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R/saveSBML.r
In SBMLR: SBML-R Interface and Analysis Tools
"saveSBML" <-
function(model,filename)
{ # takes model object of class SBML ,and maps it to an SBML model in filename.xml
fid <- file(filename, "w") # open the output file connection
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("<?xml version=\"1.0\" encoding=\"UTF-8\"?>", file=fid, sep="\n")
cat("<sbml xmlns=\"http://www.sbml.org/sbml/level2\" level=\"2\" version=\"1\">", file=fid, sep="\n")
#print(sprintf("<model id=\"%s\">",filename))
cat(sprintf("<model id=\"%s\">",id), file=fid, sep="\n")
if(nNotes>0){
cat("<notes>", file=fid, sep="\n")
cat(" <body xmlns=\"http://www.w3.org/1999/xhtml\">", file=fid, sep="\n")
for (i in 1:nNotes) cat(sprintf(" <p> %s </p>",notes[[i]]), file=fid, sep="\n")
cat(" </body>", file=fid, sep="\n")
cat("</notes>", file=fid, sep="\n")
}
if(nCompartments>0){
cat("<listOfCompartments>", file=fid, sep="\n")
for (i in 1:nCompartments)
cat(sprintf(" <compartment id=\"%s\" size=\"%g\" />",
compartments[[i]][["id"]],compartments[[i]][["size"]]), file=fid, sep="\n")
# cat(sprintf(" <compartment id=\"%s\" size=\"%g\" name=\"%s\"/>", # VV
# compartments[[i]][["id"]],compartments[[i]][["size"]],compartments[[i]][["name"]]), file=fid, sep="\n")
cat("</listOfCompartments>", file=fid, sep="\n")
}
if(nSpecies>0){
cat("<listOfSpecies>", file=fid, sep="\n")
for (i in 1:nSpecies)
cat(sprintf(" <species id=\"%s\" initialConcentration=\"%g\" compartment=\"%s\" boundaryCondition=\"%s\"/>",
species[[i]][["id"]],species[[i]][["ic"]],species[[i]][["compartment"]],
ifelse(species[[i]][["bc"]],"true","false")), file=fid, sep="\n") #VV
# species[[i]][[1]],species[[i]][[2]],species[[i]][[3]],ifelse(species[[i]][[4]],"true","false")), file=fid, sep="\n")
cat("</listOfSpecies>", file=fid, sep="\n")
}
if(nGlobalParameters>0){
cat("<listOfParameters>", file=fid, sep="\n")
for (i in 1:nGlobalParameters)
cat(sprintf(" <parameter id=\"%s\" value=\"%g\" />",names(globalParameters[i]),globalParameters[[i]]), file=fid, sep="\n")
cat("</listOfParameters>", file=fid, sep="\n")
}
if(nRules>0){
cat("<listOfRules>", file=fid, sep="\n")
for (i in 1:nRules)
{
idOutput=rules[[i]][["idOutput"]][[1]]
cat(sprintf(" <assignmentRule variable=\"%s\">",idOutput), file=fid, sep="\n")
cat(" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">", file=fid, sep="\n")
ml=saveXML(rules[[i]]$mathmlLaw,prefix=NULL,file=fid)
cat(" </math>", file=fid, sep="\n")
cat(" </assignmentRule>", file=fid, sep="\n")
