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.
#' }
#'
#' @param template NA or \code{list}
#' @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 = NA, reaction = "RHEA:15421")
.create_template <- function(template = NA, reaction = "RHEA:15421") {
if (is.list(template)) {
## check integrity (all names are present in template)
if (!"reaction_name" %in% names(template))
stop("'template' has to contain the entry 'reaction_name'")
if (!"reaction_formula" %in% names(template))
stop("'template' has to contain the entry 'reaction_formula'")
if (!"reaction_isReversible" %in% names(template))
stop("'template' has to contain the entry 'reacton_isReversible'")
if (!"reaction_geneAssociation" %in% names(template))
stop("'template' has to contain the entry 'reaction_geneAssociation'")
if (!"reaction_pathway" %in% names(template))
stop("'template' has to contain the entry 'reaction_pathway'")
## 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_formula, "character"))
stop("entry 'reaction_formula' 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'")
} else {
## this event happens if the param template is not a list
## check if reaction is in the parameter space
.check_reaction(reaction)
## create a template object (list)
template <- list(reaction_name = "", reaction_formula = "",
reaction_RHEA = reaction, reaction_isReversible = "",
reaction_geneAssociation = "", reaction_pathway = "")
## depending on the reaction, write specific reaction .formula to the
## entry reaction_.formula
## acyldhap_to_alkyldhap
if (reaction == "RHEA:36171")
.formula <- "M_AcylDHAP + M_FAO = M_H+ + M_FA + M_AlkylDHAP"
if (reaction == "RHEA:36172")
.formula <- "M_AcylDHAP + M_FAO => M_H+ + M_FA + M_AlkylDHAP"
if (reaction == "RHEA:36173")
.formula <- "M_AcylDHAP + M_FAO <= M_H+ + M_FA + M_AlkylDHAP"
if (reaction == "RHEA:36174")
.formula <- "M_AcylDHAP + M_FAO <=> M_H+ + M_FA + M_AlkylDHAP"
## alkyldhap_to_lpao
if (reaction == "RHEA:36175")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP = M_LPA-O + M_NADP"
if (reaction == "RHEA:36176")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP => M_LPA-O + M_NADP"
if (reaction == "RHEA:36177")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP <= M_LPA-O + M_NADP"
if (reaction == "RHEA:36178")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP <=> M_LPA-O + M_NADP"
if (reaction == "cerp_to_cer")
.formula <- "M_H2O + M_CerP <=> M_Pi + M_Cer"
## cdpdg_to_pgp
if (reaction == "RHEA:12593")
.formula <- "M_Glycerol-3-P + M_CDP-DG = M_H+ + M_CMP + M_PGP"
if (reaction == "RHEA:12594")
.formula <- "M_Glycerol-3-P + M_CDP-DG => M_H+ + M_CMP + M_PGP"
if (reaction == "RHEA:12595")
.formula <- "M_Glycerol-3-P + M_CDP-DG <= M_H+ + M_CMP + M_PGP"
if (reaction == "RHEA:12596")
.formula <- "M_Glycerol-3-P + M_CDP-DG <=> M_H+ + M_CMP + M_PGP"
## cdpdg_to_pi
if (reaction == "RHEA:11580")
.formula <- "M_myo-Inositol + M_CDP-DG = M_H+ + M_CMP + M_PI"
if (reaction == "RHEA:11581")
.formula <- "M_myo-Inositol + M_CDP-DG => M_H+ + M_CMP + M_PI"
if (reaction == "RHEA:11582")
.formula <- "M_myo-Inositol + M_CDP-DG <= M_H+ + M_CMP + M_PI"
if (reaction == "RHEA:11583")
.formula <- "M_myo-Inositol + M_CDP-DG <=> M_H+ + M_CMP + M_PI"
## cer_to_cerp
if (reaction == "RHEA:17929")
.formula <- "M_ATP + M_Cer <=> M_H+ + M_ADP + M_CerP"
## cer_to_glccer
if (reaction == "RHEA:12088")
.formula <- "M_UDP-Glucose + M_Cer <=> M_H+ + M_UDP + M_GlcCer"
## cer_to_sm
if (reaction == "RHEA:18765")
.formula <- "M_PC + M_Cer <=> M_1,2-DG + M_SM"
## cl_to_lcl
if (reaction == "RHEA:32935")
.formula <- "M_H2O + M_CL = M_1,2,4-LCL + M_H+ + M_FA"
if (reaction == "RHEA:32936")
.formula <- "M_H2O + M_CL => M_1,2,4-LCL + M_H+ + M_FA"
if (reaction == "RHEA:32937")
.formula <- "M_H2O + M_CL <= M_1,2,4-LCL + M_H+ + M_FA"
if (reaction == "RHEA:32938")
.formula <- "M_H2O + M_CL <=> M_1,2,4-LCL + M_H+ + M_FA"
## coa_to_acdhap
if (reaction == "RHEA:17657")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA = M_CoA + M_AcylDHAP"
if (reaction == "RHEA:17658")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA => M_CoA + M_AcylDHAP"
if (reaction == "RHEA:17659")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA <= M_CoA + M_AcylDHAP"
if (reaction == "RHEA:17660")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA <=> M_CoA + M_AcylDHAP"
## coa_to_fao
if (reaction == "RHEA:52716")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ = M_FAO + 2 M_NADP + M_CoA"
if (reaction == "RHEA:52717")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ => M_FAO + 2 M_NADP + M_CoA"
if (reaction == "RHEA:52718")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ <= M_FAO + 2 M_NADP + M_CoA"
if (reaction == "RHEA:52719")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ <=> M_FAO + 2 M_NADP + M_CoA"
## coa_to_lpa
if (reaction == "RHEA:15325")
.formula <- "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA"
if (reaction == "RHEA:15326")
.formula <- "M_Glycerol-3-P + M_AcylCoA => M_CoA + M_LPA"
if (reaction == "RHEA:15327")
.formula <- "M_Glycerol-3-P + M_AcylCoA <= M_CoA + M_LPA"
if (reaction == "RHEA:15328")
.formula <- "M_Glycerol-3-P + M_AcylCoA <=> M_CoA + M_LPA"
## dg_to_sn1mg
if (reaction %in% c("RHEA:44712", "RHEA:35663"))
.formula <- "M_H2O + M_1,2-DG = M_H+ + M_1-MG + M_FA"
if (reaction %in% c("RHEA:44713", "RHEA:35664"))
.formula <- "M_H2O + M_1,2-DG => M_H+ + M_1-MG + M_FA"
if (reaction %in% c("RHEA:44714", "RHEA:35665"))
.formula <- "M_H2O + M_1,2-DG <= M_H+ + M_1-MG + M_FA"
if (reaction %in% c("RHEA:44715", "RHEA:35666"))
.formula <- "M_H2O + M_1,2-DG <=> M_H+ + M_1-MG + M_FA"
## dg_to_sn2mg
if (reaction == "RHEA:33275")
.formula <- "M_H2O + M_1,2-DG = M_H+ + M_2-MG + M_FA"
if (reaction == "RHEA:33276")
.formula <- "M_H2O + M_1,2-DG => M_H+ + M_2-MG + M_FA"
if (reaction == "RHEA:33277")
.formula <- "M_H2O + M_1,2-DG <= M_H+ + M_2-MG + M_FA"
if (reaction == "RHEA:33278")
.formula <- "M_H2O + M_1,2-DG <=> M_H+ + M_2-MG + M_FA"
## dg_to_pa
if (reaction == "RHEA:10272")
.formula <- "M_ATP + M_1,2-DG = M_H+ + M_ADP + M_PA"
if (reaction == "RHEA:10273")
.formula <- "M_ATP + M_1,2-DG => M_H+ + M_ADP + M_PA"
if (reaction == "RHEA:10274")
.formula <- "M_ATP + M_1,2-DG <= M_H+ + M_ADP + M_PA"
if (reaction == "RHEA:10275")
.formula <- "M_ATP + M_1,2-DG <=> M_H+ + M_ADP + M_PA"
## dg_to_pc
if (reaction == "RHEA:32939")
.formula <- "M_CDP-Choline + M_1,2-DG = M_H+ + M_CMP + M_PC"
