merged master with writeSBML branch

DESCRIPTION

 Package: sybilSBML
 Type: Package
 Title: SBML Integration in Package 'Sybil'
-Version: 2.0.11
-Date: 2016-06-06
+Version: 3.0.1
+Date: 2016-12-16
 Authors@R: c(person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
 			 person("Gabriel", "Gelius-Dietrich", role = c("aut", "ctb")),
-             person("Deya", "Alzoubi", role = "ctb"))
+             person("Deya", "Alzoubi", role = "ctb"),
+             person("Ardalan", "Habil", role = "ctb"))
 Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
 Depends: R (>= 2.14.2), Matrix, sybil (>= 2.0.0)
 Imports: methods
-Description: 'SBML' (Systems Biology Markup Language) integration in 'sybil'. Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read and check 'SBML' files in 'sybil' provided.
+Description: 'SBML' (Systems Biology Markup Language) with FBC (Flux Balance Constraints) integration in 'sybil'. Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read, write, and check 'SBML' files in 'sybil' provided.
 License: GPL-3 | file LICENSE
 LazyLoad: yes
 Collate: generics.R sbmlPtrClass.R sbmlErrorClass.R sybilSBML.R
         uglyHack.R readSBMLmod.R zzz.R
-Packaged: 2015-06-06 07:11:55 UTC; jonathan
+Packaged: 2016-12-16 07:11:55 UTC; jonathan
 Author: C. Jonathan Fritzemeier [cre, ctb],
   Gabriel Gelius-Dietrich [aut, ctb],
-  Deya Alzoubi [ctb]
+  Deya Alzoubi [ctb],
+  Ardalan Habil [ctb]
 NeedsCompilation: yes
 Repository: CRAN

NAMESPACE

@@ -48,5 +48,9 @@ getSBMLunitDefinitionsList,
 getSBMLCompartList,
 getSBMLSpeciesList,
 getSBMLReactionsList,
-readSBMLmod
+readSBMLmod,
+writeSBML,
+getSBMLFbcversion,
+getSBMLmodNotes,
+getSBMLmodAnnotation
 )

R/readSBMLmod.R

@@ -247,7 +247,13 @@ parseNotesReact <- function(notes) {
           gpr <- sub("GENE[_ ]?ASSOCIATION: *", "", fields_str[j])
           gene_rule <- sybil:::.parseBoolean(gpr)
           #print(gene_rule)
+    
+      }#Ardalan Habil
+      else if (grepl("GPR[_ ]?ASSOCIATION", fields_str[j])) {
+        gpr <- sub("GPR[_ ]?ASSOCIATION: *", "", fields_str[j])
+        gene_rule <- sybil:::.parseBoolean(gpr)
       }  
+
       if (charmatch("SUBSYSTEM", fields_str[j], nomatch = -1) != -1) {
           subSyst <- sub("SUBSYSTEM: *", "", fields_str[j])
           subSyst <- sub("^S_", "", subSyst, perl = TRUE)
@@ -283,6 +289,14 @@ sbmldoc <- openSBMLfile(filename)
 
 message("OK")
 
+# warning if new Version/Level/
+SBMLlevel<- getSBMLlevel(sbmldoc)
+SBMLversion<- getSBMLversion(sbmldoc)
+FBCversion<-getSBMLFbcversion(sbmldoc)
+if(SBMLlevel == 3 && SBMLversion > 1)
+  warning(paste("No support for Level 3 Version ",SBMLversion))
+if (FBCversion > 2)
+  warning(paste("No support for Fbc Version ",FBCversion))
 
 #------------------------------------------------------------------------------#
 #                              check the model                                 #
@@ -380,6 +394,7 @@ if (mdesc == filename) {
 sybil::mod_desc(mod) <- mdesc
 
 
+
 #------------------------------------------------------------------------------#
 #                                   units                                      #
 #------------------------------------------------------------------------------#
@@ -398,7 +413,7 @@ if (is.null(compartmentsList)) {
 }
 
 missingId(compartmentsList)
-sybil::mod_compart(mod) <- compartmentsList[["id"]]
+comp_tmp_id <- compartmentsList[["id"]]
 
 
 #------------------------------------------------------------------------------#
@@ -430,6 +445,7 @@ missingId(metabolitesList)
 metSpIds        <- metabolitesList[["id"]]
 #nummet          <- getSBMLnumSpecies(sbmlmod)
 
+
 if (isTRUE(bndCond)) {
     metSpBnd <- metabolitesList[["boundaryCondition"]]
     met_id_pos <- !metSpBnd
@@ -485,12 +501,20 @@ gpr      <- character(numreact)
 hasNotes <- FALSE
 hasAnnot <- FALSE
 
+#FBC contraints @Ardalan Habil
+fbclowbnd<-reactionsList[["fbc_lowbnd"]]
+fbcuppbnd<-reactionsList[["fbc_uppbnd"]]
+fbcgprRules<-reactionsList[["fbc_gprRules"]]
+fbcObjectives<-reactionsList[["fbc_Objectives"]]
+
 for (i in 1 : numreact) {
 
     # the notes/annotations field
     notes <- reactionsList[["notes"]][i]
     annot <- reactionsList[["annotation"]][i]
     
+    # Notes und Annotation can be null ( @Ardalan Habil)
+    if(!is.null( reactionsList[["notes"]])) 				
     if (nchar(notes) > 0) {
 
         hasNotes    <- TRUE
@@ -504,7 +528,7 @@ for (i in 1 : numreact) {
 
     }
     else {
-
+	 if(!is.null( reactionsList[["annotation"]]))	
         if (nchar(annot) > 0) {
             hasAnnot    <- TRUE
             pn <- regexpr("Pathway Name: [^<]+", annot, perl = TRUE)
@@ -514,6 +538,17 @@ for (i in 1 : numreact) {
     }
      
     	
+
+    fbcgene_rule <- NA
+    if ( !is.null(fbcgprRules))
+    { 
+      fbcgene_rule<- sybil:::.parseBoolean(fbcgprRules[i])
+      
+      genes[[i]]  <- fbcgene_rule$gene      # list of genes
+      rules[i]    <- fbcgene_rule$rule       # rules
+      gpr[i]      <- fbcgprRules[i]  
+    }	
+
     # Check here if reactants and products lists exist, same for the stoichiometry slot
 