# VV replaces the last 3 lines with this, but I don't get where newtry comes from????
# In case of dirty xml file with messed up rules, we shouldn't write
# if(!(is.null(newtry$rules[[i]]$mathmlLaw)))
# { # the messed up parts.
# ml=saveXML(rules[[i]]$mathmlLaw,prefix=NULL,file=fid)
# cat(" </math>", file=fid, sep="\n")
# cat(" </assignmentRule>", file=fid, sep="\n")
# }
# else
# {
# cat(" </math>", file=fid, sep="\n")
# cat(" </assignmentRule>", file=fid, sep="\n")
# next; #move onto next rule
# }
}
cat("</listOfRules>", file=fid, sep="\n")
}
cat("<listOfReactions>", 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
cat(sprintf(" <reaction id=\"%s\" reversible=\"%s\">",reactions[[i]][["id"]],
ifelse(reactions[[i]][["reversible"]],"true","false")), file=fid, sep="\n")
reactants=reactions[[i]][["reactants"]]
if (!is.null(reactants[[1]])) {
cat(" <listOfReactants>", file=fid, sep="\n")
for (j in 1:length(reactants))
cat(sprintf(" <speciesReference species = \"%s\" />", reactants[[j]]), file=fid, sep="\n")
cat(" </listOfReactants>", file=fid, sep="\n")}
# Just switched the order of these two blocks to fix the errors
products=reactions[[i]][["products"]]
if (!is.null(products[[1]])) {
cat(" <listOfProducts>", file=fid, sep="\n")
for (j in 1:length(products))
cat(sprintf(" <speciesReference species = \"%s\" />", products[[j]]), file=fid, sep="\n")
cat(" </listOfProducts>", file=fid, sep="\n") }
modifiers=reactions[[i]][["modifiers"]]
if (!is.null(modifiers[[1]])) {
cat(" <listOfModifiers>", file=fid, sep="\n")
for (j in 1:length(modifiers))
cat(sprintf(" <modifierSpeciesReference species = \"%s\" />", modifiers[[j]]), file=fid, sep="\n")
cat(" </listOfModifiers>", file=fid, sep="\n")}
cat(" <kineticLaw>", file=fid, sep="\n")
cat(" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">", file=fid, sep="\n")
ml=saveXML(reactions[[i]]$mathmlLaw,prefix=NULL,file=fid) # annoying warnings were coming from here without file=fid
cat(" </math>", file=fid, sep="\n")
# cat(" <listOfParameters>", file=fid, sep="\n")
# parameters=reactions[[i]][["parameters"]]
# for (j in 1:length(parameters))
# if (length(parameters[[j]])==1)
# cat(sprintf(" <parameter id = \"%s\" value = \"%g\"/>", names(parameters)[j],parameters[[j]]), file=fid, sep="\n") else
# cat(sprintf(" <parameter id = \"%s\" value = \"%g\"/>", names(parameters)[j],-parameters[[j]][[1]]), file=fid, sep="\n")
# cat(" </listOfParameters>", file=fid, sep="\n") # I forgot what the else is for, i.e. when is it not 1? is it >1 or 0???
# VV replaces block above with this block.
parameters=reactions[[i]][["parameters"]]
nlocalParameters = length(parameters)
if(nlocalParameters > 0) #if local parameters exist, we write it. Else we avoid it.
{ cat(" <listOfParameters>", file=fid, sep="\n")
for (j in 1:nlocalParameters) # Write each and every local parameter.
cat(sprintf(" <parameter id = \"%s\" value = \"%g\"/>", names(parameters)[j],parameters[[j]]), file=fid, sep="\n")
cat(" </listOfParameters>", file=fid, sep="\n") }
cat(" </kineticLaw>", file=fid, sep="\n")
cat(" </reaction>", file=fid, sep="\n")
}
cat("</listOfReactions>", file=fid, sep="\n")
cat("</model>", file=fid, sep="\n")
cat("</sbml>", file=fid, sep="\n")
close(fid)
} # end write.sbml function defition
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SBMLR documentation built on Nov. 8, 2020, 6:50 p.m.
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"saveSBML" <-
function(model,filename)
{ # takes model object of class SBML ,and maps it to an SBML model in filename.xml
fid <- file(filename, "w") # open the output file connection
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("<?xml version=\"1.0\" encoding=\"UTF-8\"?>", file=fid, sep="\n")
cat("<sbml xmlns=\"http://www.sbml.org/sbml/level2\" level=\"2\" version=\"1\">", file=fid, sep="\n")
#print(sprintf("<model id=\"%s\">",filename))
cat(sprintf("<model id=\"%s\">",id), file=fid, sep="\n")
if(nNotes>0){
cat("<notes>", file=fid, sep="\n")
cat(" <body xmlns=\"http://www.w3.org/1999/xhtml\">", file=fid, sep="\n")
for (i in 1:nNotes) cat(sprintf(" <p> %s </p>",notes[[i]]), file=fid, sep="\n")
cat(" </body>", file=fid, sep="\n")
cat("</notes>", file=fid, sep="\n")
}
if(nCompartments>0){
cat("<listOfCompartments>", file=fid, sep="\n")
for (i in 1:nCompartments)
cat(sprintf(" <compartment id=\"%s\" size=\"%g\" />",
compartments[[i]][["id"]],compartments[[i]][["size"]]), file=fid, sep="\n")
# cat(sprintf(" <compartment id=\"%s\" size=\"%g\" name=\"%s\"/>", # VV
# compartments[[i]][["id"]],compartments[[i]][["size"]],compartments[[i]][["name"]]), file=fid, sep="\n")
cat("</listOfCompartments>", file=fid, sep="\n")
}
if(nSpecies>0){
cat("<listOfSpecies>", file=fid, sep="\n")
for (i in 1:nSpecies)
cat(sprintf(" <species id=\"%s\" initialConcentration=\"%g\" compartment=\"%s\" boundaryCondition=\"%s\"/>",
species[[i]][["id"]],species[[i]][["ic"]],species[[i]][["compartment"]],
ifelse(species[[i]][["bc"]],"true","false")), file=fid, sep="\n") #VV
# species[[i]][[1]],species[[i]][[2]],species[[i]][[3]],ifelse(species[[i]][[4]],"true","false")), file=fid, sep="\n")
cat("</listOfSpecies>", file=fid, sep="\n")
}
if(nGlobalParameters>0){
cat("<listOfParameters>", file=fid, sep="\n")
for (i in 1:nGlobalParameters)
cat(sprintf(" <parameter id=\"%s\" value=\"%g\" />",names(globalParameters[i]),globalParameters[[i]]), file=fid, sep="\n")
cat("</listOfParameters>", file=fid, sep="\n")
}
if(nRules>0){
cat("<listOfRules>", file=fid, sep="\n")
for (i in 1:nRules)
{
idOutput=rules[[i]][["idOutput"]][[1]]
cat(sprintf(" <assignmentRule variable=\"%s\">",idOutput), file=fid, sep="\n")
cat(" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">", file=fid, sep="\n")
ml=saveXML(rules[[i]]$mathmlLaw,prefix=NULL,file=fid)
cat(" </math>", file=fid, sep="\n")
cat(" </assignmentRule>", file=fid, sep="\n")
