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WIP, ssld import: site attributes map, initial conditions
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@danv61
danv61 committed Aug 26, 2024
1 parent f9c8bf9 commit fcb270b
Showing 1 changed file with 95 additions and 7 deletions.
102 changes: 95 additions & 7 deletions vcell-core/src/main/java/org/vcell/model/ssld/SsldUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,18 +2,20 @@

import cbit.vcell.biomodel.BioModel;
import cbit.vcell.geometry.Geometry;
import cbit.vcell.mapping.GeometryContext;
import cbit.vcell.mapping.ReactionRuleSpec;
import cbit.vcell.mapping.SimulationContext;
import cbit.vcell.mapping.SpeciesContextSpec;
import cbit.vcell.mapping.*;
import cbit.vcell.model.*;
import cbit.vcell.parser.Expression;
import org.vcell.model.rbm.*;
import org.vcell.solver.langevin.LangevinLngvWriter;
import org.vcell.util.Coordinate;
import org.vcell.util.springsalad.Colors;
import org.vcell.util.springsalad.NamedColor;

import java.awt.*;
import java.util.*;
import java.io.BufferedReader;
import java.io.*;
import java.util.List;
import java.util.prefs.Preferences;

import static org.vcell.model.ssld.TransitionReaction.ANY_STATE;
Expand All @@ -28,6 +30,9 @@ private class Mapping {
final BioModel bioModel;
SimulationContext simContext; // set late (after we construct the physiology)

Map<Site, SiteType> siteToTypeMap = new LinkedHashMap<> ();
Map<SiteType, Site> typeToSiteMap = new LinkedHashMap<> ();

Map<Molecule, MolecularType> moleculeToMolecularTypeMap = new LinkedHashMap<>();
Map<MolecularType, Molecule> molecularTypeToMoleculeMap = new LinkedHashMap<>();
Map<SiteType, MolecularComponent> typeToComponentMap = new LinkedHashMap<>();
Expand Down Expand Up @@ -82,6 +87,23 @@ SimulationContext getSimulationContext() {
return simContext;
}

void put(Site site, SiteType type) {
if(siteToTypeMap.containsKey(site)) {
throw new RuntimeException("siteToTypeMap: Duplicate Key");
}
if(typeToSiteMap.containsKey(type)) {
throw new RuntimeException("typeToSiteMap: Duplicate Key");
}
siteToTypeMap.put(site, type);
typeToSiteMap.put(type, site);
}
Site getSite(SiteType type) {
return typeToSiteMap.get(type);
}
SiteType getType(Site site) {
return siteToTypeMap.get(site);
}

void put(Molecule ssldMolecule, MolecularType mt) {
if(moleculeToMolecularTypeMap.containsKey(ssldMolecule)) {
throw new RuntimeException("moleculeToMolecularTypeMap: Duplicate Key");
Expand Down Expand Up @@ -310,11 +332,12 @@ public BioModel fromSsld(SsldModel ssldModel) throws Exception {
// String newApplicationName = bioModel.getFreeSimulationContextName();
SimulationContext springSaLaDSimContext = bioModel.addNewSimulationContext("SpringSaLaD",
SimulationContext.Application.SPRINGSALAD); // make new default SpringSaLaD application
springSaLaDSimContext.setUsingConcentration(true, false);
// we always import count, so we start with default count
// TODO: in specifications, initial conditions must be set to count; also add button to switch between count and concentration
springSaLaDSimContext.setUsingConcentration(false, false);
m.set(springSaLaDSimContext);
importApplicationFromSsld(m);


return bioModel;
}

Expand All @@ -331,9 +354,72 @@ public void importApplicationFromSsld(Mapping m) throws Exception {
ReactionRuleSpec[] rrSpecs = simContext.getReactionContext().getReactionRuleSpecs();
SpeciesContextSpec[] scSpecs = simContext.getReactionContext().getSpeciesContextSpecs();

for(SpeciesContextSpec scs : scSpecs) {
importSpeciesContextSpecForSsld(scs, m);

