Examples with MolecularTypePattern org.vcell.model.rbm.MolecularTypePattern used on opensource projects

Example 66 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class ReactionRule method getReactantComponentBondType.

public BondType getReactantComponentBondType(MolecularComponentPattern mcpProduct) {
    MolecularTypePattern mtpProduct = getProductMoleculeOfComponent(mcpProduct);
    MolecularTypePattern mtpReactant = getMatchingReactantMolecule(mtpProduct);
    if (mtpReactant == null) {
        // possible if this product has no matching explicit or implicit reactant
        return null;
    }
    for (MolecularComponentPattern mcpReactant : mtpReactant.getComponentPatternList()) {
        if (mcpReactant.getMolecularComponent() != mcpProduct.getMolecularComponent()) {
            continue;
        }
        return mcpReactant.getBondType();
    }
    return null;
}

Example 67 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class RuleParticipantSignature method getListOfMolecularTypePatternSignatures.

private static ArrayList<String> getListOfMolecularTypePatternSignatures(SpeciesPattern sp, GroupingCriteria crit) {
    ArrayList<String> mtpSignatures = new ArrayList<String>();
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        if (crit == GroupingCriteria.molecule) {
            mtpSignatures.add(mtp.getMolecularType().getName());
        } else if (crit == GroupingCriteria.rule) {
            mtpSignatures.add(mtp.getMolecularType().getName());
        } else if (crit == GroupingCriteria.full) {
            String signature = RbmUtils.toBnglString(mtp, null, CompartmentMode.hide, -1, true);
            mtpSignatures.add(signature);
        }
    }
    return mtpSignatures;
}

Example 68 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class SpeciesContext method findComponentUsage.

public void findComponentUsage(MolecularType mt, MolecularComponent mc, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    if (!hasSpeciesPattern()) {
        return;
    }
    SpeciesPattern sp = getSpeciesPattern();
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        if (mtp.getMolecularType() == mt) {
            List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
            for (MolecularComponentPattern mcp : componentPatterns) {
                if (mcp.getMolecularComponent() == mc) {
                    // here all components are always in use
                    if (mcp.getBond() != null) {
                        // we only care about the components with a bond
                        String key = sp.getDisplayName();
                        key = getDisplayType() + getDisplayName() + key;
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}

Example 69 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class SpeciesContext method checkBondsSufficiency.

private void checkBondsSufficiency(IssueContext issueContext, List<Issue> issueList, SpeciesPattern sp) {
    if (sp.getMolecularTypePatterns().size() < 2) {
        return;
    }
    int numberOfMolecularTypeCandidates = 0;
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        if (mtp.getComponentPatternList().size() > 0) {
            numberOfMolecularTypeCandidates++;
        }
    }
    if (numberOfMolecularTypeCandidates < 2) {
        // we need at least 2 molecular types with at least 1 component each
        return;
    }
    boolean atLeastOneBad = false;
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        boolean bondSpecifiedExists = false;
        for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
            if (mcp.getBondType() == BondType.Specified) {
                Bond b = mcp.getBond();
                if (b != null) {
                    bondSpecifiedExists = true;
                    break;
                }
            }
        }
        if (!bondSpecifiedExists) {
            atLeastOneBad = true;
        }
    }
    if (atLeastOneBad) {
        String msg = "Each Molecular Pattern of the Species Pattern " + sp.toString() + " needs at least one explicit Bond.\n";
        IssueSource parent = issueContext.getContextObject();
        issueList.add(new Issue(parent, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
    }
}

Example 70 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.

the class SpeciesContext method findStateUsage.

public void findStateUsage(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    if (!hasSpeciesPattern()) {
        return;
    }
    SpeciesPattern sp = getSpeciesPattern();
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        if (mtp.getMolecularType() == mt) {
            List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
            for (MolecularComponentPattern mcp : componentPatterns) {
                if (mcp.getMolecularComponent() == mc) {
                    // here some state is always in use if available
                    ComponentStatePattern csp = mcp.getComponentStatePattern();
                    if (csp == null) {
                        System.out.println("This component " + mc.getName() + " should have had some State specified.");
                        continue;
                    }
                    if ((csp.getComponentStateDefinition() == csd) && (mcp.getBond() != null)) {
                        // we only care if there's a bond
                        String key = sp.getDisplayName();
                        key = getDisplayType() + getDisplayName() + key;
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}