// <cml:name id="m1.n1" dictRef="chem4word:Synonym">m1.n1</cml:name>
private static TextualProperty GetName(XElement cmlElement)
{
var name = new TextualProperty();
name.Id = cmlElement.Attribute(CMLConstants.AttributeId)?.Value;
if (cmlElement.Attribute(CMLConstants.AttributeDictRef) == null)
{
name.FullType = CMLConstants.ValueChem4WordSynonym;
}
else
{
name.FullType = cmlElement.Attribute(CMLConstants.AttributeDictRef)?.Value;
}
// Correct import from legacy Add-In
if (string.IsNullOrEmpty(name.FullType) || name.FullType.Equals(CMLConstants.ValueNameDictUnknown))
{
name.FullType = CMLConstants.ValueChem4WordSynonym;
}
name.Value = cmlElement.Value;
return(name);
}
// <cml:formula id="m1.f1" convention="chemspider:Smiles" inline="m1.f1" concise="C 6 H 14 Li 1 N 1" />
// <cml:formula id="m1.f0" concise="C 6 H 14 Li 1 N 1" />
private static TextualProperty GetFormula(XElement cmlElement)
{
var formula = new TextualProperty();
if (cmlElement.Attribute(CMLConstants.AttributeId) != null)
{
formula.Id = cmlElement.Attribute(CMLConstants.AttributeId)?.Value;
}
if (cmlElement.Attribute(CMLConstants.AttributeConvention) == null)
{
formula.FullType = CMLConstants.ValueChem4WordFormula;
}
else
{
formula.FullType = cmlElement.Attribute(CMLConstants.AttributeConvention)?.Value;
}
// Correct import from legacy Add-In
if (string.IsNullOrEmpty(formula.FullType))
{
formula.FullType = CMLConstants.ValueChem4WordFormula;
}
if (cmlElement.Attribute(CMLConstants.AttributeInline) != null)
{
formula.Value = cmlElement.Attribute(CMLConstants.AttributeInline)?.Value;
}
return(formula);
}
// <cml:formula id="m1.f1" convention="chemspider:Smiles" inline="m1.f1" concise="C 6 H 14 Li 1 N 1" />
private XElement GetXElement(TextualProperty f, string concise)
{
XElement result = new XElement(CMLNamespaces.cml + CMLConstants.TagFormula);
if (f.Id != null)
{
result.Add(new XAttribute(CMLConstants.AttributeId, f.Id));
}
if (f.FullType != null)
{
result.Add(new XAttribute(CMLConstants.AttributeConvention, f.FullType));
}
if (f.Value != null)
{
result.Add(new XAttribute(CMLConstants.AttributeInline, f.Value));
}
if (concise != null)
{
result.Add(new XAttribute(CMLConstants.AttributeConcise, concise));
}
return(result);
}
// <cml:label id="" dictRef="chem4word:Caption" value="C19 />
private static TextualProperty GetCaption(XElement cmlElement)
{
if (cmlElement.Attribute(CMLConstants.AttributeDictRef) != null)
{
var dictrefValue = cmlElement.Attribute(CMLConstants.AttributeDictRef)?.Value;
if (dictrefValue != null && dictrefValue.Equals(CMLConstants.ValueChem4WordCaption))
{
var result = new TextualProperty();
result.FullType = CMLConstants.ValueChem4WordCaption;
if (cmlElement.Attribute(CMLConstants.AttributeId) != null)
{
result.Id = cmlElement.Attribute(CMLConstants.AttributeId)?.Value;
}
if (cmlElement.Attribute(CMLConstants.AttributeNameValue) != null)
{
result.Value = cmlElement.Attribute(CMLConstants.AttributeNameValue)?.Value;
}
result.CanBeDeleted = true;
return(result);
}
}
return(null);
}
private void ImportStructure()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
if (_lastModel != null)
{
using (new WaitCursor())
{
CMLConverter conv = new CMLConverter();
double before = _lastModel.MeanBondLength;
_lastModel.ScaleToAverageBondLength(Core.Helpers.Constants.StandardBondLength);
double after = _lastModel.MeanBondLength;
Telemetry.Write(module, "Information", $"Structure rescaled from {before.ToString("#0.00")} to {after.ToString("#0.00")}");
_lastModel.Relabel(true);
var expModel = _lastModel;
using (new WaitCursor())
{
if (expModel.Molecules.Values.Any())
{
var mol = expModel.Molecules.Values.First();
mol.Names.Clear();
if (_allResults.IupacNames != null)
{
foreach (var di in _allResults.IupacNames)
{
var cn = new TextualProperty();
cn.Value = di.data;
cn.FullType = "chebi:Iupac";
mol.Names.Add(cn);
}
}
if (_allResults.Synonyms != null)
{
foreach (var di in _allResults.Synonyms)
{
var cn = new TextualProperty();
cn.Value = di.data;
cn.FullType = "chebi:Synonym";
mol.Names.Add(cn);
}
}
Cml = conv.Export(expModel);
}
}
}
}
}
// <cml:name id="m1.n1" dictRef="chem4word:Synonym">m1.n1</cml:name>
private XElement GetNameXElement(TextualProperty name)
{
XElement result = new XElement(CMLNamespaces.cml + CMLConstants.TagName, name.Value);
