R/helper_.create_template.R
In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam
Defines functions
.create_template
Documented in
.create_template
#' @name .create_template
#'
#' @title Create template with mininum information or return a given template
#'
#' @description
#' Helper function for \code{create_reaction}.
#'
#' The function \code{.create_template} returns a data.frame of the template
#' of a given \code{reaction}. The returned data.frame is either
#' the pass-through of the given \code{template} or will be created and
#' filled with minimum information using the information from
#' \code{reaction}.
#'
#' @details
#' The function \code{.create_template} will check the \code{template} object
#' for the following information:
#'
#' \itemize{
#' \item column "reaction_name" with character entry,
#' \item column "reaction_formula" with character entry,
#' \item column "reaction_isReversible" with character entry,
#' \item column "reaction_geneAssociation" with character entry,
#' \item column "reaction_pathway" with character entry.
#' }
#'
#' If \code{template} is \code{NA} or \code{NULL}, \code{template} will be set
#' to an empty list.
#'
#' @param template \code{list}, \code{NA} or \code{NULL}
#' @param reaction \code{character(1)}
#'
#' @return data.frame
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#' and Thomas Naake, \email{thomasnaake@@googlemail.com}
#'
#' @importFrom stringi stri_replace_all_fixed stri_replace_all_regex stri_split
#'
#' @examples
#' LipidNetworkPredictR:::.create_template(template = list(), reaction = "RHEA:15421")
.create_template <- function(template = list(), reaction = "RHEA:15421") {
## checks on template, convert to empty list if template is NA or NULL
if (length(template) == 1) {
if (is.na(template))
template <- list()
}
if (length(template) == 0) {
if (is.null(template))
template <- list()
}
if (!is.list(template))
stop("'template' has to be a list")
## convert to list if template is a data.frame
if (is.data.frame(template)) {
template <- as.list(template)
}
## write reaction to reation_RHEA entry
template[["reaction_RHEA"]] <- reaction
## check integrity (all names are present in template)
if (!"reaction_name" %in% names(template))
template[["reaction_name"]] <- ""
if (!"reaction_isReversible" %in% names(template))
template[["reaction_isReversible"]] <- ""
if (!"reaction_geneAssociation" %in% names(template))
template[["reaction_geneAssociation"]] <- ""
if (!"reaction_pathway" %in% names(template))
template[["reaction_pathway"]] <- ""
if (!"reaction_constraints" %in% names(template))
template[["reaction_constraints"]] <- ""
if (!"reaction_constraints_negate" %in% names(template))
template[["reaction_constraints_negate"]] <- FALSE
## all entries are of mode character
if (!is.vector(template$reaction_name, "character"))
stop("entry 'reaction_name' is not of mode 'character'")
if (!is.vector(template$reaction_isReversible, "character"))
stop("entry 'reaction_isReversible' is not of mode 'character'")
if (!is.vector(template$reaction_geneAssociation, "character"))
stop("entry 'reaction_geneAssociation' is not of mode 'character'")
if (!is.vector(template$reaction_pathway, "character"))
stop("entry 'reaction_pathway' is not of mode 'character'")
if (is.null(template$reaction_formula)) {
## this event happens if the param template is not a list
## check if reaction is in the parameter space
.check_reaction(reaction)
## dg_to_pa
if (reaction == "RHEA:10272")
.formula <- "M_1,2-DG + M_ATP = M_PA + M_ADP + M_H+"
if (reaction == "RHEA:10273")
.formula <- "M_1,2-DG + M_ATP => M_PA + M_ADP + M_H+"
if (reaction == "RHEA:10274")
.formula <- "M_1,2-DG + M_ATP <= M_PA + M_ADP + M_H+"
if (reaction == "RHEA:10275")
.formula <- "M_1,2-DG + M_ATP <=> M_PA + M_ADP + M_H+"
## pc_to_dg
if (reaction == "RHEA:10604")
.formula <- "M_PC + M_H2O = M_1,2-DG + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:10605")
.formula <- "M_PC + M_H2O => M_1,2-DG + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:10606")
.formula <- "M_PC + M_H2O <= M_1,2-DG + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:10607")
.formula <- "M_PC + M_H2O <=> M_1,2-DG + M_H+ + M_Phosphocholine"
## dg_to_tg
if (reaction == "RHEA:10868")
.formula <- "M_1,2-DG + M_AcylCoA = M_TG + M_CoA"
if (reaction == "RHEA:10869")
.formula <- "M_1,2-DG + M_AcylCoA => M_TG + M_CoA"
if (reaction == "RHEA:10870")
.formula <- "M_1,2-DG + M_AcylCoA <= M_TG + M_CoA"
if (reaction == "RHEA:10871")
.formula <- "M_1,2-DG + M_AcylCoA <=> M_TG + M_CoA"
## cdpdg_to_pi
if (reaction == "RHEA:11580")
.formula <- "M_CDP-DG + M_myo-Inositol = M_PI + M_CMP + M_H+"
if (reaction == "RHEA:11581")
.formula <- "M_CDP-DG + M_myo-Inositol => M_PI + M_CMP + M_H+"
if (reaction == "RHEA:11582")
.formula <- "M_CDP-DG + M_myo-Inositol <= M_PI + M_CMP + M_H+"
if (reaction == "RHEA:11583")
.formula <- "M_CDP-DG + M_myo-Inositol <=> M_PI + M_CMP + M_H+"
## cer_to_glccer
if (reaction == "RHEA:12088")
.formula <- "M_Cer + M_UDP-Glucose = M_GlcCer + M_H+ + M_UDP"
if (reaction == "RHEA:12089")
.formula <- "M_Cer + M_UDP-Glucose => M_GlcCer + M_H+ + M_UDP"
if (reaction == "RHEA:12090")
.formula <- "M_Cer + M_UDP-Glucose <= M_GlcCer + M_H+ + M_UDP"
if (reaction == "RHEA:12091")
.formula <- "M_Cer + M_UDP-Glucose <=> M_GlcCer + M_H+ + M_UDP"
## cdpdg_to_pgp
if (reaction == "RHEA:12593")
.formula <- "M_CDP-DG + M_Glycerol-3-P = M_PGP + M_CMP + M_H+"
if (reaction == "RHEA:12594")
.formula <- "M_CDP-DG + M_Glycerol-3-P => M_PGP + M_CMP + M_H+"
if (reaction == "RHEA:12595")
.formula <- "M_CDP-DG + M_Glycerol-3-P <= M_PGP + M_CMP + M_H+"
if (reaction == "RHEA:12596")
.formula <- "M_CDP-DG + M_Glycerol-3-P <=> M_PGP + M_CMP + M_H+"
## sn1lpc_to_pc
if (reaction == "RHEA:12937")
.formula <- "M_1-LPC + M_AcylCoA = M_PC + M_CoA"
if (reaction == "RHEA:12938")
.formula <- "M_1-LPC + M_AcylCoA => M_PC + M_CoA"
if (reaction == "RHEA:12939")
.formula <- "M_1-LPC + M_AcylCoA <= M_PC + M_CoA"
if (reaction == "RHEA:12940")
.formula <- "M_1-LPC + M_AcylCoA <=> M_PC + M_CoA"
## pc_to_pa
if (reaction == "RHEA:14445")
.formula <- "M_PC + M_H2O = M_PA + M_Choline + M_H+"
if (reaction == "RHEA:14446")
.formula <- "M_PC + M_H2O => M_PA + M_Choline + M_H+"
if (reaction == "RHEA:14447")
.formula <- "M_PC + M_H2O <= M_PA + M_Choline + M_H+"
if (reaction == "RHEA:14448")
.formula <- "M_PC + M_H2O <=> M_PA + M_Choline + M_H+"
## sn1lpc_to_fa
if (reaction == "RHEA:15177")
.formula <- "M_1-LPC + M_H2O = M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:15178")
.formula <- "M_1-LPC + M_H2O => M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:15179")
.formula <- "M_1-LPC + M_H2O <= M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:15180")
.formula <- "M_1-LPC + M_H2O <=> M_FA + M_H+ + M_Glycerophosphocholine"
## coa_to_lpa
if (reaction == "RHEA:15325")
.formula <- "M_AcylCoA + M_Glycerol-3-P = M_LPA + M_CoA"
if (reaction == "RHEA:15326")
.formula <- "M_AcylCoA + M_Glycerol-3-P => M_LPA + M_CoA"
if (reaction == "RHEA:15327")
.formula <- "M_AcylCoA + M_Glycerol-3-P <= M_LPA + M_CoA"
if (reaction == "RHEA:15328")
.formula <- "M_AcylCoA + M_Glycerol-3-P <=> M_LPA + M_CoA"
## fa_to_coa
if (reaction %in% c("RHEA:15421", "RHEA:38883"))
.formula <- "M_FA + M_ATP + M_CoA = M_AcylCoA + M_AMP + M_PPi"
if (reaction %in% c("RHEA:15422", "RHEA:38884"))
.formula <- "M_FA + M_ATP + M_CoA => M_AcylCoA + M_AMP + M_PPi"
if (reaction %in% c("RHEA:15423", "RHEA:38885"))
.formula <- "M_FA + M_ATP + M_CoA <= M_AcylCoA + M_AMP + M_PPi"
if (reaction %in% c("RHEA:15424", "RHEA:38886"))
.formula <- "M_FA + M_ATP + M_CoA <=> M_AcylCoA + M_AMP + M_PPi"
## pc_to_sn1lpc
if (reaction == "RHEA:15801")
.formula <- "M_PC + M_H2O = M_1-LPC + M_FA + M_H+"
if (reaction == "RHEA:15802")
.formula <- "M_PC + M_H2O => M_1-LPC + M_FA + M_H+"
if (reaction == "RHEA:15803")
.formula <- "M_PC + M_H2O <= M_1-LPC + M_FA + M_H+"
if (reaction == "RHEA:15804")
.formula <- "M_PC + M_H2O <=> M_1-LPC + M_FA + M_H+"
## pa_to_cdpdg
if (reaction == "RHEA:16229")
.formula <- "M_PA + M_CTP + M_H+ = M_CDP-DG + M_PPi"
if (reaction == "RHEA:16230")
.formula <- "M_PA + M_CTP + M_H+ => M_CDP-DG + M_PPi"
if (reaction == "RHEA:16231")
.formula <- "M_PA + M_CTP + M_H+ <= M_CDP-DG + M_PPi"
if (reaction == "RHEA:16232")
.formula <- "M_PA + M_CTP + M_H+ <=> M_CDP-DG + M_PPi"
## lpep_to_pep
if (reaction == "RHEA:16245")
.formula <- "M_LPE-P + M_AcylCoA = M_PE-P + M_CoA"
if (reaction == "RHEA:16246")
.formula <- "M_LPE-P + M_AcylCoA => M_PE-P + M_CoA"
if (reaction == "RHEA:16247")
.formula <- "M_LPE-P + M_AcylCoA <= M_PE-P + M_CoA"
if (reaction == "RHEA:16248")
.formula <- "M_LPE-P + M_AcylCoA <=> M_PE-P + M_CoA"
## lpep_to_fal
if (reaction == "RHEA:16905")
.formula <- "M_1-LPE-P + M_H2O = M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16906")
.formula <- "M_1-LPE-P + M_H2O => M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16907")
.formula <- "M_1-LPE-P + M_H2O <= M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16908")
.formula <- "M_1-LPE-P + M_H2O <=> M_FAL + M_Glycerophosphoethanolamine"
## nae_to_fa
if (reaction %in% c("RHEA:17505", "RHEA:39995"))
.formula <- "M_H2O + M_NAE = M_FA + M_Ethanolamine"
if (reaction %in% c("RHEA:17506", "RHEA:39996"))
.formula <- "M_H2O + M_NAE => M_FA + M_Ethanolamine"
if (reaction %in% c("RHEA:17507", "RHEA:39997"))
.formula <- "M_H2O + M_NAE <= M_FA + M_Ethanolamine"