     # Entries for S -- the reactants
@@ -565,6 +600,16 @@ for (i in 1 : numreact) {
 #    }
 
     # the constraints
+  
+  #FBC contraints @Ardalan Habil
+  if ( !is.null(fbclowbnd) &&  !is.null(fbcuppbnd))
+  {
+    lbnd[i] <- checkupplowbnd(fbclowbnd[i])
+    ubnd[i] <- checkupplowbnd(fbcuppbnd[i])
+  }
+  #read from kinetic_law if fbc is empty 		
+  else
+  {
     parm <- reactionsList[["kinetic_law"]][[i]]
     if (is.null(parm)) {
         ubnd[i] <- def_bnd
@@ -591,9 +636,15 @@ for (i in 1 : numreact) {
             # reduced cost?  (sbml file)
         }
     }
-
   }
+  #FBC Objective @Ardalan Habil
+    if(!is.null(fbcObjectives))
+    {
+      ocof[i]<-as.numeric(fbcObjectives[i])
+    }  
+    
     
+}
 
 # ---------------------------------------------------------------------------- #
 # search for unused metabolites and unused reactions
@@ -877,7 +928,7 @@ else {
     rules  <- rules[SKIP_REACTION]
     gpr    <- gpr[SKIP_REACTION]
 
-    if (isTRUE(hasNotes)) {
+    if (isTRUE(hasNotes) ||  !is.null(fbcgprRules) ) {
         message("GPR mapping ... ", appendLF = FALSE)
 
         #allGenes <- unique(allGenes)
@@ -898,13 +949,12 @@ else {
                 geneInd <- match(genes[[i]], allGenes)
                 rxnGeneMat[i, geneInd] <- TRUE
     
-    			 # no use because new gprRule format
-#                for (j in 1 : length(geneInd)) {
-#                    pat  <- paste("x(", j, ")", sep = "")
-#                    repl <- paste("x[", geneInd[j], "]", sep = "")
-#    
-#                    rules[i] <- gsub(pat, repl, rules[i], fixed = TRUE)
-#                }
+                for (j in 1 : length(geneInd)) {
+                    pat  <- paste("x(", j, ")", sep = "")
+                    repl <- paste("x[", geneInd[j], "]", sep = "")
+    
+                    rules[i] <- gsub(pat, repl, rules[i], fixed = TRUE)
+                }
             }
         }
 
@@ -970,6 +1020,63 @@ react_name_tmp   <- sub( "\\s+$",  "",  react_name_tmp, perl = TRUE)
 sybil::react_name(mod) <- react_name_tmp
 
 
+#------------------------------------------------------------------------------#
+#                             Reaction Attr  @Ardalan                          #
+#------------------------------------------------------------------------------#
+# Test for new Slots
+if( .hasSlot(mod,"mod_attr") &&  .hasSlot(mod,"comp_attr") &&  .hasSlot(mod,"met_attr")  &&  .hasSlot(mod,"react_attr") )
+  newSybil<-TRUE
+else newSybil<-FALSE
+
+numreact<-nummet <- sum(SKIP_REACTION)
+reactannotation <- reactionsList[["annotation"]][SKIP_REACTION]
+reactnotes <- reactionsList[["notes"]][SKIP_REACTION]
+if(newSybil)
+{  
+  sybil::react_attr(mod)  <-data.frame(row.names=1:numreact)
+  #Speed optimierung durch notes NULL falls nichts drin steht
+  
+  if( !is.null(reactannotation) && length(reactannotation)==numreact  )sybil::react_attr(mod)[['annotation']]<-reactannotation
+  if( !is.null(reactnotes) && length(reactnotes)==numreact  )sybil::react_attr(mod)[['notes']]<-reactnotes
+}
+
+
+#------------------------------------------------------------------------------#
+#                         Model Attr @Ardalan                                  #
+#------------------------------------------------------------------------------#
+
+modanno<-getSBMLmodAnnotation(sbmlmod)
+modnotes<-getSBMLmodNotes(sbmlmod)
+if(newSybil)
+{
+  sybil::mod_attr(mod)  <-data.frame(row.names=1)
+  if(nchar(modanno)>1)sybil::mod_attr(mod)[['annotation']]<-modanno
+  if(nchar(modnotes)>1)sybil::mod_attr(mod)[['notes']]<-modnotes
+  
+}  
+
+
+#------------------------------------------------------------------------------#
+#                         compartments Attr @Ardalan                           #
+#------------------------------------------------------------------------------#
+# Define SKIP_COMPARTMENT FALSE= HAS NO REFERENCE
+met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
+SKIP_COMPARTMENT<- comp_tmp_id %in% unique(met_comp_tmp)
+
+  
+sybil::mod_compart(mod) <- comp_tmp_id[SKIP_COMPARTMENT]
+numcom<-length(mod_compart(mod))
+comannotation <- compartmentsList[["annotation"]][SKIP_COMPARTMENT]
+comnotes <- compartmentsList[["notes"]][SKIP_COMPARTMENT]
+if(newSybil)
+{ 
+  sybil::comp_attr(mod)  <-data.frame(row.names=1:numcom)
+  if( !is.null(comannotation) && length(comannotation)==numcom   )sybil::comp_attr(mod)[['annotation']]<-comannotation
+  if( !is.null(comnotes) && length(comnotes)==numcom  )sybil::comp_attr(mod)[['notes']]<-comnotes
+  
+}
+
+
 #------------------------------------------------------------------------------#
 #                             metabolite id's                                  #
 #------------------------------------------------------------------------------#
@@ -985,7 +1092,7 @@ sybil::met_id(mod) <- gsub("-",      "_",    met_id_tmp, fixed = TRUE)
 #                        metabolite compartments                               #
 #------------------------------------------------------------------------------#
 
-met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
+#met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
 
 sybil::met_comp(mod) <- match(met_comp_tmp, sybil::mod_compart(mod))
 
@@ -1002,6 +1109,69 @@ met_name_tmp   <- sub( "\\s+$",   "",  met_name_tmp, perl = TRUE)
 sybil::met_name(mod) <- met_name_tmp
 
