0) = PPi + AMP + CoA(16:0)",
"ATP + CoA + FA(12:0) = PPi + AMP + CoA(12:0)",
"ATP + CoA + FA(14:0) = PPi + AMP + CoA(14:0)"))
expect_equal(reactions_l[[1]][[2]]$reaction_isReversible[1:3], c("", "", ""))
expect_equal(reactions_l[[1]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[1]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[1]][[2]]$reaction_substrate[1:3],
c("ATP + CoA + FA(16:0)", "ATP + CoA + FA(12:0)", "ATP + CoA + FA(14:0)"))
expect_equal(reactions_l[[1]][[2]]$reaction_product[1:3],
c("PPi + AMP + CoA(16:0)", "PPi + AMP + CoA(12:0)", "PPi + AMP + CoA(14:0)"))
## second entry
expect_equal(names(reactions_l[[2]][[1]]), c("AcylCoA", "sn1LPA"))
expect_equal(reactions_l[[2]][[1]]$AcylCoA,
c("CoA(16:0)", "CoA(12:0)", "CoA(14:0)"))
expect_equal(reactions_l[[2]][[1]]$sn1LPA,
c("PA(16:0/0:0)", "PA(12:0/0:0)", "PA(14:0/0:0)"))
expect_equal(colnames(reactions_l[[2]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[2]][[2]]), 3)
expect_equal(reactions_l[[2]][[2]]$reaction_formula[1:3],
c("Glycerol-3-P + CoA(16:0) = CoA + PA(16:0/0:0)",
"Glycerol-3-P + CoA(12:0) = CoA + PA(12:0/0:0)",
"Glycerol-3-P + CoA(14:0) = CoA + PA(14:0/0:0)"))
expect_equal(reactions_l[[2]][[2]]$reaction_isReversible[1:3],
c("", "", ""))
expect_equal(reactions_l[[2]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[2]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[2]][[2]]$reaction_substrate[1:3],
c("Glycerol-3-P + CoA(16:0)", "Glycerol-3-P + CoA(12:0)",
"Glycerol-3-P + CoA(14:0)"))
expect_equal(reactions_l[[2]][[2]]$reaction_product[1:3],
c("CoA + PA(16:0/0:0)", "CoA + PA(12:0/0:0)", "CoA + PA(14:0/0:0)"))
## third entry
expect_equal(names(reactions_l[[3]][[1]]), c("sn1LPA", "AcylCoA", "PA"))
expect_equal(reactions_l[[3]][[1]]$sn1LPA,
c("PA(16:0/0:0)", "PA(12:0/0:0)", "PA(14:0/0:0)"))
expect_equal(reactions_l[[3]][[1]]$AcylCoA,
c("CoA(16:0)", "CoA(12:0)", "CoA(14:0)"))
expect_equal(reactions_l[[3]][[1]]$PA,
c("PA(16:0/16:0)", "PA(12:0/16:0)", "PA(14:0/16:0)", "PA(16:0/12:0)",
"PA(12:0/12:0)", "PA(14:0/12:0)", "PA(16:0/14:0)", "PA(12:0/14:0)",
"PA(14:0/14:0)"))
expect_equal(colnames(reactions_l[[3]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[3]][[2]]), 9)
expect_equal(reactions_l[[3]][[2]]$reaction_formula[1:3],
c("PA(16:0/0:0) + CoA(16:0) = CoA + PA(16:0/16:0)",
"PA(12:0/0:0) + CoA(16:0) = CoA + PA(12:0/16:0)",
"PA(14:0/0:0) + CoA(16:0) = CoA + PA(14:0/16:0)"))
expect_equal(reactions_l[[3]][[2]]$reaction_isReversible[1:3], c("", "", ""))
expect_equal(reactions_l[[3]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[3]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[3]][[2]]$reaction_substrate[1:3],
c("PA(16:0/0:0) + CoA(16:0)", "PA(12:0/0:0) + CoA(16:0)",
"PA(14:0/0:0) + CoA(16:0)"))
expect_equal(reactions_l[[3]][[2]]$reaction_product[1:3],
c("CoA + PA(16:0/16:0)", "CoA + PA(12:0/16:0)", "CoA + PA(14:0/16:0)"))
## fourth entry
expect_equal(names(reactions_l[[4]][[1]]), c("PA", "DG"))
expect_equal(reactions_l[[4]][[1]]$PA,
c("PA(16:0/16:0)", "PA(12:0/16:0)", "PA(14:0/16:0)", "PA(16:0/12:0)",
"PA(12:0/12:0)", "PA(14:0/12:0)", "PA(16:0/14:0)", "PA(12:0/14:0)",
"PA(14:0/14:0)"))
expect_equal(reactions_l[[4]][[1]]$DG,
c("DG(16:0/16:0/0:0)", "DG(12:0/16:0/0:0)", "DG(14:0/16:0/0:0)",
"DG(16:0/12:0/0:0)", "DG(12:0/12:0/0:0)", "DG(14:0/12:0/0:0)",
"DG(16:0/14:0/0:0)", "DG(12:0/14:0/0:0)", "DG(14:0/14:0/0:0)"))
expect_equal(colnames(reactions_l[[4]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[4]][[2]]), 9)
expect_equal(reactions_l[[4]][[2]]$reaction_formula[1:3],
c("H2O + PA(16:0/16:0) = Pi + DG(16:0/16:0/0:0)",
"H2O + PA(12:0/16:0) = Pi + DG(12:0/16:0/0:0)",
"H2O + PA(14:0/16:0) = Pi + DG(14:0/16:0/0:0)"))
expect_equal(reactions_l[[4]][[2]]$reaction_isReversible[1:3], c("", "", ""))
expect_equal(reactions_l[[4]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[4]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[4]][[2]]$reaction_substrate[1:3],
c("H2O + PA(16:0/16:0)", "H2O + PA(12:0/16:0)", "H2O + PA(14:0/16:0)"))
expect_equal(reactions_l[[4]][[2]]$reaction_product[1:3],
c("Pi + DG(16:0/16:0/0:0)", "Pi + DG(12:0/16:0/0:0)",
"Pi + DG(14:0/16:0/0:0)"))
})
## function create_reactions
test_that("create_reaction_adjacency_matrix works.", {
FA <- c("FA(16:0)", "FA(12:0)", "FA(14:0)")
## create data.frame with reactions and reaction order
reactions <- rbind(
c(1, "RHEA:15421", "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA", FALSE),
c(2, "RHEA:15325", "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA", FALSE),
c(3, "RHEA:19709", "M_LPA + M_AcylCoA = M_CoA + M_PA", FALSE),
c(4, "RHEA:27429", "M_H2O + M_PA = M_Pi + M_1,2-DG", FALSE))
reactions <- data.frame(order = reactions[, 1], RHEA = reactions[, 2],
reactions = reactions[, 3], directed = reactions[, 4])
reactions$order <- as.numeric(reactions$order)
reactions$directed <- as.logical(reactions$directed)
reactions_l <- create_reactions(substrates = list(FA = FA),
reactions = reactions)
## run the function
adj <- create_reaction_adjacency_matrix(reaction_l = reactions_l)
expect_equal(dim(adj), c(34, 34))
expect_equal(rownames(adj), colnames(adj))
expect_equal(rownames(adj)[1:32],
c("AMP", "ATP", "CoA", "CoA(12:0)", "CoA(14:0)", "CoA(16:0)",
"DG(12:0/12:0/0:0)", "DG(12:0/14:0/0:0)", "DG(12:0/16:0/0:0)",
"DG(14:0/12:0/0:0)", "DG(14:0/14:0/0:0)", "DG(14:0/16:0/0:0)",
"DG(16:0/12:0/0:0)", "DG(16:0/14:0/0:0)", "DG(16:0/16:0/0:0)",
"FA(12:0)", "FA(14:0)", "FA(16:0)", "Glycerol-3-P", "H2O",
"PA(12:0/0:0)", "PA(12:0/12:0)", "PA(12:0/14:0)", "PA(12:0/16:0)",
"PA(14:0/0:0)", "PA(14:0/12:0)", "PA(14:0/14:0)", "PA(14:0/16:0)",
"PA(16:0/0:0)", "PA(16:0/12:0)", "PA(16:0/14:0)", "PA(16:0/16:0)",
"Pi", "PPi")[1:32])
expect_equal(sum(adj), 78)
expect_equal(as.vector(adj[1:5, 1:5]),
c(0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0,
1, 1, 0, 0))
expect_equal(adj["PA(14:0/0:0)", "PA(14:0/16:0)"], 1)
expect_equal(adj["PA(14:0/0:0)", "Pi"], 0)
expect_equal(adj["PA(14:0/0:0)", "PPi"], 0)
expect_equal(adj["PA(14:0/0:0)", "PA(14:0/16:0)"], 1)
expect_equal(as.vector(adj["ATP", c("CoA(12:0)", "CoA(14:0)", "CoA(16:0)")]),
c(1, 1, 1))
expect_equal(as.vector(adj[c("CoA(12:0)", "CoA(14:0)", "CoA(16:0)"), "ATP"]),
c(0, 0, 0))
})
michaelwitting/wormLipidPredictR documentation built on Aug. 28, 2024, 9:39 a.m.
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## function .create_reaction
test_that(".create_reaction works", {
## acyldhap_to_alkyldhap
acyldhap <- "DHAP(18:0)"
fao <- "FAO(16:0)"
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36171")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) = H+ + FA(18:0) + DHAP(O-16:0)")
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36172")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) => H+ + FA(18:0) + DHAP(O-16:0)")
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36173")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) <= H+ + FA(18:0) + DHAP(O-16:0)")
reaction_l <- .create_reaction(substrates = list(AcylDHAP = acyldhap, FAO = fao),
template = NULL, reaction = "RHEA:36174")
expect_equal(reaction_l[[1]]$AlkylDHAP, "DHAP(O-16:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"DHAP(18:0) + FAO(16:0) <=> H+ + FA(18:0) + DHAP(O-16:0)")
## alkyldhap_to_lpao
alkyldhap <- "DHAP(O-18:0)"
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36175")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) = PA(O-18:0/0:0) + NADP+")
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36176")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) => PA(O-18:0/0:0) + NADP+")
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36177")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) <= PA(O-18:0/0:0) + NADP+")
reaction_l <- .create_reaction(substrates = list(AlkylDHAP = alkyldhap),
template = NULL, reaction = "RHEA:36178")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADPH + DHAP(O-18:0) <=> PA(O-18:0/0:0) + NADP+")
## cerp_to_cer
cerp <- "CerP(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(CerP = cerp),
template = NULL, reaction = "cerp_to_cer")