if (reaction %in% c("RHEA:17508", "RHEA:39998"))
.formula <- "M_H2O + M_NAE <=> M_FA + M_Ethanolamine"
## coa_to_acdhap
if (reaction == "RHEA:17657")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P = M_AcylDHAP + M_CoA"
if (reaction == "RHEA:17658")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P => M_AcylDHAP + M_CoA"
if (reaction == "RHEA:17659")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P <= M_AcylDHAP + M_CoA"
if (reaction == "RHEA:17660")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P <=> M_AcylDHAP + M_CoA"
## coa_to_ce
if (reaction == "RHEA:17729")
.formula <- "M_Cholesterol + M_AcylCoA = M_CE + M_CoA"
if (reaction == "RHEA:17730")
.formula <- "M_Cholesterol + M_AcylCoA => M_CE + M_CoA"
if (reaction == "RHEA:17731")
.formula <- "M_Cholesterol + M_AcylCoA <= M_CE + M_CoA"
if (reaction == "RHEA:17732")
.formula <- "M_Cholesterol + M_AcylCoA <=> M_CE + M_CoA"
## cer_to_cerp
if (reaction == "RHEA:17929")
.formula <- "M_Cer + M_ATP = M_ADP + M_CerP + M_H+"
if (reaction == "RHEA:17930")
.formula <- "M_Cer + M_ATP => M_ADP + M_CerP + M_H+"
if (reaction == "RHEA:17931")
.formula <- "M_Cer + M_ATP <= M_ADP + M_CerP + M_H+"
if (reaction == "RHEA:17932")
.formula <- "M_Cer + M_ATP <=> M_ADP + M_CerP + M_H+"
## pi_to_sn1lpi
if (reaction == "RHEA:18001")
.formula <- "M_PI + M_H2O = M_1-LPI + M_FA + M_H+"
if (reaction == "RHEA:18002")
.formula <- "M_PI + M_H2O => M_1-LPI + M_FA + M_H+"
if (reaction == "RHEA:18003")
.formula <- "M_PI + M_H2O <= M_1-LPI + M_FA + M_H+"
if (reaction == "RHEA:18004")
.formula <- "M_PI + M_H2O <=> M_1-LPI + M_FA + M_H+"
## pc_to_sn2lpc
if (reaction == "RHEA:18689")
.formula <- "M_PC + M_H2O = M_2-LPC + M_FA + M_H+"
if (reaction == "RHEA:18690")
.formula <- "M_PC + M_H2O => M_2-LPC + M_FA + M_H+"
if (reaction == "RHEA:18691")
.formula <- "M_PC + M_H2O <= M_2-LPC + M_FA + M_H+"
if (reaction == "RHEA:18692")
.formula <- "M_PC + M_H2O <=> M_2-LPC + M_FA + M_H+"
## cer_to_sm
if (reaction == "RHEA:18765")
.formula <- "M_PC + M_Cer = M_1,2-DG + M_SM"
if (reaction == "RHEA:18766")
.formula <- "M_PC + M_Cer => M_1,2-DG + M_SM"
if (reaction == "RHEA:18767")
.formula <- "M_PC + M_Cer <= M_1,2-DG + M_SM"
if (reaction == "RHEA:18768")
.formula <- "M_PC + M_Cer <=> M_1,2-DG + M_SM"
## lpa_to_pa
if (reaction == "RHEA:19709")
.formula <- "M_LPA + M_AcylCoA = M_PA + M_CoA"
if (reaction == "RHEA:19710")
.formula <- "M_LPA + M_AcylCoA => M_PA + M_CoA"
if (reaction == "RHEA:19711")
.formula <- "M_LPA + M_AcylCoA <= M_PA + M_CoA"
if (reaction == "RHEA:19712")
.formula <- "M_LPA + M_AcylCoA <=> M_PA + M_CoA"
## ps_to_pe
if (reaction == "RHEA:20828")
.formula <- "M_PS + M_H+ = M_PE + M_CO2"
if (reaction == "RHEA:20829")
.formula <- "M_PS + M_H+ => M_PE + M_CO2"
if (reaction == "RHEA:20830")
.formula <- "M_PS + M_H+ <= M_PE + M_CO2"
if (reaction == "RHEA:20831")
.formula <- "M_PS + M_H+ <=> M_PE + M_CO2"
## peo_to_pep
if (reaction == "RHEA:22956")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 = M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
if (reaction == "RHEA:22957")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 => M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
if (reaction == "RHEA:22958")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <= M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
if (reaction == "RHEA:22959")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <=> M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
## lpco_to_pco
if (reaction == "RHEA:23992")
.formula <- "M_1-LPC-O + M_AcylCoA = M_PC-O + M_CoA"
if (reaction == "RHEA:23993")
.formula <- "M_1-LPC-O + M_AcylCoA => M_PC-O + M_CoA"
if (reaction == "RHEA:23994")
.formula <- "M_1-LPC-O + M_AcylCoA <= M_PC-O + M_CoA"
if (reaction == "RHEA:23995")
.formula <- "M_1-LPC-O + M_AcylCoA <=> M_PC-O + M_CoA"
## pa_to_dg
if (reaction == "RHEA:27429")
.formula <- "M_PA + M_H2O = M_1,2-DG + M_Pi"
if (reaction == "RHEA:27430")
.formula <- "M_PA + M_H2O => M_1,2-DG + M_Pi"
if (reaction == "RHEA:27431")
.formula <- "M_PA + M_H2O <= M_1,2-DG + M_Pi"
if (reaction == "RHEA:27432")
.formula <- "M_PA + M_H2O <=> M_1,2-DG + M_Pi"
## pe_to_ps
if (reaction == "RHEA:27606")
.formula <- "M_PE + M_L-Serine = M_PS + M_Ethanolamine"
if (reaction == "RHEA:27607")
.formula <- "M_PE + M_L-Serine => M_PS + M_Ethanolamine"
if (reaction == "RHEA:27608")
.formula <- "M_PE + M_L-Serine <= M_PS + M_Ethanolamine"
if (reaction == "RHEA:27609")
.formula <- "M_PE + M_L-Serine <=> M_PS + M_Ethanolamine"
## sn2mg_to_fa
if (reaction %in% c("RHEA:32871"))
.formula <- "M_H2O + M_2-MG = M_FA + M_Glycerol + M_H+"
if (reaction %in% c("RHEA:32872"))
.formula <- "M_H2O + M_2-MG => M_FA + M_Glycerol + M_H+"
if (reaction %in% c("RHEA:32873"))
.formula <- "M_H2O + M_2-MG <= M_FA + M_Glycerol + M_H+"
if (reaction %in% c("RHEA:32874"))
.formula <- "M_H2O + M_2-MG <=> M_FA + M_Glycerol + M_H+"
## pg_to_cl
if (reaction == "RHEA:32931")
.formula <- "M_PG + M_CDP-DG = M_CL + M_CMP + M_H+"
if (reaction == "RHEA:32932")
.formula <- "M_PG + M_CDP-DG => M_CL + M_CMP + M_H+"
if (reaction == "RHEA:32933")
.formula <- "M_PG + M_CDP-DG <= M_CL + M_CMP + M_H+"
if (reaction == "RHEA:32934")
.formula <- "M_PG + M_CDP-DG <=> M_CL + M_CMP + M_H+"
## cl_to_lcl
if (reaction == "RHEA:32935")
.formula <- "M_CL + M_H2O = M_1,2,4-LCL + M_FA + M_H+"
if (reaction == "RHEA:32936")
.formula <- "M_CL + M_H2O => M_1,2,4-LCL + M_FA + M_H+"
if (reaction == "RHEA:32937")
.formula <- "M_CL + M_H2O <= M_1,2,4-LCL + M_FA + M_H+"
if (reaction == "RHEA:32938")
.formula <- "M_CL + M_H2O <=> M_1,2,4-LCL + M_FA + M_H+"
## dg_to_pc
if (reaction == "RHEA:32939")
.formula <- "M_1,2-DG + M_CDP-Choline = M_PC + M_CMP + M_H+"
if (reaction == "RHEA:32940")
.formula <- "M_1,2-DG + M_CDP-Choline => M_PC + M_CMP + M_H+"
if (reaction == "RHEA:32941")
.formula <- "M_1,2-DG + M_CDP-Choline <= M_PC + M_CMP + M_H+"
if (reaction == "RHEA:32942")
.formula <- "M_1,2-DG + M_CDP-Choline <=> M_PC + M_CMP + M_H+"
## dg_to_pe
if (reaction == "RHEA:32943")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine = M_PE + M_CMP + M_H+"
if (reaction == "RHEA:32944")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine => M_PE + M_CMP + M_H+"
if (reaction == "RHEA:32945")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine <= M_PE + M_CMP + M_H+"
if (reaction == "RHEA:32946")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine <=> M_PE + M_CMP + M_H+"
## sn2mg_to_dg
if (reaction %in% c("RHEA:32947", "RHEA:16741"))
.formula <- "M_2-MG + M_AcylCoA = M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:32948", "RHEA:16742"))
.formula <- "M_2-MG + M_AcylCoA => M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:32949", "RHEA:16743"))
.formula <- "M_2-MG + M_AcylCoA <= M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:32950", "RHEA:16744"))
.formula <- "M_2-MG + M_AcylCoA <=> M_1,2-DG + M_CoA"
## sn1lpe_to_fa
if (reaction == "RHEA:32967")
.formula <- "M_1-LPE + M_H2O = M_FA + M_H+ + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32968")
.formula <- "M_1-LPE + M_H2O => M_FA + M_H+ + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32969")
.formula <- "M_1-LPE + M_H2O <= M_FA + M_H+ + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32970")
.formula <- "M_1-LPE + M_H2O <=> M_FA + M_H+ + M_Glycerophosphoethanolamine"
## sn1lpe_to_pe
if (reaction == "RHEA:32995")
.formula <- "M_1-LPE + M_AcylCoA = M_PE + M_CoA"
if (reaction == "RHEA:32996")
.formula <- "M_1-LPE + M_AcylCoA => M_PE + M_CoA"
if (reaction == "RHEA:32997")
.formula <- "M_1-LPE + M_AcylCoA <= M_PE + M_CoA"
if (reaction == "RHEA:32998")
.formula <- "M_1-LPE + M_AcylCoA <=> M_PE + M_CoA"
## nape_to_nae
if (reaction == "RHEA:33159")
.formula <- "M_H2O + M_NAPE = M_PA + M_NAE + M_H+"
if (reaction == "RHEA:33160")
.formula <- "M_H2O + M_NAPE => M_PA + M_NAE + M_H+"
if (reaction == "RHEA:33161")
.formula <- "M_H2O + M_NAPE <= M_PA + M_NAE + M_H+"
if (reaction == "RHEA:33162")
.formula <- "M_H2O + M_NAPE <=> M_PA + M_NAE + M_H+"
## sn1lpi_to_pi
if (reaction == "RHEA:33195")
.formula <- "M_1-LPI + M_AcylCoA = M_PI + M_CoA"
if (reaction == "RHEA:33196")
.formula <- "M_1-LPI + M_AcylCoA => M_PI + M_CoA"
if (reaction == "RHEA:33197")
.formula <- "M_1-LPI + M_AcylCoA <= M_PI + M_CoA"
if (reaction == "RHEA:33198")
.formula <- "M_1-LPI + M_AcylCoA <=> M_PI + M_CoA"
## lpg_to_pg
if (reaction == "RHEA:33203")
.formula <- "M_1-LPG + M_AcylCoA = M_PG + M_CoA"
if (reaction == "RHEA:33204")
.formula <- "M_1-LPG + M_AcylCoA => M_PG + M_CoA"
if (reaction == "RHEA:33205")
.formula <- "M_1-LPG + M_AcylCoA <= M_PG + M_CoA"
if (reaction == "RHEA:33206")
.formula <- "M_1-LPG + M_AcylCoA <=> M_PG + M_CoA"
## tg_to_dg
if (reaction %in% c("RHEA:33271", "RHEA:44864"))
.formula <- "M_TG + M_H2O = M_1,2-DG + M_FA + M_H+"
if (reaction %in% c("RHEA:33272", "RHEA:44865"))
.formula <- "M_TG + M_H2O => M_1,2-DG + M_FA + M_H+"
if (reaction %in% c("RHEA:33273", "RHEA:44866"))
.formula <- "M_TG + M_H2O <= M_1,2-DG + M_FA + M_H+"
if (reaction %in% c("RHEA:33274", "RHEA:44867"))
.formula <- "M_TG + M_H2O <=> M_1,2-DG + M_FA + M_H+"
## dg_to_sn2mg
if (reaction == "RHEA:33275")
.formula <- "M_1,2-DG + M_H2O = M_2-MG + M_FA + M_H+"
if (reaction == "RHEA:33276")
.formula <- "M_1,2-DG + M_H2O => M_2-MG + M_FA + M_H+"
if (reaction == "RHEA:33277")
.formula <- "M_1,2-DG + M_H2O <= M_2-MG + M_FA + M_H+"
