AtomEnvironment AtomEnvironmentFromXmlElement(XElement environmentEl, Dictionary <string, AtomState> atomStateDict)
{
AtomEnvironment atomEnvironment = new AtomEnvironment();
atomEnvironment.name = environmentEl.Attribute("name").Value;
atomEnvironment.amber = environmentEl.Element("amber").Value;
atomEnvironment.radius = float.Parse(environmentEl.Element("radius").Value);
float r = float.Parse(environmentEl.Element("red").Value);
float g = float.Parse(environmentEl.Element("green").Value);
float b = float.Parse(environmentEl.Element("blue").Value);
atomEnvironment.color = new Color(r, g, b);
string stateName = environmentEl.Element("state").Value;
if (!atomStateDict.ContainsKey(stateName))
{
string[] keyArr = new string[atomStateDict.Keys.Count];
atomStateDict.Keys.CopyTo(keyArr, 0);
Debug.LogErrorFormat(
"State {0} not available for Atom Environment {1}. Available states for element {2}: {3}",
stateName,
atomEnvironment.name,
environmentEl.Parent.Attribute("element").Value,
string.Join(", ", keyArr)
);
}
else
{
atomEnvironment.atomState = atomStateDict [stateName];
}
foreach (XElement conditionEl in environmentEl.Elements("condition"))
{
atomEnvironment.environmentConditions.Add(EnvironmentConditionFromXmlElement(conditionEl, atomStateDict));
}
return(atomEnvironment);
}
public void GetEnvironmentFromXML()
{
elementEnvironments = new Dictionary <string, ElementEnvironment> ();
XDocument envX = FileIO.ReadXML("Assets/Resources/Data/Elements.xml");
XElement atomsX = envX.Element("elements");
foreach (XElement atomEl in atomsX.Elements("atom"))
{
ElementEnvironment elementEnvironment = new ElementEnvironment();
elementEnvironment.element = atomEl.Attribute("element").Value;
elementEnvironment.radius = float.Parse(atomEl.Element("radius").Value);
elementEnvironment.maxValency = double.Parse(atomEl.Element("maxValency").Value);
elementEnvironment.mass = float.Parse(atomEl.Element("mass").Value);
float r = float.Parse(atomEl.Element("red").Value);
float g = float.Parse(atomEl.Element("green").Value);
float b = float.Parse(atomEl.Element("blue").Value);
elementEnvironment.color = new Color(r, g, b);
foreach (XElement stateEl in atomEl.Elements("state"))
{
elementEnvironment.atomStateDict[stateEl.Attribute("name").Value] = AtomStateFromXmlElement(stateEl);
}
foreach (XElement environmentEl in atomEl.Elements("environment"))
{
AtomEnvironment atomEnvironment = AtomEnvironmentFromXmlElement(environmentEl, elementEnvironment.atomStateDict);
elementEnvironment.environmentDict[atomEnvironment.name] = atomEnvironment;
}
elementEnvironments [elementEnvironment.element] = elementEnvironment;
}
}
//Environment
public IEnumerator CalculateEnvironment(bool overwrite = true, int maxIterations = 4)
{
_busy++;
int selectionNum;
int atomNum;
int environmentCalculatedCount = 0;
Atom atom;
selection = SelectIf();
if (!overwrite)
{
for (atomNum = 0; atomNum < size; atomNum++)
{
if (atoms[atomNum].amberName != "")
{
selection.Remove(atomNum);
}
}
}
yield return(new WaitForSeconds(0.1f));
for (int iteration = 0; iteration < maxIterations; iteration++)
{
if (environmentCalculatedCount == size)
{
break;
}
for (selectionNum = selection.Count - 1; selectionNum >= 0; selectionNum--)
{
atomNum = selection[selectionNum];
atom = atoms[atomNum];
string element = atom.element;
if (!amberEnvironment.elementEnvironments.ContainsKey(element))
{
Debug.LogErrorFormat("Element {0} not included in data file", element);
selection.RemoveAt(atomNum);
continue;
}
ElementEnvironment elementEnvironment = amberEnvironment.elementEnvironments [element];
atom.mass = elementEnvironment.mass;
bool conditionMet = false;
foreach (string key in elementEnvironment.environmentDict.Keys)
{
AtomEnvironment atomEnvironment = elementEnvironment.environmentDict [key];
foreach (EnvironmentCondition environmentCondition in atomEnvironment.environmentConditions)
{
//Meets condition
if (environmentCondition.EvaluateConditions(atoms, atomNum) == 0)
{
atom.amberName = atomEnvironment.amber;
atom.atomState = atomEnvironment.atomState;
atom.vdwRadius = atomEnvironment.radius;
atom.color = atomEnvironment.color;
selection.RemoveAt(atomNum);
conditionMet = true;
break;
}
}
if (conditionMet)
{
break;
}
}
}
yield return(new WaitForSeconds(0.1f));
}
_busy--;
}
//Environment
public IEnumerator CalculateEnvironment(bool overwrite = true, int maxIterations = 4)
{
_busy++;
int atomNum;
int environmentCalculatedCount = 0;
for (atomNum = 0; atomNum < size; atomNum++)
{
selection [atomNum] = 1.0;
}
if (!overwrite)
{
for (atomNum = 0; atomNum < size; atomNum++)
{
if (atoms[atomNum].amberName != "")
{
selection [atomNum] = 0.0;
}
}
}
yield return(new WaitForSeconds(0.1f));
for (int iteration = 0; iteration < maxIterations; iteration++)
{
if (environmentCalculatedCount == size)
{
break;
}
for (atomNum = 0; atomNum < size; atomNum++)
{
if (selection [atomNum] == 0.0)
{
continue;
}
string element = atoms [atomNum].element;
if (!amberEnvironment.elementEnvironments.ContainsKey(element))
{
Debug.LogErrorFormat("Element {0} not included in data file", element);
selection [atomNum] = 0.0;
continue;
}
ElementEnvironment elementEnvironment = amberEnvironment.elementEnvironments [element];
foreach (string key in elementEnvironment.environmentDict.Keys)
{
AtomEnvironment atomEnvironment = elementEnvironment.environmentDict [key];
foreach (EnvironmentCondition environmentCondition in atomEnvironment.environmentConditions)
{
//Meets condition
if (environmentCondition.EvaluateConditions(atoms, atomNum) == 0)
{
atoms [atomNum].amberName = atomEnvironment.amber;
atoms [atomNum].atomState = atomEnvironment.atomState;
atoms [atomNum].vdwRadius = atomEnvironment.radius;
atoms [atomNum].color = atomEnvironment.color;
selection [atomNum] = 0.0;
goto CONDITIONMET;
}
}
}
CONDITIONMET :;
}
yield return(new WaitForSeconds(0.1f));
}
_busy--;
}