expect_equal(reaction_l[[1]]$Cer, "Cer(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CerP(16:0(3OH,4OH,15Me)/18:0) <=> Pi + Cer(16:0(3OH,4OH,15Me)/18:0)")
## cdpdg_to_pgp
cdpdg <- "CDP-DG(12:0(11Me)/14:0)"
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12593")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) = H+ + CMP + PGP(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12594")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) => H+ + CMP + PGP(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12595")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) <= H+ + CMP + PGP(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:12596")
expect_equal(reaction_l[[1]]$PGP, "PGP(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CDP-DG(12:0(11Me)/14:0) <=> H+ + CMP + PGP(12:0(11Me)/14:0)")
## cdpdg_to_pi
cdgdg <- "CDP-DG(12:0(11Me)/14:0)"
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11580")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) = H+ + CMP + PI(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11581")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) => H+ + CMP + PI(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11582")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) <= H+ + CMP + PI(12:0(11Me)/14:0)")
reaction_l <- .create_reaction(substrates = list(CDPDG = cdpdg),
template = NULL, reaction = "RHEA:11583")
expect_equal(reaction_l[[1]]$PI, "PI(12:0(11Me)/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"myo-Inositol + CDP-DG(12:0(11Me)/14:0) <=> H+ + CMP + PI(12:0(11Me)/14:0)")
## cer_to_cerp
cer <- "Cer(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(Cer = cer),
template = NULL, reaction = "RHEA:17929")
expect_equal(reaction_l[[1]]$CerP, "CerP(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + Cer(16:0(3OH,4OH,15Me)/18:0) <=> H+ + ADP + CerP(16:0(3OH,4OH,15Me)/18:0)")
## cer_to_glccer
cer <- "Cer(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(Cer = cer),
template = NULL, reaction = "RHEA:12088")
expect_equal(reaction_l[[1]]$GlcCer, "GlcCer(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"UDP-Glucose + Cer(16:0(3OH,4OH,15Me)/18:0) <=> H+ + UDP + GlcCer(16:0(3OH,4OH,15Me)/18:0)")
## cer_to_sm
cer <- "Cer(16:0(3OH,4OH,15Me)/18:0)"
reaction_l <- .create_reaction(substrates = list(Cer = cer),
template = NULL, reaction = "RHEA:18765")
expect_equal(reaction_l[[1]]$SM, "SM(16:0(3OH,4OH,15Me)/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC + Cer(16:0(3OH,4OH,15Me)/18:0) <=> DG + SM(16:0(3OH,4OH,15Me)/18:0)")
## cl_to_lcl
cl <- "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])"
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32935")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) = CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32936")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) => CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32937")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) <= CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
reaction_l <- .create_reaction(substrates = list(CL = cl),
template = NULL, reaction = "RHEA:32938")
expect_equal(reaction_l[[1]]$LCL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[1]]$FA, "FA(18:4(6Z,9Z,12Z,15Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) <=> CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + H+ + FA(18:4(6Z,9Z,12Z,15Z))")
## coa_to_acyldhap
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17657")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) = CoA + DHAP(18:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17658")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) => CoA + DHAP(18:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17659")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) <= CoA + DHAP(18:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:17660")
expect_equal(reaction_l[[1]]$AcylDHAP, "DHAP(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Dihydroxyacetone-P + CoA(18:0) <=> CoA + DHAP(18:0)")
## coa_to_fao
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52716")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ = FAO(18:0) + 2 NADP+ + CoA")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52717")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ => FAO(18:0) + 2 NADP+ + CoA")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52718")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ <= FAO(18:0) + 2 NADP+ + CoA")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:52719")
expect_equal(reaction_l[[1]]$FAO, "FAO(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + 2 NADPH + 2 H+ <=> FAO(18:0) + 2 NADP+ + CoA")
## coa_to_lpa
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15325")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) = CoA + PA(18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15326")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) => CoA + PA(18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15327")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) <= CoA + PA(18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:15328")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"Glycerol-3-P + CoA(18:0) <=> CoA + PA(18:0/0:0)")
## dg_to_sn1mg
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44712")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) = H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35663")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) = H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44713")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) => H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35664")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) => H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44714")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <= H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35665")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <= H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:44715")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <=> H+ + MG(18:0/0:0/0:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:35666")
expect_equal(reaction_l[[1]]$sn1MG, "MG(18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <=> H+ + MG(18:0/0:0/0:0) + FA(16:0)")
## dg_to_sn2mg
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33275")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) = H+ + MG(0:0/16:0/0:0) + FA(18:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33276")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) => H+ + MG(0:0/16:0/0:0) + FA(18:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33277")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <= H+ + MG(0:0/16:0/0:0) + FA(18:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:33278")
expect_equal(reaction_l[[1]]$sn2MG, "MG(0:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + DG(18:0/16:0/0:0) <=> H+ + MG(0:0/16:0/0:0) + FA(18:0)")
## dg_to_pa
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10272")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) = H+ + ADP + PA(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10273")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) => H+ + ADP + PA(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10274")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) <= H+ + ADP + PA(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:10275")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + DG(18:0/16:0/0:0) <=> H+ + ADP + PA(18:0/16:0)")
## dg_to_pc
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32939")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) = H+ + CMP + PC(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32940")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) => H+ + CMP + PC(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32941")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) <= H+ + CMP + PC(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32942")
expect_equal(reaction_l[[1]]$PC, "PC(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(18:0/16:0/0:0) <=> H+ + CMP + PC(18:0/16:0)")