# VV replaces the last 3 lines with this, but I don't get where newtry comes from????
# In case of dirty xml file with messed up rules, we shouldn't write
# if(!(is.null(newtry$rules[[i]]$mathmlLaw)))
# { # the messed up parts.
# ml=saveXML(rules[[i]]$mathmlLaw,prefix=NULL,file=fid)
# cat(" </math>", file=fid, sep="\n")
# cat(" </assignmentRule>", file=fid, sep="\n")
# }
# else
# {
# cat(" </math>", file=fid, sep="\n")
# cat(" </assignmentRule>", file=fid, sep="\n")
# next; #move onto next rule
# }
}
cat("</listOfRules>", file=fid, sep="\n")
}
cat("<listOfReactions>", file=fid, sep="\n")
for (i in 1:nReactions)
{
if (is.null(reactions[[i]][["reversible"]]))
print("Internal SBMLR object should have reverse flag set") else
cat(sprintf(" <reaction id=\"%s\" reversible=\"%s\">",reactions[[i]][["id"]],
ifelse(reactions[[i]][["reversible"]],"true","false")), file=fid, sep="\n")
reactants=reactions[[i]][["reactants"]]
if (!is.null(reactants[[1]])) {
cat(" <listOfReactants>", file=fid, sep="\n")
for (j in 1:length(reactants))
cat(sprintf(" <speciesReference species = \"%s\" />", reactants[[j]]), file=fid, sep="\n")
cat(" </listOfReactants>", file=fid, sep="\n")}
# Just switched the order of these two blocks to fix the errors
products=reactions[[i]][["products"]]
if (!is.null(products[[1]])) {
cat(" <listOfProducts>", file=fid, sep="\n")
for (j in 1:length(products))
cat(sprintf(" <speciesReference species = \"%s\" />", products[[j]]), file=fid, sep="\n")
cat(" </listOfProducts>", file=fid, sep="\n") }
modifiers=reactions[[i]][["modifiers"]]
if (!is.null(modifiers[[1]])) {
cat(" <listOfModifiers>", file=fid, sep="\n")
for (j in 1:length(modifiers))
cat(sprintf(" <modifierSpeciesReference species = \"%s\" />", modifiers[[j]]), file=fid, sep="\n")
cat(" </listOfModifiers>", file=fid, sep="\n")}
cat(" <kineticLaw>", file=fid, sep="\n")
cat(" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">", file=fid, sep="\n")
ml=saveXML(reactions[[i]]$mathmlLaw,prefix=NULL,file=fid) # annoying warnings were coming from here without file=fid
cat(" </math>", file=fid, sep="\n")
# cat(" <listOfParameters>", file=fid, sep="\n")
# parameters=reactions[[i]][["parameters"]]
# for (j in 1:length(parameters))
# if (length(parameters[[j]])==1)
# cat(sprintf(" <parameter id = \"%s\" value = \"%g\"/>", names(parameters)[j],parameters[[j]]), file=fid, sep="\n") else
# cat(sprintf(" <parameter id = \"%s\" value = \"%g\"/>", names(parameters)[j],-parameters[[j]][[1]]), file=fid, sep="\n")
# cat(" </listOfParameters>", file=fid, sep="\n") # I forgot what the else is for, i.e. when is it not 1? is it >1 or 0???
# VV replaces block above with this block.
parameters=reactions[[i]][["parameters"]]
nlocalParameters = length(parameters)
if(nlocalParameters > 0) #if local parameters exist, we write it. Else we avoid it.
{ cat(" <listOfParameters>", file=fid, sep="\n")
for (j in 1:nlocalParameters) # Write each and every local parameter.
cat(sprintf(" <parameter id = \"%s\" value = \"%g\"/>", names(parameters)[j],parameters[[j]]), file=fid, sep="\n")
cat(" </listOfParameters>", file=fid, sep="\n") }
cat(" </kineticLaw>", file=fid, sep="\n")
cat(" </reaction>", file=fid, sep="\n")
}
cat("</listOfReactions>", file=fid, sep="\n")
cat("</model>", file=fid, sep="\n")
cat("</sbml>", file=fid, sep="\n")
close(fid)
} # end write.sbml function defition
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R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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