 
+#------------------------------------------------------------------------------#
+#                             metabolite attr @Ardalan Habil                   #
+#------------------------------------------------------------------------------#
+
+#ChemicalFormula Charge Notes Annotation MetaID @Ardalan Habil
+
+metformula   <- metabolitesList[["chemicalFormula"]][met_id_pos][SKIP_METABOLITE]
+metcharge    <- metabolitesList[["charge"]][met_id_pos][SKIP_METABOLITE]
+
+metnotes <- metabolitesList[["notes"]][met_id_pos][SKIP_METABOLITE]
+metannotation <-   metabolitesList[["annotation"]][met_id_pos][SKIP_METABOLITE]
+
+
+metchargenote<-NULL
+metformulanote<-NULL
+# check metnotes for Formula and Charge
+if( !is.null(metnotes) && length(metnotes==nummet))
+{
+  pn <- regexpr("FORMULA: [^<]+", metnotes, perl = TRUE)
+  metformulanote <- substr(metnotes, (pn+9), pn + ((attr(pn, "match.length"))-1))
+  pn <- regexpr("CHARGE: [^<]+", metnotes, perl = TRUE)
+  metchargenote <- substr(metnotes, (pn+8), pn + ((attr(pn, "match.length"))-1))
+  metchargenote <- as.integer(metchargenote)
+  metchargenote[is.na(metchargenote)] <- 0
+}
+
+
+nummet <- sum(SKIP_METABOLITE)
+if(newSybil)
+{ 
+  # save attributes to met_attr slot
+  sybil::met_attr(mod)  <-data.frame(row.names=1:nummet)
+  if( !is.null(metformula) && length(metformula)==nummet)
+  {sybil::met_attr(mod)[['chemicalFormula']]<-metformula}
+  else{
+    if(length(metformulanote)==nummet)
+    { if(max(nchar(metformulanote)) >0)
+      sybil::met_attr(mod)[['chemicalFormula']]<-metformulanote 
+    }  
+  }
+  if( !is.null(metcharge) && length(metcharge)==nummet && sum(metcharge)!=0)
+  {sybil::met_attr(mod)[['charge']]<-metcharge}
+  else{
+    if(  length(metchargenote)==nummet)
+    {  if(max(nchar(metchargenote)) >0)
+      sybil::met_attr(mod)[['charge']]<-metchargenote 
+    }  
+  }
+  if( !is.null(metnotes) && length(metnotes)==nummet)sybil::met_attr(mod)[['notes']]<-metnotes 
+  if( !is.null(metannotation) && length(metannotation)==nummet)sybil::met_attr(mod)[['annotation']]<-metannotation
+  
+  # Save boundaryCondition when bndCond=FALSE
+  if (!isTRUE(bndCond)) {
+    metBnd <- metabolitesList[["boundaryCondition"]][met_id_pos][SKIP_METABOLITE]
+    # When all metBnd = False -> metabolite removed by extMetFlag
+    if( !is.null(metBnd) && length(metBnd)==nummet && !all(metBnd == FALSE) )sybil::met_attr(mod)[['boundaryCondition']]<-metBnd
+  }
+  
+  
+}
+
+
+
 #------------------------------------------------------------------------------#
 #                             check reversibilities                            #
 #------------------------------------------------------------------------------#

R/sybilSBML.R

@@ -124,6 +124,17 @@ getSBMLversion <- function(sbmlf) {
     return(version)
 }
 
+#------------------------------------------------------------------------------#
+
+getSBMLFbcversion <- function(sbmlf) {
+  
+  version <- .Call("getSBMLFbcversion", PACKAGE = "sybilSBML",
+                   sbmlPointer(sbmlf)
+  )
+  
+  return(version)
+}
+
 
 #------------------------------------------------------------------------------#
 
@@ -186,6 +197,28 @@ getSBMLmodName <- function(sbmlm) {
     return(modn)
 }
 
+#------------------------------------------------------------------------------#
+
+getSBMLmodNotes <- function(sbmlm) {
+  
+  modnotes <- .Call("getSBMLmodNotes", PACKAGE = "sybilSBML",
+                sbmlPointer(sbmlm)
+  )
+  
+  return(modnotes)
+}
+
+#------------------------------------------------------------------------------#
+
+getSBMLmodAnnotation <- function(sbmlm) {
+  
+  modanno <- .Call("getSBMLmodAnnotation", PACKAGE = "sybilSBML",
+                sbmlPointer(sbmlm)
+  )
+  
+  return(modanno)
+}
+
 
 #------------------------------------------------------------------------------#
 
@@ -271,10 +304,272 @@ getSBMLReactionsList <- function(sbmlm) {
 }
 
 
+#------------------------------------------------------------------------------#
+#export mod to SBML
+deformatSBMLid <- function(idstr) {
+  idstr <- gsub("-", "_DASH_", idstr, fixed = TRUE)
+  idstr <- gsub("(", "_LPAREN_", idstr, fixed = TRUE)
+  idstr <- gsub(")", "_RPAREN_", idstr, fixed = TRUE)
+  idstr <- gsub("[", "_", idstr, fixed = TRUE)
+  idstr <- gsub("]", "", idstr, fixed = TRUE)
+  idstr <- gsub(",", "_COMMA_", idstr, fixed = TRUE)
+  idstr <- gsub(".", "_PERIOD_", idstr, fixed = TRUE)
+  idstr <- gsub("'", "_APOS_", idstr, fixed = TRUE)
+  idstr <- sub("\\(e\\)$", "_e_", idstr)
+  idstr <- gsub("-", "_", idstr, fixed = TRUE)
+  return(idstr)
+}
+
+deformatGene<-function(idstr) {
+  idstr<-gsub("\\((\\S+)\\)", "\\1", idstr)
+  #idstr <- gsub("( ", "(", idstr, fixed = TRUE)
+  #idstr <- gsub(" (", "(", idstr, fixed = TRUE)
+  #idstr <- gsub(") ", ")", idstr, fixed = TRUE)
+  #idstr <- gsub(" )", ")", idstr, fixed = TRUE)
+  idstr <- gsub(":", "_", idstr, fixed = TRUE)
+  return(idstr)
+}
+
+writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml",recoverExtMet=FALSE,printNotes=TRUE,printAnnos=TRUE,validation=FALSE ){
+  if(class(morg)!="modelorg"){
+    stop("morg has to be of class modelorg\n")
+  }
   
+  ###right 
+  if(level==1)
+  { 
+    # test if Matrix has no double values
+    if( !all( S(morg) == floor(S(morg))) ) warning("Level 1 does not support double values")
+    fbcLevel=0
+      if(version != 2)
+      {
+        warning("just Level 1 Version 2 will be supported")
+        version=2
+      }
+  }else if (level==2)
+  { 
+    fbcLevel=0
+    if(version >5)
+    {
+      warning("Level 2 Version 5 will be supported")
+      version=5 
+    }
+    if(version < 1)
+    {
+      warning("Level 2 Version 1 will be supported")
+      version=1 
+    }  
+  }
+  else if (level==3)
+  { if(fbcLevel >2)fbcLevel=2
+  if(version != 1)
+  {
+    print("Level 3 Version 1 will be supported")
+    version=1 
+  }
   