## dg_to_pe
dg <- "DG(18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32943")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) = H+ + CMP + PE(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32944")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) => H+ + CMP + PE(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32945")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) <= H+ + CMP + PE(18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg),
template = NULL, reaction = "RHEA:32946")
expect_equal(reaction_l[[1]]$PE, "PE(18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(18:0/16:0/0:0) <=> H+ + CMP + PE(18:0/16:0)")
## dg_to_tg
dg <- "DG(18:0/16:0/0:0)"
acylcoa <- "CoA(14:0)"
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10868")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) = CoA + TG(18:0/16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10869")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) => CoA + TG(18:0/16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10870")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) <= CoA + TG(18:0/16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(DG = dg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:10871")
expect_equal(reaction_l[[1]]$TG, "TG(18:0/16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(14:0) + DG(18:0/16:0/0:0) <=> CoA + TG(18:0/16:0/14:0)")
## dgo_to_pco
dgo <- "DG(O-18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36179")
expect_equal(reaction_l[[1]]$PCO, "PC(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Choline + DG(O-18:0/16:0/0:0) <=> H+ + CMP + PC(O-18:0/16:0)")
## dgo_to_peo
dgo <- "DG(O-18:0/16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36187")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) = H+ + CMP + PE(O-18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36188")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) => H+ + CMP + PE(O-18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36189")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) <= H+ + CMP + PE(O-18:0/16:0)")
reaction_l <- .create_reaction(substrates = list(DGO = dgo),
template = NULL, reaction = "RHEA:36190")
expect_equal(reaction_l[[1]]$PEO, "PE(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-Ethanolamine + DG(O-18:0/16:0/0:0) <=> H+ + CMP + PE(O-18:0/16:0)")
## dhcer_to_cer
dhcer <- "Cer(d16:0(3OH,4OH)(15Me)/12:0)" ###################################################
reaction_l <- .create_reaction(substrates = list(DhCer = dhcer),
template = NULL, reaction = "dhcer_to_cer")
expect_equal(reaction_l[[1]]$Cer, "Cer(d16:0(3OH,4OH)(15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + NADH + O2 + Cer(d16:0(3OH,4OH)(15Me)/12:0) <=> 2 H2O + NAD+ + Cer(d16:0(3OH,4OH)(15Me)/12:0)")
## dhcer_to_dhsm
dhcer <- "Cer(16:1(3OH,4OH,15Me)/12:0)" ###################################################
reaction_l <- .create_reaction(substrates = list(DhCer = dhcer),
template = NULL, reaction = "RHEA:44620")
expect_equal(reaction_l[[1]]$DhSM, "SM(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC + Cer(16:1(3OH,4OH,15Me)/12:0) <=> DG + SM(16:1(3OH,4OH,15Me)/12:0)")
## dhsm_to_dhcer
dhsm <- "SM(16:1(3OH,4OH,15Me)/12:0)" ###################################################
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45300")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) = Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45301")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) => Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45302")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) <= Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(DhSM = dhsm),
template = NULL, reaction = "RHEA:45303")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:1(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:1(3OH,4OH,15Me)/12:0) <=> Phosphocholine + H+ + Cer(16:1(3OH,4OH,15Me)/12:0)")
## fa_to_coa
fa <- "FA(18:0)"
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15421")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) = PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38883")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) = PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15422")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) => PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38884")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) => PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15423")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <= PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38885")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <= PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:15424")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <=> PPi + AMP + CoA(18:0)")
reaction_l <- .create_reaction(substrates = list(FA = fa),
template = NULL, reaction = "RHEA:38886")
expect_equal(reaction_l[[1]]$AcylCoA, "CoA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + CoA + FA(18:0) <=> PPi + AMP + CoA(18:0)")
## lcl_to_cl
lcl <- "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)])"
acylcoa <- "CoA(18:4(6Z,9Z,12Z,15Z))"
reaction_l <- .create_reaction(
substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35839")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) = CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
reaction_l <- .create_reaction(substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35840")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) => CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
reaction_l <- .create_reaction(substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35841")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) <= CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
reaction_l <- .create_reaction(substrates = list(LCL = lcl, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:35842")
expect_equal(reaction_l[[1]]$CL, "CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[0:0/18:4(6Z,9Z,12Z,15Z)]) + CoA(18:4(6Z,9Z,12Z,15Z)) <=> CL(1'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)],3'-[18:4(6Z,9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)]) + CoA")
## lnape_to_gpnae
lnape <- "NAPE(14:0/0:0/0:0)"
reaction_l <- .create_reaction(substrates = list(LNAPE = lnape),
template = NULL, reaction = "RHEA:45420")
expect_equal(reaction_l[[1]]$GPNAE, "GPNAE(0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/0:0/0:0) + H2O <=> GPNAE(0:0) + FA(14:0)")
## lpa_to_pa
lpa <- "PA(18:0/0:0)"
acylcoa <- "CoA(14:0)"
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19709")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) = CoA + PA(18:0/14:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19710")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) => CoA + PA(18:0/14:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19711")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) <= CoA + PA(18:0/14:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPA = lpa, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:19712")
expect_equal(reaction_l[[1]]$PA, "PA(18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(18:0/0:0) + CoA(14:0) <=> CoA + PA(18:0/14:0)")
## lpao_to_pao
lpao <- "PA(O-18:0/0:0)"
acylcoa <- "CoA(14:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36235")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) = PA(O-18:0/14:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36236")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) => PA(O-18:0/14:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36237")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) <= PA(O-18:0/14:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPAO = lpao, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:36238")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PA(O-18:0/0:0) + CoA(14:0) <=> PA(O-18:0/14:0) + CoA")
## sn1lpc_to_fa
sn1lpc <- "PC(14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15177")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) = Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15178")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) => Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15179")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) <= Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc),