}



}

private void importSpeciesContextSpecForSsld(SpeciesContextSpec scs, Mapping m) throws Exception {

Map<MolecularComponentPattern, SiteAttributesSpec> siteAttributesMap = new LinkedHashMap<>();
Set<MolecularInternalLinkSpec> internalLinkSet = new LinkedHashSet<>();

SpeciesPattern sp = scs.getSpeciesContext().getSpeciesPattern();
MolecularTypePattern mtp = sp.getMolecularTypePatterns().get(0);
MolecularType mt = mtp.getMolecularType();
List<MolecularComponentPattern> mcpList = mtp.getComponentPatternList();

Molecule ssldMolecule = m.get(mt);
List<Site> ssldSiteArray = ssldMolecule.getSiteArray();
List<SiteType> ssldTypeArray = ssldMolecule.getTypeArray();

for(MolecularComponentPattern mcp : mcpList) {
MolecularComponent mc = mcp.getMolecularComponent();
SiteType ssldType = m.get(mc);
Site ssldSite = m.getSite(ssldType);

String ssldStructure = ssldSite.getLocation(); // structure of site, may differ from molecule structure
Structure structure = m.getBioModel().getModel().getStructure(ssldStructure);
String colorName = ssldType.getColorName();
NamedColor namedColor = Colors.getColorByName(colorName);
Coordinate coordinate = new Coordinate(ssldSite.x, ssldSite.y, ssldSite.z);

SiteAttributesSpec sas = new SiteAttributesSpec(scs, mcp, structure);
sas.setCoordinate(coordinate);
sas.setColor(namedColor);
sas.setRadius(ssldType.getRadius());
sas.setDiffusionRate(ssldType.getD());

siteAttributesMap.put(mcp, sas);
}
for(Link ssldLink : ssldMolecule.getLinkArray()) {
// ssldLink -> ssldSite1 -> ssldType1 -> mc1 -> mcp1 -> mils
// -> ssldSite2 -> ssldType2 -> mc2 -> mcp2 ->
Site ssldSite1 = ssldLink.getSite1();
Site ssldSite2 = ssldLink.getSite2();
SiteType ssldType1 = m.getType(ssldSite1);
SiteType ssldType2 = m.getType(ssldSite2);
MolecularComponent mc1 = m.get(ssldType1);
MolecularComponent mc2 = m.get(ssldType2);
MolecularComponentPattern mcp1 = mtp.getMolecularComponentPattern(mc1);
MolecularComponentPattern mcp2 = mtp.getMolecularComponentPattern(mc2);

MolecularInternalLinkSpec mils = new MolecularInternalLinkSpec(scs, mcp1, mcp2);
internalLinkSet.add(mils);
}
scs.setSiteAttributesMap(siteAttributesMap);
scs.setInternalLinkSet(internalLinkSet);

SpeciesContextSpec.SpeciesContextSpecParameter countParam = scs.getInitialCountParameter();
InitialCondition ssldIc = ssldMolecule.getInitialCondition();
Expression countExp = new Expression(ssldIc.getNumber());
countParam.setExpression(countExp);
}

public Mapping importPhysiologyFromSsld(SsldModel ssldModel) throws Exception {

ModelUnitSystem mus = ModelUnitSystem.createDefaultVCModelUnitSystem();
Expand Down Expand Up @@ -367,8 +453,10 @@ public Mapping importPhysiologyFromSsld(SsldModel ssldModel) throws Exception {
MolecularType mt = new MolecularType(ssldMolecule.getName(), model);
for(Site ssldSite : ssldMolecule.getSiteArray()) {
SiteType ssldType = ssldSite.getType();
MolecularComponent mc = new MolecularComponent(ssldType.getName());
// in vcell we only accept a 1 to 1 relationship between type and site
m.put(ssldSite, ssldType);

MolecularComponent mc = new MolecularComponent(ssldType.getName());
// site index starts at 1 in vcell, while it starts at 0 in ssld
// see also LangevinLngvWriter.writeSpeciesInfo()
// see also MolecularInternalLinkSpec.writeLink()
Expand Down

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