public MoleculeInitData(ComplexPattern _complexPattern, Dictionary <string, List <RelativeTransform> > _moleculeTransforms,
BindReaction[] _relevantBindReactions,
CollisionFreeReaction[] _relevantCollisionFreeReactions)
{
complexPattern = _complexPattern;
moleculeTransforms = _moleculeTransforms;
relevantBindReactions = _relevantBindReactions;
relevantCollisionFreeReactions = _relevantCollisionFreeReactions;
}
public bool ComplexIsReactant(ComplexPattern complexPattern)
{
foreach (ReactionCenter reactionCenter in definition.reactionCenters)
{
if (reactionCenter.reactantComplex.Matches(complexPattern))
{
return(true);
}
}
return(false);
}
protected CollisionFreeReaction[] GetRelevantCollisionFreeReactions(ComplexPattern complexPattern)
{
List <CollisionFreeReaction> reactionsList = new List <CollisionFreeReaction>();
foreach (CollisionFreeReaction reaction in collisionFreeReactions)
{
if (reaction.ComplexIsReactant(complexPattern))
{
reactionsList.Add(reaction);
}
}
return(reactionsList.ToArray());
}
protected BindReaction[] GetRelevantBindReactions(ComplexPattern complexPattern)
{
List <BindReaction> reactionsList = new List <BindReaction>();
foreach (BindReaction reaction in bindReactions)
{
if (reaction.ComplexIsReactant(complexPattern))
{
reactionsList.Add(reaction);
}
}
return(reactionsList.ToArray());
}
public ComplexConcentration(ComplexPattern _complexPattern, float _concentration)
{
complexPattern = _complexPattern;
complexPattern.Init();
concentration = _concentration;
}
protected virtual Dictionary <string, List <RelativeTransform> > CalculateMoleculeTransforms(ComplexPattern complexPattern)
{
Dictionary <string, List <RelativeTransform> > transforms = new Dictionary <string, List <RelativeTransform> >();
Vector3 averagePosition = Vector3.zero;
//temp transforms for calculation
Transform molecule1 = new GameObject("molecule1").transform;
Transform molecule2 = new GameObject("molecule2").transform;
Transform component1 = new GameObject("component1").transform;
Transform component2 = new GameObject("component2").transform;
component1.SetParent(molecule1);
component2.SetParent(molecule2);
List <ComponentPattern> foundComponents = new List <ComponentPattern>();
ComponentPattern componentPattern1, componentPattern2;
ComponentDef componentDef;
int n = 0;
foreach (string moleculeName1 in complexPattern.moleculePatterns.Keys)
{
if (!transforms.ContainsKey(moleculeName1))
{
transforms.Add(moleculeName1, new List <RelativeTransform>());
}
if (transforms.Keys.Count == 1)
{
transforms[moleculeName1].Add(new RelativeTransform(Vector3.zero, Vector3.zero));
n++;
}
for (int m1 = 0; m1 < complexPattern.moleculePatterns[moleculeName1].Count; m1++)
{
foreach (string componentName1 in complexPattern.moleculePatterns[moleculeName1][m1].componentPatterns.Keys)
{
for (int c1 = 0; c1 < complexPattern.moleculePatterns[moleculeName1][m1].componentPatterns[componentName1].Count; c1++)
{
componentPattern1 = complexPattern.moleculePatterns[moleculeName1][m1].componentPatterns[componentName1][c1];
if (foundComponents.Contains(componentPattern1))
{
continue;
}
if (complexPattern.moleculePatterns[moleculeName1][m1].componentPatterns[componentName1][c1].bound)
{
foreach (string moleculeName2 in complexPattern.moleculePatterns.Keys)
{
for (int m2 = 0; m2 < complexPattern.moleculePatterns[moleculeName2].Count; m2++)
{
if (moleculeName2 == moleculeName1 && m2 == m1)
{
continue;
}
foreach (string componentName2 in complexPattern.moleculePatterns[moleculeName2][m2].componentPatterns.Keys)
{
for (int c2 = 0; c2 < complexPattern.moleculePatterns[moleculeName2][m2].componentPatterns[componentName2].Count; c2++)
{
componentPattern2 = complexPattern.moleculePatterns[moleculeName2][m2].componentPatterns[componentName2][c2];
if (componentPattern2.bound && !foundComponents.Contains(componentPattern2) && componentPattern1.bondName == componentPattern2.bondName)
{