template = NULL, reaction = "RHEA:15180")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(14:0/0:0) <=> Glycerophosphocholine + H+ + FA(14:0)")
## sn2lpc_to_fa
sn2lpc <- "PC(0:0/14:0)"
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44696")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) = Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44697")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) => Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44698")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) <= Glycerophosphocholine + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2LPC = sn2lpc),
template = NULL, reaction = "RHEA:44699")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(0:0/14:0) <=> Glycerophosphocholine + H+ + FA(14:0)")
## sn1lpc_to_pc
sn1lpc <- "PC(14:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12937")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) = PC(14:0/18:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12938")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) => PC(14:0/18:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12939")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) <= PC(14:0/18:0) + CoA")
reaction_l <- .create_reaction(substrates = list(sn1LPC = sn1lpc, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:12940")
expect_equal(reaction_l[[1]]$PC, "PC(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(14:0/0:0) + CoA(18:0) <=> PC(14:0/18:0) + CoA")
## sn1lpe_to_fa
pe <- "PE(14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32967")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) = H+ + FA(14:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32968")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) => H+ + FA(14:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32969")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) <= H+ + FA(14:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPE = pe),
template = NULL, reaction = "RHEA:32970")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/0:0) <=> H+ + FA(14:0) + Glycerophosphoethanolamine")
## sn2lpe_to_fa
sn2lpe <- "PE(0:0/14:0)"
reaction_l <- .create_reaction(substrates = list(sn2LPE = sn2lpe),
template = NULL, reaction = "sn2lpe_to_fa")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(0:0/14:0) <=> H+ + FA(14:0) + Glycerophosphoethanolamine")
## sn1lpe_to_pe
sn1lpe <- "PE(14:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32995")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) = CoA + PE(14:0/18:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32996")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) => CoA + PE(14:0/18:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32997")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) <= CoA + PE(14:0/18:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPE = sn1lpe, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32998")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(14:0/0:0) <=> CoA + PE(14:0/18:0)")
## sn1lpi_to_pi
sn1lpi <- "PI(16:0/0:0)"
acylcoa <- "CoA(18:1(9Z))"
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33195")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) = PI(16:0/18:1(9Z)) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33196")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) => PI(16:0/18:1(9Z)) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33197")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) <= PI(16:0/18:1(9Z)) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPI = sn1lpi, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:33198")
expect_equal(reaction_l[[1]]$PI, "PI(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"PI(16:0/0:0) + CoA(18:1(9Z)) <=> PI(16:0/18:1(9Z)) + CoA")
## lpeo_to_peo
lpeo <- "PE(O-16:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(
substrates = list(sn1LPEO = lpeo, AcylCoA = acylcoa),
template = NULL, reaction = "lpeo_to_peo")
expect_equal(reaction_l[[1]]$PEO, "PE(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(O-16:0/0:0) <=> CoA + PE(O-16:0/18:0)")
## lpep_to_pep
lpep <- "PE(P-16:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16245")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16246")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16247")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
reaction_l <- .create_reaction(
substrates = list(sn1LPEP = lpep, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16248")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(18:0) + PE(P-16:0/0:0) <=> CoA + PE(P-16:0/18:0)")
## sn1mg_to_dg
sn1mg <- "MG(14:0/0:0/0:0)"
acylcoa <- "CoA(16:0)"
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38463")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) = CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39943")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) = CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38464")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) => CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39944")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) => CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38465")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <= CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39945")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <= CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:38466")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <=> CoA + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:39946")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(14:0/0:0/0:0) + CoA(16:0) <=> CoA + DG(14:0/16:0/0:0)")
## sn2mg_to_dg
sn2mg <- "MG(0:0/14:0/0:0)"
acylcoa <- "CoA(16:0)"
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32947")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) = CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16741")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) = CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32948")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) => CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16742")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) => CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32949")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <= CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16743")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <= CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:32950")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <=> CoA + DG(16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:16744")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(16:0) + MG(0:0/14:0/0:0) <=> CoA + DG(16:0/14:0/0:0)")
## sn1mg_to_fa
sn1mg <- "MG(14:0/0:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34019")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) = Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34020")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) => Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34021")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) <= Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:34022")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(14:0/0:0/0:0) <=> Glycerol + H+ + FA(14:0)")
## sn2mg_to_fa
sn2mg <- "MG(0:0/14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32871")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) = Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32872")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) => Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32873")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) <= Glycerol + H+ + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "RHEA:32874")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + MG(0:0/14:0/0:0) <=> Glycerol + H+ + FA(14:0)")
