public void SdfImportBasicParafuchsin()
{
SdFileConverter mc = new SdFileConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("BasicParafuchsin.txt"));
// Basic sanity checks
Assert.True(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
var mol = m.Molecules.Values.First();
Assert.True(mol.Molecules.Count == 2,
$"Expected 2 Child Molecules; Got {mol.Molecules.Count}");
Assert.True(m.TotalAtomsCount == 41, $"Expected 41 Atoms; Got {m.TotalAtomsCount}");
Assert.True(m.TotalBondsCount == 42, $"Expected 42 Bonds; Got {m.TotalBondsCount}");
// Check that we got three rings
var mol2 = mol.Molecules.Values.Skip(1).First();
Assert.True(mol2.Rings.Count == 3,
$"Expected 3 Rings; Got {mol2.Rings.Count}");
string molstring = mc.Export(m);
mc = new SdFileConverter();
Model m2 = mc.Import(molstring);
}
private void ExportAs_SelectedIndexChanged(object sender, EventArgs e)
{
if (lastModel != null)
{
string result = string.Empty;
switch (ExportAs.SelectedIndex)
{
case 1:
var cmlConverter = new CMLConverter();
result = cmlConverter.Export(lastModel);
break;
case 2:
var sdFileConverter = new SdFileConverter();
result = sdFileConverter.Export(lastModel);
break;
case 3:
var jsonConverter = new JSONConverter();
result = jsonConverter.Export(lastModel);
break;
}
if (!string.IsNullOrEmpty(result))
{
//Clipboard.SetText(result);
//MessageBox.Show("Last loaded model exported to clipboard as CML");
textBox1.Text = result + Environment.NewLine;
}
}
ExportAs.SelectedIndex = 0;
LoadStructure.Focus();
}
private void SaveStructure_Click(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
CMLConverter cmlConverter = new CMLConverter();
Model m = cmlConverter.Import(_lastCml);
m.CustomXmlPartGuid = "";
string filter = "CML molecule files (*.cml, *.xml)|*.cml;*.xml|MDL molecule files (*.mol, *.sdf)|*.mol;*.sdf";
using (SaveFileDialog sfd = new SaveFileDialog {
Filter = filter
})
{
DialogResult dr = sfd.ShowDialog();
if (dr == DialogResult.OK)
{
FileInfo fi = new FileInfo(sfd.FileName);
_telemetry.Write(module, "Information", $"Exporting to '{fi.Name}'");
string fileType = Path.GetExtension(sfd.FileName).ToLower();
switch (fileType)
{
case ".cml":
case ".xml":
string temp = "<?xml version=\"1.0\" encoding=\"utf-8\"?>"
+ Environment.NewLine
+ cmlConverter.Export(m);
File.WriteAllText(sfd.FileName, temp);
break;
case ".mol":
case ".sdf":
// https://www.chemaxon.com/marvin-archive/6.0.2/marvin/help/formats/mol-csmol-doc.html
double before = m.MeanBondLength;
// Set bond length to 1.54 angstroms (Å)
m.ScaleToAverageBondLength(1.54);
double after = m.MeanBondLength;
_telemetry.Write(module, "Information", $"Structure rescaled from {before.ToString("#0.00")} to {after.ToString("#0.00")}");
SdFileConverter converter = new SdFileConverter();
File.WriteAllText(sfd.FileName, converter.Export(m));
break;
}
}
}
}
catch (Exception exception)
{
_telemetry.Write(module, "Exception", $"Exception: {exception.Message}");
_telemetry.Write(module, "Exception(Data)", $"Exception: {exception}");
MessageBox.Show(exception.StackTrace, exception.Message);
}
}
public void SdfImportBasicParafuchsin()
{
SdFileConverter mc = new SdFileConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("BasicParafuchsin.txt"));
// Basic sanity checks
Assert.IsTrue(m.Molecules.Count == 2, $"Expected 2 Molecules; Got {m.Molecules.Count}");
Assert.IsTrue(m.AllAtoms.Count == 41, $"Expected 41 Atoms; Got {m.AllAtoms.Count}");
Assert.IsTrue(m.AllBonds.Count == 42, $"Expected 42 Bonds; Got {m.AllBonds.Count}");
// Check that we got two rings