+  }else {
+    stop(" Support just for Level 1,2 and 3 \n")
+  }
   
+  ##All GENES### 
+  allgenes<- unique(unlist(genes(morg)))
+  allgenes<-allgenes[allgenes != ""]
   
   
+  ##EXCHANGE REACTIONS##
+  ex <- findExchReact(morg)
+  ex_react<-NULL
+  # if recoverExtMet== FALSE => null for ex_react
+  if( (!is.null(ex)) && (recoverExtMet) )
+  {
+    if(!(all(diag(S(morg)[met_pos(ex), react_pos(ex)])==-1)))
+      stop("exchange reactions with Scoeff different than -1\n")
+    ex_react<-as.integer(react_pos(ex))
+  }
+  
+  ### Build wrapper for C Function #####
+  
+  
+  ##Met Attribute###
+  com_meta_id<- NULL
+  met_meta_id<- NULL
+  com_notes <- NULL
+  com_annotation<- NULL
+  met_notes<- NULL
+  met_anno<- NULL
+  met_bnd<- NULL
+  met_charge<-NULL
+  met_formula<-NULL
+  
+  react_notes<-NULL
+  react_anno<-NULL
+  
+  mod_notes<-NULL
+  mod_anno<-NULL
+  
+  #subsystem
+  # is subsystem Empty
+  if(length( colnames(subSys(morg)))==1 && colnames(subSys(morg))[1]=="" ) modhasubSys<-FALSE
+  else modhasubSys<-TRUE
+  
+  newsubS<- NULL
+
+  if( .hasSlot(morg,"mod_attr") &&  .hasSlot(morg,"comp_attr") &&  .hasSlot(morg,"met_attr")  &&  .hasSlot(morg,"react_attr") )
+    newSybil<-TRUE
+  else newSybil<-FALSE
+  ### Start newSybil attr
+  if(newSybil)
+  { 
+    if(("notes" %in% colnames(mod_attr(morg))) && (printNotes) ) mod_notes<-as.character(mod_attr(morg)[['notes']])
+    if(("annotation" %in% colnames(mod_attr(morg))) && (printAnnos) ) mod_annotation<-as.character(mod_attr(morg)[['annotation']])
+    
+    if(("notes" %in% colnames(comp_attr(morg)))    && (printNotes) ) com_notes<-as.character(as.list((comp_attr(morg)[['notes']])))
+    if(("annotation" %in% colnames(comp_attr(morg))) && (printAnnos)  ) com_annotation<-as.character(as.list((comp_attr(morg)[['annotation']])))
+    
+    if("charge" %in% colnames(met_attr(morg))) met_charge<- as.integer(as.list((met_attr(morg)[['charge']])))
+    if("chemicalFormula" %in% colnames(met_attr(morg))) met_formula<-as.character(as.list((met_attr(morg)[['chemicalFormula']])))
+    if(("annotation" %in% colnames(met_attr(morg))) && (printAnnos)) met_anno<-as.character(as.list((met_attr(morg)[['annotation']])))
+    if("boundaryCondition" %in% colnames(met_attr(morg))) met_bnd<-as.logical(as.list((met_attr(morg)[['boundaryCondition']])))
+    
+    if(("notes" %in% colnames(met_attr(morg))) && (printNotes) )
+    {   # delete Formular and charge from notes to do
+      met_notes<-as.character(as.list((met_attr(morg)[['notes']])))
+      if (!is.null(met_charge) || !is.null(met_formula))
+      {  
+        for ( i in 1:met_num(morg)) 
+        {
+          
+          if(nchar(met_notes[i])> 8)
+          { 
+            # Have Assocation in Notes?yes: replace no: append
+            
+            if (regexpr("html:p", met_notes[i], fixed = TRUE) == -1)tag <- "p"
+            else tag <- "html:p"
+            
+            
+            if (!is.null(met_formula))
+            {    
+              haveform<-grepl("FORMULA: [^<]+",met_notes[i])
+              #Have Gene if not ->no need to write in FBC2
+              if(haveform)
+              {  
+                if(fbcLevel==0)met_notes[i]<-sub("FORMULA: [^<]+",paste("FORMULA: ",met_formula[i], sep = ""), met_notes[i], perl = TRUE)
+                else met_notes[i]<-sub(paste("<",tag,">","FORMULA: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE)
+              }    
+              else if(fbcLevel==0) met_notes[i]<-gsub("</notes>",paste("<",tag,">","FORMULA: ",met_formula[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i])
+            }
+            if (!is.null(met_charge))
+            {    
+              havecharge<-grepl("CHARGE: [^<]+",met_notes[i])
+              #Have Subsystem
+              if(havecharge)
+              {  
+                if(fbcLevel !=0 || (level==2 && version==1 ))
+                  met_notes[i]<-sub(paste("<",tag,">","CHARGE: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE)
+                else met_notes[i]<-sub("CHARGE: [^<]+",paste("CHARGE: ",met_charge[i], sep = ""), met_notes[i], perl = TRUE)
                 