if (name.Id != null)
{
result.Add(new XAttribute(CMLConstants.AttributeId, name.Id));
}
if (name.FullType != null)
{
result.Add(new XAttribute(CMLConstants.AttributeDictRef, name.FullType));
}
return(result);
}
// <cml:label id="m1.l1" dictRef="chem4word:Label "value="C19"/>
private XElement GetLabelXElement(TextualProperty label)
{
XElement result = new XElement(CMLNamespaces.cml + CMLConstants.TagLabel);
if (label.Id != null)
{
result.Add(new XAttribute(CMLConstants.AttributeId, label.Id));
}
result.Add(new XAttribute(CMLConstants.AttributeDictRef, CMLConstants.ValueChem4WordLabel));
if (label.Value != null)
{
result.Add(new XAttribute(CMLConstants.AttributeNameValue, label.Value));
}
return(result);
}
// <cml:label id="" dictRef="chem4word:Label" value="C19 />
private static TextualProperty GetLabel(XElement cmlElement)
{
var result = new TextualProperty();
result.FullType = CMLConstants.ValueChem4WordLabel;
if (cmlElement.Attribute(CMLConstants.AttributeId) != null)
{
result.Id = cmlElement.Attribute(CMLConstants.AttributeId)?.Value;
}
if (cmlElement.Attribute(CMLConstants.AttributeNameValue) != null)
{
result.Value = cmlElement.Attribute(CMLConstants.AttributeNameValue)?.Value;
}
result.CanBeDeleted = true;
return(result);
}
private void ImportStructure()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
using (new WaitCursor())
{
CMLConverter conv = new CMLConverter();
var expModel = _lastModel;
expModel.Relabel(true);
using (new WaitCursor())
{
expModel.Molecules.Values.First().Names.Clear();
if (_allResults.IupacNames != null)
{
foreach (var di in _allResults.IupacNames)
{
var cn = new TextualProperty();
cn.Value = di.data;
cn.FullType = "chebi:Iupac";
expModel.Molecules.Values.First().Names.Add(cn);
}
}
if (_allResults.Synonyms != null)
{
foreach (var di in _allResults.Synonyms)
{
var cn = new TextualProperty();
cn.Value = di.data;
cn.FullType = "chebi:Synonym";
expModel.Molecules.Values.First().Names.Add(cn);
}
}
Cml = conv.Export(expModel);
}
}
}
public void CheckNamesCanBeAltered()
{
Model model = new Model();
Molecule molecule = new Molecule();
molecule.Id = "m1";
model.AddMolecule(molecule);
molecule.Parent = model;
var name = new TextualProperty();
name.FullType = "";
name.Value = "";
molecule.Names.Add(name);
Assert.True(molecule.Names.Count == 1, "Expected count to be 1");
Assert.Equal("", molecule.Names[0].FullType);
molecule.Names[0].FullType = "dictref";
Assert.Equal("dictref", molecule.Names[0].FullType);
}
public void CheckFormulasCanBeAltered()
{
Model model = new Model();
Molecule molecule = new Molecule();
molecule.Id = "m1";
model.AddMolecule(molecule);
molecule.Parent = model;
var formula = new TextualProperty();
formula.FullType = "";
formula.Value = "";
molecule.Formulas.Add(formula);
Assert.True(molecule.Formulas.Count == 1, "Expected count to be 1");
Assert.Equal("", molecule.Formulas[0].FullType);
molecule.Formulas[0].FullType = "convention";
Assert.Equal("convention", molecule.Formulas[0].FullType);
}
public override SdfState ImportFromStream(StreamReader reader, Molecule molecule, out string message)
{
message = null;
_molecule = molecule;
SdfState result = SdfState.Null;
try
{
bool isFormula = false;
string internalName = "";
while (!reader.EndOfStream)
{
string line = SdFileConverter.GetNextLine(reader); //reader.ReadLine();;
if (!string.IsNullOrEmpty(line))
{
if (line.Equals(MDLConstants.SDF_END))
{
// End of SDF Section
result = SdfState.EndOfData;
break;
}
if (line.StartsWith(">"))
{
// Clear existing Property Name
internalName = string.Empty;
// See if we can find the property in our translation table
foreach (var property in _propertyTypes)
{
if (line.Equals(property.ExternalName))
{
isFormula = property.IsFormula;
internalName = property.InternalName;
break;
}
}
}
else
{
// Property Data
if (!string.IsNullOrEmpty(internalName))
{
if (isFormula)
{
var formula = new TextualProperty();
formula.FullType = internalName;
formula.Value = line;
_molecule.Formulas.Add(formula);
}
else
{
var name = new TextualProperty();
name.FullType = internalName;
name.Value = line;
_molecule.Names.Add(name);
}
}
}
}
else
{
internalName = string.Empty;
}
}
}
catch (System.Exception ex)
{
Debug.WriteLine(ex.Message);
result = SdfState.Error;
}
return(result);
}