Assert.IsTrue(m.Molecules.SelectMany(m1 => m1.Rings).Count() == 3, $"Expected 2 Rings; Got {m.Molecules.SelectMany(m1 => m1.Rings).Count()}");
string molstring = mc.Export(m);
mc = new SdFileConverter();
Model m2 = mc.Import(molstring);
}
private void LayoutStructure_Click(object sender, EventArgs e)
{
var data = new LayoutResult();
var cc = new CMLConverter();
var sc = new SdFileConverter();
string molfile = sc.Export(cc.Import(_lastCml));
try
{
using (HttpClient httpClient = new HttpClient())
{
var formData = new List <KeyValuePair <string, string> >();
formData.Add(new KeyValuePair <string, string>("mol", molfile));
formData.Add(new KeyValuePair <string, string>("machine", SystemHelper.GetMachineId()));
formData.Add(new KeyValuePair <string, string>("version", "1.2.3.4"));
#if DEBUG
formData.Add(new KeyValuePair <string, string>("debug", "true"));
#endif
var content = new FormUrlEncodedContent(formData);
httpClient.Timeout = TimeSpan.FromSeconds(15);
httpClient.DefaultRequestHeaders.Add("user-agent", "Chem4Word");
try
{
var response = httpClient.PostAsync("https://chemicalservices-staging.azurewebsites.net/api/Layout", content).Result;
if (response.Content != null)
{
var responseContent = response.Content;
var jsonContent = responseContent.ReadAsStringAsync().Result;
try
{
data = JsonConvert.DeserializeObject <LayoutResult>(jsonContent);
}
catch (Exception e3)
{
//Telemetry.Write(module, "Exception", e3.Message);
//Telemetry.Write(module, "Exception(Data)", jsonContent);
Debug.WriteLine(e3.Message);
}
if (data != null)
{
if (data.Messages.Any())
{
//Telemetry.Write(module, "Timing", string.Join(Environment.NewLine, data.Messages));
}
if (data.Errors.Any())
{
//Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, data.Errors));
}
if (!string.IsNullOrEmpty(data.Molecule))
{
var model = sc.Import(data.Molecule);
model.EnsureBondLength(20, false);
if (string.IsNullOrEmpty(model.CustomXmlPartGuid))
{
model.CustomXmlPartGuid = Guid.NewGuid().ToString("N");
}
var clone = cc.Import(_lastCml);
_undoStack.Push(clone);
_lastCml = cc.Export(model);
ShowChemistry("", model);
}
}
}
}
catch (Exception e2)
{
//Telemetry.Write(module, "Exception", e2.Message);
//Telemetry.Write(module, "Exception", e2.ToString());
Debug.WriteLine(e2.Message);
}
}
}
catch (Exception e1)
{
//Telemetry.Write(module, "Exception", e1.Message);
//Telemetry.Write(module, "Exception", e1.ToString());
Debug.WriteLine(e1.Message);
}
}
public static int CalculateProperties(List <Molecule> newMolecules)
{
string module = $"{Product}.{Class}.{MethodBase.GetCurrentMethod().Name}()";
var molConverter = new SdFileConverter();
int changedProperties = 0;
int newProperties = 0;
int webServiceCalls = newMolecules.Count + 1;
Progress pb = new Progress();
pb.TopLeft = Globals.Chem4WordV3.WordTopLeft;
pb.Value = 0;
pb.Maximum = webServiceCalls;
foreach (var molecule in newMolecules)
{
Model temp = new Model();
var mol = molecule.Copy();
temp.AddMolecule(mol);
// GitHub: Issue #9 https://github.com/Chem4Word/Version3/issues/9
int maxAtomicNumber = temp.MaxAtomicNumber;
int minAtomicNumber = temp.MinAtomicNumber;
var invalidBonds = new List <Bond>();
if (mol.Bonds.Any())
{
invalidBonds = mol.Bonds.Where(b => b.OrderValue != null && (CtabProcessor.MdlBondType(b.Order) < 1 || CtabProcessor.MdlBondType(b.Order) > 4)).ToList();
}
var calculatedNames = new List <TextualProperty>();
var calculatedFormulae = new List <TextualProperty>();
if (mol.HasFunctionalGroups || invalidBonds.Any() || minAtomicNumber < 1 || maxAtomicNumber > 118)
{
// IUPAC InChi (1.05) generator does not support Mdl Bond Types < 1 or > 4 or Elements < 1 or > 118 or 'our' functional groups