                 
+              }  
+              else if(fbcLevel==0) if(level!=2 && version!=1) met_notes[i]<-gsub("</notes>",paste("<",tag,">","CHARGE: ",met_charge[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i])
+            }
+          }
+        }  
+      }
+      
+    }
+    if(("annotation" %in% colnames(react_attr(morg))) && (printAnnos)) react_anno<-as.character(as.list((react_attr(morg)[['annotation']])))
+    
+    # Merge Notes with "our" Notes and make sure gpr Rules from gpr
+    if(("notes" %in% colnames(react_attr(morg))) && (printNotes))
+    {
+      react_notes<-as.character(as.list((react_attr(morg)[['notes']])))
+      # using
+      #  SubSystem EXISTIERT nicht colnames(subSys(ec))
+      
+      for ( i in 1:react_num(morg)) 
+      {
+        # using the for loop
+        if(modhasubSys)newsubS[i]<- paste(names(which(subSys(morg)[i,])), collapse=", ")   
+        if(nchar(react_notes[i])> 8)
+        { 
+          # Have Association in Notes? yes: replace no: append
+          
+          if (regexpr("html:p", react_notes[i], fixed = TRUE) == -1)tag <- "p"
+          else tag <- "html:p"
+          
+          havegene<-grepl("GENE[_ ]?ASSOCIATION: [^<]+",react_notes[i])
+          havesub<-grepl("SUBSYSTEM: [^<]+",react_notes[i])
+          
+          #Have Gene if not ->no need to write in FBC2
+          if(havegene)
+          {
+            if(fbcLevel==2) react_notes[i]<-sub(paste("<",tag,">","GENE[_ ]?ASSOCIATION: [^<]+","</",tag,">",sep = ""),"",react_notes[i], perl = TRUE)
+            else react_notes[i]<-sub("GENE[_ ]?ASSOCIATION: [^<]+",paste("GENE_ASSOCIATION: ",gpr(morg)[i], sep = ""), react_notes[i], perl = TRUE)
+          }
+          else if(fbcLevel!=2)react_notes[i]<-gsub("</notes>",paste("<",tag,">","GENE_ASSOCIATION: ",gpr(morg)[i],"</",tag,">","\n</notes>",sep = ""),react_notes[i])
+          
+          #Have Subsystem
+          if(havesub)react_notes[i]<-sub("SUBSYSTEM: [^<]+",paste("SUBSYSTEM: ",newsubS[i], sep = ""), react_notes[i], perl = TRUE)
+          else if(modhasubSys) react_notes[i]<-gsub("</notes>",paste("<",tag,">","SUBSYSTEM: ",newsubS[i],"</",tag,">","\n</notes>",sep = ""),react_notes[i])
+        }
+      }  
+    }  
+    
+    
+  } ####END newSybil attr
+  
+  # Subsystem
+  if(is.null(newsubS) && !(modhasubSys) ) for ( i in 1:react_num(morg)) {newsubS[i]<- paste(names(which(subSys(morg)[i,])), collapse=", ")}
+  
+  newmet_id <- paste0("M_", (deformatSBMLid(met_id(morg))))
+  #newmet_id <- sub("\\[(\\w)\\]$", "_\\1",  newmet_id) # append compartment id, if in postfix with square brkts
+  
+  newreact_id <- paste0("R_", deformatSBMLid(react_id(morg)))
+  newmet_comp<-mod_compart(morg)[met_comp(morg)]
+  
+  
+  success <-.Call("exportSBML", PACKAGE = "sybilSBML",
+                  as.integer(version),
+                  as.integer(level),
+                  as.integer(fbcLevel),
+                  as.character(filename),
+                  SYBIL_SETTINGS("MAXIMUM"),
+                  as.character(mod_desc(morg)),
+                  as.character(mod_name(morg)),
+                  as.character(mod_compart(morg)),
+                  as.character(newmet_id),
+                  as.character(met_name(morg)),
+                  as.character(newmet_comp),
+                  met_formula,
+                  met_charge,
+                  as.character(newreact_id),
+                  as.character(react_name(morg)),
+                  as.logical(react_rev(morg)),
+                  as.numeric(lowbnd(morg)),
+                  as.numeric(uppbnd(morg)),
+                  as.integer(obj_coef(morg)),
+                  as.character(newsubS),
+                  as.character(deformatGene(gpr(morg))),
+                  as.numeric(shrinkMatrix(morg,j=1:react_num(morg))),
+                  mod_notes,
+                  mod_anno,
+                  com_notes,   
+                  com_annotation, 
+                  met_notes,      
+                  met_anno,
+                  met_bnd,
+                  react_notes,
+                  react_anno,
+                  ex_react,
+                  as.character(deformatGene(allgenes))
+  )
+# SUCESS MESSAGES
+  if(success)
+  {
+    message(paste("Wrote file ",filename,"\n",sep=""), appendLF = FALSE);
+    if (validation)print(validateSBMLdocument(filename));
+  }  
+  else  message(paste("Could not write file ",filename,"\n",sep=""), appendLF = FALSE);
+  return (success)
+}
\ No newline at end of file

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for sybilSBML 2.0.8.
+# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.0.
 #
-# Report bugs to <geliudie@uni-duesseldorf.de>.
+# Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -267,8 +267,8 @@ fi
     $as_echo "$0: be upgraded to zsh 4.3.4 or later."
   else
     $as_echo "$0: Please tell bug-autoconf@gnu.org and
-$0: geliudie@uni-duesseldorf.de about your system,
-$0: including any error possibly output before this
+$0: clausjonathan.fritzemeier@uni-duesseldorf.de about your
+$0: system, including any error possibly output before this
 $0: message. Then install a modern shell, or manually run
 $0: the script under such a shell if you do have one."
   fi
@@ -580,9 +580,9 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='sybilSBML'
 PACKAGE_TARNAME='sybilsbml'
-PACKAGE_VERSION='2.0.8'
-PACKAGE_STRING='sybilSBML 2.0.8'
-PACKAGE_BUGREPORT='geliudie@uni-duesseldorf.de'
+PACKAGE_VERSION='3.0.0'
+PACKAGE_STRING='sybilSBML 3.0.0'
+PACKAGE_BUGREPORT='clausjonathan.fritzemeier@uni-duesseldorf.de'
 PACKAGE_URL=''
 
 # Factoring default headers for most tests.
@@ -1230,7 +1230,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures sybilSBML 2.0.8 to adapt to many kinds of systems.
+\`configure' configures sybilSBML 3.0.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1291,7 +1291,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of sybilSBML 2.0.8:";;
+     short | recursive ) echo "Configuration of sybilSBML 3.0.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1315,7 +1315,7 @@ Some influential environment variables:
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
 
-Report bugs to <geliudie@uni-duesseldorf.de>.
+Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>.
 _ACEOF
 ac_status=$?
 fi
@@ -1378,7 +1378,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-sybilSBML configure 2.0.8
+sybilSBML configure 3.0.0
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1537,9 +1537,9 @@ $as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
 $as_echo "$as_me: WARNING: $2:     section \"Present But Cannot Be Compiled\"" >&2;}
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
 $as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
-( $as_echo "## ------------------------------------------ ##
-## Report this to geliudie@uni-duesseldorf.de ##
-## ------------------------------------------ ##"
+( $as_echo "## ----------------------------------------------------------- ##
+## Report this to clausjonathan.fritzemeier@uni-duesseldorf.de ##
+## ----------------------------------------------------------- ##"
      ) | sed "s/^/$as_me: WARNING:     /" >&2
     ;;
 esac
@@ -1676,11 +1676,78 @@ fi
   as_fn_set_status $ac_retval
 
 } # ac_fn_c_try_link
+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_c_check_func ()
+{
+  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char $2 (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+  eval "$3=yes"
+else
+  eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_func
 cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by sybilSBML $as_me 2.0.8, which was
+It was created by sybilSBML $as_me 3.0.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -3528,6 +3595,101 @@ else
 fi
 