if (reaction == "RHEA:33278")
.formula <- "M_1,2-DG + M_H2O <=> M_2-MG + M_FA + M_H+"
## cerp_to_cer
if (reaction == "RHEA:33743")
.formula <- "M_H2O + M_CerP = M_Pi + M_Cer"
if (reaction == "RHEA:33744")
.formula <- "M_H2O + M_CerP => M_Pi + M_Cer"
if (reaction == "RHEA:33745")
.formula <- "M_H2O + M_CerP <= M_Pi + M_Cer"
if (reaction == "RHEA:33746")
.formula <- "M_H2O + M_CerP <=> M_Pi + M_Cer"
## sn1mg_to_lpa
if (reaction == "RHEA:33747")
.formula <- "M_1-MG + M_ATP = M_LPA + M_ADP + M_H+"
if (reaction == "RHEA:33748")
.formula <- "M_1-MG + M_ATP => M_LPA + M_ADP + M_H+"
if (reaction == "RHEA:33749")
.formula <- "M_1-MG + M_ATP <= M_LPA + M_ADP + M_H+"
if (reaction == "RHEA:33750")
.formula <- "M_1-MG + M_ATP <=> M_LPA + M_ADP + M_H+"
## pgp_to_pg
if (reaction == "RHEA:33751")
.formula <- "M_PGP + M_H2O = M_PG + M_Pi"
if (reaction == "RHEA:33752")
.formula <- "M_PGP + M_H2O => M_PG + M_Pi"
if (reaction == "RHEA:33753")
.formula <- "M_PGP + M_H2O <= M_PG + M_Pi"
if (reaction == "RHEA:33754")
.formula <- "M_PGP + M_H2O <=> M_PG + M_Pi"
## sn1mg_to_fa
if (reaction == "RHEA:34019")
.formula <- "M_1-MG + M_H2O = M_FA + M_Glycerol + M_H+"
if (reaction == "RHEA:34020")
.formula <- "M_1-MG + M_H2O => M_FA + M_Glycerol + M_H+"
if (reaction == "RHEA:34021")
.formula <- "M_1-MG + M_H2O <= M_FA + M_Glycerol + M_H+"
if (reaction == "RHEA:34022")
.formula <- "M_1-MG + M_H2O <=> M_FA + M_Glycerol + M_H+"
## dg_to_sn1mg
if (reaction %in% c("RHEA:35663", "RHEA:44712"))
.formula <- "M_1,2-DG + M_H2O = M_1-MG + M_FA + M_H+"
if (reaction %in% c("RHEA:35664", "RHEA:44713"))
.formula <- "M_1,2-DG + M_H2O => M_1-MG + M_FA + M_H+"
if (reaction %in% c("RHEA:35665", "RHEA:44714"))
.formula <- "M_1,2-DG + M_H2O <= M_1-MG + M_FA + M_H+"
if (reaction %in% c("RHEA:35666", "RHEA:44715"))
.formula <- "M_1,2-DG + M_H2O <=> M_1-MG + M_FA + M_H+"
## lcl_to_cl
if (reaction == "RHEA:35839")
.formula <- "M_1,2,4-LCL + M_AcylCoA = M_CL + M_CoA"
if (reaction == "RHEA:35840")
.formula <- "M_1,2,4-LCL + M_AcylCoA => M_CL + M_CoA"
if (reaction == "RHEA:35841")
.formula <- "M_1,2,4-LCL + M_AcylCoA <= M_CL + M_CoA"
if (reaction == "RHEA:35842")
.formula <- "M_1,2,4-LCL + M_AcylCoA <=> M_CL + M_CoA"
## lpco_to_mgo
if (reaction == "RHEA:36083")
.formula <- "M_1-LPC-O + M_H2O = M_1-MG-O + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:36084")
.formula <- "M_1-LPC-O + M_H2O => M_1-MG-O + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:36085")
.formula <- "M_1-LPC-O + M_H2O <= M_1-MG-O + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:36086")
.formula <- "M_1-LPC-O + M_H2O <=> M_1-MG-O + M_H+ + M_Phosphocholine"
## acyldhap_to_alkyldhap
if (reaction == "RHEA:36171")
.formula <- "M_AcylDHAP + M_FAO = M_AlkylDHAP + M_FA + M_H+"
if (reaction == "RHEA:36172")
.formula <- "M_AcylDHAP + M_FAO => M_AlkylDHAP + M_FA + M_H+"
if (reaction == "RHEA:36173")
.formula <- "M_AcylDHAP + M_FAO <= M_AlkylDHAP + M_FA + M_H+"
if (reaction == "RHEA:36174")
.formula <- "M_AcylDHAP + M_FAO <=> M_AlkylDHAP + M_FA + M_H+"
## alkyldhap_to_lpao
if (reaction == "RHEA:36175")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH = M_LPA-O + M_NADP"
if (reaction == "RHEA:36176")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH => M_LPA-O + M_NADP"
if (reaction == "RHEA:36177")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH <= M_LPA-O + M_NADP"
if (reaction == "RHEA:36178")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH <=> M_LPA-O + M_NADP"
## dgo_to_pco
if (reaction == "RHEA:36179")
.formula <- "M_DG-O + M_CDP-Choline = M_PC-O + M_CMP + M_H+"
if (reaction == "RHEA:36180")
.formula <- "M_DG-O + M_CDP-Choline => M_PC-O + M_CMP + M_H+"
if (reaction == "RHEA:36181")
.formula <- "M_DG-O + M_CDP-Choline <= M_PC-O + M_CMP + M_H+"
if (reaction == "RHEA:36182")
.formula <- "M_DG-O + M_CDP-Choline <=> M_PC-O + M_CMP + M_H+"
## dgo_to_peo
if (reaction == "RHEA:36187")
.formula <- "M_DG-O + M_CDP-Ethanolamine = M_PE-O + M_CMP + M_H+"
if (reaction == "RHEA:36188")
.formula <- "M_DG-O + M_CDP-Ethanolamine => M_PE-O + M_CMP + M_H+"
if (reaction == "RHEA:36189")
.formula <- "M_DG-O + M_CDP-Ethanolamine <= M_PE-O + M_CMP + M_H+"
if (reaction == "RHEA:36190")
.formula <- "M_DG-O + M_CDP-Ethanolamine <=> M_PE-O + M_CMP + M_H+"
## pep_to_lpep
if (reaction == "RHEA:36195")
.formula <- "M_PE-P + M_H2O = M_LPE-P + M_FA + M_H+"
if (reaction == "RHEA:36196")
.formula <- "M_PE-P + M_H2O => M_LPE-P + M_FA + M_H+"
if (reaction == "RHEA:36197")
.formula <- "M_PE-P + M_H2O <= M_LPE-P + M_FA + M_H+"
if (reaction == "RHEA:36198")
.formula <- "M_PE-P + M_H2O <=> M_LPE-P + M_FA + M_H+"
## lpep_to_mgp
if (reaction == "RHEA:36199")
.formula <- "M_1-LPE-P + M_H2O = M_1-MG-P + M_H+ + M_Phosphoethanolamine"
if (reaction == "RHEA:36200")
.formula <- "M_1-LPE-P + M_H2O => M_1-MG-P + M_H+ + M_Phosphoethanolamine"
if (reaction == "RHEA:36201")
.formula <- "M_1-LPE-P + M_H2O <= M_1-MG-P + M_H+ + M_Phosphoethanolamine"
if (reaction == "RHEA:36202")
.formula <- "M_1-LPE-P + M_H2O <=> M_1-MG-P + M_H+ + M_Phosphoethanolamine"
## lpep_to_lpap
if (reaction == "RHEA:36203")
.formula <- "M_1-LPE-P + M_H2O = M_LPA-P + M_Ethanolamine + M_H+"
if (reaction == "RHEA:36204")
.formula <- "M_1-LPE-P + M_H2O => M_LPA-P + M_Ethanolamine + M_H+"
if (reaction == "RHEA:36205")
.formula <- "M_1-LPE-P + M_H2O <= M_LPA-P + M_Ethanolamine + M_H+"
if (reaction == "RHEA:36206")
.formula <- "M_1-LPE-P + M_H2O <=> M_LPA-P + M_Ethanolamine + M_H+"
## pco_to_lpco
if (reaction == "RHEA:36231")
.formula <- "M_PC-O + M_H2O = M_LPC-O + M_FA + M_H+"
if (reaction == "RHEA:36232")
.formula <- "M_PC-O + M_H2O => M_LPC-O + M_FA + M_H+"
if (reaction == "RHEA:36233")
.formula <- "M_PC-O + M_H2O <= M_LPC-O + M_FA + M_H+"
if (reaction == "RHEA:36234")
.formula <- "M_PC-O + M_H2O <=> M_LPC-O + M_FA + M_H+"
## lpao_to_pao
if (reaction == "RHEA:36235")
.formula <- "M_LPA-O + M_AcylCoA = M_PA-O + M_CoA"
if (reaction == "RHEA:36236")
.formula <- "M_LPA-O + M_AcylCoA => M_PA-O + M_CoA"
if (reaction == "RHEA:36237")
.formula <- "M_LPA-O + M_AcylCoA <= M_PA-O + M_CoA"
if (reaction == "RHEA:36238")
.formula <- "M_LPA-O + M_AcylCoA <=> M_PA-O + M_CoA"
## pao_to_dgo
if (reaction == "RHEA:36239")
.formula <- "M_PA-O + M_H2O = M_DG-O + M_Pi"
if (reaction == "RHEA:36240")
.formula <- "M_PA-O + M_H2O => M_DG-O + M_Pi"
if (reaction == "RHEA:36241")
.formula <- "M_PA-O + M_H2O <= M_DG-O + M_Pi"
if (reaction == "RHEA:36242")
.formula <- "M_PA-O + M_H2O <=> M_DG-O + M_Pi"
## sn1mg_to_dg
if (reaction %in% c("RHEA:38463", "RHEA:39943"))
.formula <- "M_1-MG + M_AcylCoA = M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:38464", "RHEA:39944"))
.formula <- "M_1-MG + M_AcylCoA => M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:38465", "RHEA:39945"))
.formula <- "M_1-MG + M_AcylCoA <= M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:38466", "RHEA:39946"))
.formula <- "M_1-MG + M_AcylCoA <=> M_1,2-DG + M_CoA"
## lpco_to_lpao
if (reaction == "RHEA:39927")
.formula <- "M_1-LPC-O + M_H2O = M_1-LPA-O + M_Choline + M_H+"
if (reaction == "RHEA:39928")
.formula <- "M_1-LPC-O + M_H2O => M_1-LPA-O + M_Choline + M_H+"
if (reaction == "RHEA:39929")
.formula <- "M_1-LPC-O + M_H2O <= M_1-LPA-O + M_Choline + M_H+"
if (reaction == "RHEA:39930")
.formula <- "M_1-LPC-O + M_H2O <=> M_1-LPA-O + M_Choline + M_H+"
## pi_to_dg
if (reaction == "RHEA:43484")
.formula <- "M_PI + M_H2O = M_myo-Inositol-1-P + M_1,2-DG + M_H+"
if (reaction == "RHEA:43485")
.formula <- "M_PI + M_H2O => M_myo-Inositol-1-P + M_1,2-DG + M_H+"
if (reaction == "RHEA:43486")
.formula <- "M_PI + M_H2O <= M_myo-Inositol-1-P + M_1,2-DG + M_H+"
if (reaction == "RHEA:43487")
.formula <- "M_PI + M_H2O <=> M_myo-Inositol-1-P + M_1,2-DG + M_H+"
## pe_to_sn2lpe
if (reaction == "RHEA:44408")
.formula <- "M_PE + M_H2O = M_2-LPE + M_FA + M_H+"
if (reaction == "RHEA:44409")
.formula <- "M_PE + M_H2O => M_2-LPE + M_FA + M_H+"
if (reaction == "RHEA:44410")
.formula <- "M_PE + M_H2O <= M_2-LPE + M_FA + M_H+"
if (reaction == "RHEA:44411")
.formula <- "M_PE + M_H2O <=> M_2-LPE + M_FA + M_H+"
## pg_to_sn1lpg
if (reaction == "RHEA:44416")
.formula <- "M_PG + M_H2O = M_1-LPG + M_FA + M_H+"
if (reaction == "RHEA:44417")
.formula <- "M_PG + M_H2O => M_1-LPG + M_FA + M_H+"
if (reaction == "RHEA:44418")
.formula <- "M_PG + M_H2O <= M_1-LPG + M_FA + M_H+"
if (reaction == "RHEA:44419")
.formula <- "M_PG + M_H2O <=> M_1-LPG + M_FA + M_H+"
## pe_to_sn1lpe
if (reaction == "RHEA:44604")
.formula <- "M_PE + M_H2O = M_1-LPE + M_FA + M_H+"
if (reaction == "RHEA:44605")
.formula <- "M_PE + M_H2O => M_1-LPE + M_FA + M_H+"
if (reaction == "RHEA:44606")
.formula <- "M_PE + M_H2O <= M_1-LPE + M_FA + M_H+"
if (reaction == "RHEA:44607")
.formula <- "M_PE + M_H2O <=> M_1-LPE + M_FA + M_H+"
## dhcer_to_dhsm
if (reaction == "RHEA:44620")
.formula <- "M_PC + M_DhCer = M_1,2-DG + M_DhSM"
if (reaction == "RHEA:44621")
.formula <- "M_PC + M_DhCer => M_1,2-DG + M_DhSM"
if (reaction == "RHEA:44622")
.formula <- "M_PC + M_DhCer <= M_1,2-DG + M_DhSM"
if (reaction == "RHEA:44623")
.formula <- "M_PC + M_DhCer <=> M_1,2-DG + M_DhSM"
## sn2lpc_to_fa
if (reaction == "RHEA:44696")
.formula <- "M_2-LPC + M_H2O = M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:44697")
.formula <- "M_2-LPC + M_H2O => M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:44698")