## sn1mg_to_lpa
sn1mg <- "MG(14:0/0:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33747")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) = H+ + ADP + PA(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33748")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) => H+ + ADP + PA(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33749")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) <= H+ + ADP + PA(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1MG = sn1mg),
template = NULL, reaction = "RHEA:33750")
expect_equal(reaction_l[[1]]$sn1LPA, "PA(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"ATP + MG(14:0/0:0/0:0) <=> H+ + ADP + PA(14:0/0:0)")
## sn2mg_to_sn1mg
sn2mg <- "MG(0:0/14:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn2MG = sn2mg),
template = NULL, reaction = "sn2mg_to_sn1mg")
expect_equal(reaction_l[[1]]$sn1MG, "MG(14:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"MG(0:0/14:0/0:0) <=> MG(14:0/0:0/0:0)")
## nae_to_fa
nae <- "NAE(18:0)"
reaction_l <- .create_reaction(substrates = list(NAE = nae),
template = NULL, reaction = "nae_to_fa")
expect_equal(reaction_l[[1]]$FA, "FA(18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + NAE(18:0) <=> Ethanolamine + H+ + FA(18:0)")
## nape_to_lnape
nape <- "NAPE(14:0/16:0/18:0)"
reaction_l <- .create_reaction(substrates = list(NAPE = nape),
template = NULL, reaction = "nape_to_lnape")
expect_equal(reaction_l[[1]]$LNAPE, "NAPE(14:0/0:0/18:0)")
expect_equal(reaction_l[[1]]$FA, "FA(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/16:0/18:0) + H2O <=> NAPE(14:0/0:0/18:0) + FA(16:0)")
## nape_to_nae
nape <- "NAPE(14:0/16:0/18:0)"
reaction_l <- .create_reaction(substrates = list(NAPE = nape),
template = NULL, reaction = "nape_to_nae")
expect_equal(reaction_l[[1]]$NAE, "NAE(18:0)")
expect_equal(reaction_l[[1]]$PA, "PA(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/16:0/18:0) + H2O <=> NAE(18:0) + PA(14:0/16:0)")
## nape_to_pnae
nape <- "NAPE(14:0/16:0/18:0)"
reaction_l <- .create_reaction(substrates = list(NAPE = nape),
template = NULL, reaction = "nape_to_pnae")
expect_equal(reaction_l[[1]]$PNAE, "PNAE(18:0)")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(14:0/16:0/18:0) + H2O <=> PNAE(18:0) + DG(14:0/16:0/0:0)")
## napeo_to_nae
napeo <- "NAPE(O-18:0/16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(NAPEO = napeo),
template = NULL, reaction = "napeo_to_nae")
expect_equal(reaction_l[[1]]$NAE, "NAE(14:0)")
expect_equal(reaction_l[[1]]$PAO, "PA(O-18:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"NAPE(O-18:0/16:0/14:0) + H2O <=> NAE(14:0) + PA(O-18:0/16:0)")
## pa_to_cdpdg
pa <- "PA(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16229")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) = PPi + CDP-DG(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16230")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) => PPi + CDP-DG(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16231")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) <= PPi + CDP-DG(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:16232")
expect_equal(reaction_l[[1]]$CDPDG, "CDP-DG(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CTP + PA(14:0/16:0) <=> PPi + CDP-DG(14:0/16:0)")
## pa_to_dg
pa <- "PA(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27429")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) = Pi + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27430")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) => Pi + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27431")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) <= Pi + DG(14:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PA = pa),
template = NULL, reaction = "RHEA:27432")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(14:0/16:0) <=> Pi + DG(14:0/16:0/0:0)")
## pao_to_dgo
pao <- "PA(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36239")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) = Pi + DG(O-16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36240")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) => Pi + DG(O-16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36241")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) <= Pi + DG(O-16:0/14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PAO = pao),
template = NULL, reaction = "RHEA:36242")
expect_equal(reaction_l[[1]]$DGO, "DG(O-16:0/14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PA(O-16:0/14:0) <=> Pi + DG(O-16:0/14:0/0:0)")
## pc_to_dg
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10604")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) = Phosphocholine + DG(20:0/18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10605")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) => Phosphocholine + DG(20:0/18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10606")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) <= Phosphocholine + DG(20:0/18:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:10607")
expect_equal(reaction_l[[1]]$DG, "DG(20:0/18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(20:0/18:0) <=> Phosphocholine + DG(20:0/18:0/0:0)")
## pc_to_sn1lpc
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15801")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) = PC(16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15802")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) => PC(16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15803")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <= PC(16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:15804")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <=> PC(16:0/0:0) + FA(14:0)")
## pc_to_sn2lpc
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18689")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) = PC(0:0/14:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18690")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) => PC(0:0/14:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18691")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <= PC(0:0/14:0) + FA(16:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:18692")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <=> PC(0:0/14:0) + FA(16:0)")
## pc_to_pa
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14445")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) = Choline + PA(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14446")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) => Choline + PA(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14447")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <= Choline + PA(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:14448")
expect_equal(reaction_l[[1]]$PA, "PA(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(16:0/14:0) <=> Choline + PA(16:0/14:0)")
## pc_to_ps
pc <- "PC(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45088")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) = Choline + PS(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45089")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) => Choline + PS(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45090")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) <= Choline + PS(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PC = pc),
template = NULL, reaction = "RHEA:45091")
expect_equal(reaction_l[[1]]$PS, "PS(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PC(16:0/14:0) <=> Choline + PS(16:0/14:0)")
## pco_to_lpco
pco <- "PC(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36231")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) = H+ + PC(O-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36232")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) => H+ + PC(O-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36233")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) <= H+ + PC(O-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PCO = pco),
template = NULL, reaction = "RHEA:36234")
expect_equal(reaction_l[[1]]$sn1LPCO, "PC(O-16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/14:0) <=> H+ + PC(O-16:0/0:0) + FA(14:0)")
