public IReadOnlyList <IAtomType> ReadAtomTypes()
{
var ret = new List <IAtomType>();
var doc = XElement.Load(input);
foreach (var atomTypeElm in doc.Elements(XName_AtomType))
{
var anAtomType = builder.NewAtomType("H");
anAtomType.AtomicNumber = 0;
anAtomType.AtomTypeName = atomTypeElm.Attribute(XName_ID)?.Value;
int piBondCount = 0;
int neighborCount = 0;
BondOrder maxBondOrder = BondOrder.Unset;
double bondOrderSum = 0.0;
foreach (var elm in atomTypeElm.Elements())
{
if (elm.Name == XName_hasElement)
{
var aa = elm.Attribute(XName_rdf_resource)?.Value;
anAtomType.Symbol = aa.Substring(aa.IndexOf('#') + 1);
}
else if (elm.Name == XName_formalBondType)
{
neighborCount++;
var aa = elm.Attribute(XName_rdf_resource)?.Value;
var bondType = aa.Substring(aa.IndexOf('#') + 1);
int bondOrder = 0;
switch (bondType)
{
case "single":
bondOrder = 1;
break;
case "double":
bondOrder = 2;
break;
case "triple":
bondOrder = 3;
break;
case "quadruple":
bondOrder = 4;
break;
default:
throw new Exception();
}
maxBondOrder = BondManipulator.GetMaximumBondOrder(maxBondOrder, (BondOrder)bondOrder);
piBondCount += (bondOrder - 1);
bondOrderSum += bondOrder;
}
else if (elm.Name == XName_hybridization)
{
var aa = elm.Attribute(XName_rdf_resource)?.Value;
var hybridization = aa.Substring(aa.IndexOf('#') + 1);
anAtomType.Hybridization = HybridizationTools.ToHybridization(hybridization);
}
else if (elm.Name == XName_formalCharge)
{
anAtomType.FormalCharge = int.Parse(elm.Value, NumberFormatInfo.InvariantInfo);
}
else if (elm.Name == XName_formalNeighbourCount)
{
neighborCount = int.Parse(elm.Value, NumberFormatInfo.InvariantInfo);
}
else if (elm.Name == XName_lonePairCount)
{
anAtomType.SetProperty(CDKPropertyName.LonePairCount, int.Parse(elm.Value, NumberFormatInfo.InvariantInfo));
}
else if (elm.Name == XName_singleElectronCount)
{
anAtomType.SetProperty(CDKPropertyName.SingleElectronCount, int.Parse(elm.Value, NumberFormatInfo.InvariantInfo));
}
else if (elm.Name == XName_piBondCount)
{
piBondCount = int.Parse(elm.Value, NumberFormatInfo.InvariantInfo);
}
}
anAtomType.SetProperty(CDKPropertyName.PiBondCount, piBondCount);
anAtomType.FormalNeighbourCount = neighborCount;
if (maxBondOrder != BondOrder.Unset)
{
anAtomType.MaxBondOrder = maxBondOrder;
}
if (bondOrderSum > 0.1)
{
anAtomType.BondOrderSum = bondOrderSum;
}
ret.Add(anAtomType);
}
return(ret);
}