.formula <- "M_2-LPC + M_H2O <= M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:44699")
.formula <- "M_2-LPC + M_H2O <=> M_FA + M_H+ + M_Glycerophosphocholine"
## pc_to_ps
if (reaction == "RHEA:45088")
.formula <- "M_PC + M_L-Serine = M_PS + M_Choline"
if (reaction == "RHEA:45089")
.formula <- "M_PC + M_L-Serine => M_PS + M_Choline"
if (reaction == "RHEA:45090")
.formula <- "M_PC + M_L-Serine <= M_PS + M_Choline"
if (reaction == "RHEA:45091")
.formula <- "M_PC + M_L-Serine <=> M_PS + M_Choline"
## pe_to_nape_sn1
if (reaction == "RHEA:45188")
.formula <- "M_PC + M_PE = M_2-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45189")
.formula <- "M_PC + M_PE => M_2-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45190")
.formula <- "M_PC + M_PE <= M_2-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45191")
.formula <- "M_PC + M_PE <=> M_2-LPC + M_H+ + M_NAPE"
## pe_to_nape_sn2
if (reaction == "RHEA:45192")
.formula <- "M_PC + M_PE = M_1-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45193")
.formula <- "M_PC + M_PE => M_1-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45194")
.formula <- "M_PC + M_PE <= M_1-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45195")
.formula <- "M_PC + M_PE <=> M_1-LPC + M_H+ + M_NAPE"
## dhsm_to_dhcer
if (reaction == "RHEA:45300")
.formula <- "M_DhSM + M_H2O = M_DhCer + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:45301")
.formula <- "M_DhSM + M_H2O => M_DhCer + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:45302")
.formula <- "M_DhSM + M_H2O <= M_DhCer + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:45303")
.formula <- "M_DhSM + M_H2O <=> M_DhCer + M_H+ + M_Phosphocholine"
## lnape_to_gpnae
if (reaction == "RHEA:45420")
.formula <- "M_H2O + M_LNAPE = M_FA + M_H+ + M_GPNAE"
if (reaction == "RHEA:45421")
.formula <- "M_H2O + M_LNAPE => M_FA + M_H+ + M_GPNAE"
if (reaction == "RHEA:45422")
.formula <- "M_H2O + M_LNAPE <= M_FA + M_H+ + M_GPNAE"
if (reaction == "RHEA:45423")
.formula <- "M_H2O + M_LNAPE <=> M_FA + M_H+ + M_GPNAE"
## nape_to_lnape
if (reaction == "RHEA:45460")
.formula <- "M_H2O + M_NAPE = M_FA + M_H+ + M_LNAPE"
if (reaction == "RHEA:45461")
.formula <- "M_H2O + M_NAPE => M_FA + M_H+ + M_LNAPE"
if (reaction == "RHEA:45462")
.formula <- "M_H2O + M_NAPE <= M_FA + M_H+ + M_LNAPE"
if (reaction == "RHEA:45463")
.formula <- "M_H2O + M_NAPE <=> M_FA + M_H+ + M_LNAPE"
## dhcer_to_cer
if (reaction == "RHEA:46544")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 = 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
if (reaction == "RHEA:46545")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 => 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
if (reaction == "RHEA:46546")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <= 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
if (reaction == "RHEA:46547")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <=> 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
## sm_to_cer
if (reaction == "RHEA:45644")
.formula <- "M_H2O + M_SM = M_H+ + M_Cer + M_Phosphocholine"
if (reaction == "RHEA:45645")
.formula <- "M_H2O + M_SM => M_H+ + M_Cer + M_Phosphocholine"
if (reaction == "RHEA:45646")
.formula <- "M_H2O + M_SM <= M_H+ + M_Cer + M_Phosphocholine"
if (reaction == "RHEA:45647")
.formula <- "M_H2O + M_SM <=> M_H+ + M_Cer + M_Phosphocholine"
## coa_to_fao
if (reaction == "RHEA:52716")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH = M_FAO + M_CoA + 2 M_NADP"
if (reaction == "RHEA:52717")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH => M_FAO + M_CoA + 2 M_NADP"
if (reaction == "RHEA:52718")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH <= M_FAO + M_CoA + 2 M_NADP"
if (reaction == "RHEA:52719")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH <=> M_FAO + M_CoA + 2 M_NADP"
## sphinga_to_dhcer
if (reaction == "RHEA:53424")
.formula <- "M_AcylCoA + M_Sphinganine = M_DhCer + M_CoA + M_H+"
if (reaction == "RHEA:53425")
.formula <- "M_AcylCoA + M_Sphinganine => M_DhCer + M_CoA + M_H+"
if (reaction == "RHEA:53426")
.formula <- "M_AcylCoA + M_Sphinganine <= M_DhCer + M_CoA + M_H+"
if (reaction == "RHEA:53427")
.formula <- "M_AcylCoA + M_Sphinganine <=> M_DhCer + M_CoA + M_H+"
## pep_to_napep_sn1
if (reaction == "RHEA:63596")
.formula <- "M_PE-P + M_PC = M_2-LPC + M_H+ + M_NAPEP"
if (reaction == "RHEA:63597")
.formula <- "M_PE-P + M_PC => M_2-LPC + M_H+ + M_NAPEP"
if (reaction == "RHEA:63598")
.formula <- "M_PE-P + M_PC <= M_2-LPC + M_H+ + M_NAPEP"
if (reaction == "RHEA:63599")
.formula <- "M_PE-P + M_PC <=> M_2-LPC + M_H+ + M_NAPEP"
## pe_to_dg
if (reaction == "RHEA:78951")
.formula <- "M_H2O + M_PE = M_P-Ethanolamine + M_1,2-DG + M_H+"
if (reaction == "RHEA:78952")
.formula <- "M_H2O + M_PE => M_P-Ethanolamine + M_1,2-DG + M_H+"
if (reaction == "RHEA:78953")
.formula <- "M_H2O + M_PE <= M_P-Ethanolamine + M_1,2-DG + M_H+"
if (reaction == "RHEA:78954")
.formula <- "M_H2O + M_PE <=> M_P-Ethanolamine + M_1,2-DG + M_H+"
## sn2lpe_to_fa
if (reaction == "sn2lpe_to_fa")
.formula <- "M_2-LPE + M_H2O <=> M_FA + M_H+ + M_Glycerophosphoethanolamine"
## lpeo_to_peo
if (reaction == "lpeo_to_peo")
.formula <- "M_AcylCoA + M_LPE-O <=> M_CoA + M_PE-O"
## sn2mg_to_sn1mg
if (reaction == "sn2mg_to_sn1mg")
.formula <- "M_2-MG <=> M_1-MG"
## nape_to_pnae
if (reaction == "nape_to_pnae")
.formula <- "M_NAPE + M_H2O <=> M_PNAE + M_1,2-DG"
## napeo_to_nae
if (reaction == "napeo_to_nae")
.formula <- "M_NAPEO + M_H2O <=> M_NAE + M_PA-O"
## pe_to_pa
if (reaction == "pe_to_pa")
.formula <- "M_PE + M_H2O <=> M_PA + M_Ethanolamine + M_H+"
## peo_to_lpeo
if (reaction == "peo_to_lpeo")
.formula <- "M_PE-O + M_H2O <=> M_LPE-O + M_FA + M_H+"
## peo_to_napeo_sn1
if (reaction == "peo_to_napeo_sn1")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_2-LPC"
## peo_to_napeo_sn2
if (reaction == "peo_to_napeo_sn2")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_1-LPC"
## pep_to_napep_sn2
if (reaction == "pep_to_napep_sn2")
.formula <- "M_PE-P + M_PC <=> M_NAPEP + M_1-LPC"
template$reaction_formula <- .formula
}
## fill using reaction_formula
## split the template$reaction_formula into substrates and products
.formula_tmp <- template$reaction_formula
.formula_tmp <- stringi::stri_replace_all_regex(str = .formula_tmp,
pattern = ">|<", replacement = "")
.formula_tmp <- stringi::stri_split(str = .formula_tmp, fixed = "=")[[1]]
.formula_substrate <- .formula_tmp[1]
.formula_product <- .formula_tmp[2]
## remove the "+" and the trailing spaces for substrates and products
.formula_substrate <- stringi::stri_split(str = .formula_substrate,
regex = "[ ][+][ ]")[[1]]
.formula_substrate <- stringi::stri_replace_all_regex(str = .formula_substrate,
pattern = "^ | $", replacement = "")
.formula_product <- stringi::stri_split(str = .formula_product,
regex = "[ ][+][ ]")[[1]]
.formula_product <- stringi::stri_replace_all_regex(str = .formula_product,
pattern = "^ | $", replacement = "")
## write the substrates and products to the template
template$reaction_substrate <- .formula_substrate
template$reaction_product <- .formula_product
## fill using reaction_formula_chebi
## add ChEBI ids using the mapping table
.mappingTable <- mappingTable()
inds <- which(.mappingTable == reaction, arr.ind = TRUE)[, "row"]
.mappingTable <- .mappingTable[inds, ]
## find the corresponding CHEBIs for substrates
substrate_tmp <- stringi::stri_split(template$reaction_substrate, regex = "[ ]")
.formula_substrate <- lapply(substrate_tmp, function(substrate_tmp_i) {
inds_match <- match(substrate_tmp_i, .mappingTable[, 1])
res <- .mappingTable[inds_match, 3, drop = FALSE]
res[is.na(inds_match)] <- substrate_tmp_i[is.na(inds_match)]
paste(res, collapse = " ")
}) |>
unlist()
## find the corresponding CHEBIs for products
product_tmp <- stringi::stri_split(template$reaction_product, regex = "[ ]")
.formula_product <- lapply(product_tmp, function(product_tmp_i) {
inds_match <- match(product_tmp_i, .mappingTable[, 1])
res <- .mappingTable[inds_match, 3, drop = FALSE]
res[is.na(inds_match)] <- product_tmp_i[is.na(inds_match)]
paste(res, collapse = " ")
}) |>
unlist()
## determine the reaction direction
patterns <- c("<=>", "<=", "=>", "=")
matches <- sapply(patterns, function(p) grepl(p, template$reaction_formula))
reaction_type <- names(which(matches)[1])
## assemble the reaction_formula_chebi
template$reaction_formula_chebi <- paste(
paste(.formula_substrate, collapse = " + "), reaction_type,
paste(.formula_product, collapse = " + "), collapse = " ")
## write the substrates and products to the template
template$reaction_substrate_chebi <- .formula_substrate
template$reaction_product_chebi <- .formula_product
## return the template object
template
}
michaelwitting/wormLipidPredictR documentation built on Jan. 30, 2025, 12:30 a.m.
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Defines functions .create_template
Documented in .create_template
#' @name .create_template
#'
#' @title Create template with mininum information or return a given template
#'
#' @description
#' Helper function for \code{create_reaction}.
#'
#' The function \code{.create_template} returns a data.frame of the template
#' of a given \code{reaction}. The returned data.frame is either
#' the pass-through of the given \code{template} or will be created and
#' filled with minimum information using the information from
#' \code{reaction}.