if (reaction == "RHEA:32940")
.formula <- "M_CDP-Choline + M_1,2-DG => M_H+ + M_CMP + M_PC"
if (reaction == "RHEA:32941")
.formula <- "M_CDP-Choline + M_1,2-DG <= M_H+ + M_CMP + M_PC"
if (reaction == "RHEA:32942")
.formula <- "M_CDP-Choline + M_1,2-DG <=> M_H+ + M_CMP + M_PC"
## dg_to_pe
if (reaction == "RHEA:32943")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG = M_H+ + M_CMP + M_PE"
if (reaction == "RHEA:32944")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG => M_H+ + M_CMP + M_PE"
if (reaction == "RHEA:32945")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG <= M_H+ + M_CMP + M_PE"
if (reaction == "RHEA:32946")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG <=> M_H+ + M_CMP + M_PE"
## dg_to_tg
if (reaction == "RHEA:10868")
.formula <- "M_AcylCoA + M_1,2-DG = M_CoA + M_TG"
if (reaction == "RHEA:10869")
.formula <- "M_AcylCoA + M_1,2-DG => M_CoA + M_TG"
if (reaction == "RHEA:10870")
.formula <- "M_AcylCoA + M_1,2-DG <= M_CoA + M_TG"
if (reaction == "RHEA:10871")
.formula <- "M_AcylCoA + M_1,2-DG <=> M_CoA + M_TG"
## dgo_to_pco
if (reaction == "RHEA:36179")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
if (reaction == "RHEA:36180")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
if (reaction == "RHEA:36181")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
if (reaction == "RHEA:36182")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
## dgo_to_peo
if (reaction %in% c("RHEA:36187"))
.formula <- "M_CDP-Ethanolamine + M_DG-O = M_H+ + M_CMP + M_PE-O"
if (reaction %in% c("RHEA:36188"))
.formula <- "M_CDP-Ethanolamine + M_DG-O => M_H+ + M_CMP + M_PE-O"
if (reaction %in% c("RHEA:36189"))
.formula <- "M_CDP-Ethanolamine + M_DG-O <= M_H+ + M_CMP + M_PE-O"
if (reaction %in% c("RHEA:36190"))
.formula <- "M_CDP-Ethanolamine + M_DG-O <=> M_H+ + M_CMP + M_PE-O"
if (reaction == "dhcer_to_cer")
.formula <- "M_H+ + M_NADH + M_O2 + M_DhCer <=> 2 M_H2O + M_NAD + M_Cer"
## dhcer_to_dhsm
if (reaction == "RHEA:44620")
.formula <- "M_PC + M_DhCer <=> M_1,2-DG + M_DhSM"
## dhsm_to_dhcer
if (reaction == "RHEA:45300")
.formula <- "M_H2O + M_DhSM = M_Phosphocholine + M_H+ + M_DhCer"
if (reaction == "RHEA:45301")
.formula <- "M_H2O + M_DhSM => M_Phosphocholine + M_H+ + M_DhCer"
if (reaction == "RHEA:45302")
.formula <- "M_H2O + M_DhSM <= M_Phosphocholine + M_H+ + M_DhCer"
if (reaction == "RHEA:45303")
.formula <- "M_H2O + M_DhSM <=> M_Phosphocholine + M_H+ + M_DhCer"
## fa_to_coa
if (reaction %in% c("RHEA:15421", "RHEA:38883"))
.formula <- "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA"
if (reaction %in% c("RHEA:15422", "RHEA:38884"))
.formula <- "M_ATP + M_CoA + M_FA => M_PPi + M_AMP + M_AcylCoA"
if (reaction %in% c("RHEA:15423", "RHEA:38885"))
.formula <- "M_ATP + M_CoA + M_FA <= M_PPi + M_AMP + M_AcylCoA"
if (reaction %in% c("RHEA:15424", "RHEA:38886"))
.formula <- "M_ATP + M_CoA + M_FA <=> M_PPi + M_AMP + M_AcylCoA"
## 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"
if (reaction == "RHEA:45420") ## lnape_to_gpnae
.formula <- "M_LNAPE + M_H2O <=> M_gpnae + M_FA"
## lpa_to_pa
if (reaction == "RHEA:19709")
.formula <- "M_LPA + M_AcylCoA = M_CoA + M_PA"
if (reaction == "RHEA:19710")
.formula <- "M_LPA + M_AcylCoA => M_CoA + M_PA"
if (reaction == "RHEA:19711")
.formula <- "M_LPA + M_AcylCoA <= M_CoA + M_PA"
if (reaction == "RHEA:19712")
.formula <- "M_LPA + M_AcylCoA <=> M_CoA + M_PA"
## 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"
## sn1lpc_to_fa
if (reaction == "RHEA:15177")
.formula <- "M_H2O + M_1-LPC = M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:15178")
.formula <- "M_H2O + M_1-LPC => M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:15179")
.formula <- "M_H2O + M_1-LPC <= M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:15180")
.formula <- "M_H2O + M_1-LPC <=> M_Glycerophosphocholine + M_H+ + M_FA"
## sn2lpc_to_fa
if (reaction == "RHEA:44696")
.formula <- "M_H2O + M_2-LPC = M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:44697")
.formula <- "M_H2O + M_2-LPC => M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:44698")
.formula <- "M_H2O + M_2-LPC <= M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:44699")
.formula <- "M_H2O + M_2-LPC <=> M_Glycerophosphocholine + M_H+ + M_FA"
## 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"
## lpco_to_pco
if (reaction == "RHEA:23992")
.formula <- "1-LPC-O + AcylCoA = PC-O + CoA"
if (reaction == "RHEA:23993")
.formula <- "1-LPC-O + AcylCoA => PC-O + CoA"
if (reaction == "RHEA:23994")
.formula <- "1-LPC-O + AcylCoA <= PC-O + CoA"
if (reaction == "RHEA:23995")
.formula <- "1-LPC-O + AcylCoA <=> PC-O + CoA"
## sn1lpe_to_fa
if (reaction == "RHEA:32967")
.formula <- "M_H2O + M_1-LPE = M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32968")
.formula <- "M_H2O + M_1-LPE => M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32969")
.formula <- "M_H2O + M_1-LPE <= M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32970")
.formula <- "M_H2O + M_1-LPE <=> M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "sn2lpe_to_fa")
.formula <- "M_H2O + M_2-LPE <=> M_H+ + M_FA + M_Glycerophosphoethanolamine"
## sn1lpe_to_pe
if (reaction == "RHEA:32995")
.formula <- "M_AcylCoA + M_1-LPE = M_CoA + M_PE"
if (reaction == "RHEA:32996")
.formula <- "M_AcylCoA + M_1-LPE => M_CoA + M_PE"
if (reaction == "RHEA:32997")
.formula <- "M_AcylCoA + M_1-LPE <= M_CoA + M_PE"
if (reaction == "RHEA:32998")
.formula <- "M_AcylCoA + M_1-LPE <=> M_CoA + M_PE"
## 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"
if (reaction == "lpeo_to_peo")
.formula <- "M_AcylCoA + M_ak2lgpe <=> M_CoA + M_PE-O"
## lpep_to_pep
if (reaction == "RHEA:16245")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
if (reaction == "RHEA:16246")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
if (reaction == "RHEA:16247")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
if (reaction == "RHEA:16248")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
## sn1mg_to_dg
if (reaction %in% c("RHEA:38463", "RHEA:39943"))
.formula <- "M_1-MG + M_AcylCoA = M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:38464", "RHEA:39944"))
.formula <- "M_1-MG + M_AcylCoA => M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:38465", "RHEA:39945"))
.formula <- "M_1-MG + M_AcylCoA <= M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:38466", "RHEA:39946"))
