Examples with SpeciesContext cbit.vcell.model.SpeciesContext used on opensource projects

Example 11 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class AnnotationMapping method annotation2BioPaxObject.

public String annotation2BioPaxObject(BioModel bioModel, Identifiable identifiable) {
    String name = "";
    String type = "";
    ArrayList<String> componentInfo = getComponentInfo(bioModel, identifiable);
    if (componentInfo.size() > 0) {
        name = componentInfo.get(0);
        type = componentInfo.get(1);
    }
    String info = type + " : " + name;
    HashMap<String, String> refInfo = getRefInfo(bioModel, identifiable);
    // otherwise, create object and add link
    if (type.equals(VCID.CLASS_SPECIES)) {
        // lookup name by speciesContext
        ArrayList<SpeciesContext> speciesContextArrList = new ArrayList<SpeciesContext>(Arrays.asList(new SpeciesContext[] { bioModel.getModel().getSpeciesContext(name) }));
        if (speciesContextArrList.get(0) == null) {
            speciesContextArrList.clear();
            // lookup name by species
            for (int i = 0; i < bioModel.getModel().getSpeciesContexts().length; i++) {
                if (bioModel.getModel().getSpeciesContexts()[i].getSpecies().getCommonName().equals(name)) {
                    speciesContextArrList.add(bioModel.getModel().getSpeciesContexts()[i]);
                }
            }
        }
        for (int i = 0; i < speciesContextArrList.size(); i++) {
            SpeciesContext speciesContext = speciesContextArrList.get(i);
            if (bioModel.getRelationshipModel().getRelationshipObjects(speciesContext).size() == 0) {
                ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
                ArrayList<String> refName = getNameRef(xRef, name);
                BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_PHYSICALENTITY);
                if (bpObject == null) {
                    bpObject = createPhysicalEntity(xRef, refName, name);
                    bioModel.getPathwayModel().add(bpObject);
                }
                if (!isLinked(bioModel, bpObject, speciesContext)) {
                    // create linkage
                    RelationshipObject newRelationship = new RelationshipObject(speciesContext, bpObject);
                    bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
                    return info;
                }
            }
        }
    } else if (type.equals(VCID.CLASS_BIOMODEL)) {
    // BioPaxObject bpObject = bioModel.getPathwayModel().findFromName(refName.get(0), "Pathway");
    // if(bpObject == null){
    // bpObject = createPathway(componentInfo, refInfo);
    // bioModel.getPathwayModel().add(bpObject);
    // return info;
    // }
    } else if (type.equals(VCID.CLASS_REACTION_STEP)) {
        ReactionStep reactionStep = bioModel.getModel().getReactionStep(name);
        ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
        ArrayList<String> refName = getNameRef(xRef, name);
        if (bioModel.getRelationshipModel().getRelationshipObjects(reactionStep).size() == 0) {
            BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_INTERACTION);
            if (bpObject == null) {
                bpObject = createInteraction(reactionStep, xRef, refName);
                bioModel.getPathwayModel().add(bpObject);
            }
            if (!isLinked(bioModel, bpObject, reactionStep)) {
                // create linkage
                RelationshipObject newRelationship = new RelationshipObject(reactionStep, bpObject);
                bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
                return info;
            }
        }
    }
    return null;
}

Example 12 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class RbmNetworkGenerator method generateModel.

