Refactor code for SBML2PRISM
This commit is contained in:
LukasBuecherl
parent
a93e650de2
commit
4bf6c6e1e6
1 changed files with 82 additions and 241 deletions
|
|
@ -14,58 +14,23 @@
|
|||
package edu.utah.ece.async.ibiosim.conversion;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.FileWriter;
|
||||
import java.io.FilenameFilter;
|
||||
import java.io.IOException;
|
||||
import java.net.URI;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.HashSet;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
import javax.xml.stream.XMLStreamException;
|
||||
|
||||
import org.sbml.jsbml.Compartment;
|
||||
import org.sbml.jsbml.Model;
|
||||
import org.sbml.jsbml.ModifierSpeciesReference;
|
||||
import org.sbml.jsbml.Parameter;
|
||||
import org.sbml.jsbml.Reaction;
|
||||
import org.sbml.jsbml.SBMLDocument;
|
||||
import org.sbml.jsbml.SBMLReader;
|
||||
import org.sbml.jsbml.Species;
|
||||
import org.sbml.jsbml.SpeciesReference;
|
||||
import org.sbml.jsbml.ext.comp.CompModelPlugin;
|
||||
import org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin;
|
||||
import org.sbml.jsbml.ext.comp.CompSBasePlugin;
|
||||
import org.sbml.jsbml.ext.comp.ExternalModelDefinition;
|
||||
import org.sbml.jsbml.ext.comp.ReplacedBy;
|
||||
import org.sbml.jsbml.ext.comp.ReplacedElement;
|
||||
import org.sbolstandard.core2.AccessType;
|
||||
import org.sbolstandard.core2.ComponentDefinition;
|
||||
import org.sbolstandard.core2.DirectionType;
|
||||
import org.sbolstandard.core2.EDAMOntology;
|
||||
import org.sbolstandard.core2.FunctionalComponent;
|
||||
import org.sbolstandard.core2.Interaction;
|
||||
import org.sbolstandard.core2.Module;
|
||||
import org.sbolstandard.core2.ModuleDefinition;
|
||||
import org.sbolstandard.core2.RefinementType;
|
||||
import org.sbolstandard.core2.SBOLConversionException;
|
||||
import org.sbolstandard.core2.SBOLDocument;
|
||||
import org.sbolstandard.core2.SBOLReader;
|
||||
import org.sbolstandard.core2.SBOLValidationException;
|
||||
import org.sbolstandard.core2.Sequence;
|
||||
import org.sbolstandard.core2.SequenceOntology;
|
||||
import org.sbolstandard.core2.SystemsBiologyOntology;
|
||||
import org.sbolstandard.core2.TopLevel;
|
||||
|
||||
import edu.utah.ece.async.ibiosim.dataModels.biomodel.annotation.AnnotationUtility;
|
||||
import edu.utah.ece.async.ibiosim.dataModels.biomodel.parser.BioModel;
|
||||
import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
|
||||
import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
|
||||
|
||||
|
||||
/**
|
||||
* Perform conversion from SBML to PRISM.
|
||||
|
|
@ -76,10 +41,11 @@ import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
|
|||
* Contributors </a>
|
||||
* @version %I%
|
||||
*/
|
||||
|
||||
public class SBML2PRISM {
|
||||
|
||||
/*
|
||||
* Convert SBML to Prism Input: SBMLDocument, File Output: void
|
||||
* Convert SBML to Prism. Input: SBMLDocument, File, bound. Output: void
|
||||
*
|
||||
* Function takes in a SBML document and writes the prism conversion of the file
|
||||
* in the same directory. The function also translates the constraint into a
|
||||
|
|
@ -90,33 +56,41 @@ public class SBML2PRISM {
|
|||
* To run the converter use the following command: java -jar
|
||||
* conversion/target/iBioSim-conversion-3.1.0-SNAPSHOT-jar-with-dependencies.jar
|
||||
* -l PRISM YOURSBMLFILE.xml
|
||||
*
|
||||
* The function also allows the translation into a bound model by simply adding the flag
|
||||
* -bound
|
||||
*/
|
||||
|
||||
public static void convertSBML2PRISM(SBMLDocument sbmlDoc, String filename, boolean unbound) throws IOException {
|
||||
Model model = sbmlDoc.getModel();
|
||||
File file = new File(filename.replace(".xml", ".sm"));
|
||||
|
||||
// Opening and writing preamble to the file
|
||||
FileWriter out = new FileWriter(file);
|
||||
out.write("// File generated by SBML-to-PRISM converter\n");
|
||||
out.write("// Original file: " + filename + "\n");
|
||||
out.write("// @GeneticLogicLab\n");
|
||||
out.write("\n");
|