.formula <- "M_1-MG + M_AcylCoA <=> M_CoA + M_1,2-DG"
## sn2mg_to_dg
if (reaction %in% c("RHEA:32947", "RHEA:16741"))
.formula <- "M_AcylCoA + M_1-MG = M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:32948", "RHEA:16742"))
.formula <- "M_AcylCoA + M_1-MG => M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:32949", "RHEA:16743"))
.formula <- "M_AcylCoA + M_1-MG <= M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:32950", "RHEA:16744"))
.formula <- "M_AcylCoA + M_1-MG <=> M_CoA + M_1,2-DG"
## sn1mg_to_fa
if (reaction == "RHEA:34019")
.formula <- "M_H2O + M_1-MG = M_Glycerol + M_H+ + M_FA"
if (reaction == "RHEA:34020")
.formula <- "M_H2O + M_1-MG => M_Glycerol + M_H+ + M_FA"
if (reaction == "RHEA:34021")
.formula <- "M_H2O + M_1-MG <= M_Glycerol + M_H+ + M_FA"
if (reaction == "RHEA:34022")
.formula <- "M_H2O + M_1-MG <=> M_Glycerol + M_H+ + M_FA"
## sn2mg_to_fa
if (reaction %in% c("RHEA:32871"))
.formula <- "M_H2O + M_2-MG = M_Glycerol + M_H+ + M_FA"
if (reaction %in% c("RHEA:32872"))
.formula <- "M_H2O + M_2-MG => M_Glycerol + M_H+ + M_FA"
if (reaction %in% c("RHEA:32873"))
.formula <- "M_H2O + M_2-MG <= M_Glycerol + M_H+ + M_FA"
if (reaction %in% c("RHEA:32874"))
.formula <- "M_H2O + M_2-MG <=> M_Glycerol + M_H+ + M_FA"
## sn1mg_to_lpa
if (reaction == "RHEA:33747")
.formula <- "M_ATP + M_1-MG = M_H+ + M_ADP + M_LPA"
if (reaction == "RHEA:33748")
.formula <- "M_ATP + M_1-MG => M_H+ + M_ADP + M_LPA"
if (reaction == "RHEA:33749")
.formula <- "M_ATP + M_1-MG <= M_H+ + M_ADP + M_LPA"
if (reaction == "RHEA:33750")
.formula <- "M_ATP + M_1-MG <=> M_H+ + M_ADP + M_LPA"
if (reaction == "sn2mg_to_sn1mg")
.formula <- "M_2-MG <=> M_1-MG"
if (reaction == "nae_to_fa")
.formula <- "M_H2O + M_NAE <=> M_Ethanolamine + M_H+ + M_FA"
if (reaction == "nape_to_lnape")
.formula <- "M_NAPE + M_H2O <=> M_LNAPE + M_FA"
if (reaction == "nape_to_nae")
.formula <- "M_NAPE + M_H2O <=> M_NAE + M_PA"
if (reaction == "nape_to_pnae")
.formula <- "M_NAPE + M_H2O <=> M_PNAE + M_1,2-DG"
if (reaction == "napeo_to_nae")
.formula <- "M_NAPEO + M_H2O <=> M_NAE + M_PA-O"
## pa_to_cdpdg
if (reaction == "RHEA:16229")
.formula <- "M_CTP + M_PA = M_PPi + M_CDP-DG"
if (reaction == "RHEA:16230")
.formula <- "M_CTP + M_PA => M_PPi + M_CDP-DG"
if (reaction == "RHEA:16231")
.formula <- "M_CTP + M_PA <= M_PPi + M_CDP-DG"
if (reaction == "RHEA:16232")
.formula <- "M_CTP + M_PA <=> M_PPi + M_CDP-DG"
## pa_to_dg
if (reaction == "RHEA:27429")
.formula <- "M_H2O + M_PA = M_Pi + M_1,2-DG"
if (reaction == "RHEA:27430")
.formula <- "M_H2O + M_PA => M_Pi + M_1,2-DG"
if (reaction == "RHEA:27431")
.formula <- "M_H2O + M_PA <= M_Pi + M_1,2-DG"
if (reaction == "RHEA:27432")
.formula <- "M_H2O + M_PA <=> M_Pi + M_1,2-DG"
## pao_to_dgo
if (reaction == "RHEA:36239")
.formula <- "M_H2O + M_PA-O = M_Pi + M_DG-O"
if (reaction == "RHEA:36240")
.formula <- "M_H2O + M_PA-O => M_Pi + M_DG-O"
if (reaction == "RHEA:36241")
.formula <- "M_H2O + M_PA-O <= M_Pi + M_DG-O"
if (reaction == "RHEA:36242")
.formula <- "M_H2O + M_PA-O <=> M_Pi + M_DG-O"
## pc_to_dg
if (reaction == "RHEA:10604")
.formula <- "M_H2O + M_PC = M_Phosphocholine + M_1,2-DG"
if (reaction == "RHEA:10605")
.formula <- "M_H2O + M_PC => M_Phosphocholine + M_1,2-DG"
if (reaction == "RHEA:10606")
.formula <- "M_H2O + M_PC <= M_Phosphocholine + M_1,2-DG"
if (reaction == "RHEA:10607")
.formula <- "M_H2O + M_PC <=> M_Phosphocholine + M_1,2-DG"
## pc_to_sn1lpc
if (reaction == "RHEA:15801")
.formula <- "M_H2O + M_PC = M_1-LPC + M_FA"
if (reaction == "RHEA:15802")
.formula <- "M_H2O + M_PC => M_1-LPC + M_FA"
if (reaction == "RHEA:15803")
.formula <- "M_H2O + M_PC <= M_1-LPC + M_FA"
if (reaction == "RHEA:15804")
.formula <- "M_H2O + M_PC <=> M_1-LPC + M_FA"
## pc_to_sn2lpc
if (reaction == "RHEA:18689")
.formula <- "M_H2O + M_PC = M_2-LPC + M_FA"
if (reaction == "RHEA:18690")
.formula <- "M_H2O + M_PC => M_2-LPC + M_FA"
if (reaction == "RHEA:18691")
.formula <- "M_H2O + M_PC <= M_2-LPC + M_FA"
if (reaction == "RHEA:18692")
.formula <- "M_H2O + M_PC <=> M_2-LPC + M_FA"
## pc_to_pa
if (reaction == "RHEA:14445")
.formula <- "M_H2O + M_PC = M_Choline + M_PA"
if (reaction == "RHEA:14446")
.formula <- "M_H2O + M_PC => M_Choline + M_PA"
if (reaction == "RHEA:14447")
.formula <- "M_H2O + M_PC <= M_Choline + M_PA"
if (reaction == "RHEA:14448")
.formula <- "M_H2O + M_PC <=> M_Choline + M_PA"
## pc_to_ps
if (reaction == "RHEA:45088") ##
.formula <- "M_L-Serine + M_PC = M_Choline + M_PS"
if (reaction == "RHEA:45089") ##
.formula <- "M_L-Serine + M_PC => M_Choline + M_PS"
if (reaction == "RHEA:45090") ##
.formula <- "M_L-Serine + M_PC <= M_Choline + M_PS"
if (reaction == "RHEA:45091") ##
.formula <- "M_L-Serine + M_PC <=> M_Choline + M_PS"
## pco_to_lpco
if (reaction == "RHEA:36231")
.formula <- "M_H2O + M_PC-O = M_H+ + M_LPC-O + M_FA"
if (reaction == "RHEA:36232")
.formula <- "M_H2O + M_PC-O => M_H+ + M_LPC-O + M_FA"
if (reaction == "RHEA:36233")
.formula <- "M_H2O + M_PC-O <= M_H+ + M_LPC-O + M_FA"
if (reaction == "RHEA:36234")
.formula <- "M_H2O + M_PC-O <=> M_H+ + M_LPC-O + M_FA"
## lpco_to_lpao
if (reaction == "RHEA:39927")
.formula <- "M_H2O + M_1-LPC-O = M_1-LPA-O + M_H+ + M_Choline"
if (reaction == "RHEA:39928")
.formula <- "M_H2O + M_1-LPC-O => M_1-LPA-O + M_H+ + M_Choline"
if (reaction == "RHEA:39929")
.formula <- "M_H2O + M_1-LPC-O <= M_1-LPA-O + M_H+ + M_Choline"
if (reaction == "RHEA:39930")
.formula <- "M_H2O + M_1-LPC-O <=> M_1-LPA-O + M_H+ + M_Choline"
## lpco_to_mgo
if (reaction == "RHEA:36083")
.formula <- "M_H2O + M_1-LPC-O = M_H+ + M_Phosphocholine + M_1-MG-O"
if (reaction == "RHEA:36084")
.formula <- "M_H2O + M_1-LPC-O => M_H+ + M_Phosphocholine + M_1-MG-O"
if (reaction == "RHEA:36085")
.formula <- "M_H2O + M_1-LPC-O <= M_H+ + M_Phosphocholine + M_1-MG-O"
if (reaction == "RHEA:36086")
.formula <- "M_H2O + M_1-LPC-O <=> M_H+ + M_Phosphocholine + M_1-MG-O"
## 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"
## pe_to_dg
if (reaction == "pe_to_dg")
.formula <- "M_H2O + M_PE <=> M_P-Ethanolamine + M_1,2-DG"
## pe_to_sn1lpe
if (reaction == "RHEA:44604")
.formula <- "M_H2O + M_PE = M_H+ + M_FA + M_1-LPE"
if (reaction == "RHEA:44605")
.formula <- "M_H2O + M_PE => M_H+ + M_FA + M_1-LPE"
if (reaction == "RHEA:44606")
.formula <- "M_H2O + M_PE <= M_H+ + M_FA + M_1-LPE"
if (reaction == "RHEA:44607")
.formula <- "M_H2O + M_PE <=> M_H+ + M_FA + M_1-LPE"
## pe_to_sn2lpe
if (reaction == "RHEA:44408")
