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

Example 16 with MolecularTypePattern

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

the class RbmObservable method resolveStates.

// TODO: this will have to go once we get rid of ComponentStatePattern
// use as a stopgap measure to eliminate a bug where the ComponentStatePattern is null
// instead of being Any (which happens when the MolecularComponent has states defined)
private void resolveStates() {
    for (SpeciesPattern sp : speciesPatternList) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                if (mcp.getComponentStatePattern() == null && mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                    ComponentStatePattern csp = new ComponentStatePattern();
                    mcp.setComponentStatePattern(csp);
                }
            }
        }
    }
}

Example 17 with MolecularTypePattern

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

the class RbmObservable method findStateUsage.

public void findStateUsage(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    for (SpeciesPattern sp : getSpeciesPatternList()) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        // we don't care about these
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        // found mc in use
                        // now let's look at component state definition
                        ComponentStatePattern csp = mcp.getComponentStatePattern();
                        if (csp == null) {
                            continue;
                        }
                        if (csp.getComponentStateDefinition() == csd) {
                            String key = sp.getDisplayName();
                            key = getDisplayType() + getDisplayName() + key;
                            usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                        }
                    }
                }
            }
        }
    }
}

Example 18 with MolecularTypePattern

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

the class RbmObservable method resolveBonds.

private void resolveBonds() {
    for (SpeciesPattern sp : speciesPatternList) {
        List<MolecularTypePattern> molecularTypePatterns = sp.getMolecularTypePatterns();
        for (int i = 0; i < molecularTypePatterns.size(); ++i) {
            molecularTypePatterns.get(i).setIndex(i + 1);
        }
        sp.resolveBonds();
    }
}

Example 19 with MolecularTypePattern

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

the class ReactionRule method removeMatch.

public void removeMatch(String keyToRemove) {
    // no need to specify where the key is, we remove it from everywhere
    if (keyToRemove == null || keyToRemove.equals("*")) {
        // nothing to remove if key is bad or no key
        return;
    }
    int matches = 0;
    for (ReactionRuleParticipant participant : reactantPatterns) {
        List<MolecularTypePattern> molecularTypePatterns = participant.getSpeciesPattern().getMolecularTypePatterns();
        for (MolecularTypePattern mtp : molecularTypePatterns) {
            if (mtp.hasExplicitParticipantMatch() && mtp.getParticipantMatchLabel().equals(keyToRemove)) {
                mtp.setParticipantMatchLabel("*");
                matches++;
            }
        }
    }
    for (ReactionRuleParticipant participant : productPatterns) {
        List<MolecularTypePattern> molecularTypePatterns = participant.getSpeciesPattern().getMolecularTypePatterns();
        for (MolecularTypePattern mtp : molecularTypePatterns) {
            if (mtp.hasExplicitParticipantMatch() && mtp.getParticipantMatchLabel().equals(keyToRemove)) {
                mtp.setParticipantMatchLabel("*");
                matches++;
            }
        }
    }
    if (matches > 1) {
        throw new RuntimeException("Found more than one MolecularTypePatterns to remove matching the key " + keyToRemove);
    }
}

Example 20 with MolecularTypePattern

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

the class ReactionRule method populateMaps.

public List<MolecularTypePattern> populateMaps(MolecularType mt, ReactionRuleParticipantType type) {
    List<MolecularTypePattern> mtpList = new ArrayList<MolecularTypePattern>();
    List<? extends ReactionRuleParticipant> patterns = (type == ReactionRuleParticipantType.Reactant) ? reactantPatterns : productPatterns;
    for (ReactionRuleParticipant participant : patterns) {
        List<MolecularTypePattern> molecularTypePatterns = participant.getSpeciesPattern().getMolecularTypePatterns();
        for (MolecularTypePattern mtp : molecularTypePatterns) {
            if (mtp.getMolecularType() == mt) {
                mtpList.add(mtp);
            }
        }
    }
    return mtpList;
}