private void NormalizeCoords(Molecule mol, COMPOUND_TYPES type, int id)
{
if (mol == null) return;
//First we get the region we are working in
RectangleF region;
if (type == COMPOUND_TYPES.Reactant) region = reactantRegions[id];
else if (type == COMPOUND_TYPES.Reagent) region = reagentRegions[0]; //we only ever have one reagent region
else region = productRegions[id];
//we get the bounds of the raw copy for initial sizing for the given region
mol.Bounds = GetBoundingBox(mol, region);
PointF center = new PointF(region.X + region.Width / 2, region.Y + region.Height / 2);
//The scale values for x and y are then calculated
//We want to keep the same ratio so we get the ratio, find the max sx can be and then calculte sy from that
float ratio = mol.Bounds.Width/mol.Bounds.Height;
double sx = 40; //region.Width / mol.Bounds.Width-30;
double sy = 30; //ratio / sx;
foreach (Node atom in mol.Atoms.Values)
{
double ox = atom.Position.X;
double oy = atom.Position.Y;
double x = (ox * sx + center.X);
double y = (oy * sy + center.Y);
atom.Position = new Vector3(x, y, 0);
//Finally we go through the bonds and update their nodes, due to some error in copying
foreach (Bond bond in mol.Bonds)
{
if (bond.Node1.ID == atom.ID)
bond.Node1 = atom;
else if (bond.Node2.ID == atom.ID)
bond.Node2 = atom;
}
//and again go through one more time to calculate the paths
foreach (Bond bond in mol.Bonds)
{
bond.CalculateBoundPath();
}
}
//We also need to get the new size of the bounding box and get the bounds for each bond
mol.Bounds = GetBoundingBox(mol, region);
}
private static void WriteBlock(XmlDocument doc, XmlElement pparent, Edit edit, List<int> fileIDs, ObservableCollection<Compound> compounds, COMPOUND_TYPES type)
{
//First we have a counter to keep track of rc1, rc2 etc
int counter = 0;
foreach (Compound comp in compounds)
{
//First we determine what element this will belong to
string parentname = string.Empty;
switch (type)
{
case COMPOUND_TYPES.Reactant:
parentname = "reactant";
break;
case COMPOUND_TYPES.Reagent:
parentname = "reagent";
break;
case COMPOUND_TYPES.Product:
parentname = "product";
break;
}
XmlElement parent = doc.CreateElement(parentname);
//Fileid is generated on the fly
XmlElement fileid = doc.CreateElement("fileid");
comp.FileID = GenerateFileID(fileIDs);
fileid.InnerText = comp.FileID.ToString();
//Local id is also generated on the fly we simply pass our counter and type
XmlElement localid = doc.CreateElement("localid");
localid.InnerText = GenerateLocalID(counter, type);
//The name is a copy of our compoud name
XmlElement name = doc.CreateElement("name");
name.InnerText = comp.Name;
//Copy over ref id
XmlElement refid = doc.CreateElement("refid");
refid.InnerText = comp.RefName;
//Same for formula
XmlElement formula = doc.CreateElement("formula");
formula.InnerText = comp.Formula;
//And same for state
XmlElement state = doc.CreateElement("state");
state.InnerText = comp.State.ToString();
//density is the same, but it has a temperature <--- NOT DONE
XmlElement density = doc.CreateElement("density"); // at temp x
density.InnerText = comp.Density.ToString(); //THIS IS NOT COMPLETE; DENSITY EXISTS AT A GIVEN TEMP
density.SetAttribute("temp", "25");
XmlElement islimiting = doc.CreateElement("islimiting");
islimiting.InnerText = comp.IsLimiting.ToString();
XmlElement isTarget = doc.CreateElement("istarget");
isTarget.InnerText = comp.IsTarget.ToString();
//The mols have a unit so we look into the dictionary to get the value at whatever unit
XmlElement mols = doc.CreateElement("mols"); // unit
mols.InnerText = comp.MolsValue.ToString();
mols.SetAttribute("unit", comp.MolsUnit);
mols.SetAttribute("unit_power", comp.Mols.Power.ToString());
//The mass is also at a unit so just the same, however some compounds are measured
//not in mass but by volume so we check this and output null if thats the case
XmlElement mass = doc.CreateElement("mass"); //unit
if (comp.MassValue > 0)
{
mass.InnerText = comp.MassValue.ToString();
mass.SetAttribute("unit", comp.MassUnit);
mass.SetAttribute("unit_power", comp.Mass.Power.ToString());
}
else
{
mass.InnerText = "null";
mass.SetAttribute("unit", "mol");
mass.SetAttribute("unit_power", "0");
}
//and likewise for the volume, sometimes things are measured by mass and not volume
XmlElement volume = doc.CreateElement("volume"); //unit