.formula <- "M_H2O + M_PE = M_H+ + M_FA + M_2-LPE"
if (reaction == "RHEA:44409")
.formula <- "M_H2O + M_PE => M_H+ + M_FA + M_2-LPE"
if (reaction == "RHEA:44410")
.formula <- "M_H2O + M_PE <= M_H+ + M_FA + M_2-LPE"
if (reaction == "RHEA:44411")
.formula <- "M_H2O + M_PE <=> M_H+ + M_FA + M_2-LPE"
if (reaction == "pe_to_nape_sn1")
.formula <- "M_PE + M_PC <=> M_NAPE + M_2-LPC"
if (reaction == "pe_to_nape_sn2")
.formula <- "M_PE + M_PC <=> M_NAPE + M_1-LPC"
if (reaction == "pe_to_pa")
.formula <- "M_H2O + M_PE <=> M_Ethanolamine + M_H+ + M_PA"
## pe_to_ps
if (reaction == "RHEA:27606")
.formula <- "M_L-Serine + M_PE = M_Ethanolamine + M_PS"
if (reaction == "RHEA:27607")
.formula <- "M_L-Serine + M_PE => M_Ethanolamine + M_PS"
if (reaction == "RHEA:27608")
.formula <- "M_L-Serine + M_PE <= M_Ethanolamine + M_PS"
if (reaction == "RHEA:27609")
.formula <- "M_L-Serine + M_PE <=> M_Ethanolamine + M_PS"
if (reaction == "peo_to_lpeo")
.formula <- "M_H2O + M_PE-O <=> M_H+ + M_LPE-O + M_FA"
if (reaction == "peo_to_napeo_sn1")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_2-LPC"
if (reaction == "peo_to_napeo_sn2")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_1-LPC"
## 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"
## pep_to_lpep
if (reaction == "RHEA:36195")
.formula <- "M_H2O + M_PE-P = M_H+ + M_LPE-P + M_FA"
if (reaction == "RHEA:36196")
.formula <- "M_H2O + M_PE-P => M_H+ + M_LPE-P + M_FA"
if (reaction == "RHEA:36197")
.formula <- "M_H2O + M_PE-P <= M_H+ + M_LPE-P + M_FA"
if (reaction == "RHEA:36198")
.formula <- "M_H2O + M_PE-P <=> M_H+ + M_LPE-P + M_FA"
## lpep_to_fal
if (reaction == "RHEA:16905")
.formula <- "M_H2O + M_1-LPE-P = M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16906")
.formula <- "M_H2O + M_1-LPE-P => M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16907")
.formula <- "M_H2O + M_1-LPE-P <= M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16908")
.formula <- "M_H2O + M_1-LPE-P <=> M_FAL + M_Glycerophosphoethanolamine"
## lpep_to_lpap
if (reaction == "RHEA:36203")
.formula <- "M_H2O + M_1-LPE-P = M_LPA-P + M_H+ + M_Ethanolamine"
if (reaction == "RHEA:36204")
.formula <- "M_H2O + M_1-LPE-P => M_LPA-P + M_H+ + M_Ethanolamine"
if (reaction == "RHEA:36205")
.formula <- "M_H2O + M_1-LPE-P <= M_LPA-P + M_H+ + M_Ethanolamine"
if (reaction == "RHEA:36206")
.formula <- "M_H2O + M_1-LPE-P <=> M_LPA-P + M_H+ + M_Ethanolamine"
## lpep_to_mgp
if (reaction == "RHEA:36199")
.formula <- "M_H2O + M_1-LPE-P = M_Phosphoethanolamine + M_H+ + M_1-MG-P"
if (reaction == "RHEA:36200")
.formula <- "M_H2O + M_1-LPE-P => M_Phosphoethanolamine + M_H+ + M_1-MG-P"
if (reaction == "RHEA:36201")
.formula <- "M_H2O + M_1-LPE-P <= M_Phosphoethanolamine + M_H+ + M_1-MG-P"
if (reaction == "RHEA:36202")
.formula <- "M_H2O + M_1-LPE-P <=> M_Phosphoethanolamine + M_H+ + M_1-MG-P"
## pep_to_napep_sn1
if (reaction == "pep_to_napep_sn1")
.formula <- "M_PE-P + M_PC <=> M_NAPEP + M_2-LPC"
## pep_to_napep_sn2
if (reaction == "pep_to_napep_sn2")
.formula <- "M_PE-P + M_PC <=> M_NAPEP + M_1-LPC"
## pg_to_cl
if (reaction == "RHEA:32931")
.formula <- "M_CDP-DG + M_PG = M_H+ + M_CMP + M_CL"
if (reaction == "RHEA:32932")
.formula <- "M_CDP-DG + M_PG => M_H+ + M_CMP + M_CL"
if (reaction == "RHEA:32933")
.formula <- "M_CDP-DG + M_PG <= M_H+ + M_CMP + M_CL"
if (reaction == "RHEA:32934")
.formula <- "M_CDP-DG + M_PG <=> M_H+ + M_CMP + M_CL"
## pgp_to_pg
if (reaction == "RHEA:33751")
.formula <- "M_H2O + M_pgp = M_Pi + M_PG"
if (reaction == "RHEA:33752")
.formula <- "M_H2O + M_pgp => M_Pi + M_PG"
if (reaction == "RHEA:33753")
.formula <- "M_H2O + M_pgp <= M_Pi + M_PG"
if (reaction == "RHEA:33754")
.formula <- "M_H2O + M_pgp <=> M_Pi + M_PG"
## pi_to_dg
if (reaction == "RHEA:43484")
.formula <- "M_H2O + M_PI = M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
if (reaction == "RHEA:43485")
.formula <- "M_H2O + M_PI => M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
if (reaction == "RHEA:43486")
.formula <- "M_H2O + M_PI <= M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
if (reaction == "RHEA:43487")
.formula <- "M_H2O + M_PI <=> M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
## pi_to_sn1lpi
if (reaction == "RHEA:18001")
.formula <- "M_H2O + M_PI = M_1-LPI + M_H+ + M_FA"
if (reaction == "RHEA:18002")
.formula <- "M_H2O + M_PI => M_1-LPI + M_H+ + M_FA"
if (reaction == "RHEA:18003")
.formula <- "M_H2O + M_PI <= M_1-LPI + M_H+ + M_FA"
if (reaction == "RHEA:18004")
.formula <- "M_H2O + M_PI <=> M_1-LPI + M_H+ + M_FA"
## ps_to_pe
if (reaction == "RHEA:20828")
.formula <- "M_H+ + M_PS = M_CO2 + M_PE"
if (reaction == "RHEA:20829")
.formula <- "M_H+ + M_PS => M_CO2 + M_PE"
if (reaction == "RHEA:20830")
.formula <- "M_H+ + M_PS <= M_CO2 + M_PE"
if (reaction == "RHEA:20831")
.formula <- "M_H+ + M_PS <=> M_CO2 + M_PE"
if (reaction == "sm_to_cer")
.formula <- "M_H2O + M_SM <=> M_Phosphocholine + M_H+ + M_Cer"
## sphinga_to_dhcer
if (reaction == "RHEA:53424")
.formula <- "M_AcylCoA + M_Sphinganine = M_CoA + M_DhCer"
if (reaction == "RHEA:53425")
.formula <- "M_AcylCoA + M_Sphinganine => M_CoA + M_DhCer"
if (reaction == "RHEA:53426")
.formula <- "M_AcylCoA + M_Sphinganine <= M_CoA + M_DhCer"
if (reaction == "RHEA:53427")
.formula <- "M_AcylCoA + M_Sphinganine <=> M_CoA + M_DhCer"
## tg_to_dg
if (reaction %in% c("RHEA:33271", "RHEA:44864"))
.formula <- "M_H2O + M_TG = M_H+ + M_FA + M_1,2-DG"
if (reaction %in% c("RHEA:33272", "RHEA:44865"))
.formula <- "M_H2O + M_TG => M_H+ + M_FA + M_1,2-DG"
if (reaction %in% c("RHEA:33273", "RHEA:44866"))
.formula <- "M_H2O + M_TG <= M_H+ + M_FA + M_1,2-DG"
if (reaction %in% c("RHEA:33274", "RHEA:44867"))
.formula <- "M_H2O + M_TG <=> M_H+ + M_FA + M_1,2-DG"
template$reaction_formula <- .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_fixed(str = .formula_substrate,
pattern = " ", replacement = "")
.formula_product <- stringi::stri_split(str = .formula_product,
regex = "[+]")[[1]]
.formula_product <- stringi::stri_replace_all_fixed(str = .formula_product,
pattern = " ", replacement = "")
## write the substrates and products to the template
template$reaction_substrate <- .formula_substrate
template$reaction_product <- .formula_product
## return the template object
template
}
michaelwitting/wormLipidPredictR documentation built on July 1, 2023, 9:20 p.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.