#'
#' @details
#' The function \code{.create_template} will check the \code{template} object
#' for the following information:
#'
#' \itemize{
#' \item column "reaction_name" with character entry,
#' \item column "reaction_formula" with character entry,
#' \item column "reaction_isReversible" with character entry,
#' \item column "reaction_geneAssociation" with character entry,
#' \item column "reaction_pathway" with character entry.
#' }
#'
#' If \code{template} is \code{NA} or \code{NULL}, \code{template} will be set
#' to an empty list.
#'
#' @param template \code{list}, \code{NA} or \code{NULL}
#' @param reaction \code{character(1)}
#'
#' @return data.frame
#'
#' @author Michael Witting, \email{michael.witting@@helmholtz-muenchen.de}
#' and Thomas Naake, \email{thomasnaake@@googlemail.com}
#'
#' @importFrom stringi stri_replace_all_fixed stri_replace_all_regex stri_split
#'
#' @examples
#' LipidNetworkPredictR:::.create_template(template = list(), reaction = "RHEA:15421")
.create_template <- function(template = list(), reaction = "RHEA:15421") {
## checks on template, convert to empty list if template is NA or NULL
if (length(template) == 1) {
if (is.na(template))
template <- list()
}
if (length(template) == 0) {
if (is.null(template))
template <- list()
}
if (!is.list(template))
stop("'template' has to be a list")
## convert to list if template is a data.frame
if (is.data.frame(template)) {
template <- as.list(template)
}
## write reaction to reation_RHEA entry
template[["reaction_RHEA"]] <- reaction
## check integrity (all names are present in template)
if (!"reaction_name" %in% names(template))
template[["reaction_name"]] <- ""
if (!"reaction_isReversible" %in% names(template))
template[["reaction_isReversible"]] <- ""
if (!"reaction_geneAssociation" %in% names(template))
template[["reaction_geneAssociation"]] <- ""
if (!"reaction_pathway" %in% names(template))
template[["reaction_pathway"]] <- ""
if (!"reaction_constraints" %in% names(template))
template[["reaction_constraints"]] <- ""
if (!"reaction_constraints_negate" %in% names(template))
template[["reaction_constraints_negate"]] <- FALSE
## all entries are of mode character
if (!is.vector(template$reaction_name, "character"))
stop("entry 'reaction_name' is not of mode 'character'")
if (!is.vector(template$reaction_isReversible, "character"))
stop("entry 'reaction_isReversible' is not of mode 'character'")
if (!is.vector(template$reaction_geneAssociation, "character"))
stop("entry 'reaction_geneAssociation' is not of mode 'character'")
if (!is.vector(template$reaction_pathway, "character"))
stop("entry 'reaction_pathway' is not of mode 'character'")
if (is.null(template$reaction_formula)) {
## this event happens if the param template is not a list
## check if reaction is in the parameter space
.check_reaction(reaction)
## dg_to_pa
if (reaction == "RHEA:10272")
.formula <- "M_1,2-DG + M_ATP = M_PA + M_ADP + M_H+"
if (reaction == "RHEA:10273")
.formula <- "M_1,2-DG + M_ATP => M_PA + M_ADP + M_H+"
if (reaction == "RHEA:10274")
.formula <- "M_1,2-DG + M_ATP <= M_PA + M_ADP + M_H+"
if (reaction == "RHEA:10275")
.formula <- "M_1,2-DG + M_ATP <=> M_PA + M_ADP + M_H+"
## pc_to_dg
if (reaction == "RHEA:10604")
.formula <- "M_PC + M_H2O = M_1,2-DG + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:10605")
.formula <- "M_PC + M_H2O => M_1,2-DG + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:10606")
.formula <- "M_PC + M_H2O <= M_1,2-DG + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:10607")
.formula <- "M_PC + M_H2O <=> M_1,2-DG + M_H+ + M_Phosphocholine"
## dg_to_tg
if (reaction == "RHEA:10868")
.formula <- "M_1,2-DG + M_AcylCoA = M_TG + M_CoA"
if (reaction == "RHEA:10869")
.formula <- "M_1,2-DG + M_AcylCoA => M_TG + M_CoA"
if (reaction == "RHEA:10870")
.formula <- "M_1,2-DG + M_AcylCoA <= M_TG + M_CoA"
if (reaction == "RHEA:10871")
.formula <- "M_1,2-DG + M_AcylCoA <=> M_TG + M_CoA"
## cdpdg_to_pi
if (reaction == "RHEA:11580")
.formula <- "M_CDP-DG + M_myo-Inositol = M_PI + M_CMP + M_H+"
if (reaction == "RHEA:11581")
.formula <- "M_CDP-DG + M_myo-Inositol => M_PI + M_CMP + M_H+"
if (reaction == "RHEA:11582")
.formula <- "M_CDP-DG + M_myo-Inositol <= M_PI + M_CMP + M_H+"
if (reaction == "RHEA:11583")
.formula <- "M_CDP-DG + M_myo-Inositol <=> M_PI + M_CMP + M_H+"
## cer_to_glccer
if (reaction == "RHEA:12088")
.formula <- "M_Cer + M_UDP-Glucose = M_GlcCer + M_H+ + M_UDP"
if (reaction == "RHEA:12089")
.formula <- "M_Cer + M_UDP-Glucose => M_GlcCer + M_H+ + M_UDP"
if (reaction == "RHEA:12090")
.formula <- "M_Cer + M_UDP-Glucose <= M_GlcCer + M_H+ + M_UDP"
if (reaction == "RHEA:12091")
.formula <- "M_Cer + M_UDP-Glucose <=> M_GlcCer + M_H+ + M_UDP"
## cdpdg_to_pgp
if (reaction == "RHEA:12593")
.formula <- "M_CDP-DG + M_Glycerol-3-P = M_PGP + M_CMP + M_H+"
if (reaction == "RHEA:12594")
.formula <- "M_CDP-DG + M_Glycerol-3-P => M_PGP + M_CMP + M_H+"
if (reaction == "RHEA:12595")
.formula <- "M_CDP-DG + M_Glycerol-3-P <= M_PGP + M_CMP + M_H+"
if (reaction == "RHEA:12596")
.formula <- "M_CDP-DG + M_Glycerol-3-P <=> M_PGP + M_CMP + M_H+"
## sn1lpc_to_pc
if (reaction == "RHEA:12937")
.formula <- "M_1-LPC + M_AcylCoA = M_PC + M_CoA"
if (reaction == "RHEA:12938")
.formula <- "M_1-LPC + M_AcylCoA => M_PC + M_CoA"
if (reaction == "RHEA:12939")
.formula <- "M_1-LPC + M_AcylCoA <= M_PC + M_CoA"
if (reaction == "RHEA:12940")
.formula <- "M_1-LPC + M_AcylCoA <=> M_PC + M_CoA"
## pc_to_pa
if (reaction == "RHEA:14445")
.formula <- "M_PC + M_H2O = M_PA + M_Choline + M_H+"
if (reaction == "RHEA:14446")
.formula <- "M_PC + M_H2O => M_PA + M_Choline + M_H+"
if (reaction == "RHEA:14447")
.formula <- "M_PC + M_H2O <= M_PA + M_Choline + M_H+"
if (reaction == "RHEA:14448")
.formula <- "M_PC + M_H2O <=> M_PA + M_Choline + M_H+"
## sn1lpc_to_fa
if (reaction == "RHEA:15177")
.formula <- "M_1-LPC + M_H2O = M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:15178")
.formula <- "M_1-LPC + M_H2O => M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:15179")
.formula <- "M_1-LPC + M_H2O <= M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:15180")
.formula <- "M_1-LPC + M_H2O <=> M_FA + M_H+ + M_Glycerophosphocholine"
## coa_to_lpa
if (reaction == "RHEA:15325")
.formula <- "M_AcylCoA + M_Glycerol-3-P = M_LPA + M_CoA"
if (reaction == "RHEA:15326")
.formula <- "M_AcylCoA + M_Glycerol-3-P => M_LPA + M_CoA"
if (reaction == "RHEA:15327")
.formula <- "M_AcylCoA + M_Glycerol-3-P <= M_LPA + M_CoA"
if (reaction == "RHEA:15328")
.formula <- "M_AcylCoA + M_Glycerol-3-P <=> M_LPA + M_CoA"
## fa_to_coa
if (reaction %in% c("RHEA:15421", "RHEA:38883"))
.formula <- "M_FA + M_ATP + M_CoA = M_AcylCoA + M_AMP + M_PPi"
if (reaction %in% c("RHEA:15422", "RHEA:38884"))
.formula <- "M_FA + M_ATP + M_CoA => M_AcylCoA + M_AMP + M_PPi"
if (reaction %in% c("RHEA:15423", "RHEA:38885"))
.formula <- "M_FA + M_ATP + M_CoA <= M_AcylCoA + M_AMP + M_PPi"
if (reaction %in% c("RHEA:15424", "RHEA:38886"))
.formula <- "M_FA + M_ATP + M_CoA <=> M_AcylCoA + M_AMP + M_PPi"
## pc_to_sn1lpc
if (reaction == "RHEA:15801")
.formula <- "M_PC + M_H2O = M_1-LPC + M_FA + M_H+"
if (reaction == "RHEA:15802")
.formula <- "M_PC + M_H2O => M_1-LPC + M_FA + M_H+"
if (reaction == "RHEA:15803")
.formula <- "M_PC + M_H2O <= M_1-LPC + M_FA + M_H+"
if (reaction == "RHEA:15804")
.formula <- "M_PC + M_H2O <=> M_1-LPC + M_FA + M_H+"
## pa_to_cdpdg
if (reaction == "RHEA:16229")
.formula <- "M_PA + M_CTP + M_H+ = M_CDP-DG + M_PPi"
if (reaction == "RHEA:16230")
.formula <- "M_PA + M_CTP + M_H+ => M_CDP-DG + M_PPi"
if (reaction == "RHEA:16231")
.formula <- "M_PA + M_CTP + M_H+ <= M_CDP-DG + M_PPi"
if (reaction == "RHEA:16232")
.formula <- "M_PA + M_CTP + M_H+ <=> M_CDP-DG + M_PPi"
## lpep_to_pep
if (reaction == "RHEA:16245")
.formula <- "M_LPE-P + M_AcylCoA = M_PE-P + M_CoA"
if (reaction == "RHEA:16246")
.formula <- "M_LPE-P + M_AcylCoA => M_PE-P + M_CoA"
if (reaction == "RHEA:16247")
.formula <- "M_LPE-P + M_AcylCoA <= M_PE-P + M_CoA"
if (reaction == "RHEA:16248")
.formula <- "M_LPE-P + M_AcylCoA <=> M_PE-P + M_CoA"
## lpep_to_fal
if (reaction == "RHEA:16905")
.formula <- "M_1-LPE-P + M_H2O = M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16906")
.formula <- "M_1-LPE-P + M_H2O => M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16907")
.formula <- "M_1-LPE-P + M_H2O <= M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16908")
.formula <- "M_1-LPE-P + M_H2O <=> M_FAL + M_Glycerophosphoethanolamine"
## nae_to_fa
if (reaction %in% c("RHEA:17505", "RHEA:39995"))
.formula <- "M_H2O + M_NAE = M_FA + M_Ethanolamine"
if (reaction %in% c("RHEA:17506", "RHEA:39996"))
.formula <- "M_H2O + M_NAE => M_FA + M_Ethanolamine"
if (reaction %in% c("RHEA:17507", "RHEA:39997"))
.formula <- "M_H2O + M_NAE <= M_FA + M_Ethanolamine"
if (reaction %in% c("RHEA:17508", "RHEA:39998"))
.formula <- "M_H2O + M_NAE <=> M_FA + M_Ethanolamine"
## coa_to_acdhap
if (reaction == "RHEA:17657")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P = M_AcylDHAP + M_CoA"