 
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for readSBML in -lsbml" >&5
+$as_echo_n "checking for readSBML in -lsbml... " >&6; }
+if ${ac_cv_lib_sbml_readSBML+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsbml  $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char readSBML ();
+int
+main ()
+{
+return readSBML ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+  ac_cv_lib_sbml_readSBML=yes
+else
+  ac_cv_lib_sbml_readSBML=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sbml_readSBML" >&5
+$as_echo "$ac_cv_lib_sbml_readSBML" >&6; }
+if test "x$ac_cv_lib_sbml_readSBML" = xyes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBSBML 1
+_ACEOF
+
+  LIBS="-lsbml $LIBS"
+
+else
+  as_fn_error $? "Could not link to libSBML:
+      use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker." "$LINENO" 5
+fi
+
+
+ac_fn_c_check_header_compile "$LINENO" "sbml/packages/fbc/common/FbcExtensionTypes.h" "ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" "#include <sbml/SBMLTypes.h>
+"
+if test "x$ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" = xyes; then :
+
+else
+  as_fn_error $? "Could not find specific FBC header of libSBML:
+      make sure your libSBML version is >= 5.13." "$LINENO" 5
+fi
+
+
+
+#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#		make sure your libSBML version is >= 5.13.]))
+
+for ac_func in SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound
+do :
+  as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+  cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+else
+  as_fn_error $? "Could not find specific FBC function of libSBML:
+		make sure your libSBML version is >= 5.13." "$LINENO" 5
+fi
+done
+
+
+#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#      make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBMLExtensionRegistry_getRegisteredPackages], [sbml], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#      make sure your libSBML version is >= 5.13.]))
+
+
+
+#AC_SEARCH_LIBS([GeneProductAssociation_setAssociation], [sbml], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#      make sure your libSBML version is >= 5.13.]))
+
+
 
 
 
@@ -4077,7 +4239,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by sybilSBML $as_me 2.0.8, which was
+This file was extended by sybilSBML $as_me 3.0.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -4124,13 +4286,13 @@ Usage: $0 [OPTION]... [TAG]...
 Configuration files:
 $config_files
 
-Report bugs to <geliudie@uni-duesseldorf.de>."
+Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>."
 
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-sybilSBML config.status 2.0.8
+sybilSBML config.status 3.0.0
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

-AC_INIT([sybilSBML], [2.0.8], [geliudie@uni-duesseldorf.de])
+AC_INIT([sybilSBML], [3.0.0], [clausjonathan.fritzemeier@uni-duesseldorf.de])
 
 dnl # --------------------------------------------------------------------
 dnl # global (environment) variables
@@ -236,6 +236,38 @@ AC_SEARCH_LIBS([readSBML], [sbml], ,
     AC_MSG_ERROR([Could not link to libSBML:
       use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.]))
 
+AC_CHECK_LIB([sbml], [readSBML], ,
+    AC_MSG_ERROR([Could not link to libSBML:
+      use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.]))
+
+AC_CHECK_HEADER([sbml/packages/fbc/common/FbcExtensionTypes.h], ,
+ AC_MSG_ERROR([Could not find specific FBC header of libSBML:
+      make sure your libSBML version is >= 5.13.]),
+      [#include <sbml/SBMLTypes.h>])
+
+#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#		make sure your libSBML version is >= 5.13.]))
+
+AC_CHECK_FUNCS([SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound], ,
+	AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+		make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#      make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBMLExtensionRegistry_getRegisteredPackages], [sbml], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#      make sure your libSBML version is >= 5.13.]))
+
+
+
+#AC_SEARCH_LIBS([GeneProductAssociation_setAssociation], [sbml], ,
+#    AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+#      make sure your libSBML version is >= 5.13.]))
+
+
 
 dnl # --------------------------------------------------------------------
 dnl # substitute src/Makevars

inst/NEWS.Rd

@@ -4,7 +4,24 @@
 \title{sybilSBML News}
 \encoding{UTF-8}
 
-\newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+\newcommand{\CRANpkg}{\href{https://cran.r-project.org/package=#1}{\pkg{#1}}}
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 3.0.1 2016-12-16}{
+  \itemize{
+    \item sybilSBML now supports writing of SBML files.
+    \item The new FBC additional package for SBML is now fully integrated.
+    \item Urls in NEWS file are now in default style.
+  }
+}
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 2.0.11 2015-07-03}{
+  \itemize{
+    \item \code{gprRules}-Slot in \code{modelorg} has changed. Thus 
+    \code{readSBMLmod} had to be updated.
+  }
+}
 
 % ---------------------------------------------------------------------------- %
 \section{Changes in version 2.0.11 2015-07-03}{

inst/doc/sybilSBML.R

+### R code from vignette source 'sybilSBML.Rnw'
+### Encoding: UTF-8
+
+###################################################
+### code chunk number 1: sybilSBML.Rnw:85-87 (eval = FALSE)
+###################################################
+## library(sybilSBML)
+## model <- readSBMLmod("<model>.xml")
+
+
+###################################################
+### code chunk number 2: sybilSBML.Rnw:103-106
+###################################################
+library(sybilSBML)
+mp     <- system.file(package = "sybilSBML", "extdata")
+ec_mod <- file.path(mp, "ecoli_core_model.xml")
+
+
+###################################################
+### code chunk number 3: sybilSBML.Rnw:109-110
+###################################################
+mod <- readSBMLmod(ec_mod, bndCond = FALSE)
+
+
+###################################################
+### code chunk number 4: sybilSBML.Rnw:123-124
+###################################################
+err <- validateSBMLdocument(ec_mod)
+
+

