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);
}
/// <summary>
/// Reads the atom types from the data file.
/// </summary>
/// <returns><see cref="IEnumerable{T}"/> with atom types. Is empty if some reading error occurred.</returns>
public IEnumerable <IAtomType> ReadAtomTypes()
{
var settings = new XmlReaderSettings
{
ValidationType = ValidationType.None,
ValidationFlags = System.Xml.Schema.XmlSchemaValidationFlags.None
};
XmlReader reader = XmlReader.Create(input, settings);
var doc = XElement.Load(reader);
var nAtomType = doc.Name.Namespace + "atomType";
var nAtom = doc.Name.Namespace + "atom";
var nLabel = doc.Name.Namespace + "label";
var nScalar = doc.Name.Namespace + "scalar";
foreach (var elementAtomType in doc.Elements(nAtomType))
{
var atomType = builder.NewAtomType("R");
atomType.AtomTypeName = elementAtomType.Attribute("id")?.Value;
foreach (var elm in elementAtomType.Descendants())
{
// lazy compare
switch (elm.Name.LocalName)
{
case "atom":
atomType.Symbol = elm.Attribute("elementType")?.Value;
var sFormalCharge = elm.Attribute("formalCharge")?.Value;
if (sFormalCharge != null)
{
atomType.FormalCharge = int.Parse(sFormalCharge, NumberFormatInfo.InvariantInfo);
}
break;
case "label":
var aValue = elm.Attribute("value");
if (aValue != null)
{
if (atomType.AtomTypeName != null)
{
atomType.Id = atomType.AtomTypeName;
}
atomType.AtomTypeName = aValue.Value;
}
break;
case "scalar":
var dictRef = elm.Attribute("dictRef")?.Value;
var value = string.IsNullOrWhiteSpace(elm.Value) ? null : elm.Value;
if (value != null)
{
switch (dictRef)
{
case "cdk:bondOrderSum":
atomType.BondOrderSum = double.Parse(value, NumberFormatInfo.InvariantInfo);
break;
case "cdk:maxBondOrder":
atomType.MaxBondOrder = (BondOrder)(int)double.Parse(value, NumberFormatInfo.InvariantInfo);
break;
case "cdk:formalNeighbourCount":
atomType.FormalNeighbourCount = (int)double.Parse(value, NumberFormatInfo.InvariantInfo);
break;
case "cdk:valency":
atomType.Valency = (int)double.Parse(value, NumberFormatInfo.InvariantInfo);
break;
case "cdk:formalCharge":
atomType.FormalCharge = (int)double.Parse(value, NumberFormatInfo.InvariantInfo);
break;
case "cdk:hybridization":
atomType.Hybridization = HybridizationTools.ToHybridization(value);
break;
case "cdk:DA":
switch (value)
{
case "A":
atomType.IsHydrogenBondAcceptor |= true;
break;
case "D":
atomType.IsHydrogenBondDonor |= true;
break;
default:
Trace.TraceWarning($"Unrecognized H-bond donor/acceptor pattern in configuration file: {value}");
break;
}
break;
case "cdk:sphericalMatcher":
atomType.SetProperty(CDKPropertyName.SphericalMatcher, value);
break;
case "cdk:ringSize":
atomType.SetProperty(CDKPropertyName.PartOfRingOfSize, int.Parse(value, NumberFormatInfo.InvariantInfo));
break;
case "cdk:ringConstant":
atomType.SetProperty(CDKPropertyName.ChemicalGroupConstant, int.Parse(value, NumberFormatInfo.InvariantInfo));
break;
case "cdk:aromaticAtom":
atomType.IsAromatic |= true;
break;
case "emboss:vdwrad":
break;
case "cdk:piBondCount":
atomType.SetProperty(CDKPropertyName.PiBondCount, int.Parse(value, NumberFormatInfo.InvariantInfo));
break;
case "cdk:lonePairCount":
atomType.SetProperty(CDKPropertyName.LonePairCount, int.Parse(value, NumberFormatInfo.InvariantInfo));
break;
default:
break;
}
}
break;
default:
break;
}
}
yield return(atomType);
}
yield break;
}