if (reaction == "RHEA:17658")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P => M_AcylDHAP + M_CoA"
if (reaction == "RHEA:17659")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P <= M_AcylDHAP + M_CoA"
if (reaction == "RHEA:17660")
.formula <- "M_AcylCoA + M_Dihydroxyacetone-P <=> M_AcylDHAP + M_CoA"
## coa_to_ce
if (reaction == "RHEA:17729")
.formula <- "M_Cholesterol + M_AcylCoA = M_CE + M_CoA"
if (reaction == "RHEA:17730")
.formula <- "M_Cholesterol + M_AcylCoA => M_CE + M_CoA"
if (reaction == "RHEA:17731")
.formula <- "M_Cholesterol + M_AcylCoA <= M_CE + M_CoA"
if (reaction == "RHEA:17732")
.formula <- "M_Cholesterol + M_AcylCoA <=> M_CE + M_CoA"
## cer_to_cerp
if (reaction == "RHEA:17929")
.formula <- "M_Cer + M_ATP = M_ADP + M_CerP + M_H+"
if (reaction == "RHEA:17930")
.formula <- "M_Cer + M_ATP => M_ADP + M_CerP + M_H+"
if (reaction == "RHEA:17931")
.formula <- "M_Cer + M_ATP <= M_ADP + M_CerP + M_H+"
if (reaction == "RHEA:17932")
.formula <- "M_Cer + M_ATP <=> M_ADP + M_CerP + M_H+"
## pi_to_sn1lpi
if (reaction == "RHEA:18001")
.formula <- "M_PI + M_H2O = M_1-LPI + M_FA + M_H+"
if (reaction == "RHEA:18002")
.formula <- "M_PI + M_H2O => M_1-LPI + M_FA + M_H+"
if (reaction == "RHEA:18003")
.formula <- "M_PI + M_H2O <= M_1-LPI + M_FA + M_H+"
if (reaction == "RHEA:18004")
.formula <- "M_PI + M_H2O <=> M_1-LPI + M_FA + M_H+"
## pc_to_sn2lpc
if (reaction == "RHEA:18689")
.formula <- "M_PC + M_H2O = M_2-LPC + M_FA + M_H+"
if (reaction == "RHEA:18690")
.formula <- "M_PC + M_H2O => M_2-LPC + M_FA + M_H+"
if (reaction == "RHEA:18691")
.formula <- "M_PC + M_H2O <= M_2-LPC + M_FA + M_H+"
if (reaction == "RHEA:18692")
.formula <- "M_PC + M_H2O <=> M_2-LPC + M_FA + M_H+"
## cer_to_sm
if (reaction == "RHEA:18765")
.formula <- "M_PC + M_Cer = M_1,2-DG + M_SM"
if (reaction == "RHEA:18766")
.formula <- "M_PC + M_Cer => M_1,2-DG + M_SM"
if (reaction == "RHEA:18767")
.formula <- "M_PC + M_Cer <= M_1,2-DG + M_SM"
if (reaction == "RHEA:18768")
.formula <- "M_PC + M_Cer <=> M_1,2-DG + M_SM"
## lpa_to_pa
if (reaction == "RHEA:19709")
.formula <- "M_LPA + M_AcylCoA = M_PA + M_CoA"
if (reaction == "RHEA:19710")
.formula <- "M_LPA + M_AcylCoA => M_PA + M_CoA"
if (reaction == "RHEA:19711")
.formula <- "M_LPA + M_AcylCoA <= M_PA + M_CoA"
if (reaction == "RHEA:19712")
.formula <- "M_LPA + M_AcylCoA <=> M_PA + M_CoA"
## ps_to_pe
if (reaction == "RHEA:20828")
.formula <- "M_PS + M_H+ = M_PE + M_CO2"
if (reaction == "RHEA:20829")
.formula <- "M_PS + M_H+ => M_PE + M_CO2"
if (reaction == "RHEA:20830")
.formula <- "M_PS + M_H+ <= M_PE + M_CO2"
if (reaction == "RHEA:20831")
.formula <- "M_PS + M_H+ <=> M_PE + M_CO2"
## peo_to_pep
if (reaction == "RHEA:22956")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 = M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
if (reaction == "RHEA:22957")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 => M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
if (reaction == "RHEA:22958")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <= M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
if (reaction == "RHEA:22959")
.formula <- "M_PE-O + M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <=> M_PE-P + M_Fe3+-cytochrome_b5 + 2 M_H2O"
## lpco_to_pco
if (reaction == "RHEA:23992")
.formula <- "M_1-LPC-O + M_AcylCoA = M_PC-O + M_CoA"
if (reaction == "RHEA:23993")
.formula <- "M_1-LPC-O + M_AcylCoA => M_PC-O + M_CoA"
if (reaction == "RHEA:23994")
.formula <- "M_1-LPC-O + M_AcylCoA <= M_PC-O + M_CoA"
if (reaction == "RHEA:23995")
.formula <- "M_1-LPC-O + M_AcylCoA <=> M_PC-O + M_CoA"
## pa_to_dg
if (reaction == "RHEA:27429")
.formula <- "M_PA + M_H2O = M_1,2-DG + M_Pi"
if (reaction == "RHEA:27430")
.formula <- "M_PA + M_H2O => M_1,2-DG + M_Pi"
if (reaction == "RHEA:27431")
.formula <- "M_PA + M_H2O <= M_1,2-DG + M_Pi"
if (reaction == "RHEA:27432")
.formula <- "M_PA + M_H2O <=> M_1,2-DG + M_Pi"
## pe_to_ps
if (reaction == "RHEA:27606")
.formula <- "M_PE + M_L-Serine = M_PS + M_Ethanolamine"
if (reaction == "RHEA:27607")
.formula <- "M_PE + M_L-Serine => M_PS + M_Ethanolamine"
if (reaction == "RHEA:27608")
.formula <- "M_PE + M_L-Serine <= M_PS + M_Ethanolamine"
if (reaction == "RHEA:27609")
.formula <- "M_PE + M_L-Serine <=> M_PS + M_Ethanolamine"
## sn2mg_to_fa
if (reaction %in% c("RHEA:32871"))
.formula <- "M_H2O + M_2-MG = M_FA + M_Glycerol + M_H+"
if (reaction %in% c("RHEA:32872"))
.formula <- "M_H2O + M_2-MG => M_FA + M_Glycerol + M_H+"
if (reaction %in% c("RHEA:32873"))
.formula <- "M_H2O + M_2-MG <= M_FA + M_Glycerol + M_H+"
if (reaction %in% c("RHEA:32874"))
.formula <- "M_H2O + M_2-MG <=> M_FA + M_Glycerol + M_H+"
## pg_to_cl
if (reaction == "RHEA:32931")
.formula <- "M_PG + M_CDP-DG = M_CL + M_CMP + M_H+"
if (reaction == "RHEA:32932")
.formula <- "M_PG + M_CDP-DG => M_CL + M_CMP + M_H+"
if (reaction == "RHEA:32933")
.formula <- "M_PG + M_CDP-DG <= M_CL + M_CMP + M_H+"
if (reaction == "RHEA:32934")
.formula <- "M_PG + M_CDP-DG <=> M_CL + M_CMP + M_H+"
## cl_to_lcl
if (reaction == "RHEA:32935")
.formula <- "M_CL + M_H2O = M_1,2,4-LCL + M_FA + M_H+"
if (reaction == "RHEA:32936")
.formula <- "M_CL + M_H2O => M_1,2,4-LCL + M_FA + M_H+"
if (reaction == "RHEA:32937")
.formula <- "M_CL + M_H2O <= M_1,2,4-LCL + M_FA + M_H+"
if (reaction == "RHEA:32938")
.formula <- "M_CL + M_H2O <=> M_1,2,4-LCL + M_FA + M_H+"
## dg_to_pc
if (reaction == "RHEA:32939")
.formula <- "M_1,2-DG + M_CDP-Choline = M_PC + M_CMP + M_H+"
if (reaction == "RHEA:32940")
.formula <- "M_1,2-DG + M_CDP-Choline => M_PC + M_CMP + M_H+"
if (reaction == "RHEA:32941")
.formula <- "M_1,2-DG + M_CDP-Choline <= M_PC + M_CMP + M_H+"
if (reaction == "RHEA:32942")
.formula <- "M_1,2-DG + M_CDP-Choline <=> M_PC + M_CMP + M_H+"
## dg_to_pe
if (reaction == "RHEA:32943")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine = M_PE + M_CMP + M_H+"
if (reaction == "RHEA:32944")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine => M_PE + M_CMP + M_H+"
if (reaction == "RHEA:32945")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine <= M_PE + M_CMP + M_H+"
if (reaction == "RHEA:32946")
.formula <- "M_1,2-DG + M_CDP-Ethanolamine <=> M_PE + M_CMP + M_H+"
## sn2mg_to_dg
if (reaction %in% c("RHEA:32947", "RHEA:16741"))
.formula <- "M_2-MG + M_AcylCoA = M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:32948", "RHEA:16742"))
.formula <- "M_2-MG + M_AcylCoA => M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:32949", "RHEA:16743"))
.formula <- "M_2-MG + M_AcylCoA <= M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:32950", "RHEA:16744"))
.formula <- "M_2-MG + M_AcylCoA <=> M_1,2-DG + M_CoA"
## sn1lpe_to_fa
if (reaction == "RHEA:32967")
.formula <- "M_1-LPE + M_H2O = M_FA + M_H+ + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32968")
.formula <- "M_1-LPE + M_H2O => M_FA + M_H+ + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32969")
.formula <- "M_1-LPE + M_H2O <= M_FA + M_H+ + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32970")
.formula <- "M_1-LPE + M_H2O <=> M_FA + M_H+ + M_Glycerophosphoethanolamine"
## sn1lpe_to_pe
if (reaction == "RHEA:32995")
.formula <- "M_1-LPE + M_AcylCoA = M_PE + M_CoA"
if (reaction == "RHEA:32996")
.formula <- "M_1-LPE + M_AcylCoA => M_PE + M_CoA"
if (reaction == "RHEA:32997")
.formula <- "M_1-LPE + M_AcylCoA <= M_PE + M_CoA"
if (reaction == "RHEA:32998")
.formula <- "M_1-LPE + M_AcylCoA <=> M_PE + M_CoA"
## nape_to_nae
if (reaction == "RHEA:33159")
.formula <- "M_H2O + M_NAPE = M_PA + M_NAE + M_H+"
if (reaction == "RHEA:33160")
.formula <- "M_H2O + M_NAPE => M_PA + M_NAE + M_H+"
if (reaction == "RHEA:33161")
.formula <- "M_H2O + M_NAPE <= M_PA + M_NAE + M_H+"
if (reaction == "RHEA:33162")
.formula <- "M_H2O + M_NAPE <=> M_PA + M_NAE + M_H+"
## sn1lpi_to_pi
if (reaction == "RHEA:33195")
.formula <- "M_1-LPI + M_AcylCoA = M_PI + M_CoA"
if (reaction == "RHEA:33196")
.formula <- "M_1-LPI + M_AcylCoA => M_PI + M_CoA"
if (reaction == "RHEA:33197")
.formula <- "M_1-LPI + M_AcylCoA <= M_PI + M_CoA"
if (reaction == "RHEA:33198")
.formula <- "M_1-LPI + M_AcylCoA <=> M_PI + M_CoA"
## lpg_to_pg
if (reaction == "RHEA:33203")
.formula <- "M_1-LPG + M_AcylCoA = M_PG + M_CoA"
if (reaction == "RHEA:33204")
.formula <- "M_1-LPG + M_AcylCoA => M_PG + M_CoA"
if (reaction == "RHEA:33205")
.formula <- "M_1-LPG + M_AcylCoA <= M_PG + M_CoA"
if (reaction == "RHEA:33206")
.formula <- "M_1-LPG + M_AcylCoA <=> M_PG + M_CoA"
## tg_to_dg
if (reaction %in% c("RHEA:33271", "RHEA:44864"))
.formula <- "M_TG + M_H2O = M_1,2-DG + M_FA + M_H+"
if (reaction %in% c("RHEA:33272", "RHEA:44865"))
.formula <- "M_TG + M_H2O => M_1,2-DG + M_FA + M_H+"
if (reaction %in% c("RHEA:33273", "RHEA:44866"))
.formula <- "M_TG + M_H2O <= M_1,2-DG + M_FA + M_H+"
if (reaction %in% c("RHEA:33274", "RHEA:44867"))
.formula <- "M_TG + M_H2O <=> M_1,2-DG + M_FA + M_H+"
## dg_to_sn2mg
if (reaction == "RHEA:33275")
.formula <- "M_1,2-DG + M_H2O = M_2-MG + M_FA + M_H+"
if (reaction == "RHEA:33276")
.formula <- "M_1,2-DG + M_H2O => M_2-MG + M_FA + M_H+"
if (reaction == "RHEA:33277")