if (comp.VolumeValue > 0)
{
volume.InnerText = comp.VolumeValue.ToString();
volume.SetAttribute("unit", "l");
volume.SetAttribute("unit_power", comp.Volume.Power.ToString());
}
else
{
volume.InnerText = "null";
volume.SetAttribute("unit", "l");
volume.SetAttribute("unit_power", "0");
}
XmlElement solvent = doc.CreateElement("solvent");
if (!string.IsNullOrEmpty(comp.SolventName))
{
solvent.InnerText = comp.SolventName;
solvent.SetAttribute("conc", comp.Solution.Concentration.Value.ToString());
solvent.SetAttribute("conc_unit", comp.Solution.Concentration.UnitType);
solvent.SetAttribute("unit_power", comp.Solution.Concentration.Power.ToString());
}
else
{
solvent.InnerText = "null";
solvent.SetAttribute("conc", "null");
solvent.SetAttribute("conc_unit", "mol/l");
solvent.SetAttribute("unit_power", "0");
}
//Now we have to append all of these as children to the parent element given
parent.AppendChild(fileid); parent.AppendChild(localid); parent.AppendChild(name); parent.AppendChild(refid);
parent.AppendChild(formula); parent.AppendChild(state); parent.AppendChild(density); parent.AppendChild(islimiting); parent.AppendChild(isTarget);
parent.AppendChild(mols); parent.AppendChild(mass); parent.AppendChild(volume); parent.AppendChild(solvent);
//NOw that we have added all of the elements we add this parent element to our parents parent, giving us the correct format
pparent.AppendChild(parent);
counter++;
}
}
private static ObservableCollection<Compound> ReadBlock(XmlNodeList compoundList, COMPOUND_TYPES type)
{
ObservableCollection<Compound> returnList = new ObservableCollection<Compound>();
foreach (XmlNode node in compoundList)
{
string localid = string.Empty;
string name = string.Empty;
string refid = string.Empty;
int fileid = 0; //In the files each compound is recognized by a five digit number, so we can attach mol data
int state = 0;
string formula = string.Empty;
float density = 0.0f;
Unit mols = new Unit(0, "mol", (int)UNIT_POWERS.none);
Unit mass = new Unit(0, "g", (int)UNIT_POWERS.none);
Unit volume = new Unit(0, "l", (int)UNIT_POWERS.none);
Solution solvent = new Solution("null", new Unit(0, "mol/l", (int)UNIT_POWERS.none));
bool isLimiting = false;
bool isTarget = false;
foreach (XmlNode inner in node.ChildNodes)
{
switch (inner.Name)
{
case "fileid":
fileid = int.Parse(inner.InnerText); break;
case "localid":
localid = inner.InnerText; break;
case "name":
name = inner.InnerText; break;
case "refid":
refid = inner.InnerText; break;
case "formula":
formula = inner.InnerText; break;
case "state":
string text = inner.InnerText;
if (text == "solid") state = 0;
if (text == "liquid") state = 1;
if (text == "gas") state = 2;
if (text == "solvated") state = 3;
break;
case "islimiting":
isLimiting = bool.Parse(inner.InnerText);
break;
case "istarget":
isTarget = bool.Parse(inner.InnerText);
break;
case "density":
if (inner.InnerText == "null") break;
density = float.Parse(inner.InnerText); break;
case "mols":
if(inner.InnerText == "null") break;
mols = new Unit(double.Parse(inner.InnerText), inner.Attributes["unit"].Value, int.Parse(inner.Attributes["unit_power"].Value));
break;
case "mass":
if (inner.InnerText == "null") break;
mass = new Unit(double.Parse(inner.InnerText), inner.Attributes["unit"].Value, int.Parse(inner.Attributes["unit_power"].Value));
break;
case "volume":
if (inner.InnerText == "null") break;
volume = new Unit(double.Parse(inner.InnerText), inner.Attributes["unit"].Value, int.Parse(inner.Attributes["unit_power"].Value));
break;
case "solvent":
if (inner.InnerText == "null") break;
solvent = new Solution(inner.InnerText, new Unit(float.Parse(inner.Attributes["conc"].Value), inner.Attributes["conc_unit"].Value, int.Parse(inner.Attributes["unit_power"].Value)));
break;
}
}
Compound c = new Compound(name, refid, localid, fileid, (int)type, state, isLimiting, isTarget, formula, density, mols, mass, volume, solvent);
Console.WriteLine(c.ToString());
returnList.Add(c);
}
return returnList;
}
//We need to be able to generate an local id for an edit such as rc1 or p1
private static string GenerateLocalID(int counter, COMPOUND_TYPES type)
{
switch (type)
{
case COMPOUND_TYPES.Reactant:
return "rc" + counter;
case COMPOUND_TYPES.Reagent:
return "rg" + counter;
case COMPOUND_TYPES.Product:
return "p" + counter;
}
return string.Empty;
}