public static void generateModel(BioModel bioModel, String netfile) throws Exception {
    Model model = bioModel.getModel();
    Map<String, SpeciesContext> speciesMap = new HashMap<String, SpeciesContext>();
    Map<String, ReactionStep> reactionMap = new HashMap<String, ReactionStep>();
    List<ReactionLine> reactionLineList = new ArrayList<ReactionLine>();
    BufferedReader br = new BufferedReader(new StringReader(netfile));
    int reversibleCount = 0;
    int reactionCount = 0;
    while (true) {
        String line = br.readLine();
        if (line == null) {
            break;
        }
        line = line.trim();
        if (line.equals(BEGIN_PARAMETERS)) {
            while (true) {
                String line2 = br.readLine();
                line2 = line2.trim();
                if (line2.length() == 0) {
                    continue;
                }
                if (line2.equals(END_PARAMETERS)) {
                    break;
                }
                StringTokenizer st = new StringTokenizer(line2);
                String token1 = st.nextToken();
                String token2 = st.nextToken();
                String token3 = st.nextToken();
                ModelParameter mp = model.new ModelParameter(token2, new Expression(token3), Model.ROLE_UserDefined, bioModel.getModel().getUnitSystem().getInstance_TBD());
                model.addModelParameter(mp);
            }
        } else if (line.equals(BEGIN_SPECIES)) {
            while (true) {
                String line2 = br.readLine();
                line2 = line2.trim();
                if (line2.length() == 0) {
                    continue;
                }
                if (line2.equals(END_SPECIES)) {
                    break;
                }
                StringTokenizer st = new StringTokenizer(line2);
                // no
                String token1 = st.nextToken();
                // pattern
                String token2 = st.nextToken();
                // initial condition
                String token3 = st.nextToken();
                String newname = token2.replaceAll("\\.", "_");
                newname = newname.replaceAll("[\\(,][a-zA-Z]\\w*", "");
                newname = newname.replaceAll("~|!\\d*", "");
                newname = newname.replaceAll("\\(\\)", "");
                newname = newname.replaceAll("\\)", "");
                SpeciesContext sc = model.createSpeciesContext(model.getStructure(0));
                sc.setName(newname);
                bioModel.getVCMetaData().setFreeTextAnnotation(sc, token2);
                bioModel.getVCMetaData().setFreeTextAnnotation(sc.getSpecies(), token2);
                speciesMap.put(token1, sc);
            }
        } else if (line.equals(BEGIN_REACTIONS)) {
            while (true) {
                String line2 = br.readLine();
                line2 = line2.trim();
                if (line2.length() == 0) {
                    continue;
                }
                if (line2.equals(END_REACTIONS)) {
                    break;
                }
                ++reactionCount;
                StringTokenizer st = new StringTokenizer(line2);
                String token1 = st.nextToken();
                // reactants
                String token2 = st.nextToken();
                // products
                String token3 = st.nextToken();
                // rate
                String token4 = st.nextToken();
                String token5 = st.nextToken();
                boolean bFoundReversible = false;
                Expression rate = new Expression(token4);
                for (ReactionLine rl : reactionLineList) {
                    if (token2.equals(rl.products) && token3.equals(rl.reactants) && token5.equals(rl.ruleLabel + "r")) {
                        ReactionStep rs = reactionMap.get(rl.no);
                        ((MassActionKinetics) rs.getKinetics()).getReverseRateParameter().setExpression(rate);
                        reactionLineList.remove(rl);
                        bFoundReversible = true;
                        break;
                    }
                }
                if (bFoundReversible) {
                    ++reversibleCount;
                    continue;
                }
                ReactionLine rl = new ReactionLine(token1, token2, token3, token5);
                reactionLineList.add(rl);
                SimpleReaction reaction = model.createSimpleReaction(model.getStructure(0));
                reactionMap.put(token1, reaction);
                reaction.setModel(model);
                bioModel.getVCMetaData().setFreeTextAnnotation(reaction, line2);
                MassActionKinetics kinetics = new MassActionKinetics(reaction);
                reaction.setKinetics(kinetics);
                st = new StringTokenizer(token2, ",");
                while (st.hasMoreTokens()) {
                    String t = st.nextToken();
                    SpeciesContext sc = speciesMap.get(t);
                    if (sc != null) {
                        boolean bExists = false;
                        for (ReactionParticipant rp : reaction.getReactionParticipants()) {
                            if (rp instanceof Reactant && rp.getSpeciesContext() == sc) {
                                rp.setStoichiometry(rp.getStoichiometry() + 1);
                                bExists = true;
                                break;
                            }
                        }
                        if (!bExists) {
                            reaction.addReactant(sc, 1);
                        }
                    }
                }
                st = new StringTokenizer(token3, ",");
                while (st.hasMoreTokens()) {
                    String t = st.nextToken();
                    SpeciesContext sc = speciesMap.get(t);
                    if (sc != null) {
                        boolean bExists = false;
                        for (ReactionParticipant rp : reaction.getReactionParticipants()) {
                            if (rp instanceof Product && rp.getSpeciesContext() == sc) {
                                rp.setStoichiometry(rp.getStoichiometry() + 1);
                                bExists = true;
                                break;
                            }
                        }
                        if (!bExists) {
                            reaction.addProduct(sc, 1);
                        }
                    }
                }
                kinetics.getForwardRateParameter().setExpression(rate);
            }
        }
    }
    System.out.println(model.getNumSpecies() + " species added");
    System.out.println(model.getNumReactions() + " reactions added");
    System.out.println(reversibleCount + " reversible reactions found");
    if (reactionCount != model.getNumReactions() + reversibleCount) {
        throw new RuntimeException("Reactions are not imported correctly!");
    }
}