.formula <- "M_1,2-DG + M_H2O <= M_2-MG + M_FA + M_H+"
if (reaction == "RHEA:33278")
.formula <- "M_1,2-DG + M_H2O <=> M_2-MG + M_FA + M_H+"
## cerp_to_cer
if (reaction == "RHEA:33743")
.formula <- "M_H2O + M_CerP = M_Pi + M_Cer"
if (reaction == "RHEA:33744")
.formula <- "M_H2O + M_CerP => M_Pi + M_Cer"
if (reaction == "RHEA:33745")
.formula <- "M_H2O + M_CerP <= M_Pi + M_Cer"
if (reaction == "RHEA:33746")
.formula <- "M_H2O + M_CerP <=> M_Pi + M_Cer"
## sn1mg_to_lpa
if (reaction == "RHEA:33747")
.formula <- "M_1-MG + M_ATP = M_LPA + M_ADP + M_H+"
if (reaction == "RHEA:33748")
.formula <- "M_1-MG + M_ATP => M_LPA + M_ADP + M_H+"
if (reaction == "RHEA:33749")
.formula <- "M_1-MG + M_ATP <= M_LPA + M_ADP + M_H+"
if (reaction == "RHEA:33750")
.formula <- "M_1-MG + M_ATP <=> M_LPA + M_ADP + M_H+"
## pgp_to_pg
if (reaction == "RHEA:33751")
.formula <- "M_PGP + M_H2O = M_PG + M_Pi"
if (reaction == "RHEA:33752")
.formula <- "M_PGP + M_H2O => M_PG + M_Pi"
if (reaction == "RHEA:33753")
.formula <- "M_PGP + M_H2O <= M_PG + M_Pi"
if (reaction == "RHEA:33754")
.formula <- "M_PGP + M_H2O <=> M_PG + M_Pi"
## sn1mg_to_fa
if (reaction == "RHEA:34019")
.formula <- "M_1-MG + M_H2O = M_FA + M_Glycerol + M_H+"
if (reaction == "RHEA:34020")
.formula <- "M_1-MG + M_H2O => M_FA + M_Glycerol + M_H+"
if (reaction == "RHEA:34021")
.formula <- "M_1-MG + M_H2O <= M_FA + M_Glycerol + M_H+"
if (reaction == "RHEA:34022")
.formula <- "M_1-MG + M_H2O <=> M_FA + M_Glycerol + M_H+"
## dg_to_sn1mg
if (reaction %in% c("RHEA:35663", "RHEA:44712"))
.formula <- "M_1,2-DG + M_H2O = M_1-MG + M_FA + M_H+"
if (reaction %in% c("RHEA:35664", "RHEA:44713"))
.formula <- "M_1,2-DG + M_H2O => M_1-MG + M_FA + M_H+"
if (reaction %in% c("RHEA:35665", "RHEA:44714"))
.formula <- "M_1,2-DG + M_H2O <= M_1-MG + M_FA + M_H+"
if (reaction %in% c("RHEA:35666", "RHEA:44715"))
.formula <- "M_1,2-DG + M_H2O <=> M_1-MG + M_FA + M_H+"
## lcl_to_cl
if (reaction == "RHEA:35839")
.formula <- "M_1,2,4-LCL + M_AcylCoA = M_CL + M_CoA"
if (reaction == "RHEA:35840")
.formula <- "M_1,2,4-LCL + M_AcylCoA => M_CL + M_CoA"
if (reaction == "RHEA:35841")
.formula <- "M_1,2,4-LCL + M_AcylCoA <= M_CL + M_CoA"
if (reaction == "RHEA:35842")
.formula <- "M_1,2,4-LCL + M_AcylCoA <=> M_CL + M_CoA"
## lpco_to_mgo
if (reaction == "RHEA:36083")
.formula <- "M_1-LPC-O + M_H2O = M_1-MG-O + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:36084")
.formula <- "M_1-LPC-O + M_H2O => M_1-MG-O + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:36085")
.formula <- "M_1-LPC-O + M_H2O <= M_1-MG-O + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:36086")
.formula <- "M_1-LPC-O + M_H2O <=> M_1-MG-O + M_H+ + M_Phosphocholine"
## acyldhap_to_alkyldhap
if (reaction == "RHEA:36171")
.formula <- "M_AcylDHAP + M_FAO = M_AlkylDHAP + M_FA + M_H+"
if (reaction == "RHEA:36172")
.formula <- "M_AcylDHAP + M_FAO => M_AlkylDHAP + M_FA + M_H+"
if (reaction == "RHEA:36173")
.formula <- "M_AcylDHAP + M_FAO <= M_AlkylDHAP + M_FA + M_H+"
if (reaction == "RHEA:36174")
.formula <- "M_AcylDHAP + M_FAO <=> M_AlkylDHAP + M_FA + M_H+"
## alkyldhap_to_lpao
if (reaction == "RHEA:36175")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH = M_LPA-O + M_NADP"
if (reaction == "RHEA:36176")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH => M_LPA-O + M_NADP"
if (reaction == "RHEA:36177")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH <= M_LPA-O + M_NADP"
if (reaction == "RHEA:36178")
.formula <- "M_AlkylDHAP + M_H+ + M_NADPH <=> M_LPA-O + M_NADP"
## dgo_to_pco
if (reaction == "RHEA:36179")
.formula <- "M_DG-O + M_CDP-Choline = M_PC-O + M_CMP + M_H+"
if (reaction == "RHEA:36180")
.formula <- "M_DG-O + M_CDP-Choline => M_PC-O + M_CMP + M_H+"
if (reaction == "RHEA:36181")
.formula <- "M_DG-O + M_CDP-Choline <= M_PC-O + M_CMP + M_H+"
if (reaction == "RHEA:36182")
.formula <- "M_DG-O + M_CDP-Choline <=> M_PC-O + M_CMP + M_H+"
## dgo_to_peo
if (reaction == "RHEA:36187")
.formula <- "M_DG-O + M_CDP-Ethanolamine = M_PE-O + M_CMP + M_H+"
if (reaction == "RHEA:36188")
.formula <- "M_DG-O + M_CDP-Ethanolamine => M_PE-O + M_CMP + M_H+"
if (reaction == "RHEA:36189")
.formula <- "M_DG-O + M_CDP-Ethanolamine <= M_PE-O + M_CMP + M_H+"
if (reaction == "RHEA:36190")
.formula <- "M_DG-O + M_CDP-Ethanolamine <=> M_PE-O + M_CMP + M_H+"
## pep_to_lpep
if (reaction == "RHEA:36195")
.formula <- "M_PE-P + M_H2O = M_LPE-P + M_FA + M_H+"
if (reaction == "RHEA:36196")
.formula <- "M_PE-P + M_H2O => M_LPE-P + M_FA + M_H+"
if (reaction == "RHEA:36197")
.formula <- "M_PE-P + M_H2O <= M_LPE-P + M_FA + M_H+"
if (reaction == "RHEA:36198")
.formula <- "M_PE-P + M_H2O <=> M_LPE-P + M_FA + M_H+"
## lpep_to_mgp
if (reaction == "RHEA:36199")
.formula <- "M_1-LPE-P + M_H2O = M_1-MG-P + M_H+ + M_Phosphoethanolamine"
if (reaction == "RHEA:36200")
.formula <- "M_1-LPE-P + M_H2O => M_1-MG-P + M_H+ + M_Phosphoethanolamine"
if (reaction == "RHEA:36201")
.formula <- "M_1-LPE-P + M_H2O <= M_1-MG-P + M_H+ + M_Phosphoethanolamine"
if (reaction == "RHEA:36202")
.formula <- "M_1-LPE-P + M_H2O <=> M_1-MG-P + M_H+ + M_Phosphoethanolamine"
## lpep_to_lpap
if (reaction == "RHEA:36203")
.formula <- "M_1-LPE-P + M_H2O = M_LPA-P + M_Ethanolamine + M_H+"
if (reaction == "RHEA:36204")
.formula <- "M_1-LPE-P + M_H2O => M_LPA-P + M_Ethanolamine + M_H+"
if (reaction == "RHEA:36205")
.formula <- "M_1-LPE-P + M_H2O <= M_LPA-P + M_Ethanolamine + M_H+"
if (reaction == "RHEA:36206")
.formula <- "M_1-LPE-P + M_H2O <=> M_LPA-P + M_Ethanolamine + M_H+"
## pco_to_lpco
if (reaction == "RHEA:36231")
.formula <- "M_PC-O + M_H2O = M_LPC-O + M_FA + M_H+"
if (reaction == "RHEA:36232")
.formula <- "M_PC-O + M_H2O => M_LPC-O + M_FA + M_H+"
if (reaction == "RHEA:36233")
.formula <- "M_PC-O + M_H2O <= M_LPC-O + M_FA + M_H+"
if (reaction == "RHEA:36234")
.formula <- "M_PC-O + M_H2O <=> M_LPC-O + M_FA + M_H+"
## lpao_to_pao
if (reaction == "RHEA:36235")
.formula <- "M_LPA-O + M_AcylCoA = M_PA-O + M_CoA"
if (reaction == "RHEA:36236")
.formula <- "M_LPA-O + M_AcylCoA => M_PA-O + M_CoA"
if (reaction == "RHEA:36237")
.formula <- "M_LPA-O + M_AcylCoA <= M_PA-O + M_CoA"
if (reaction == "RHEA:36238")
.formula <- "M_LPA-O + M_AcylCoA <=> M_PA-O + M_CoA"
## pao_to_dgo
if (reaction == "RHEA:36239")
.formula <- "M_PA-O + M_H2O = M_DG-O + M_Pi"
if (reaction == "RHEA:36240")
.formula <- "M_PA-O + M_H2O => M_DG-O + M_Pi"
if (reaction == "RHEA:36241")
.formula <- "M_PA-O + M_H2O <= M_DG-O + M_Pi"
if (reaction == "RHEA:36242")
.formula <- "M_PA-O + M_H2O <=> M_DG-O + M_Pi"
## sn1mg_to_dg
if (reaction %in% c("RHEA:38463", "RHEA:39943"))
.formula <- "M_1-MG + M_AcylCoA = M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:38464", "RHEA:39944"))
.formula <- "M_1-MG + M_AcylCoA => M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:38465", "RHEA:39945"))
.formula <- "M_1-MG + M_AcylCoA <= M_1,2-DG + M_CoA"
if (reaction %in% c("RHEA:38466", "RHEA:39946"))
.formula <- "M_1-MG + M_AcylCoA <=> M_1,2-DG + M_CoA"
## lpco_to_lpao
if (reaction == "RHEA:39927")
.formula <- "M_1-LPC-O + M_H2O = M_1-LPA-O + M_Choline + M_H+"
if (reaction == "RHEA:39928")
.formula <- "M_1-LPC-O + M_H2O => M_1-LPA-O + M_Choline + M_H+"
if (reaction == "RHEA:39929")
.formula <- "M_1-LPC-O + M_H2O <= M_1-LPA-O + M_Choline + M_H+"
if (reaction == "RHEA:39930")
.formula <- "M_1-LPC-O + M_H2O <=> M_1-LPA-O + M_Choline + M_H+"
## pi_to_dg
if (reaction == "RHEA:43484")
.formula <- "M_PI + M_H2O = M_myo-Inositol-1-P + M_1,2-DG + M_H+"
if (reaction == "RHEA:43485")
.formula <- "M_PI + M_H2O => M_myo-Inositol-1-P + M_1,2-DG + M_H+"
if (reaction == "RHEA:43486")
.formula <- "M_PI + M_H2O <= M_myo-Inositol-1-P + M_1,2-DG + M_H+"
if (reaction == "RHEA:43487")
.formula <- "M_PI + M_H2O <=> M_myo-Inositol-1-P + M_1,2-DG + M_H+"
## pe_to_sn2lpe
if (reaction == "RHEA:44408")
.formula <- "M_PE + M_H2O = M_2-LPE + M_FA + M_H+"
if (reaction == "RHEA:44409")
.formula <- "M_PE + M_H2O => M_2-LPE + M_FA + M_H+"
if (reaction == "RHEA:44410")
.formula <- "M_PE + M_H2O <= M_2-LPE + M_FA + M_H+"
if (reaction == "RHEA:44411")
.formula <- "M_PE + M_H2O <=> M_2-LPE + M_FA + M_H+"
## pg_to_sn1lpg
if (reaction == "RHEA:44416")
.formula <- "M_PG + M_H2O = M_1-LPG + M_FA + M_H+"
if (reaction == "RHEA:44417")
.formula <- "M_PG + M_H2O => M_1-LPG + M_FA + M_H+"
if (reaction == "RHEA:44418")
.formula <- "M_PG + M_H2O <= M_1-LPG + M_FA + M_H+"
if (reaction == "RHEA:44419")
.formula <- "M_PG + M_H2O <=> M_1-LPG + M_FA + M_H+"
## pe_to_sn1lpe
if (reaction == "RHEA:44604")
.formula <- "M_PE + M_H2O = M_1-LPE + M_FA + M_H+"
if (reaction == "RHEA:44605")
.formula <- "M_PE + M_H2O => M_1-LPE + M_FA + M_H+"
if (reaction == "RHEA:44606")
.formula <- "M_PE + M_H2O <= M_1-LPE + M_FA + M_H+"
if (reaction == "RHEA:44607")
.formula <- "M_PE + M_H2O <=> M_1-LPE + M_FA + M_H+"
## dhcer_to_dhsm
if (reaction == "RHEA:44620")
.formula <- "M_PC + M_DhCer = M_1,2-DG + M_DhSM"
if (reaction == "RHEA:44621")
.formula <- "M_PC + M_DhCer => M_1,2-DG + M_DhSM"
if (reaction == "RHEA:44622")
.formula <- "M_PC + M_DhCer <= M_1,2-DG + M_DhSM"
if (reaction == "RHEA:44623")