||||
out.write("ctmc\n");
|
||||
out.write("\n");
|
||||
|
||||
// Set bound limit if bound model is selected
|
||||
if (unbound) {
|
||||
convertSBML2PRISMUnbound(sbmlDoc, filename);
|
||||
out.write("// const int MAX_AMOUNT = ADD VALUE \n");
|
||||
out.write("\n");
|
||||
} else {
|
||||
convertSBML2PRISMbound(sbmlDoc, filename);
|
||||
double maxAmount = 0.0;
|
||||
for (int i = 0; i < model.getSpeciesCount(); i++) {
|
||||
Species species = model.getSpecies(i);
|
||||
if (species.getInitialAmount() > maxAmount) {
|
||||
maxAmount = species.getInitialAmount();
|
||||
}
|
||||
}
|
||||
out.write(" const int MAX_AMOUNT = " + (int) maxAmount + ";\n");
|
||||
out.write("\n"); out.write("\n");
|
||||
}
|
||||
}
|
||||
|
||||
private static void convertSBML2PRISMUnbound(SBMLDocument sbmlDoc, String filename) throws IOException {
|
||||
Model model = sbmlDoc.getModel();
|
||||
File file = new File(filename.replace(".xml", ".sm"));
|
||||
|
||||
// Opening and writing preamble to the file
|
||||
FileWriter out = new FileWriter(file);
|
||||
out.write("// File generated by SBML-to-PRISM converter\n");
|
||||
out.write("// Original file: " + filename + "\n");
|
||||
out.write("// @GeneticLogicLab\n");
|
||||
out.write("\n");
|
||||
out.write("ctmc\n");
|
||||
out.write("\n");
|
||||
|
||||
out.write("// const int MAX_AMOUNT = ADD VALUE \n");
|
||||
out.write("\n");
|
||||
|
||||
|
||||
// Identify compartments and their size
|
||||
out.write("// Compartment size\n");
|
||||
|
||||
|
|
@ -124,7 +98,6 @@ public class SBML2PRISM {
|
|||
Compartment compartment = model.getCompartment(i);
|
||||
out.write("const double " + checkReservedKeywordPrism(compartment.getId()) + " = " + compartment.getSize()
|
||||
+ ";\n");
|
||||
|
||||
}
|
||||
|
||||
out.write("\n");
|
||||
|
|
@ -147,15 +120,28 @@ public class SBML2PRISM {
|
|||
// For function checkReservedKeywordPrism see below
|
||||
Species species = model.getSpecies(i);
|
||||
out.write("// Species " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("// const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
|
||||
out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("\n");
|
||||
out.write(" // " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
|
||||
+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
|
||||
+ ";\n");
|
||||
out.write(" " + checkReservedKeywordPrism(species.getId()) + " : " + "int init "
|
||||
+ (int) (species.getInitialAmount()) + ";\n");
|
||||
out.write("\n");
|
||||
|
||||
if (unbound) {
|
||||
out.write("// const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
|
||||
out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("\n");
|
||||
out.write(" // " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
|
||||
+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
|
||||
+ ";\n");
|
||||
out.write(" " + checkReservedKeywordPrism(species.getId()) + " : " + "int init "
|
||||
+ (int) (species.getInitialAmount()) + ";\n");
|
||||
out.write("\n");
|
||||
} else {
|
||||
out.write("const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
|
||||
out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("\n");
|
||||
out.write(" " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
|
||||
+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
|
||||
+ ";\n");
|
||||
out.write(" // " + checkReservedKeywordPrism(species.getId()) + " : " + "int init "
|
||||
+ (int) (species.getInitialAmount()) + ";\n");
|
||||
out.write("\n");
|
||||
}
|
||||
|
||||
// Iterate over reactions
|
||||
for (int j = 0; j < model.getReactionCount(); j++) {
|
||||
|
|
@ -174,12 +160,24 @@ public class SBML2PRISM {
|
|||
+ checkReservedKeywordPrism(species.getId()) + "-" + (int) reactant.getStoichiometry()
|
||||
+ ");\n");
|
||||
} else if (product != null) {
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReservedKeywordPrism(species.getId()) + " >= " + "0 -> ("
|
||||
+ checkReservedKeywordPrism(species.getId()) + "\'="
|
||||
+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
|
||||