#' }
#'
#' @param template NA or \code{list}
#' @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 = NA, reaction = "RHEA:15421")
.create_template <- function(template = NA, reaction = "RHEA:15421") {
if (is.list(template)) {
## check integrity (all names are present in template)
if (!"reaction_name" %in% names(template))
stop("'template' has to contain the entry 'reaction_name'")
if (!"reaction_formula" %in% names(template))
stop("'template' has to contain the entry 'reaction_formula'")
if (!"reaction_isReversible" %in% names(template))
stop("'template' has to contain the entry 'reacton_isReversible'")
if (!"reaction_geneAssociation" %in% names(template))
stop("'template' has to contain the entry 'reaction_geneAssociation'")
if (!"reaction_pathway" %in% names(template))
stop("'template' has to contain the entry 'reaction_pathway'")
## 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_formula, "character"))
stop("entry 'reaction_formula' 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'")
} else {
## this event happens if the param template is not a list
## check if reaction is in the parameter space
.check_reaction(reaction)
## create a template object (list)
template <- list(reaction_name = "", reaction_formula = "",
reaction_RHEA = reaction, reaction_isReversible = "",
reaction_geneAssociation = "", reaction_pathway = "")
## depending on the reaction, write specific reaction .formula to the
## entry reaction_.formula
## acyldhap_to_alkyldhap
if (reaction == "RHEA:36171")
.formula <- "M_AcylDHAP + M_FAO = M_H+ + M_FA + M_AlkylDHAP"
if (reaction == "RHEA:36172")
.formula <- "M_AcylDHAP + M_FAO => M_H+ + M_FA + M_AlkylDHAP"
if (reaction == "RHEA:36173")
.formula <- "M_AcylDHAP + M_FAO <= M_H+ + M_FA + M_AlkylDHAP"
if (reaction == "RHEA:36174")
.formula <- "M_AcylDHAP + M_FAO <=> M_H+ + M_FA + M_AlkylDHAP"
## alkyldhap_to_lpao
if (reaction == "RHEA:36175")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP = M_LPA-O + M_NADP"
if (reaction == "RHEA:36176")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP => M_LPA-O + M_NADP"
if (reaction == "RHEA:36177")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP <= M_LPA-O + M_NADP"
if (reaction == "RHEA:36178")
.formula <- "M_H+ + M_NADPH + M_AlkylDHAP <=> M_LPA-O + M_NADP"
if (reaction == "cerp_to_cer")
.formula <- "M_H2O + M_CerP <=> M_Pi + M_Cer"
## cdpdg_to_pgp
if (reaction == "RHEA:12593")
.formula <- "M_Glycerol-3-P + M_CDP-DG = M_H+ + M_CMP + M_PGP"
if (reaction == "RHEA:12594")
.formula <- "M_Glycerol-3-P + M_CDP-DG => M_H+ + M_CMP + M_PGP"
if (reaction == "RHEA:12595")
.formula <- "M_Glycerol-3-P + M_CDP-DG <= M_H+ + M_CMP + M_PGP"
if (reaction == "RHEA:12596")
.formula <- "M_Glycerol-3-P + M_CDP-DG <=> M_H+ + M_CMP + M_PGP"
## cdpdg_to_pi
if (reaction == "RHEA:11580")
.formula <- "M_myo-Inositol + M_CDP-DG = M_H+ + M_CMP + M_PI"
if (reaction == "RHEA:11581")
.formula <- "M_myo-Inositol + M_CDP-DG => M_H+ + M_CMP + M_PI"
if (reaction == "RHEA:11582")
.formula <- "M_myo-Inositol + M_CDP-DG <= M_H+ + M_CMP + M_PI"
if (reaction == "RHEA:11583")
.formula <- "M_myo-Inositol + M_CDP-DG <=> M_H+ + M_CMP + M_PI"
## cer_to_cerp
if (reaction == "RHEA:17929")
.formula <- "M_ATP + M_Cer <=> M_H+ + M_ADP + M_CerP"
## cer_to_glccer
if (reaction == "RHEA:12088")
.formula <- "M_UDP-Glucose + M_Cer <=> M_H+ + M_UDP + M_GlcCer"
## cer_to_sm
if (reaction == "RHEA:18765")
.formula <- "M_PC + M_Cer <=> M_1,2-DG + M_SM"
## cl_to_lcl
if (reaction == "RHEA:32935")
.formula <- "M_H2O + M_CL = M_1,2,4-LCL + M_H+ + M_FA"
if (reaction == "RHEA:32936")
.formula <- "M_H2O + M_CL => M_1,2,4-LCL + M_H+ + M_FA"
if (reaction == "RHEA:32937")
.formula <- "M_H2O + M_CL <= M_1,2,4-LCL + M_H+ + M_FA"
if (reaction == "RHEA:32938")
.formula <- "M_H2O + M_CL <=> M_1,2,4-LCL + M_H+ + M_FA"
## coa_to_acdhap
if (reaction == "RHEA:17657")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA = M_CoA + M_AcylDHAP"
if (reaction == "RHEA:17658")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA => M_CoA + M_AcylDHAP"
if (reaction == "RHEA:17659")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA <= M_CoA + M_AcylDHAP"
if (reaction == "RHEA:17660")
.formula <- "M_Dihydroxyacetone-P + M_AcylCoA <=> M_CoA + M_AcylDHAP"
## coa_to_fao
if (reaction == "RHEA:52716")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ = M_FAO + 2 M_NADP + M_CoA"
if (reaction == "RHEA:52717")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ => M_FAO + 2 M_NADP + M_CoA"
if (reaction == "RHEA:52718")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ <= M_FAO + 2 M_NADP + M_CoA"
if (reaction == "RHEA:52719")
.formula <- "M_AcylCoA + 2 M_NADPH + 2 M_H+ <=> M_FAO + 2 M_NADP + M_CoA"
## coa_to_lpa
if (reaction == "RHEA:15325")
.formula <- "M_Glycerol-3-P + M_AcylCoA = M_CoA + M_LPA"
if (reaction == "RHEA:15326")
.formula <- "M_Glycerol-3-P + M_AcylCoA => M_CoA + M_LPA"
if (reaction == "RHEA:15327")
.formula <- "M_Glycerol-3-P + M_AcylCoA <= M_CoA + M_LPA"
if (reaction == "RHEA:15328")
.formula <- "M_Glycerol-3-P + M_AcylCoA <=> M_CoA + M_LPA"
## dg_to_sn1mg
if (reaction %in% c("RHEA:44712", "RHEA:35663"))
.formula <- "M_H2O + M_1,2-DG = M_H+ + M_1-MG + M_FA"
if (reaction %in% c("RHEA:44713", "RHEA:35664"))
.formula <- "M_H2O + M_1,2-DG => M_H+ + M_1-MG + M_FA"
if (reaction %in% c("RHEA:44714", "RHEA:35665"))
.formula <- "M_H2O + M_1,2-DG <= M_H+ + M_1-MG + M_FA"
if (reaction %in% c("RHEA:44715", "RHEA:35666"))
.formula <- "M_H2O + M_1,2-DG <=> M_H+ + M_1-MG + M_FA"
## dg_to_sn2mg
if (reaction == "RHEA:33275")
.formula <- "M_H2O + M_1,2-DG = M_H+ + M_2-MG + M_FA"
if (reaction == "RHEA:33276")
.formula <- "M_H2O + M_1,2-DG => M_H+ + M_2-MG + M_FA"
if (reaction == "RHEA:33277")
.formula <- "M_H2O + M_1,2-DG <= M_H+ + M_2-MG + M_FA"
if (reaction == "RHEA:33278")
.formula <- "M_H2O + M_1,2-DG <=> M_H+ + M_2-MG + M_FA"
## dg_to_pa
if (reaction == "RHEA:10272")
.formula <- "M_ATP + M_1,2-DG = M_H+ + M_ADP + M_PA"
if (reaction == "RHEA:10273")
.formula <- "M_ATP + M_1,2-DG => M_H+ + M_ADP + M_PA"
if (reaction == "RHEA:10274")
.formula <- "M_ATP + M_1,2-DG <= M_H+ + M_ADP + M_PA"
if (reaction == "RHEA:10275")
.formula <- "M_ATP + M_1,2-DG <=> M_H+ + M_ADP + M_PA"
## dg_to_pc
if (reaction == "RHEA:32939")
.formula <- "M_CDP-Choline + M_1,2-DG = M_H+ + M_CMP + M_PC"
if (reaction == "RHEA:32940")
.formula <- "M_CDP-Choline + M_1,2-DG => M_H+ + M_CMP + M_PC"
if (reaction == "RHEA:32941")
.formula <- "M_CDP-Choline + M_1,2-DG <= M_H+ + M_CMP + M_PC"
if (reaction == "RHEA:32942")
.formula <- "M_CDP-Choline + M_1,2-DG <=> M_H+ + M_CMP + M_PC"
## dg_to_pe
if (reaction == "RHEA:32943")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG = M_H+ + M_CMP + M_PE"
if (reaction == "RHEA:32944")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG => M_H+ + M_CMP + M_PE"
if (reaction == "RHEA:32945")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG <= M_H+ + M_CMP + M_PE"
if (reaction == "RHEA:32946")
.formula <- "M_CDP-Ethanolamine + M_1,2-DG <=> M_H+ + M_CMP + M_PE"
## dg_to_tg
if (reaction == "RHEA:10868")
.formula <- "M_AcylCoA + M_1,2-DG = M_CoA + M_TG"
if (reaction == "RHEA:10869")
.formula <- "M_AcylCoA + M_1,2-DG => M_CoA + M_TG"
if (reaction == "RHEA:10870")
.formula <- "M_AcylCoA + M_1,2-DG <= M_CoA + M_TG"
if (reaction == "RHEA:10871")
.formula <- "M_AcylCoA + M_1,2-DG <=> M_CoA + M_TG"
## dgo_to_pco
if (reaction == "RHEA:36179")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
if (reaction == "RHEA:36180")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
if (reaction == "RHEA:36181")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
if (reaction == "RHEA:36182")
.formula <- "M_CDP-Choline + M_DG-O <=> M_H+ + M_CMP + M_PC-O"
## dgo_to_peo
if (reaction %in% c("RHEA:36187"))
.formula <- "M_CDP-Ethanolamine + M_DG-O = M_H+ + M_CMP + M_PE-O"
if (reaction %in% c("RHEA:36188"))
.formula <- "M_CDP-Ethanolamine + M_DG-O => M_H+ + M_CMP + M_PE-O"
if (reaction %in% c("RHEA:36189"))
.formula <- "M_CDP-Ethanolamine + M_DG-O <= M_H+ + M_CMP + M_PE-O"
if (reaction %in% c("RHEA:36190"))
.formula <- "M_CDP-Ethanolamine + M_DG-O <=> M_H+ + M_CMP + M_PE-O"
if (reaction == "dhcer_to_cer")
.formula <- "M_H+ + M_NADH + M_O2 + M_DhCer <=> 2 M_H2O + M_NAD + M_Cer"
## dhcer_to_dhsm
if (reaction == "RHEA:44620")
.formula <- "M_PC + M_DhCer <=> M_1,2-DG + M_DhSM"
## dhsm_to_dhcer
if (reaction == "RHEA:45300")
.formula <- "M_H2O + M_DhSM = M_Phosphocholine + M_H+ + M_DhCer"
if (reaction == "RHEA:45301")
.formula <- "M_H2O + M_DhSM => M_Phosphocholine + M_H+ + M_DhCer"
if (reaction == "RHEA:45302")
.formula <- "M_H2O + M_DhSM <= M_Phosphocholine + M_H+ + M_DhCer"
if (reaction == "RHEA:45303")
.formula <- "M_H2O + M_DhSM <=> M_Phosphocholine + M_H+ + M_DhCer"
## fa_to_coa
if (reaction %in% c("RHEA:15421", "RHEA:38883"))
.formula <- "M_ATP + M_CoA + M_FA = M_PPi + M_AMP + M_AcylCoA"
if (reaction %in% c("RHEA:15422", "RHEA:38884"))
.formula <- "M_ATP + M_CoA + M_FA => M_PPi + M_AMP + M_AcylCoA"
if (reaction %in% c("RHEA:15423", "RHEA:38885"))
.formula <- "M_ATP + M_CoA + M_FA <= M_PPi + M_AMP + M_AcylCoA"
if (reaction %in% c("RHEA:15424", "RHEA:38886"))
.formula <- "M_ATP + M_CoA + M_FA <=> M_PPi + M_AMP + M_AcylCoA"
## 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"
if (reaction == "RHEA:45420") ## lnape_to_gpnae
.formula <- "M_LNAPE + M_H2O <=> M_gpnae + M_FA"
## lpa_to_pa
if (reaction == "RHEA:19709")
.formula <- "M_LPA + M_AcylCoA = M_CoA + M_PA"
if (reaction == "RHEA:19710")
.formula <- "M_LPA + M_AcylCoA => M_CoA + M_PA"
if (reaction == "RHEA:19711")
.formula <- "M_LPA + M_AcylCoA <= M_CoA + M_PA"
if (reaction == "RHEA:19712")
.formula <- "M_LPA + M_AcylCoA <=> M_CoA + M_PA"
## 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"
## sn1lpc_to_fa
if (reaction == "RHEA:15177")
.formula <- "M_H2O + M_1-LPC = M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:15178")
.formula <- "M_H2O + M_1-LPC => M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:15179")
.formula <- "M_H2O + M_1-LPC <= M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:15180")
.formula <- "M_H2O + M_1-LPC <=> M_Glycerophosphocholine + M_H+ + M_FA"
## sn2lpc_to_fa
if (reaction == "RHEA:44696")
.formula <- "M_H2O + M_2-LPC = M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:44697")
.formula <- "M_H2O + M_2-LPC => M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:44698")
.formula <- "M_H2O + M_2-LPC <= M_Glycerophosphocholine + M_H+ + M_FA"
if (reaction == "RHEA:44699")
.formula <- "M_H2O + M_2-LPC <=> M_Glycerophosphocholine + M_H+ + M_FA"
## 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"
## lpco_to_pco
if (reaction == "RHEA:23992")
.formula <- "1-LPC-O + AcylCoA = PC-O + CoA"
if (reaction == "RHEA:23993")
.formula <- "1-LPC-O + AcylCoA => PC-O + CoA"
if (reaction == "RHEA:23994")
.formula <- "1-LPC-O + AcylCoA <= PC-O + CoA"
if (reaction == "RHEA:23995")
.formula <- "1-LPC-O + AcylCoA <=> PC-O + CoA"
## sn1lpe_to_fa
if (reaction == "RHEA:32967")
.formula <- "M_H2O + M_1-LPE = M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32968")
.formula <- "M_H2O + M_1-LPE => M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32969")
.formula <- "M_H2O + M_1-LPE <= M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:32970")
.formula <- "M_H2O + M_1-LPE <=> M_H+ + M_FA + M_Glycerophosphoethanolamine"
if (reaction == "sn2lpe_to_fa")
.formula <- "M_H2O + M_2-LPE <=> M_H+ + M_FA + M_Glycerophosphoethanolamine"
## sn1lpe_to_pe
if (reaction == "RHEA:32995")
.formula <- "M_AcylCoA + M_1-LPE = M_CoA + M_PE"
if (reaction == "RHEA:32996")
.formula <- "M_AcylCoA + M_1-LPE => M_CoA + M_PE"
if (reaction == "RHEA:32997")
.formula <- "M_AcylCoA + M_1-LPE <= M_CoA + M_PE"
if (reaction == "RHEA:32998")
.formula <- "M_AcylCoA + M_1-LPE <=> M_CoA + M_PE"
## 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"
if (reaction == "lpeo_to_peo")
.formula <- "M_AcylCoA + M_ak2lgpe <=> M_CoA + M_PE-O"
## lpep_to_pep
if (reaction == "RHEA:16245")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
if (reaction == "RHEA:16246")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
if (reaction == "RHEA:16247")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
if (reaction == "RHEA:16248")
.formula <- "M_AcylCoA + M_LPE-P <=> M_CoA + M_PE-P"
## sn1mg_to_dg
if (reaction %in% c("RHEA:38463", "RHEA:39943"))
.formula <- "M_1-MG + M_AcylCoA = M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:38464", "RHEA:39944"))
.formula <- "M_1-MG + M_AcylCoA => M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:38465", "RHEA:39945"))
.formula <- "M_1-MG + M_AcylCoA <= M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:38466", "RHEA:39946"))