.formula <- "M_PC + M_DhCer <=> M_1,2-DG + M_DhSM"
## sn2lpc_to_fa
if (reaction == "RHEA:44696")
.formula <- "M_2-LPC + M_H2O = M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:44697")
.formula <- "M_2-LPC + M_H2O => M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:44698")
.formula <- "M_2-LPC + M_H2O <= M_FA + M_H+ + M_Glycerophosphocholine"
if (reaction == "RHEA:44699")
.formula <- "M_2-LPC + M_H2O <=> M_FA + M_H+ + M_Glycerophosphocholine"
## pc_to_ps
if (reaction == "RHEA:45088")
.formula <- "M_PC + M_L-Serine = M_PS + M_Choline"
if (reaction == "RHEA:45089")
.formula <- "M_PC + M_L-Serine => M_PS + M_Choline"
if (reaction == "RHEA:45090")
.formula <- "M_PC + M_L-Serine <= M_PS + M_Choline"
if (reaction == "RHEA:45091")
.formula <- "M_PC + M_L-Serine <=> M_PS + M_Choline"
## pe_to_nape_sn1
if (reaction == "RHEA:45188")
.formula <- "M_PC + M_PE = M_2-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45189")
.formula <- "M_PC + M_PE => M_2-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45190")
.formula <- "M_PC + M_PE <= M_2-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45191")
.formula <- "M_PC + M_PE <=> M_2-LPC + M_H+ + M_NAPE"
## pe_to_nape_sn2
if (reaction == "RHEA:45192")
.formula <- "M_PC + M_PE = M_1-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45193")
.formula <- "M_PC + M_PE => M_1-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45194")
.formula <- "M_PC + M_PE <= M_1-LPC + M_H+ + M_NAPE"
if (reaction == "RHEA:45195")
.formula <- "M_PC + M_PE <=> M_1-LPC + M_H+ + M_NAPE"
## dhsm_to_dhcer
if (reaction == "RHEA:45300")
.formula <- "M_DhSM + M_H2O = M_DhCer + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:45301")
.formula <- "M_DhSM + M_H2O => M_DhCer + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:45302")
.formula <- "M_DhSM + M_H2O <= M_DhCer + M_H+ + M_Phosphocholine"
if (reaction == "RHEA:45303")
.formula <- "M_DhSM + M_H2O <=> M_DhCer + M_H+ + M_Phosphocholine"
## lnape_to_gpnae
if (reaction == "RHEA:45420")
.formula <- "M_H2O + M_LNAPE = M_FA + M_H+ + M_GPNAE"
if (reaction == "RHEA:45421")
.formula <- "M_H2O + M_LNAPE => M_FA + M_H+ + M_GPNAE"
if (reaction == "RHEA:45422")
.formula <- "M_H2O + M_LNAPE <= M_FA + M_H+ + M_GPNAE"
if (reaction == "RHEA:45423")
.formula <- "M_H2O + M_LNAPE <=> M_FA + M_H+ + M_GPNAE"
## nape_to_lnape
if (reaction == "RHEA:45460")
.formula <- "M_H2O + M_NAPE = M_FA + M_H+ + M_LNAPE"
if (reaction == "RHEA:45461")
.formula <- "M_H2O + M_NAPE => M_FA + M_H+ + M_LNAPE"
if (reaction == "RHEA:45462")
.formula <- "M_H2O + M_NAPE <= M_FA + M_H+ + M_LNAPE"
if (reaction == "RHEA:45463")
.formula <- "M_H2O + M_NAPE <=> M_FA + M_H+ + M_LNAPE"
## dhcer_to_cer
if (reaction == "RHEA:46544")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 = 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
if (reaction == "RHEA:46545")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 => 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
if (reaction == "RHEA:46546")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <= 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
if (reaction == "RHEA:46547")
.formula <- "M_DhCer + 2 M_Fe2+-cytochrome_b5 + 2 M_H+ + M_O2 <=> 2 M_Fe3+-cytochrome_b5 + M_Cer + 2 M_H2O"
## sm_to_cer
if (reaction == "RHEA:45644")
.formula <- "M_H2O + M_SM = M_H+ + M_Cer + M_Phosphocholine"
if (reaction == "RHEA:45645")
.formula <- "M_H2O + M_SM => M_H+ + M_Cer + M_Phosphocholine"
if (reaction == "RHEA:45646")
.formula <- "M_H2O + M_SM <= M_H+ + M_Cer + M_Phosphocholine"
if (reaction == "RHEA:45647")
.formula <- "M_H2O + M_SM <=> M_H+ + M_Cer + M_Phosphocholine"
## coa_to_fao
if (reaction == "RHEA:52716")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH = M_FAO + M_CoA + 2 M_NADP"
if (reaction == "RHEA:52717")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH => M_FAO + M_CoA + 2 M_NADP"
if (reaction == "RHEA:52718")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH <= M_FAO + M_CoA + 2 M_NADP"
if (reaction == "RHEA:52719")
.formula <- "M_AcylCoA + 2 M_H+ + 2 M_NADPH <=> M_FAO + M_CoA + 2 M_NADP"
## sphinga_to_dhcer
if (reaction == "RHEA:53424")
.formula <- "M_AcylCoA + M_Sphinganine = M_DhCer + M_CoA + M_H+"
if (reaction == "RHEA:53425")
.formula <- "M_AcylCoA + M_Sphinganine => M_DhCer + M_CoA + M_H+"
if (reaction == "RHEA:53426")
.formula <- "M_AcylCoA + M_Sphinganine <= M_DhCer + M_CoA + M_H+"
if (reaction == "RHEA:53427")
.formula <- "M_AcylCoA + M_Sphinganine <=> M_DhCer + M_CoA + M_H+"
## pep_to_napep_sn1
if (reaction == "RHEA:63596")
.formula <- "M_PE-P + M_PC = M_2-LPC + M_H+ + M_NAPEP"
if (reaction == "RHEA:63597")
.formula <- "M_PE-P + M_PC => M_2-LPC + M_H+ + M_NAPEP"
if (reaction == "RHEA:63598")
.formula <- "M_PE-P + M_PC <= M_2-LPC + M_H+ + M_NAPEP"
if (reaction == "RHEA:63599")
.formula <- "M_PE-P + M_PC <=> M_2-LPC + M_H+ + M_NAPEP"
## pe_to_dg
if (reaction == "RHEA:78951")
.formula <- "M_H2O + M_PE = M_P-Ethanolamine + M_1,2-DG + M_H+"
if (reaction == "RHEA:78952")
.formula <- "M_H2O + M_PE => M_P-Ethanolamine + M_1,2-DG + M_H+"
if (reaction == "RHEA:78953")
.formula <- "M_H2O + M_PE <= M_P-Ethanolamine + M_1,2-DG + M_H+"
if (reaction == "RHEA:78954")
.formula <- "M_H2O + M_PE <=> M_P-Ethanolamine + M_1,2-DG + M_H+"
## sn2lpe_to_fa
if (reaction == "sn2lpe_to_fa")
.formula <- "M_2-LPE + M_H2O <=> M_FA + M_H+ + M_Glycerophosphoethanolamine"
## lpeo_to_peo
if (reaction == "lpeo_to_peo")
.formula <- "M_AcylCoA + M_LPE-O <=> M_CoA + M_PE-O"
## sn2mg_to_sn1mg
if (reaction == "sn2mg_to_sn1mg")
.formula <- "M_2-MG <=> M_1-MG"
## nape_to_pnae
if (reaction == "nape_to_pnae")
.formula <- "M_NAPE + M_H2O <=> M_PNAE + M_1,2-DG"
## napeo_to_nae
if (reaction == "napeo_to_nae")
.formula <- "M_NAPEO + M_H2O <=> M_NAE + M_PA-O"
## pe_to_pa
if (reaction == "pe_to_pa")
.formula <- "M_PE + M_H2O <=> M_PA + M_Ethanolamine + M_H+"
## peo_to_lpeo
if (reaction == "peo_to_lpeo")
.formula <- "M_PE-O + M_H2O <=> M_LPE-O + M_FA + M_H+"
## peo_to_napeo_sn1
if (reaction == "peo_to_napeo_sn1")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_2-LPC"
## peo_to_napeo_sn2
if (reaction == "peo_to_napeo_sn2")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_1-LPC"
## pep_to_napep_sn2
if (reaction == "pep_to_napep_sn2")
.formula <- "M_PE-P + M_PC <=> M_NAPEP + M_1-LPC"
template$reaction_formula <- .formula
}
## fill using reaction_formula
## split the template$reaction_formula into substrates and products
.formula_tmp <- template$reaction_formula
.formula_tmp <- stringi::stri_replace_all_regex(str = .formula_tmp,
pattern = ">|<", replacement = "")
.formula_tmp <- stringi::stri_split(str = .formula_tmp, fixed = "=")[[1]]
.formula_substrate <- .formula_tmp[1]
.formula_product <- .formula_tmp[2]
## remove the "+" and the trailing spaces for substrates and products
.formula_substrate <- stringi::stri_split(str = .formula_substrate,
regex = "[ ][+][ ]")[[1]]
.formula_substrate <- stringi::stri_replace_all_regex(str = .formula_substrate,
pattern = "^ | $", replacement = "")
.formula_product <- stringi::stri_split(str = .formula_product,
regex = "[ ][+][ ]")[[1]]
.formula_product <- stringi::stri_replace_all_regex(str = .formula_product,
pattern = "^ | $", replacement = "")
## write the substrates and products to the template
template$reaction_substrate <- .formula_substrate
template$reaction_product <- .formula_product
## fill using reaction_formula_chebi
## add ChEBI ids using the mapping table
.mappingTable <- mappingTable()
inds <- which(.mappingTable == reaction, arr.ind = TRUE)[, "row"]
.mappingTable <- .mappingTable[inds, ]
## find the corresponding CHEBIs for substrates
substrate_tmp <- stringi::stri_split(template$reaction_substrate, regex = "[ ]")
.formula_substrate <- lapply(substrate_tmp, function(substrate_tmp_i) {
inds_match <- match(substrate_tmp_i, .mappingTable[, 1])
res <- .mappingTable[inds_match, 3, drop = FALSE]
res[is.na(inds_match)] <- substrate_tmp_i[is.na(inds_match)]
paste(res, collapse = " ")
}) |>
unlist()
## find the corresponding CHEBIs for products
product_tmp <- stringi::stri_split(template$reaction_product, regex = "[ ]")
.formula_product <- lapply(product_tmp, function(product_tmp_i) {
inds_match <- match(product_tmp_i, .mappingTable[, 1])
res <- .mappingTable[inds_match, 3, drop = FALSE]
res[is.na(inds_match)] <- product_tmp_i[is.na(inds_match)]
paste(res, collapse = " ")
}) |>
unlist()
## determine the reaction direction
patterns <- c("<=>", "<=", "=>", "=")
matches <- sapply(patterns, function(p) grepl(p, template$reaction_formula))
reaction_type <- names(which(matches)[1])
## assemble the reaction_formula_chebi
template$reaction_formula_chebi <- paste(
paste(.formula_substrate, collapse = " + "), reaction_type,
paste(.formula_product, collapse = " + "), collapse = " ")
## write the substrates and products to the template
template$reaction_substrate_chebi <- .formula_substrate
template$reaction_product_chebi <- .formula_product
## return the template object
template
}
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