inst/doc/sybilSBML.Rnw

+\documentclass[a4paper,headings=small]{scrartcl}
+\usepackage[english]{babel}
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
+\usepackage{textcomp,lmodern}
+\typearea[current]{last}
+\usepackage{fixltx2e,mparhack,mathdots}
+
+\usepackage{natbib}
+%\usepackage{hyperref}
+
+\usepackage{microtype}
+
+\newcommand{\Comp}[1]{\texttt{#1}}
+% bash command prompt
+\DeclareRobustCommand{\PROMPTL}{\Comp{\$}}
+
+% just a bash command
+\DeclareRobustCommand{\COML}[1]{%
+    \small{\PROMPTL\Comp{ #1}}
+}
+% bash command with quote environment
+\DeclareRobustCommand{\COMML}[1]{%
+    \begin{quote}%
+        \small{\PROMPTL\Comp{ #1}}
+    \end{quote}
+}
+
+\addtolength{\skip\footins}{0.5\baselineskip}
+\usepackage{fnpos}
+
+
+% \hypersetup{
+% 	pdftitle = {sybilSBML -- Quick Start},
+% 	pdfauthor = {Gabriel Gelius-Dietrich},
+% 	pdfsubject = {SBML support for SyBiL},
+% 	pdfkeywords = {SBML},
+%     pdfborder = {0 0 0},
+%     pdfhighlight = {/N}
+% }
+
+
+\newcommand{\pkg}[1]{\emph{#1}}
+\newcommand{\CRANpkg}[1]{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+%\newcommand{\pkgname}{\CRANpkg{sybilSBML}}
+\newcommand{\pkgname}{\emph{sybilSBML}}
+\newcommand{\prgname}[1]{\textsc{#1}}
+
+
+\begin{document}
+\title{sybilSBML -- Quick Start}
+%\VignetteIndexEntry{Package sybilSBML -- Quick Start}
+%\VignettePackage{sybilSBML}
+\author{Gabriel Gelius-Dietrich}
+
+\maketitle
+
+
+\section{Introduction}
+
+The package \pkgname{} is an addition to package
+\pkg{sybil}\footnote{\texttt{http://CRAN.R-project.org/package=sybil}}
+providing support for
+metabolic networks written in SBML (Systems Biology Markup Language), in
+particular those developed by Bernhard \O. Palsson's
+lab\footnote{\texttt{http://gcrg.ucsd.edu/}} and those from the BiGG
+database\footnote{\texttt{http://bigg.ucsd.edu/}} \citep{Schellenberger:2010fk}.
+\nocite{Becker:2007uq,Schellenberger:2011fk}
+
+
+\section{Installation}
+
+The package \pkgname{} depends on a working installation of
+LibSBML \citep{Bornstein:2008uq} available from the SBML
+homepage\footnote{\texttt{http://www.sbml.org/}, libSBML version 5.6.0 or higher}
+(in particular libraries and header files).
+See \Comp{INSTALL} for installation instructions and platform specific details.
+
+
+\section{Usage}
+
+The package \pkgname{} provides the command \Comp{readSBMLmod()} which reads
+SBML formated files and returns instances of class \Comp{modelorg}.
+
+<<eval=FALSE>>=
+library(sybilSBML)
+model <- readSBMLmod("<model>.xml")
+@
+
+
+\section{Input files}
+
+The function \Comp{readSBMLmod()} reads metabolic network models written in
+SBML format (Systems Biology Markup Language).  Among the models available in
+this de-facto standard format are in particular those developed by
+Bernhard \O. Palsson's lab.
+
+The file \Comp{ecoli\_core\_model.xml} (in \Comp{extdata/}) contains an
+exemplarily metabolic network written in SBML for the core energy metabolism
+of \emph{E.~coli} \citep{Palsson:2006fk,Orth:2010fk}.
+The exact location of the file can be retrieved with the \Comp{system.file()}
+command:
+<<>>=
+library(sybilSBML)
+mp     <- system.file(package = "sybilSBML", "extdata")
+ec_mod <- file.path(mp, "ecoli_core_model.xml")
+@
+The model can be read in by using the command \Comp{readSBMLmod()}:
+<<print=true>>=
+mod <- readSBMLmod(ec_mod, bndCond = FALSE)
+@
+The metabolite id's of the SBML files are written in the format
+\Comp{M\_<metabolite abbreviation>\_<compartment abbreviation>}. The compartment
+abbreviation is a one letter abbreviation, e.\,g. \Comp{c} for cytosol.  All
+metabolites outside the system boundary belong to compartment \Comp{b}.  Those
+metabolites are transported into or outside the system.  As long as they are
+mentioned, the network is closed.  The function \Comp{readSBMLmod()} will remove
+them in order to produce an open network.
+
+\section{Validation of input files}
+
+SBML files can be validated by using the command \Comp{validateSBMLdocument()}:
+<<>>=
+err <- validateSBMLdocument(ec_mod)
+@
+The variable \Comp{err} is of class \Comp{sbmlError}, storing error messages
+generated by the validation procedure.
+
+\bibliographystyle{abbrvnat}
+\bibliography{sybilSBML}
+
+\end{document}

man/getSBMLFbcversion.Rd

+\name{getSBMLFbcversion}
+\alias{getSBMLFbcversion}
+
+\title{
+  Get SBML Version
+}
+
+\description{
+  Retrieve SBML FBC version of SBML file.
+}
+
+\usage{
+  getSBMLFbcversion(sbmlf)
+}
+
+\arguments{
+  \item{sbmlf}{
+    An object of class \code{\linkS4class{sbmlPtr}} as returned by
+    \code{\link{openSBMLfile}}. This is basically a pointer to a SBML document.
+  }
+}
+
+\value{
+  A single integer value containing the SBML FBC version of the SBML file.
+}
+
+\references{
+  Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+  LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+  880--881.
+}
+
+\author{
+  Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+  Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\seealso{
+  \code{\link{openSBMLfile}}, \code{\linkS4class{sbmlPtr}}
+}
+
+\keyword{ IO }
\ No newline at end of file

man/getSBMLmodAnnotation.Rd

+\name{getSBMLmodAnnotation}
+\alias{getSBMLmodAnnotation}
+
+\title{
+  Get Model Annotation
+}
+
+\description{
+  Retrieve model annotation of a SBML model
+}
+
+\usage{
+  getSBMLmodAnnotation(sbmlm)
+}
+
+\arguments{
+  \item{sbmlm}{
+    An object of class \code{\linkS4class{sbmlPtr}} as returned by
+    \code{\link{getSBMLmodel}}. This is basically a pointer to a SBML model.
+  }
+}
+
+\value{
+  A single character string containing the model annotation of the SBML model.
+}
+
+\references{
+  Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+  LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+  880--881.
+}
+
+\author{
+  Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+  Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\seealso{
+  \code{\link{getSBMLmodel}}, \code{\linkS4class{sbmlPtr}}
+}
+
+\keyword{ IO }
\ No newline at end of file

man/getSBMLmodNotes.Rd

+\name{getSBMLmodNotes}
+\alias{getSBMLmodNotes}
+
+\title{
+  Get Model Note
+}
+
+\description{
+  Retrieve model notes of a SBML model
+}
+
+\usage{
+  getSBMLmodNotes(sbmlm)
+}
+
+\arguments{
+  \item{sbmlm}{
+    An object of class \code{\linkS4class{sbmlPtr}} as returned by
+    \code{\link{getSBMLmodel}}. This is basically a pointer to a SBML model.
+  }
+}
+
+\value{
+  A single character string containing the model notes of the SBML model.
+}
+
+\references{
+  Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+  LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+  880--881.
+}
+
+\author{
+  Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+  Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\seealso{
+  \code{\link{getSBMLmodel}}, \code{\linkS4class{sbmlPtr}}
+}
+
+\keyword{ IO }
\ No newline at end of file