## lpco_to_lpao
sn1lpco <- "PC(O-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39927")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) = PA(O-16:0/0:0) + H+ + Choline")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39928")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) => PA(O-16:0/0:0) + H+ + Choline")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39929")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <= PA(O-16:0/0:0) + H+ + Choline")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:39930")
expect_equal(reaction_l[[1]]$sn1LPAO, "PA(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <=> PA(O-16:0/0:0) + H+ + Choline")
## lpco_to_mgo
sn1lpco <- "PC(O-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36083")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) = H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36084")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) => H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36085")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <= H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPCO = sn1lpco),
template = NULL, reaction = "RHEA:36086")
expect_equal(reaction_l[[1]]$sn1MGO, "MG(O-16:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PC(O-16:0/0:0) <=> H+ + Phosphocholine + MG(O-16:0/0:0/0:0)")
## lpco_to_pco
sn1lpco <- "PC(O-16:0/0:0)"
acylcoa <- "CoA(18:0)"
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23992")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) = PC(O-16:0/18:0) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23993")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) => PC(O-16:0/18:0) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23994")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) <= PC(O-16:0/18:0) + CoA")
reaction_l <- .create_reaction(
substrates = list(sn1LPCO = sn1lpco, AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:23995")
expect_equal(reaction_l[[1]]$PCO, "PC(O-16:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PC(O-16:0/0:0) + CoA(18:0) <=> PC(O-16:0/18:0) + CoA")
## pe_to_dg
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "pe_to_dg")
expect_equal(reaction_l[[1]]$DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> P-Ethanolamine + DG(14:0/16:0/0:0)")
## pe_to_sn1lpe
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44604")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) = H+ + FA(16:0) + PE(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44605")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) => H+ + FA(16:0) + PE(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44606")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <= H+ + FA(16:0) + PE(14:0/0:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44607")
expect_equal(reaction_l[[1]]$sn1LPE, "PE(14:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> H+ + FA(16:0) + PE(14:0/0:0)")
## pe_to_sn2lpe
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44408")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) = H+ + FA(16:0) + PE(0:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44409")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) => H+ + FA(16:0) + PE(0:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44410")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <= H+ + FA(16:0) + PE(0:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:44411")
expect_equal(reaction_l[[1]]$sn2LPE, "PE(0:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> H+ + FA(16:0) + PE(0:0/14:0)")
## pe_to_nape_sn1
pe <- "PE(14:0/16:0)"
pc <- "PC(18:0/20:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe, PC = pc),
template = NULL, reaction = "pe_to_nape_sn1")
expect_equal(reaction_l[[1]]$NAPE, "NAPE(14:0/16:0/18:0)")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/20:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(14:0/16:0) + PC(18:0/20:0) <=> NAPE(14:0/16:0/18:0) + PC(0:0/20:0)")
## pe_to_nape_sn2
pe <- "PE(14:0/16:0)"
pc <- "PC(18:0/20:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe, PC = pc),
template = NULL, reaction = "pe_to_nape_sn2")
expect_equal(reaction_l[[1]]$NAPE, "NAPE(14:0/16:0/20:0)")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(18:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(14:0/16:0) + PC(18:0/20:0) <=> NAPE(14:0/16:0/20:0) + PC(18:0/0:0)")
## pe_to_pa
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "pe_to_pa")
expect_equal(reaction_l[[1]]$PA, "PA(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(14:0/16:0) <=> Ethanolamine + H+ + PA(14:0/16:0)")
## pe_to_ps
pe <- "PE(14:0/16:0)"
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27606")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) = Ethanolamine + PS(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27607")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) => Ethanolamine + PS(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27608")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) <= Ethanolamine + PS(14:0/16:0)")
reaction_l <- .create_reaction(substrates = list(PE = pe),
template = NULL, reaction = "RHEA:27609")
expect_equal(reaction_l[[1]]$PS, "PS(14:0/16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"L-Serine + PE(14:0/16:0) <=> Ethanolamine + PS(14:0/16:0)")
## peo_to_lpeo
peo <- "PE(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "peo_to_lpeo")
expect_equal(reaction_l[[1]]$sn1LPEO, "PE(O-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(O-16:0/14:0) <=> H+ + PE(O-16:0/0:0) + FA(14:0)")
## peo_to_napeo_sn1
peo <- "PE(O-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo, PC = pc),
template = NULL, reaction = "peo_to_napeo_sn1") ################
expect_equal(reaction_l[[1]]$NAPEO, "NAPE(O-16:0/14:0/20:0)")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + PC(20:0/18:0) <=> NAPE(O-16:0/14:0/20:0) + PC(0:0/18:0)")
## peo_to_napeo_sn2
peo <- "PE(O-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo, PC = pc),
template = NULL, reaction = "peo_to_napeo_sn2")
expect_equal(reaction_l[[1]]$NAPEO, "NAPE(O-16:0/14:0/18:0)")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(20:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + PC(20:0/18:0) <=> NAPE(O-16:0/14:0/18:0) + PC(20:0/0:0)")
## peo_to_pep
peo <- "PE(O-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22956")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 = PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22957")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 => PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22958")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 <= PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
reaction_l <- .create_reaction(substrates = list(PEO = peo),
template = NULL, reaction = "RHEA:22959")
expect_equal(reaction_l[[1]]$PEP, "PE(P-16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(O-16:0/14:0) + Fe2+-cytochrome b5 + 2 H+ + O2 <=> PE(P-16:0/14:0) + Fe3+-cytochrome b5 + 2 H2O")
## pep_to_lpep
pep <- "PE(P-16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36195")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) = H+ + PE(P-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36196")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) => H+ + PE(P-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36197")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) <= H+ + PE(P-16:0/0:0) + FA(14:0)")
reaction_l <- .create_reaction(substrates = list(PEP = pep),
template = NULL, reaction = "RHEA:36198")
expect_equal(reaction_l[[1]]$sn1LPEP, "PE(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/14:0) <=> H+ + PE(P-16:0/0:0) + FA(14:0)")
## lpep_to_fal
sn1lpep <- "PE(P-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16905")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) = FAL(16:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16906")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) => FAL(16:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16907")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <= FAL(16:0) + Glycerophosphoethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:16908")