foundComponents.Add(componentPattern1);
foundComponents.Add(componentPattern2);
molecule1.position = transforms[moleculeName1][m1].position;
molecule1.rotation = Quaternion.Euler(transforms[moleculeName1][m1].rotation);
componentDef = complexPattern.moleculePatterns[moleculeName1][m1].moleculeDef.componentDefs[componentName1][c1];
componentDef.transformOnMolecule.Apply(molecule1, component1);
molecule2.position = Vector3.zero;
molecule2.rotation = Quaternion.identity;
componentDef = complexPattern.moleculePatterns[moleculeName2][m2].moleculeDef.componentDefs[componentName2][c2];
componentDef.transformOnMolecule.Apply(molecule2, component2);
molecule2.position = component1.TransformPoint(component2.InverseTransformPoint(molecule2.position));
molecule2.rotation = molecule2.rotation * Quaternion.Inverse(component2.rotation) * component1.rotation;
if (!transforms.ContainsKey(moleculeName2))
{
transforms.Add(moleculeName2, new List <RelativeTransform>());
n++;
}
transforms[moleculeName2].Add(new RelativeTransform(molecule2.position, molecule2.rotation.eulerAngles));
averagePosition += transforms[moleculeName2][m2].position;
}
}
}
}
}
}
}
}
}
}
averagePosition /= n;
foreach (string moleculeName in transforms.Keys)
{
foreach (RelativeTransform t in transforms[moleculeName])
{
t.position -= averagePosition;
}
}
Destroy(molecule1.gameObject);
Destroy(molecule2.gameObject);
return(transforms);
}
public bool Matches(ComplexPattern other)
{
//UnityEngine.Profiling.Profiler.BeginSample("Comparisons");
Dictionary <MoleculePattern, int> thisComponentsInState = new Dictionary <MoleculePattern, int>();
Dictionary <MoleculePattern, int> otherComponentsInState = new Dictionary <MoleculePattern, int>();
foreach (string moleculeName in moleculePatterns.Keys)
{
if (!other.moleculePatterns.ContainsKey(moleculeName)) //does this type of molecule exist in the other?
{
//Debug.Log( "molecule " + moleculeName + " doesn't exist in other" );
return(false);
}
foreach (MoleculePattern thisMoleculePattern in moleculePatterns[moleculeName]) //how many of our molecules are in each state?
{
if (!thisComponentsInState.ContainsKey(thisMoleculePattern))
{
thisComponentsInState[thisMoleculePattern] = 1;
}
else
{
thisComponentsInState[thisMoleculePattern]++;
}
}
foreach (MoleculePattern otherMoleculePattern in other.moleculePatterns[moleculeName]) //how many of the other's molecules are in each state?
{
if (!otherComponentsInState.ContainsKey(otherMoleculePattern))
{
otherComponentsInState[otherMoleculePattern] = 1;
}
else
{
otherComponentsInState[otherMoleculePattern]++;
}
}
foreach (MoleculePattern thisMoleculePattern in thisComponentsInState.Keys) //does the other at least have as many molecules in each state as we do?
{
MoleculePattern matchingMoleculePattern = null;
foreach (MoleculePattern otherMoleculePattern in otherComponentsInState.Keys)
{
if (thisMoleculePattern.Matches(otherMoleculePattern))
{
matchingMoleculePattern = otherMoleculePattern;
break;
}
}
if (matchingMoleculePattern == null)
{
//Debug.Log( "there are no " + moleculeName + " molecules that match pattern " + thisMoleculePattern );
return(false);
}
if (otherComponentsInState[matchingMoleculePattern] < thisComponentsInState[thisMoleculePattern])
{
//Debug.Log( "number of " + moleculeName + " molecules that match pattern " + thisMoleculePattern + " is "
//+ otherComponentsInState[matchingMoleculePattern] + " when it should be at least " + thisComponentsInState[thisMoleculePattern] );
return(false);
}
}
thisComponentsInState.Clear();
otherComponentsInState.Clear();
}
//UnityEngine.Profiling.Profiler.EndSample();
return(true);
}
public void SetToProductState(ComplexPattern productComplex, Molecule molecule1, MoleculePattern productMolecule1, Molecule molecule2, MoleculePattern productMolecule2)
{
productComplex.SetStateOfComplex(molecule1, productMolecule1, molecule2, productMolecule2);
ConnectBoundComponents();
}