man/writeSBML.Rd

+\name{writeSBML}
+\alias{writeSBML}
+
+\encoding{utf8}
+
+\title{Exports a Metabolic Network in SBML Format}
+
+\description{
+  The function exports a metabolic network from S4 object of the class \code{\link{modelorg}} in SBML format. The function returns TRUE if the SBML file is successfully built.
+}
+
+\usage{
+  writeSBML(morg=NULL,level=2,version=4,fbcLevel=0,
+             filename="export.xml",
+             recoverExtMet=FALSE,
+             printNotes=TRUE,
+             printAnnos=TRUE,
+             validation=FALSE)
+
+}
+
+\arguments{
+  \item{morg}{
+    An S4 object of the class \code{\link[sybil]{modelorg}}.
+  }
+  \item{level}{
+    A single integer value containing the SBML level for the exporting SBML file. \cr
+    Default: \code{2}.
+  }
+   \item{version}{
+    A single integer value containing the SBML version for the exporting SBML file. \cr
+    Default: \code{4}.
+  }
+  \item{fbcLevel}{
+    A single integer value containing the fbc package version for the exporting SBML file. \cr
+    Default: \code{2}.
+  }
+   \item{filename}{
+    SBML filename for exporting the model.
+    Default: \code{"export.xml"}.
+  }
+  \item{recoverExtMet}{
+    Boolean: recover external metabolites and refer them to compartment \code{"BOUNDARY"}.\cr 
+    Default: \code{FALSE}.
+  }
+  \item{printNotes}{
+    Boolean: print Notes from original SBML file .\cr
+    Default: \code{TRUE}.
+  }
+  \item{printAnnos}{
+    Boolean: print Annotations from original SBML file .\cr
+    Default: \code{TRUE}.
+  }
+  \item{validation}{
+    Boolean: print containing errors for xml file .\cr
+    Default: \code{TRUE}.
+  }
+
+}
+
+\details{
+  The library \code{libSBML} is used to export a \code{\link[sybil]{modelorg}}
+  to a SBML file.
+
+}
+
+\value{
+  A single boolean value for a successful export .
+}
+
+\references{
+  The BiGG database \url{http://bigg.ucsd.edu/}.
+
+  Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+  LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+  880--881.
+
+  Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. Ø., (2010)
+  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic
+  reconstructions. \emph{BMC Bioinformatics} \bold{11}, 213.
+
+  Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø.  and
+  Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with
+  constraint-based models: the COBRA Toolbox. \emph{Nat Protoc} \bold{2},
+  727--738.
+
+  Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D.,
+  Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S.,
+  Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of
+  cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
+  \emph{Nat Protoc} \bold{6}, 1290--1307.
+}
+
+\author{
+  Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+  Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\note{
+  The function \code{writeSBML} makes use of the library
+  \code{libSBML} (\url{http://www.sbml.org}).
+}
+
+\seealso{
+  \code{\link{readSBMLmod}}
+}
+
+\examples{
+  dir  <- system.file(package = "sybilSBML", "extdata")
+  file <- file.path(dir, "ecoli_core_model.xml")
+  mod  <- readSBMLmod(file, bndCond = FALSE)
+  writeSBML(mod,level=3,version=1,fbcLevel=2)
+}
+
+\keyword{ IO }
+

src/init.c

@@ -45,6 +45,8 @@ static const R_CallMethodDef callMethods[] = {
     {"getSBMLmodel",               (DL_FUNC) &getSBMLmodel,               2},
     {"getSBMLmodId",               (DL_FUNC) &getSBMLmodId,               1},
     {"getSBMLmodName",             (DL_FUNC) &getSBMLmodName,             1},
+    {"getSBMLmodNotes",            (DL_FUNC) &getSBMLmodNotes,            1},
+    {"getSBMLmodAnnotation",       (DL_FUNC) &getSBMLmodAnnotation,       1},
     {"getSBMLnumCompart",          (DL_FUNC) &getSBMLnumCompart,          1},
     {"getSBMLnumSpecies",          (DL_FUNC) &getSBMLnumSpecies,          1},
     {"getSBMLnumReactions",        (DL_FUNC) &getSBMLnumReactions,        1},
@@ -52,6 +54,8 @@ static const R_CallMethodDef callMethods[] = {
     {"getSBMLCompartList",         (DL_FUNC) &getSBMLCompartList,         1},
     {"getSBMLSpeciesList",         (DL_FUNC) &getSBMLSpeciesList,         1},
     {"getSBMLReactionsList",       (DL_FUNC) &getSBMLReactionsList,       1},
+    {"exportSBML",                 (DL_FUNC) &exportSBML,                 33},
+    {"getSBMLFbcversion",          (DL_FUNC) &getSBMLFbcversion,          1},
     {NULL, NULL, 0}
 };
 
@@ -62,5 +66,3 @@ void R_init_sybilSBML(DllInfo *info) {
     R_registerRoutines(info, NULL, callMethods, NULL, NULL);
     R_useDynamicSymbols(info, FALSE);
 }
\ No newline at end of file
-
-

src/sybilSBML.h

@@ -63,6 +63,9 @@ SEXP getSBMLlevel(SEXP sbmldoc);
 /* get sbml document version */
 SEXP getSBMLversion(SEXP sbmldoc);
 
+/* get sbml document FBC version */
+SEXP getSBMLFbcversion(SEXP sbmldoc);
+
 /* validate SBML document */
 SEXP validateDocument(SEXP sbmldoc);
 
@@ -78,6 +81,12 @@ SEXP getSBMLmodId(SEXP sbmlmod);
 /* get model name */
 SEXP getSBMLmodName(SEXP sbmlmod);
 
+/* get model notes */
+SEXP getSBMLmodNotes(SEXP sbmlmod);
+
+/* get model annotation */
+SEXP getSBMLmodAnnotation(SEXP sbmlmod);
+
 /* get number of compartments */
 SEXP getSBMLnumCompart(SEXP sbmlmod);
 
@@ -98,3 +107,6 @@ SEXP getSBMLSpeciesList(SEXP sbmlmod);
 
 /* get list of reactions */
 SEXP getSBMLReactionsList(SEXP sbmlmod);
+
+/* export Modelorg to SBML*/
+SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react, SEXP allgenes);
\ No newline at end of file