+ ");\n");
|
||||
|
||||
if (unbound) {
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReservedKeywordPrism(species.getId()) + " >= " + "0 -> ("
|
||||
+ checkReservedKeywordPrism(species.getId()) + "\'="
|
||||
+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
|
||||
+ ");\n");
|
||||
} else {
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReservedKeywordPrism(species.getId()) + " <= " + checkReservedKeywordPrism(species.getId()) + "_MAX-"
|
||||
+ (int) product.getStoichiometry() + " -> ("
|
||||
+ checkReservedKeywordPrism(species.getId()) + "\'="
|
||||
+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
|
||||
+ ");\n");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -235,169 +233,21 @@ public class SBML2PRISM {
|
|||
|
||||
out.close();
|
||||
|
||||
// Write Properties File
|
||||
File property = new File(filename.replace(".xml", ".props"));
|
||||
FileWriter property_out = new FileWriter(property);
|
||||
|
||||
// Property preamble
|
||||
property_out.write("// File generated by SBML-to-PRISM converter\n");
|
||||
property_out.write("// Original file: " + filename + "\n");
|
||||
property_out.write("// @GeneticLogicLab\n");
|
||||
property_out.write("\n");
|
||||
|
||||
for (int i = 0; i < model.getConstraintCount(); i++) {
|
||||
// Get and write translation of constraint
|
||||
property_out.write(checkReserveKeywordMath(
|
||||
SBMLutilities.convertMath2PrismProperty(model.getConstraint(i).getMath()), model));
|
||||
}
|
||||
|
||||
property_out.close();
|
||||
writePRISMProperty(filename, model);
|
||||
|
||||
}
|
||||
|
||||
private static void convertSBML2PRISMbound(SBMLDocument sbmlDoc, String filename) throws IOException {
|
||||
Model model = sbmlDoc.getModel();
|
||||
File file = new File(filename.replace(".xml", ".sm"));
|
||||
|
||||
// Opening and writing preamble to the file
|
||||
FileWriter out = new FileWriter(file);
|
||||
out.write("// File generated by SBML-to-PRISM converter\n");
|
||||
out.write("// Original file: " + filename + "\n");
|
||||
out.write("// @GeneticLogicLab\n");
|
||||
out.write("\n");
|
||||
out.write("ctmc\n");
|
||||
out.write("\n");
|
||||
|
||||
double maxAmount = 0.0;
|
||||
for (int i = 0; i < model.getSpeciesCount(); i++) {
|
||||
Species species = model.getSpecies(i);
|
||||
if (species.getInitialAmount() > maxAmount) {
|
||||
maxAmount = species.getInitialAmount();
|
||||
}
|
||||
}
|
||||
|
||||
out.write(" const int MAX_AMOUNT = " + (int) maxAmount + ";\n");
|
||||
out.write("\n");
|
||||
|
||||
// Identify compartments and their size
|
||||
out.write("// Compartment size\n");
|
||||
|
||||
for (int i = 0; i < model.getCompartmentCount(); i++) {
|
||||
Compartment compartment = model.getCompartment(i);
|
||||
out.write("const double " + checkReservedKeywordPrism(compartment.getId()) + " = " + compartment.getSize()
|
||||
+ ";\n");
|
||||
|
||||
}
|
||||
|
||||
out.write("\n");
|
||||
|
||||
// Identify model parameters
|
||||
out.write("// Model parameters\n");
|
||||
|
||||
for (int i = 0; i < model.getParameterCount(); i++) {
|
||||
Parameter parameter = model.getParameter(i);
|
||||
out.write("const double " + checkReservedKeywordPrism(parameter.getId()) + " = " + parameter.getValue()
|
||||
+ "; // " + parameter.getName() + "\n"); // if not null name
|
||||
|
||||
}
|
||||
|
||||
out.write("\n");
|
||||
|
||||
// Identify model species
|
||||
for (int i = 0; i < model.getSpeciesCount(); i++) {
|
||||
|
||||
// Write out syntax
|
||||
// For function checkReservedKeywordPrism see below
|
||||
Species species = model.getSpecies(i);
|
||||
out.write("// Species " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
|
||||
out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("\n");
|
||||
out.write(" " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
|
||||
+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
|
||||
+ ";\n");
|
||||
out.write(" // " + checkReservedKeywordPrism(species.getId()) + " : " + "int init "
|
||||
+ (int) (species.getInitialAmount()) + ";\n");