.formula <- "M_1-MG + M_AcylCoA <=> M_CoA + M_1,2-DG"
## sn2mg_to_dg
if (reaction %in% c("RHEA:32947", "RHEA:16741"))
.formula <- "M_AcylCoA + M_1-MG = M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:32948", "RHEA:16742"))
.formula <- "M_AcylCoA + M_1-MG => M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:32949", "RHEA:16743"))
.formula <- "M_AcylCoA + M_1-MG <= M_CoA + M_1,2-DG"
if (reaction %in% c("RHEA:32950", "RHEA:16744"))
.formula <- "M_AcylCoA + M_1-MG <=> M_CoA + M_1,2-DG"
## sn1mg_to_fa
if (reaction == "RHEA:34019")
.formula <- "M_H2O + M_1-MG = M_Glycerol + M_H+ + M_FA"
if (reaction == "RHEA:34020")
.formula <- "M_H2O + M_1-MG => M_Glycerol + M_H+ + M_FA"
if (reaction == "RHEA:34021")
.formula <- "M_H2O + M_1-MG <= M_Glycerol + M_H+ + M_FA"
if (reaction == "RHEA:34022")
.formula <- "M_H2O + M_1-MG <=> M_Glycerol + M_H+ + M_FA"
## sn2mg_to_fa
if (reaction %in% c("RHEA:32871"))
.formula <- "M_H2O + M_2-MG = M_Glycerol + M_H+ + M_FA"
if (reaction %in% c("RHEA:32872"))
.formula <- "M_H2O + M_2-MG => M_Glycerol + M_H+ + M_FA"
if (reaction %in% c("RHEA:32873"))
.formula <- "M_H2O + M_2-MG <= M_Glycerol + M_H+ + M_FA"
if (reaction %in% c("RHEA:32874"))
.formula <- "M_H2O + M_2-MG <=> M_Glycerol + M_H+ + M_FA"
## sn1mg_to_lpa
if (reaction == "RHEA:33747")
.formula <- "M_ATP + M_1-MG = M_H+ + M_ADP + M_LPA"
if (reaction == "RHEA:33748")
.formula <- "M_ATP + M_1-MG => M_H+ + M_ADP + M_LPA"
if (reaction == "RHEA:33749")
.formula <- "M_ATP + M_1-MG <= M_H+ + M_ADP + M_LPA"
if (reaction == "RHEA:33750")
.formula <- "M_ATP + M_1-MG <=> M_H+ + M_ADP + M_LPA"
if (reaction == "sn2mg_to_sn1mg")
.formula <- "M_2-MG <=> M_1-MG"
if (reaction == "nae_to_fa")
.formula <- "M_H2O + M_NAE <=> M_Ethanolamine + M_H+ + M_FA"
if (reaction == "nape_to_lnape")
.formula <- "M_NAPE + M_H2O <=> M_LNAPE + M_FA"
if (reaction == "nape_to_nae")
.formula <- "M_NAPE + M_H2O <=> M_NAE + M_PA"
if (reaction == "nape_to_pnae")
.formula <- "M_NAPE + M_H2O <=> M_PNAE + M_1,2-DG"
if (reaction == "napeo_to_nae")
.formula <- "M_NAPEO + M_H2O <=> M_NAE + M_PA-O"
## pa_to_cdpdg
if (reaction == "RHEA:16229")
.formula <- "M_CTP + M_PA = M_PPi + M_CDP-DG"
if (reaction == "RHEA:16230")
.formula <- "M_CTP + M_PA => M_PPi + M_CDP-DG"
if (reaction == "RHEA:16231")
.formula <- "M_CTP + M_PA <= M_PPi + M_CDP-DG"
if (reaction == "RHEA:16232")
.formula <- "M_CTP + M_PA <=> M_PPi + M_CDP-DG"
## pa_to_dg
if (reaction == "RHEA:27429")
.formula <- "M_H2O + M_PA = M_Pi + M_1,2-DG"
if (reaction == "RHEA:27430")
.formula <- "M_H2O + M_PA => M_Pi + M_1,2-DG"
if (reaction == "RHEA:27431")
.formula <- "M_H2O + M_PA <= M_Pi + M_1,2-DG"
if (reaction == "RHEA:27432")
.formula <- "M_H2O + M_PA <=> M_Pi + M_1,2-DG"
## pao_to_dgo
if (reaction == "RHEA:36239")
.formula <- "M_H2O + M_PA-O = M_Pi + M_DG-O"
if (reaction == "RHEA:36240")
.formula <- "M_H2O + M_PA-O => M_Pi + M_DG-O"
if (reaction == "RHEA:36241")
.formula <- "M_H2O + M_PA-O <= M_Pi + M_DG-O"
if (reaction == "RHEA:36242")
.formula <- "M_H2O + M_PA-O <=> M_Pi + M_DG-O"
## pc_to_dg
if (reaction == "RHEA:10604")
.formula <- "M_H2O + M_PC = M_Phosphocholine + M_1,2-DG"
if (reaction == "RHEA:10605")
.formula <- "M_H2O + M_PC => M_Phosphocholine + M_1,2-DG"
if (reaction == "RHEA:10606")
.formula <- "M_H2O + M_PC <= M_Phosphocholine + M_1,2-DG"
if (reaction == "RHEA:10607")
.formula <- "M_H2O + M_PC <=> M_Phosphocholine + M_1,2-DG"
## pc_to_sn1lpc
if (reaction == "RHEA:15801")
.formula <- "M_H2O + M_PC = M_1-LPC + M_FA"
if (reaction == "RHEA:15802")
.formula <- "M_H2O + M_PC => M_1-LPC + M_FA"
if (reaction == "RHEA:15803")
.formula <- "M_H2O + M_PC <= M_1-LPC + M_FA"
if (reaction == "RHEA:15804")
.formula <- "M_H2O + M_PC <=> M_1-LPC + M_FA"
## pc_to_sn2lpc
if (reaction == "RHEA:18689")
.formula <- "M_H2O + M_PC = M_2-LPC + M_FA"
if (reaction == "RHEA:18690")
.formula <- "M_H2O + M_PC => M_2-LPC + M_FA"
if (reaction == "RHEA:18691")
.formula <- "M_H2O + M_PC <= M_2-LPC + M_FA"
if (reaction == "RHEA:18692")
.formula <- "M_H2O + M_PC <=> M_2-LPC + M_FA"
## pc_to_pa
if (reaction == "RHEA:14445")
.formula <- "M_H2O + M_PC = M_Choline + M_PA"
if (reaction == "RHEA:14446")
.formula <- "M_H2O + M_PC => M_Choline + M_PA"
if (reaction == "RHEA:14447")
.formula <- "M_H2O + M_PC <= M_Choline + M_PA"
if (reaction == "RHEA:14448")
.formula <- "M_H2O + M_PC <=> M_Choline + M_PA"
## pc_to_ps
if (reaction == "RHEA:45088") ##
.formula <- "M_L-Serine + M_PC = M_Choline + M_PS"
if (reaction == "RHEA:45089") ##
.formula <- "M_L-Serine + M_PC => M_Choline + M_PS"
if (reaction == "RHEA:45090") ##
.formula <- "M_L-Serine + M_PC <= M_Choline + M_PS"
if (reaction == "RHEA:45091") ##
.formula <- "M_L-Serine + M_PC <=> M_Choline + M_PS"
## pco_to_lpco
if (reaction == "RHEA:36231")
.formula <- "M_H2O + M_PC-O = M_H+ + M_LPC-O + M_FA"
if (reaction == "RHEA:36232")
.formula <- "M_H2O + M_PC-O => M_H+ + M_LPC-O + M_FA"
if (reaction == "RHEA:36233")
.formula <- "M_H2O + M_PC-O <= M_H+ + M_LPC-O + M_FA"
if (reaction == "RHEA:36234")
.formula <- "M_H2O + M_PC-O <=> M_H+ + M_LPC-O + M_FA"
## lpco_to_lpao
if (reaction == "RHEA:39927")
.formula <- "M_H2O + M_1-LPC-O = M_1-LPA-O + M_H+ + M_Choline"
if (reaction == "RHEA:39928")
.formula <- "M_H2O + M_1-LPC-O => M_1-LPA-O + M_H+ + M_Choline"
if (reaction == "RHEA:39929")
.formula <- "M_H2O + M_1-LPC-O <= M_1-LPA-O + M_H+ + M_Choline"
if (reaction == "RHEA:39930")
.formula <- "M_H2O + M_1-LPC-O <=> M_1-LPA-O + M_H+ + M_Choline"
## lpco_to_mgo
if (reaction == "RHEA:36083")
.formula <- "M_H2O + M_1-LPC-O = M_H+ + M_Phosphocholine + M_1-MG-O"
if (reaction == "RHEA:36084")
.formula <- "M_H2O + M_1-LPC-O => M_H+ + M_Phosphocholine + M_1-MG-O"
if (reaction == "RHEA:36085")
.formula <- "M_H2O + M_1-LPC-O <= M_H+ + M_Phosphocholine + M_1-MG-O"
if (reaction == "RHEA:36086")
.formula <- "M_H2O + M_1-LPC-O <=> M_H+ + M_Phosphocholine + M_1-MG-O"
## 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"
## pe_to_dg
if (reaction == "pe_to_dg")
.formula <- "M_H2O + M_PE <=> M_P-Ethanolamine + M_1,2-DG"
## pe_to_sn1lpe
if (reaction == "RHEA:44604")
.formula <- "M_H2O + M_PE = M_H+ + M_FA + M_1-LPE"
if (reaction == "RHEA:44605")
.formula <- "M_H2O + M_PE => M_H+ + M_FA + M_1-LPE"
if (reaction == "RHEA:44606")
.formula <- "M_H2O + M_PE <= M_H+ + M_FA + M_1-LPE"
if (reaction == "RHEA:44607")
.formula <- "M_H2O + M_PE <=> M_H+ + M_FA + M_1-LPE"
