SBMLR: SBML-R Interface and Analysis Tools

"saveSBMLR" <-
  function(model,filename)
  {  # takes model and maps it to a SBMLR file
    fid <- file(filename,"w")  # open the output file connection
    cat("#",filename,"\n", file=fid, sep="")  
    cat("model=list( \n", file=fid, sep="\n")
    
    #sbml=model[["sbml"]]
    id=model[["id"]]
    notes=model[["notes"]]
    #htmlNotes=model[["htmlNotes"]]
    compartments=model[["compartments"]]
    species=model[["species"]]
    globalParameters=model[["globalParameters"]]
    rules=model[["rules"]]
    reactions=model[["reactions"]]
    units=model[["units"]]
    
    nNotes=length(notes)
    nCompartments=length(compartments)
    nReactions=length(reactions)
    nSpecies=length(species)
    nGlobalParameters=length(globalParameters)
    nRules=length(rules)
    nUnits=length(units)
    
    #cat("sbml=c(level=", sbml[2],", version=",sbml[3],"),\n\n", file=fid,sep="" )
    cat("id=\"",id,"\",\n\n", file=fid, sep=""  )
    #cat("htmlNotes=c(\"",toString(htmlNotes),"\"),\n", file=fid, sep="\n")
    
    if(nNotes>0){
      cat("notes=c(", file=fid, sep="\n")
      for (i in 1:nNotes) 
        cat(sprintf("\"%s\"%s", notes[[i]],ifelse(i==nNotes,"\n),\n",",")), file=fid, sep="\n")
    }
    
    if(nCompartments>0){
      cat("compartments=list(", file=fid, sep="\n")
      for (i in 1:nCompartments) 
        cat(sprintf("list(id=\"%s\", size = %g)%s", compartments[[i]][["id"]],compartments[[i]][["size"]],
                    ifelse(i==nCompartments,"\n),\n",",")),     file=fid, sep="\n")
    }
    
    if(nSpecies>0){
      cat("species=list(", file=fid, sep="\n")
      for (i in 1:nSpecies) 
        cat(sprintf("list(id=\"%s\",ic=%8g,    compartment=\"%s\",bc=%7s)%s",species[[i]][["id"]],species[[i]][["ic"]],
                    species[[i]][["compartment"]],ifelse(species[[i]][["bc"]],"TRUE","FALSE"),
                    ifelse(i==nSpecies,"\n),\n",",") ), file=fid, sep="\n")
    }
    
    if(nGlobalParameters>0){
      cat("globalParameters=list(", file=fid, sep="")
      for (i in 1:nGlobalParameters) 
        cat(sprintf("%s=%g%s", names(globalParameters[i]),globalParameters[[i]],
                    ifelse(i==nGlobalParameters,"),\n",",") ), file=fid, sep="\n")
    }
    
    if(nRules>0){
      cat("\n\n#BEGIN the Rules Section\nrules=list(", file=fid, sep="\n")
      for (i in 1:nRules)
      {
        idOutput=rules[[i]][["idOutput"]]
        inputs=rules[[i]][["inputs"]]
        strLaw=rules[[i]][["strLaw"]]
        #      cat(sprintf("list(idOutput=\"%s\",",substitute(idOutput)),file=fid, sep="\n")
        cat(sprintf("list(idOutput=\"%s\",",idOutput),file=fid, sep="\n") 
        ni=length(inputs)
        if (ni>0){cat("inputs=c(", file=fid, sep="")
                  for (k in 1:ni) cat(sprintf("\"%s\"%s",inputs[k],ifelse(k==ni,"),\n",",")  ), file=fid, sep="")}
        cat(sprintf("strLaw = \"%s\"",strLaw),file=fid, sep="\n")
        cat(sprintf("%s",ifelse(i==nRules,")),\n# END of the Rules Section","),\n")  ), file=fid, sep="\n")
      }  # end for loop on rules
    } # end if there are rules
    
    if(nReactions>0){
      cat("\n\n#BEGIN the Reaction Section \nreactions=list(", file=fid, sep="\n")
      for (i in 1:nReactions)
      {
        if (is.null(reactions[[i]][["reversible"]])) 
          print("Internal SBMLR object should have reverse flag set") 
        else {
          if (reactions[[i]][["reversible"]]) 
            cat(sprintf("list( id=\"%s\", reversible=TRUE,",reactions[[i]][["id"]]),file=fid, sep="\n")
          else
            cat(sprintf("list( id=\"%s\", ",reactions[[i]][["id"]]),file=fid, sep="\n") 
        }
        #       cat(sprintf("list( id=\"%s\", reversible=%s,",reactions[[i]][["id"]],
        #                   ifelse(reactions[[i]][["reversible"]],"TRUE","FALSE")),file=fid, sep="\n")
        law=reactions[[i]][["law"]]
        parameters=reactions[[i]][["parameters"]]
        reactants=reactions[[i]][["reactants"]]
        modifiers=reactions[[i]][["modifiers"]]
        products=reactions[[i]][["products"]]
        strLaw=reactions[[i]][["strLaw"]]
        nr=length(reactants)
        if (nr>0){cat("reactants=c(", file=fid, sep="")
                  for (k in 1:nr) cat(sprintf("\"%s\"%s",reactants[k], ifelse(k==nr,"),\n",",")  ),
                                      file=fid, sep="")}
        nm=length(modifiers)
        if (nm>0){cat("modifiers=c(", file=fid, sep="")
                  for (k in 1:nm) cat(sprintf("\"%s\"%s",modifiers[k], ifelse(k==nm,"),\n",",")  ), 
                                      file=fid, sep="")}
        np=length(products)
        if (np>0){cat("products=c(", file=fid, sep="")
                  for (k in 1:np) cat(sprintf("\"%s\"%s",products[k], ifelse(k==np,"),\n",",")  ), 
                                      file=fid, sep="")}
        npa=length(parameters)
        if (npa>0){cat("parameters=c(", file=fid, sep="")
                   for (k in 1:npa) cat(sprintf("%s = %g%s",names(parameters)[k],as.numeric(parameters[k]),
                                                ifelse(k==npa,"),\n",",")), file=fid, sep="")}
        # always have a law
        cat(sprintf("strLaw=\"%s\"\n",strLaw), file=fid, sep="")
        #if (funcLaw) {
        #cat("law=", file=fid, sep=" ")
        #tt=deparse(law,width=500)  # this only works well for functions. lists do not dump that pretty
        #write(tt,fid)
        #} 
        cat(sprintf("%s",ifelse(i==nReactions,")) #END of the Reaction Section\n\n","),\n")),
            file=fid, sep="\n")
      }  # end for loop on reactions
    } # end if there are reactions
    # state Units in Notes from here on out!
    cat(")  # END of the Model!", file=fid, sep="\n")
    close(fid)
  } # end saveSBMLR function definition