Example 13 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class RbmNetworkGenerator method writeSpeciesSortedAlphabetically.

public static void writeSpeciesSortedAlphabetically(PrintWriter writer, Model model, SimulationContext simulationContext, CompartmentMode compartmentMode) {
    writer.println(BEGIN_SPECIES);
    SpeciesContext[] speciesContexts = model.getSpeciesContexts();
    int i = 1;
    for (SpeciesContext sc : speciesContexts) {
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        writer.println(i + " " + RbmUtils.toBnglStringSortedAlphabetically(simulationContext, sc, compartmentMode));
        i++;
    }
    writer.println(END_SPECIES);
    writer.println();
}

Example 14 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class RbmNetworkGenerator method writeSpecies.

public static void writeSpecies(PrintWriter writer, Model model, SimulationContext simulationContext, CompartmentMode compartmentMode) {
    writer.println(BEGIN_SPECIES);
    SpeciesContext[] speciesContexts = model.getSpeciesContexts();
    int i = 1;
    for (SpeciesContext sc : speciesContexts) {
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        // writer.println("@" + sc.getStructure().getName() + ":" + RbmUtils.toBnglString(simulationContext, sc, compartmentMode));
        writer.println(i + " " + RbmUtils.toBnglString(simulationContext, sc, compartmentMode));
        i++;
    }
    writer.println(END_SPECIES);
    writer.println();
}

Example 15 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class RbmUtils method findStructure.

// not used; instead of this we should recover the structure of the rule that produced this reaction
@Deprecated
public static Structure findStructure(Model model, HashMap<Integer, String> speciesMap, BNGReaction forwardBNGReaction) {
    Structure ours = null;
    for (int j = 0; j < forwardBNGReaction.getReactants().length; j++) {
        BNGSpecies s = forwardBNGReaction.getReactants()[j];
        String scName = speciesMap.get(s.getNetworkFileIndex());
        SpeciesContext sc = model.getSpeciesContext(scName);
        Structure theirs = sc.getStructure();
        if (ours == null || ours.getDimension() > theirs.getDimension()) {
            ours = theirs;
        }
    }
    for (int j = 0; j < forwardBNGReaction.getProducts().length; j++) {
        BNGSpecies s = forwardBNGReaction.getProducts()[j];
        String scName = speciesMap.get(s.getNetworkFileIndex());
        SpeciesContext sc = model.getSpeciesContext(scName);
        Structure theirs = sc.getStructure();
        if (ours == null || ours.getDimension() > theirs.getDimension()) {
            ours = theirs;
        }
    }
    if (ours == null) {
        ours = model.getStructure(0);
    }
    return ours;
}