## pe_to_sn2lpe
if (reaction == "RHEA:44408")
.formula <- "M_H2O + M_PE = M_H+ + M_FA + M_2-LPE"
if (reaction == "RHEA:44409")
.formula <- "M_H2O + M_PE => M_H+ + M_FA + M_2-LPE"
if (reaction == "RHEA:44410")
.formula <- "M_H2O + M_PE <= M_H+ + M_FA + M_2-LPE"
if (reaction == "RHEA:44411")
.formula <- "M_H2O + M_PE <=> M_H+ + M_FA + M_2-LPE"
if (reaction == "pe_to_nape_sn1")
.formula <- "M_PE + M_PC <=> M_NAPE + M_2-LPC"
if (reaction == "pe_to_nape_sn2")
.formula <- "M_PE + M_PC <=> M_NAPE + M_1-LPC"
if (reaction == "pe_to_pa")
.formula <- "M_H2O + M_PE <=> M_Ethanolamine + M_H+ + M_PA"
## pe_to_ps
if (reaction == "RHEA:27606")
.formula <- "M_L-Serine + M_PE = M_Ethanolamine + M_PS"
if (reaction == "RHEA:27607")
.formula <- "M_L-Serine + M_PE => M_Ethanolamine + M_PS"
if (reaction == "RHEA:27608")
.formula <- "M_L-Serine + M_PE <= M_Ethanolamine + M_PS"
if (reaction == "RHEA:27609")
.formula <- "M_L-Serine + M_PE <=> M_Ethanolamine + M_PS"
if (reaction == "peo_to_lpeo")
.formula <- "M_H2O + M_PE-O <=> M_H+ + M_LPE-O + M_FA"
if (reaction == "peo_to_napeo_sn1")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_2-LPC"
if (reaction == "peo_to_napeo_sn2")
.formula <- "M_PE-O + M_PC <=> M_NAPEO + M_1-LPC"
## 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"
## pep_to_lpep
if (reaction == "RHEA:36195")
.formula <- "M_H2O + M_PE-P = M_H+ + M_LPE-P + M_FA"
if (reaction == "RHEA:36196")
.formula <- "M_H2O + M_PE-P => M_H+ + M_LPE-P + M_FA"
if (reaction == "RHEA:36197")
.formula <- "M_H2O + M_PE-P <= M_H+ + M_LPE-P + M_FA"
if (reaction == "RHEA:36198")
.formula <- "M_H2O + M_PE-P <=> M_H+ + M_LPE-P + M_FA"
## lpep_to_fal
if (reaction == "RHEA:16905")
.formula <- "M_H2O + M_1-LPE-P = M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16906")
.formula <- "M_H2O + M_1-LPE-P => M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16907")
.formula <- "M_H2O + M_1-LPE-P <= M_FAL + M_Glycerophosphoethanolamine"
if (reaction == "RHEA:16908")
.formula <- "M_H2O + M_1-LPE-P <=> M_FAL + M_Glycerophosphoethanolamine"
## lpep_to_lpap
if (reaction == "RHEA:36203")
.formula <- "M_H2O + M_1-LPE-P = M_LPA-P + M_H+ + M_Ethanolamine"
if (reaction == "RHEA:36204")
.formula <- "M_H2O + M_1-LPE-P => M_LPA-P + M_H+ + M_Ethanolamine"
if (reaction == "RHEA:36205")
.formula <- "M_H2O + M_1-LPE-P <= M_LPA-P + M_H+ + M_Ethanolamine"
if (reaction == "RHEA:36206")
.formula <- "M_H2O + M_1-LPE-P <=> M_LPA-P + M_H+ + M_Ethanolamine"
## lpep_to_mgp
if (reaction == "RHEA:36199")
.formula <- "M_H2O + M_1-LPE-P = M_Phosphoethanolamine + M_H+ + M_1-MG-P"
if (reaction == "RHEA:36200")
.formula <- "M_H2O + M_1-LPE-P => M_Phosphoethanolamine + M_H+ + M_1-MG-P"
if (reaction == "RHEA:36201")
.formula <- "M_H2O + M_1-LPE-P <= M_Phosphoethanolamine + M_H+ + M_1-MG-P"
if (reaction == "RHEA:36202")
.formula <- "M_H2O + M_1-LPE-P <=> M_Phosphoethanolamine + M_H+ + M_1-MG-P"
## pep_to_napep_sn1
if (reaction == "pep_to_napep_sn1")
.formula <- "M_PE-P + M_PC <=> M_NAPEP + M_2-LPC"
## pep_to_napep_sn2
if (reaction == "pep_to_napep_sn2")
.formula <- "M_PE-P + M_PC <=> M_NAPEP + M_1-LPC"
## pg_to_cl
if (reaction == "RHEA:32931")
.formula <- "M_CDP-DG + M_PG = M_H+ + M_CMP + M_CL"
if (reaction == "RHEA:32932")
.formula <- "M_CDP-DG + M_PG => M_H+ + M_CMP + M_CL"
if (reaction == "RHEA:32933")
.formula <- "M_CDP-DG + M_PG <= M_H+ + M_CMP + M_CL"
if (reaction == "RHEA:32934")
.formula <- "M_CDP-DG + M_PG <=> M_H+ + M_CMP + M_CL"
## pgp_to_pg
if (reaction == "RHEA:33751")
.formula <- "M_H2O + M_pgp = M_Pi + M_PG"
if (reaction == "RHEA:33752")
.formula <- "M_H2O + M_pgp => M_Pi + M_PG"
if (reaction == "RHEA:33753")
.formula <- "M_H2O + M_pgp <= M_Pi + M_PG"
if (reaction == "RHEA:33754")
.formula <- "M_H2O + M_pgp <=> M_Pi + M_PG"
## pi_to_dg
if (reaction == "RHEA:43484")
.formula <- "M_H2O + M_PI = M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
if (reaction == "RHEA:43485")
.formula <- "M_H2O + M_PI => M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
if (reaction == "RHEA:43486")
.formula <- "M_H2O + M_PI <= M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
if (reaction == "RHEA:43487")
.formula <- "M_H2O + M_PI <=> M_myo-Inositol-1-P + M_H+ + M_1,2-DG"
## pi_to_sn1lpi
if (reaction == "RHEA:18001")
.formula <- "M_H2O + M_PI = M_1-LPI + M_H+ + M_FA"
if (reaction == "RHEA:18002")
.formula <- "M_H2O + M_PI => M_1-LPI + M_H+ + M_FA"
if (reaction == "RHEA:18003")
.formula <- "M_H2O + M_PI <= M_1-LPI + M_H+ + M_FA"
if (reaction == "RHEA:18004")
.formula <- "M_H2O + M_PI <=> M_1-LPI + M_H+ + M_FA"
## ps_to_pe
if (reaction == "RHEA:20828")
.formula <- "M_H+ + M_PS = M_CO2 + M_PE"
if (reaction == "RHEA:20829")
.formula <- "M_H+ + M_PS => M_CO2 + M_PE"
if (reaction == "RHEA:20830")
.formula <- "M_H+ + M_PS <= M_CO2 + M_PE"
if (reaction == "RHEA:20831")
.formula <- "M_H+ + M_PS <=> M_CO2 + M_PE"
if (reaction == "sm_to_cer")
.formula <- "M_H2O + M_SM <=> M_Phosphocholine + M_H+ + M_Cer"
## sphinga_to_dhcer
if (reaction == "RHEA:53424")
.formula <- "M_AcylCoA + M_Sphinganine = M_CoA + M_DhCer"
if (reaction == "RHEA:53425")
.formula <- "M_AcylCoA + M_Sphinganine => M_CoA + M_DhCer"
if (reaction == "RHEA:53426")
.formula <- "M_AcylCoA + M_Sphinganine <= M_CoA + M_DhCer"
if (reaction == "RHEA:53427")
.formula <- "M_AcylCoA + M_Sphinganine <=> M_CoA + M_DhCer"
## tg_to_dg
if (reaction %in% c("RHEA:33271", "RHEA:44864"))
.formula <- "M_H2O + M_TG = M_H+ + M_FA + M_1,2-DG"
if (reaction %in% c("RHEA:33272", "RHEA:44865"))
.formula <- "M_H2O + M_TG => M_H+ + M_FA + M_1,2-DG"
if (reaction %in% c("RHEA:33273", "RHEA:44866"))
.formula <- "M_H2O + M_TG <= M_H+ + M_FA + M_1,2-DG"
if (reaction %in% c("RHEA:33274", "RHEA:44867"))
.formula <- "M_H2O + M_TG <=> M_H+ + M_FA + M_1,2-DG"
template$reaction_formula <- .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_fixed(str = .formula_substrate,
pattern = " ", replacement = "")
.formula_product <- stringi::stri_split(str = .formula_product,
regex = "[+]")[[1]]
.formula_product <- stringi::stri_replace_all_fixed(str = .formula_product,
pattern = " ", replacement = "")
## write the substrates and products to the template
template$reaction_substrate <- .formula_substrate
template$reaction_product <- .formula_product
## return the template object
template
}
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