public bool ParseLine(MoleculeDefinition molecule, string line)
{
var regexCoordLine = "[ ]+(\\d+)[ ]+(\\d+)[ ]+(\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)";
bool isLookingForActualInput = index > InitialLines.Length - 1;
if (isLookingForActualInput)
{
var match = Regex.Match(line, regexCoordLine);
if (match.Success)
{
var atomicNumber = int.Parse(match.Groups [2].Value.Trim());
var x = float.Parse(match.Groups [4].Value.Trim());
var y = float.Parse(match.Groups [5].Value.Trim());
var z = float.Parse(match.Groups [6].Value.Trim());
molecule.Atoms.Add(new AtomDefinition()
{
Position = new Vector3(x, y, z),
Element = AssetDatabase.FindAssets("t:Element")
.Select(e => AssetDatabase.LoadAssetAtPath <Element>(AssetDatabase.GUIDToAssetPath(e)))
.Where(e => e != null && e.AtomicNumber == atomicNumber).FirstOrDefault()
});
return(true);
}
else
{
index = 0;
return(false);
}
}
else
{
string desiredLine = InitialLines [index];
if (line.Equals(desiredLine))
{
index++;
if (index == InitialLines.Length)
{
molecule.Atoms.Clear();
}
return(true);
}
index = 0;
return(false);
}
}
public override void OnImportAsset(AssetImportContext ctx)
{
var lines = File.ReadAllLines(ctx.assetPath);
int modeCoordinates = 0;
int maxModeCoordinates = 0;
var coordParser = new CoordinateParser();
var modeParser = new ModeParser();
MoleculeDefinition molecule = new MoleculeDefinition();
foreach (var line in lines)
{
coordParser.ParseLine(molecule, line);
modeParser.ParseLine(molecule, line);
if (molecule.VibrationalModes.Count > 0)
{
var regexBond = " ! R\\d+ +R\\((\\d+),(\\d+)\\)";
var match = Regex.Match(line, regexBond);
if (match.Success)
{
var atom1 = int.Parse(match.Groups [1].Value) - 1;
var atom2 = int.Parse(match.Groups [2].Value) - 1;
molecule.Bonds.Add(new BondDefinition()
{
AtomIndex1 = atom1, AtomIndex2 = atom2
});
}
}
}
ctx.AddObjectToAsset("Data", molecule);
ctx.SetMainObject(molecule);
}
/// Creates a molecule from a definition. NOTE: Does not actually create it in game, for this then call CreateMoleculeGraphic
public Molecule CreateMolecule(MoleculeDefinition definition)
{
var molecule = new Molecule(definition);
foreach (var atomDefinition in definition.Atoms)
{
var atom = new Atom(molecule, atomDefinition);
molecule.Atoms.Add(atom);
}
foreach (var modeDefinition in definition.VibrationalModes)
{
var mode = new VibrationalMode(molecule, modeDefinition);
molecule.VibrationalModes.Add(mode);
}
foreach (var bondDefinition in definition.Bonds)
{
var bond = new Bond(molecule, bondDefinition);
molecule.Bonds.Add(bond);
}
return(molecule);
}
public bool ParseLine(MoleculeDefinition molecule, string line)
{
string freqLineRegex = " Frequencies --[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)";
string pointsLineRegex = "[ ]+ \\d+[ ]+ \\d+[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)";
int blockSize = 7 + molecule.Atoms.Count;
//var regexCoordLine = "[ ]+(\\d+)[ ]+(\\d+)[ ]+(\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)[ ]+(-?\\d+.\\d+)";
bool isLookingForActualInput = index > InitialLines.Length - 1;
if (isLookingForActualInput)
{
if (line.Count() == 0)
{
index = 0;
return(false);
}
else
{
if (freqIndex == 2)
{
var match = Regex.Match(line, freqLineRegex);
CurrentModes.Clear();
for (var i = 1; i <= 3; i++)
{
var freq = float.Parse(match.Groups [i].Value);
var mode = new VibrationalModeDefinition();
mode.Wavenumber = freq;
CurrentModes.Add(mode);
}
}
if (freqIndex >= 7)
{
var match = Regex.Match(line, pointsLineRegex);
for (var i = 0; i <= 2; i++)
{
Debug.Log(line);
Debug.Log(match.Success);
var x = float.Parse(match.Groups [1 + i * 3].Value);
var y = float.Parse(match.Groups [2 + i * 3].Value);
var z = float.Parse(match.Groups [3 + i * 3].Value);
CurrentModes [i].Displacements.Add(new Vector3(x, y, z));
}
}
freqIndex++;
if (freqIndex == blockSize)
{
freqIndex = 0;
molecule.VibrationalModes.AddRange(CurrentModes);
CurrentModes.Clear();
}
}
return(true);
}
else
{
string desiredLine = InitialLines [index];
if (line.Equals(desiredLine))
{
index++;
//if (index == InitialLines.Length) {
// molecule.Atoms.Clear ();
//}
return(true);
}
index = 0;
return(false);
}
}
public Molecule(MoleculeDefinition definition)
{
}