#region Set Default properties
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Not sending structure to Web Service; HasFunctionalGroups: {mol.HasFunctionalGroups} Invalid Bonds: {invalidBonds?.Count} Min Atomic Number: {minAtomicNumber} Max Atomic Number: {maxAtomicNumber}");
calculatedNames.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordInchiName, Value = "Unable to calculate"
});
//calculatedNames.Add(new TextualProperty { FullType = CMLConstants.ValueChem4WordAuxInfoName, Value = "Unable to calculate" });
calculatedNames.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordInchiKeyName, Value = "Unable to calculate"
});
calculatedFormulae.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordResolverFormulaName, Value = "Not requested"
});
calculatedNames.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordResolverIupacName, Value = "Not requested"
});
calculatedFormulae.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordResolverSmilesName, Value = "Not requested"
});
#endregion Set Default properties
}
else
{
pb.Show();
pb.Increment(1);
pb.Message = $"Calculating InChiKey and Resolving Names using Chem4Word Web Service for molecule {molecule.Id}";
#region Obtain Calculated Properties
try
{
string afterMolFile = molConverter.Export(temp);
ChemicalServices cs = new ChemicalServices(Globals.Chem4WordV3.Telemetry);
var csr = cs.GetChemicalServicesResult(afterMolFile);
if (csr?.Properties != null && csr.Properties.Any())
{
var first = csr.Properties[0];
if (first != null)
{
var value = string.IsNullOrEmpty(first.Inchi) ? "Not found" : first.Inchi;
calculatedNames.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordInchiName, Value = value
});
//value = string.IsNullOrEmpty(first.AuxInfo) ? "Not found" : first.AuxInfo;
//calculatedNames.Add(new TextualProperty { FullType = CMLConstants.ValueChem4WordAuxInfoName, Value = value });
value = string.IsNullOrEmpty(first.InchiKey) ? "Not found" : first.InchiKey;
calculatedNames.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordInchiKeyName, Value = value
});
value = string.IsNullOrEmpty(first.Formula) ? "Not found" : first.Formula;
calculatedFormulae.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordResolverFormulaName, Value = value
});
value = string.IsNullOrEmpty(first.Name) ? "Not found" : first.Name;
calculatedNames.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordResolverIupacName, Value = value
});
value = string.IsNullOrEmpty(first.Smiles) ? "Not found" : first.Smiles;
calculatedFormulae.Add(new TextualProperty {
FullType = CMLConstants.ValueChem4WordResolverSmilesName, Value = value
});
}
}
}
catch (Exception e)
{
Globals.Chem4WordV3.Telemetry.Write(module, "Exception", $"{e}");
}
#endregion Obtain Calculated Properties
}
#region Merge in properties
foreach (var formula in calculatedFormulae)
{
var target = molecule.Formulas.FirstOrDefault(f => f.FullType.Equals(formula.FullType));
if (target == null)
{
molecule.Formulas.Add(formula);
newProperties++;
}
else
{
if (!target.Value.Equals(formula.Value))
{
target.Value = formula.Value;
changedProperties++;
}
}
}
foreach (var name in calculatedNames)
{
var target = molecule.Names.FirstOrDefault(f => f.FullType.Equals(name.FullType));
if (target == null)
{
molecule.Names.Add(name);
newProperties++;
}
else
{
if (!target.Value.Equals(name.Value))
{
target.Value = name.Value;
changedProperties++;
}
}
}
#endregion Merge in properties
}
pb.Value = 0;
pb.Hide();
pb.Close();
return(changedProperties + newProperties);
}