expect_equal(reaction_l[[1]]$FAL, "FAL(16:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <=> FAL(16:0) + Glycerophosphoethanolamine")
## lpep_to_lpap
sn1lpep <- "PE(P-16:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36203")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) = PA(P-16:0/0:0) + H+ + Ethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36204")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) => PA(P-16:0/0:0) + H+ + Ethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36205")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <= PA(P-16:0/0:0) + H+ + Ethanolamine")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36206")
expect_equal(reaction_l[[1]]$sn1LPAP, "PA(P-16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-16:0/0:0) <=> PA(P-16:0/0:0) + H+ + Ethanolamine")
## lpep_to_mgp
sn1lpep <- "PE(P-18:0/0:0)"
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36199")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) = Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36200")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) => Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36201")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) <= Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
reaction_l <- .create_reaction(substrates = list(sn1LPEP = sn1lpep),
template = NULL, reaction = "RHEA:36202")
expect_equal(reaction_l[[1]]$sn1MGP, "MG(P-18:0/0:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PE(P-18:0/0:0) <=> Phosphoethanolamine + H+ + MG(P-18:0/0:0/0:0)")
## pep_to_napep_sn1
pep <- "PE(P-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEP = pep, PC = pc),
template = NULL, reaction = "pep_to_napep_sn1")
expect_equal(reaction_l[[1]]$NAPEP, "NAPE(P-16:0/14:0/20:0)")
expect_equal(reaction_l[[1]]$sn2LPC, "PC(0:0/18:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(P-16:0/14:0) + PC(20:0/18:0) <=> NAPE(P-16:0/14:0/20:0) + PC(0:0/18:0)")
## pep_to_napep_sn2
pep <- "PE(P-16:0/14:0)"
pc <- "PC(20:0/18:0)"
reaction_l <- .create_reaction(substrates = list(PEP = pep, PC = pc),
template = NULL, reaction = "pep_to_napep_sn2")
expect_equal(reaction_l[[1]]$NAPEP, "NAPE(P-16:0/14:0/18:0)")
expect_equal(reaction_l[[1]]$sn1LPC, "PC(20:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"PE(P-16:0/14:0) + PC(20:0/18:0) <=> NAPE(P-16:0/14:0/18:0) + PC(20:0/0:0)")
## pg_to_cl
pg <- "PG(18:4(6Z,9Z,12Z,15Z)/14:0)"
cdpdg <- "CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0)"
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32931")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) = H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32932")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) => H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32933")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) <= H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
reaction_l <- .create_reaction(substrates = list(PG = pg, CDPDG = cdpdg),
template = NULL, reaction = "RHEA:32934")
expect_equal(reaction_l[[1]]$CL,
"CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
expect_equal(reaction_l[[2]]$reaction_formula,
"CDP-DG(18:4(6Z,9Z,12Z,15Z)/14:0) + PG(18:4(6Z,9Z,12Z,15Z)/14:0) <=> H+ + CMP + CL(1'-[18:4(6Z,9Z,12Z,15Z)/14:0],3'-[18:4(6Z,9Z,12Z,15Z)/14:0])")
## pgp_to_pg
pgp <- "PGP(16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33751")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) = Pi + PG(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33752")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) => Pi + PG(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33753")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) <= Pi + PG(16:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PGP = pgp),
template = NULL, reaction = "RHEA:33754")
expect_equal(reaction_l[[1]]$PG, "PG(16:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PGP(16:0/14:0) <=> Pi + PG(16:0/14:0)")
## pi_to_dg
pi <- "PI(16:0/18:1(9Z))"
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43484")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) = myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43485")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) => myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43486")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <= myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:43487")
expect_equal(reaction_l[[1]]$DG, "DG(16:0/18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <=> myo-Inositol-1-P + H+ + DG(16:0/18:1(9Z))")
## pi_to_sn1lpi
pi <- "PI(16:0/18:1(9Z))"
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18001")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) = PI(16:0/0:0) + H+ + FA(18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18002")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) => PI(16:0/0:0) + H+ + FA(18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18003")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <= PI(16:0/0:0) + H+ + FA(18:1(9Z))")
reaction_l <- .create_reaction(substrates = list(PI = pi),
template = NULL, reaction = "RHEA:18004")
expect_equal(reaction_l[[1]]$sn1LPI, "PI(16:0/0:0)")
expect_equal(reaction_l[[1]]$FA, "FA(18:1(9Z))")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + PI(16:0/18:1(9Z)) <=> PI(16:0/0:0) + H+ + FA(18:1(9Z))")
## ps_to_pe
ps <- "PS(14:0/14:0)"
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20828")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) = CO2 + PE(14:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20829")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) => CO2 + PE(14:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20830")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) <= CO2 + PE(14:0/14:0)")
reaction_l <- .create_reaction(substrates = list(PS = ps),
template = NULL, reaction = "RHEA:20831")
expect_equal(reaction_l[[1]]$PE, "PE(14:0/14:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H+ + PS(14:0/14:0) <=> CO2 + PE(14:0/14:0)")
## sm_to_cer
sm <- "SM(16:0(3OH,4OH,15Me)/12:0)"
reaction_l <- .create_reaction(substrates = list(SM = sm),
template = NULL, reaction = "sm_to_cer")
expect_equal(reaction_l[[1]]$Cer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"H2O + SM(16:0(3OH,4OH,15Me)/12:0) <=> Phosphocholine + H+ + Cer(16:0(3OH,4OH,15Me)/12:0)")
## sphinga_to_dhcer
acylcoa <- "CoA(12:0)" ###############################################################
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53424")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) = CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53425")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) => CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53426")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) <= CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
reaction_l <- .create_reaction(substrates = list(AcylCoA = acylcoa),
template = NULL, reaction = "RHEA:53427")
expect_equal(reaction_l[[1]]$DhCer, "Cer(16:0(3OH,4OH,15Me)/12:0)")
expect_equal(reaction_l[[2]]$reaction_formula,
"CoA(12:0) + SPH(d16:0(1OH,3OH)(15Me)) <=> CoA + Cer(16:0(3OH,4OH,15Me)/12:0)")
## should be: "CoA(12:0) + SPH(16:0(1OH,3OH,15Me)) <=> CoA + Cer(16:0(3OH,4OH,15Me)/12:0)"
## tg_to_dg
tg <- "TG(18:0/16:0/14:0)"
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33271")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44864")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) = H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33272")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44865")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) => H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33273")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44866")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <= H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:33274")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(14:0) + DG(18:0/16:0/0:0)")
reaction_l <- .create_reaction(substrates = list(TG = tg),
template = NULL, reaction = "RHEA:44867")
expect_equal(reaction_l[[1]]$sn1Loss_DG, "DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn1Loss_FA, "FA(18:0)")