|
||||
out.write("\n");
|
||||
|
||||
// Iterate over reactions
|
||||
for (int j = 0; j < model.getReactionCount(); j++) {
|
||||
Reaction reaction = model.getReaction(j);
|
||||
|
||||
// Identify reactants and products
|
||||
SpeciesReference reactant = reaction.getReactantForSpecies(species.getId());
|
||||
SpeciesReference product = reaction.getProductForSpecies(species.getId());
|
||||
|
||||
if (reactant != null) {
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReservedKeywordPrism(species.getId()) + " > "
|
||||
+ (int) (reactant.getStoichiometry() - 1) + " -> ("
|
||||
+ checkReservedKeywordPrism(species.getId()) + "\'="
|
||||
+ checkReservedKeywordPrism(species.getId()) + "-" + (int) reactant.getStoichiometry()
|
||||
+ ");\n");
|
||||
} else if (product != null) {
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + "\n");
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReservedKeywordPrism(species.getId()) + " <= " + checkReservedKeywordPrism(species.getId()) + "_MAX-"
|
||||
+ (int) product.getStoichiometry() + " -> ("
|
||||
+ checkReservedKeywordPrism(species.getId()) + "\'="
|
||||
+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
|
||||
+ ");\n");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
out.write("\n");
|
||||
out.write("endmodule\n");
|
||||
out.write("\n");
|
||||
}
|
||||
|
||||
// Identify reaction rate
|
||||
out.write("// Reaction rates\n");
|
||||
out.write("module reaction_rates\n");
|
||||
out.write("\n");
|
||||
|
||||
for (int i = 0; i < model.getReactionCount(); i++) {
|
||||
Reaction reaction = model.getReaction(i);
|
||||
|
||||
// Write state transitions
|
||||
out.write(" // " + checkReservedKeywordPrism(reaction.getId()) + ": -> ");
|
||||
for (int j = 0; j < reaction.getProductCount(); j++) {
|
||||
out.write(checkReservedKeywordPrism(reaction.getProduct(j).getSpecies()) + " ");
|
||||
}
|
||||
out.write("\n");
|
||||
|
||||
// Get the math for the reaction rate
|
||||
out.write(" [" + checkReservedKeywordPrism(reaction.getId()) + "] "
|
||||
+ checkReserveKeywordMath(
|
||||
SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model)
|
||||
+ " > 0 -> " + "("
|
||||
+ checkReserveKeywordMath(
|
||||
SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model)
|
||||
+ ") : true;\n");
|
||||
out.write("\n");
|
||||
|
||||
}
|
||||
out.write("endmodule\n");
|
||||
|
||||
out.write("\n");
|
||||
|
||||
// Identify rewards
|
||||
out.write("// Reward structures (one per species)");
|
||||
out.write("\n");
|
||||
|
||||
for (int i = 0; i < model.getSpeciesCount(); i++) {
|
||||
Species species = model.getSpecies(i);
|
||||
|
||||
out.write("// Reward " + (i + 1) + ": " + checkReservedKeywordPrism(species.getId()) + "\n");
|
||||
out.write("rewards " + "\"" + checkReservedKeywordPrism(species.getId()) + "\" true : "
|
||||
+ checkReservedKeywordPrism(species.getId()) + "; endrewards\n");
|
||||
|
||||
}
|
||||
|
||||
out.close();
|
||||
|
||||
|
||||
/*
|
||||
* Writes PRISM property Input: (String) filename, (Model) model
|
||||
* Output: void
|
||||
*
|
||||
* Function checks the constraints of a SBML model and translates it
|
||||
* into the PRISM syntax. The properties are then written into a
|
||||
* .props file.
|
||||
*/
|
||||
private static void writePRISMProperty(String filename, Model model) throws IOException
|
||||
{
|
||||
// Write Properties File
|
||||
File property = new File(filename.replace(".xml", ".props"));
|
||||
FileWriter property_out = new FileWriter(property);
|
||||
|
|
@ -415,7 +265,6 @@ public class SBML2PRISM {
|
|||
}
|
||||
|
||||
property_out.close();
|
||||
|
||||
}
|
||||
|
||||
/*
|
||||
|
|
@ -500,11 +349,3 @@ public class SBML2PRISM {
|
|||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
BioModel bioModel = BioModel.createBioModel(properties.getDirectory(), this);
|
||||
bioModel.load(filename);
|
||||
if (bioModel.flattenModel(true) != null) {}
|
||||
bioModel.getSBMLDocument()
|
||||
*/
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue