/// <summary>
/// Loads the CML data into the in-memory model
/// </summary>
/// <param name="data">Object variable containing well-formed and compliant CML</param>
/// <returns></returns>
public Model Import(object data)
{
Model newModel = new Model();
if (data != null)
{
XDocument modelDoc = XDocument.Parse((string)data);
var root = modelDoc.Root;
// Only import if not null
var customXmlPartGuid = CML.GetCustomXmlPartGuid(root);
if (customXmlPartGuid != null && !string.IsNullOrEmpty(customXmlPartGuid.Value))
{
newModel.CustomXmlPartGuid = customXmlPartGuid.Value;
}
var moleculeElements = CML.GetMolecules(root);
foreach (XElement meElement in moleculeElements)
{
newModel.Molecules.Add(CreateMolecule(meElement));
}
// Can't use RebuildMolecules() as it trashes the formulae and labels
//newModel.RebuildMolecules();
newModel.RefreshMolecules();
foreach (Molecule molecule in newModel.Molecules)
{
molecule.RebuildRings();
// Ensure ConciseFormula has been calculated
if (string.IsNullOrEmpty(molecule.ConciseFormula))
{
molecule.ConciseFormula = molecule.CalculatedFormula();
}
}
newModel.Relabel(true);
}
return(newModel);
}
/// <summary>
/// Creates a bond from the CML
/// </summary>
/// <param name="cmlElement"></param>
/// <returns></returns>
public Bond CreateBond(XElement cmlElement)
{
Bond newBond = new Bond();
BondDirection?dir = null;
var dirAttr = cmlElement.Attribute(CML.c4w + "placement");
if (dirAttr != null)
{
BondDirection temp;
if (Enum.TryParse(dirAttr.Value, out temp))
{
dir = temp;
}
}
newBond.Id = cmlElement.Attribute("id")?.Value;
newBond.Order = cmlElement.Attribute("order")?.Value;
if (dir != null)
{
newBond.Placement = dir.Value;
}
var stereoElems = CML.GetStereo(cmlElement);
if (stereoElems.Any())
{
var stereo = stereoElems[0].Value;
switch (stereo)
{
case "N":
newBond.Stereo = BondStereo.None;
break;
case "W":
newBond.Stereo = BondStereo.Wedge;
break;
case "H":
newBond.Stereo = BondStereo.Hatch;
break;
case "S":
newBond.Stereo = BondStereo.Indeterminate;
break;
case "C":
newBond.Stereo = BondStereo.Cis;
break;
case "T":
newBond.Stereo = BondStereo.Trans;
break;
default:
newBond.Stereo = BondStereo.None;
break;
}
}
return(newBond);
}
/// <summary>
/// Creates a molecule from a CML representation
/// </summary>
/// <param name="cmlElement">CML containing the molecule representation</param>
/// <returns>Molecule object</returns>
private Molecule CreateMolecule(XElement cmlElement)
{
var m = new Molecule();
m.Id = cmlElement.Attribute("id")?.Value;
var childMolecules = CML.GetMolecules(cmlElement);
var atomElements = CML.GetAtoms(cmlElement);
var bondElements = CML.GetBonds(cmlElement);
var nameElements = GetNames(cmlElement);
var formulaElements = GetFormulas(cmlElement);
Dictionary <string, Atom> newAtoms = new Dictionary <string, Atom>();
foreach (XElement childElement in childMolecules)
{
var newMol = CreateMolecule(childElement);
m.Molecules.Add(newMol);
}
foreach (XElement atomElement in atomElements)
{
var newAtom = CreateAtom(atomElement);
newAtoms[newAtom.Id] = newAtom; //store the reference to help us build bonds
m.Atoms.Add(newAtom);
}
foreach (XElement bondElement in bondElements)
{
var newBond = CreateBond(bondElement);
string[] atomRefs = bondElement.Attribute("atomRefs2")?.Value.Split(' ');
if (atomRefs?.Length == 2)
{
newBond.StartAtom = newAtoms[atomRefs[0]];
newBond.EndAtom = newAtoms[atomRefs[1]];
m.Bonds.Add(newBond);
}
}
foreach (XElement nameElement in nameElements)
{
var newName = XmlToName(nameElement);
m.ChemicalNames.Add(newName);
}
foreach (XElement formulaElement in formulaElements)
{
// Only import Concise Once
if (string.IsNullOrEmpty(m.ConciseFormula))
{
m.ConciseFormula = XmlToConsiseFormula(formulaElement);
}
var formula = XmlToFormula(formulaElement);
if (formula.IsValid)
{
m.Formulas.Add(formula);
}
}
return(m);
}
/// <summary>
/// Creates a molecule from a CML representation
/// </summary>
/// <param name="cmlElement">CML containing the molecule representation</param>
/// <returns>Molecule object</returns>
private Molecule CreateMolecule(XElement cmlElement)
{
var m = new Molecule();
m.Id = cmlElement.Attribute("id")?.Value;
var childMolecules = CML.GetMolecules(cmlElement);
var atomElements = CML.GetAtoms(cmlElement);
var bondElements = CML.GetBonds(cmlElement);
var nameElements = GetNames(cmlElement);
var formulaElements = GetFormulas(cmlElement);
Dictionary <string, Atom> newAtoms = new Dictionary <string, Atom>();
foreach (XElement childElement in childMolecules)
{
var newMol = CreateMolecule(childElement);
m.Molecules.Add(newMol);
}
foreach (XElement atomElement in atomElements)
{
List <string> messages = new List <string>();
var newAtom = CreateAtom(atomElement, out messages);
if (messages.Count > 0)
{
m.Errors.AddRange(messages);
}
if (newAtom != null)
{
newAtoms[newAtom.Id] = newAtom; //store the reference to help us build bonds
m.Atoms.Add(newAtom);
}
}
foreach (XElement bondElement in bondElements)
{
string message = "";
var newBond = CreateBond(bondElement, out message);
if (!string.IsNullOrEmpty(message))
{
m.Errors.Add(message);
}
string[] atomRefs = bondElement.Attribute("atomRefs2")?.Value.Split(' ');
if (atomRefs?.Length == 2)
{
Atom startAtom = null;
if (newAtoms.ContainsKey(atomRefs[0]))
{
startAtom = newAtoms[atomRefs[0]];
}
else
{
m.Errors.Add($"Can't find atom '{atomRefs[0]}' of {bondElement}");
}
Atom endAtom = null;
if (newAtoms.ContainsKey(atomRefs[1]))
{
endAtom = newAtoms[atomRefs[1]];
}
else
{
m.Errors.Add($"Can't find atom '{atomRefs[1]}' of {bondElement}");
}
if (startAtom != null && endAtom != null)
{
newBond.StartAtom = startAtom;
newBond.EndAtom = endAtom;
m.Bonds.Add(newBond);
}
}
}
foreach (XElement nameElement in nameElements)
{
var newName = XmlToName(nameElement);
m.ChemicalNames.Add(newName);
}
foreach (XElement formulaElement in formulaElements)
{
// Only import Concise Once
if (string.IsNullOrEmpty(m.ConciseFormula))
{
m.ConciseFormula = XmlToConsiseFormula(formulaElement);
}
var formula = XmlToFormula(formulaElement);
if (formula.IsValid)
{
m.Formulas.Add(formula);
}
}
return(m);
}