expect_equal(reaction_l[[1]]$sn3Loss_DG, "DG(18:0/16:0/0:0)")
expect_equal(reaction_l[[1]]$sn3Loss_FA, "FA(14:0)")
expect_equal(reaction_l[[2]]$reaction_formula[1],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(18:0) + DG(14:0/16:0/0:0)")
expect_equal(reaction_l[[2]]$reaction_formula[2],
"H2O + TG(18:0/16:0/14:0) <=> H+ + FA(14:0) + DG(18:0/16:0/0:0)")
})
## function create_reactions
test_that("create_reactions works.", {
FA <- c("FA(16:0)", "FA(12:0)", "FA(14:0)")
## create data.frame with reactions and reaction order
reactions <- rbind(
c(1, "RHEA:15421", "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA", FALSE),
c(2, "RHEA:15325", "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA", FALSE),
c(3, "RHEA:19709", "M_LPA + M_AcylCoA = M_CoA + M_PA", FALSE),
c(4, "RHEA:27429", "M_H2O + M_PA = M_Pi + M_1,2-DG", FALSE))
reactions <- data.frame(order = reactions[, 1], RHEA = reactions[, 2],
reactions = reactions[, 3], directed = reactions[, 4])
reactions$order <- as.numeric(reactions$order)
reactions$directed <- as.logical(reactions$directed)
## run the function
reactions_l <- create_reactions(substrates = list(FA = FA),
reactions = reactions)
expect_equal(length(reactions_l), 4)
## first entry
expect_equal(names(reactions_l[[1]][[1]]), c("FA", "AcylCoA"))
expect_equal(reactions_l[[1]][[1]]$FA,
c("FA(16:0)", "FA(12:0)", "FA(14:0)"))
expect_equal(reactions_l[[1]][[1]]$AcylCoA,
c("CoA(16:0)", "CoA(12:0)", "CoA(14:0)"))
expect_equal(colnames(reactions_l[[1]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[1]][[2]]), 3)
expect_equal(reactions_l[[1]][[2]]$reaction_formula[1:3],
c("ATP + CoA + FA(16:0) = PPi + AMP + CoA(16:0)",
"ATP + CoA + FA(12:0) = PPi + AMP + CoA(12:0)",
"ATP + CoA + FA(14:0) = PPi + AMP + CoA(14:0)"))
expect_equal(reactions_l[[1]][[2]]$reaction_isReversible[1:3], c("", "", ""))
expect_equal(reactions_l[[1]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[1]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[1]][[2]]$reaction_substrate[1:3],
c("ATP + CoA + FA(16:0)", "ATP + CoA + FA(12:0)", "ATP + CoA + FA(14:0)"))
expect_equal(reactions_l[[1]][[2]]$reaction_product[1:3],
c("PPi + AMP + CoA(16:0)", "PPi + AMP + CoA(12:0)", "PPi + AMP + CoA(14:0)"))
## second entry
expect_equal(names(reactions_l[[2]][[1]]), c("AcylCoA", "sn1LPA"))
expect_equal(reactions_l[[2]][[1]]$AcylCoA,
c("CoA(16:0)", "CoA(12:0)", "CoA(14:0)"))
expect_equal(reactions_l[[2]][[1]]$sn1LPA,
c("PA(16:0/0:0)", "PA(12:0/0:0)", "PA(14:0/0:0)"))
expect_equal(colnames(reactions_l[[2]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[2]][[2]]), 3)
expect_equal(reactions_l[[2]][[2]]$reaction_formula[1:3],
c("Glycerol-3-P + CoA(16:0) = CoA + PA(16:0/0:0)",
"Glycerol-3-P + CoA(12:0) = CoA + PA(12:0/0:0)",
"Glycerol-3-P + CoA(14:0) = CoA + PA(14:0/0:0)"))
expect_equal(reactions_l[[2]][[2]]$reaction_isReversible[1:3],
c("", "", ""))
expect_equal(reactions_l[[2]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[2]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[2]][[2]]$reaction_substrate[1:3],
c("Glycerol-3-P + CoA(16:0)", "Glycerol-3-P + CoA(12:0)",
"Glycerol-3-P + CoA(14:0)"))
expect_equal(reactions_l[[2]][[2]]$reaction_product[1:3],
c("CoA + PA(16:0/0:0)", "CoA + PA(12:0/0:0)", "CoA + PA(14:0/0:0)"))
## third entry
expect_equal(names(reactions_l[[3]][[1]]), c("sn1LPA", "AcylCoA", "PA"))
expect_equal(reactions_l[[3]][[1]]$sn1LPA,
c("PA(16:0/0:0)", "PA(12:0/0:0)", "PA(14:0/0:0)"))
expect_equal(reactions_l[[3]][[1]]$AcylCoA,
c("CoA(16:0)", "CoA(12:0)", "CoA(14:0)"))
expect_equal(reactions_l[[3]][[1]]$PA,
c("PA(16:0/16:0)", "PA(12:0/16:0)", "PA(14:0/16:0)", "PA(16:0/12:0)",
"PA(12:0/12:0)", "PA(14:0/12:0)", "PA(16:0/14:0)", "PA(12:0/14:0)",
"PA(14:0/14:0)"))
expect_equal(colnames(reactions_l[[3]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[3]][[2]]), 9)
expect_equal(reactions_l[[3]][[2]]$reaction_formula[1:3],
c("PA(16:0/0:0) + CoA(16:0) = CoA + PA(16:0/16:0)",
"PA(12:0/0:0) + CoA(16:0) = CoA + PA(12:0/16:0)",
"PA(14:0/0:0) + CoA(16:0) = CoA + PA(14:0/16:0)"))
expect_equal(reactions_l[[3]][[2]]$reaction_isReversible[1:3], c("", "", ""))
expect_equal(reactions_l[[3]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[3]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[3]][[2]]$reaction_substrate[1:3],
c("PA(16:0/0:0) + CoA(16:0)", "PA(12:0/0:0) + CoA(16:0)",
"PA(14:0/0:0) + CoA(16:0)"))
expect_equal(reactions_l[[3]][[2]]$reaction_product[1:3],
c("CoA + PA(16:0/16:0)", "CoA + PA(12:0/16:0)", "CoA + PA(14:0/16:0)"))
## fourth entry
expect_equal(names(reactions_l[[4]][[1]]), c("PA", "DG"))
expect_equal(reactions_l[[4]][[1]]$PA,
c("PA(16:0/16:0)", "PA(12:0/16:0)", "PA(14:0/16:0)", "PA(16:0/12:0)",
"PA(12:0/12:0)", "PA(14:0/12:0)", "PA(16:0/14:0)", "PA(12:0/14:0)",
"PA(14:0/14:0)"))
expect_equal(reactions_l[[4]][[1]]$DG,
c("DG(16:0/16:0/0:0)", "DG(12:0/16:0/0:0)", "DG(14:0/16:0/0:0)",
"DG(16:0/12:0/0:0)", "DG(12:0/12:0/0:0)", "DG(14:0/12:0/0:0)",
"DG(16:0/14:0/0:0)", "DG(12:0/14:0/0:0)", "DG(14:0/14:0/0:0)"))
expect_equal(colnames(reactions_l[[4]][[2]]),
c("reaction_name", "reaction_formula", "reaction_isReversible",
"reaction_geneAssociation", "reaction_pathway",
"reaction_substrate", "reaction_product"))
expect_equal(nrow(reactions_l[[4]][[2]]), 9)
expect_equal(reactions_l[[4]][[2]]$reaction_formula[1:3],
c("H2O + PA(16:0/16:0) = Pi + DG(16:0/16:0/0:0)",
"H2O + PA(12:0/16:0) = Pi + DG(12:0/16:0/0:0)",
"H2O + PA(14:0/16:0) = Pi + DG(14:0/16:0/0:0)"))
expect_equal(reactions_l[[4]][[2]]$reaction_isReversible[1:3], c("", "", ""))
expect_equal(reactions_l[[4]][[2]]$reaction_geneAssociation[1:3],
c("", "", ""))
expect_equal(reactions_l[[4]][[2]]$reaction_pathway[1:3], c("", "", ""))
expect_equal(reactions_l[[4]][[2]]$reaction_substrate[1:3],
c("H2O + PA(16:0/16:0)", "H2O + PA(12:0/16:0)", "H2O + PA(14:0/16:0)"))
expect_equal(reactions_l[[4]][[2]]$reaction_product[1:3],
c("Pi + DG(16:0/16:0/0:0)", "Pi + DG(12:0/16:0/0:0)",
"Pi + DG(14:0/16:0/0:0)"))
})
## function create_reactions
test_that("create_reaction_adjacency_matrix works.", {
FA <- c("FA(16:0)", "FA(12:0)", "FA(14:0)")
## create data.frame with reactions and reaction order
reactions <- rbind(
c(1, "RHEA:15421", "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA", FALSE),
c(2, "RHEA:15325", "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA", FALSE),
c(3, "RHEA:19709", "M_LPA + M_AcylCoA = M_CoA + M_PA", FALSE),
c(4, "RHEA:27429", "M_H2O + M_PA = M_Pi + M_1,2-DG", FALSE))
reactions <- data.frame(order = reactions[, 1], RHEA = reactions[, 2],
reactions = reactions[, 3], directed = reactions[, 4])
reactions$order <- as.numeric(reactions$order)
reactions$directed <- as.logical(reactions$directed)
reactions_l <- create_reactions(substrates = list(FA = FA),
reactions = reactions)
## run the function
adj <- create_reaction_adjacency_matrix(reaction_l = reactions_l)
expect_equal(dim(adj), c(34, 34))
expect_equal(rownames(adj), colnames(adj))
expect_equal(rownames(adj)[1:32],
c("AMP", "ATP", "CoA", "CoA(12:0)", "CoA(14:0)", "CoA(16:0)",
"DG(12:0/12:0/0:0)", "DG(12:0/14:0/0:0)", "DG(12:0/16:0/0:0)",
"DG(14:0/12:0/0:0)", "DG(14:0/14:0/0:0)", "DG(14:0/16:0/0:0)",
"DG(16:0/12:0/0:0)", "DG(16:0/14:0/0:0)", "DG(16:0/16:0/0:0)",
"FA(12:0)", "FA(14:0)", "FA(16:0)", "Glycerol-3-P", "H2O",
"PA(12:0/0:0)", "PA(12:0/12:0)", "PA(12:0/14:0)", "PA(12:0/16:0)",
"PA(14:0/0:0)", "PA(14:0/12:0)", "PA(14:0/14:0)", "PA(14:0/16:0)",
"PA(16:0/0:0)", "PA(16:0/12:0)", "PA(16:0/14:0)", "PA(16:0/16:0)",
"Pi", "PPi")[1:32])
expect_equal(sum(adj), 78)
expect_equal(as.vector(adj[1:5, 1:5]),
c(0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0,
1, 1, 0, 0))
expect_equal(adj["PA(14:0/0:0)", "PA(14:0/16:0)"], 1)
expect_equal(adj["PA(14:0/0:0)", "Pi"], 0)
expect_equal(adj["PA(14:0/0:0)", "PPi"], 0)
expect_equal(adj["PA(14:0/0:0)", "PA(14:0/16:0)"], 1)
expect_equal(as.vector(adj["ATP", c("CoA(12:0)", "CoA(14:0)", "CoA(16:0)")]),
c(1, 1, 1))
expect_equal(as.vector(adj[c("CoA(12:0)", "CoA(14:0)", "CoA(16:0)"), "ATP"]),
c(0, 0, 0))
})
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