private void HandleDataContextChanged()
{
ChemistryModel chemistryModel = null;
if (Chemistry is string)
{
var data = Chemistry as string;
if (!string.IsNullOrEmpty(data))
{
if (data.StartsWith("<"))
{
var conv = new CMLConverter();
chemistryModel = conv.Import(data);
}
if (data.Contains("M END"))
{
var conv = new SdFileConverter();
chemistryModel = conv.Import(data);
}
}
}
else
{
if (Chemistry != null && !(Chemistry is ChemistryModel))
{
throw new ArgumentException("Object must be of type 'Chem4Word.Model.Model'.");
}
chemistryModel = Chemistry as ChemistryModel;
}
if (chemistryModel != null)
{
if (chemistryModel.AllAtoms.Count > 0)
{
chemistryModel.RescaleForXaml(Constants.StandardBondLength * 2);
Debug.WriteLine($"Ring count == {chemistryModel.Molecules.SelectMany(m => m.Rings).Count()}");
if (ShowCarbonLabels)
{
foreach (var atom in chemistryModel.AllAtoms)
{
if (atom.Element.Equals(Globals.PeriodicTable.C))
{
atom.ShowSymbol = true;
}
}
}
Placeholder.DataContext = chemistryModel;
}
else
{
Placeholder.DataContext = null;
}
}
else
{
Placeholder.DataContext = null;
}
}
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 UpdateDisplay()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
ErrorsAndWarnings.Text = "";
using (new WaitCursor())
{
var tag = ResultsListView.SelectedItems[0]?.Tag;
if (tag is LiteEntity le && !string.IsNullOrEmpty(le.chebiId))
{
ChebiId = le.chebiId;
var chemStructure = GetChemStructure(le);
if (!string.IsNullOrEmpty(chemStructure))
{
_lastMolfile = ConvertToWindows(chemStructure);
SdFileConverter sdConverter = new SdFileConverter();
_lastModel = sdConverter.Import(chemStructure);
if (_lastModel.AllWarnings.Count > 0 || _lastModel.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", chemStructure);
List <string> lines = new List <string>();
if (_lastModel.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, _lastModel.AllErrors));
lines.Add("Errors(s)");
lines.AddRange(_lastModel.AllErrors);
}
if (_lastModel.AllWarnings.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, _lastModel.AllWarnings));
lines.Add("Warnings(s)");
lines.AddRange(_lastModel.AllWarnings);
}
ErrorsAndWarnings.Text = string.Join(Environment.NewLine, lines);
}
if (_lastModel.MeanBondLength < Core.Helpers.Constants.MinimumBondLength - Core.Helpers.Constants.BondLengthTolerance ||
_lastModel.MeanBondLength > Core.Helpers.Constants.MaximumBondLength + Core.Helpers.Constants.BondLengthTolerance)
{
_lastModel.ScaleToAverageBondLength(Core.Helpers.Constants.StandardBondLength);
}
display1.Chemistry = _lastModel;
}
else
{
_lastModel = null;
_lastMolfile = String.Empty;
display1.Chemistry = null;
ErrorsAndWarnings.Text = "No structure available.";
}
EnableImport();
}
}
}
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)", $"Exception: {exception}");
MessageBox.Show(exception.StackTrace, exception.Message);
}
}
private void HandleDataContextChanged()
{
Model chemistryModel = null;
if (Chemistry is string)
{
var data = Chemistry as string;
if (!string.IsNullOrEmpty(data))
{
if (data.StartsWith("<"))
{
var conv = new CMLConverter();
chemistryModel = conv.Import(data);
chemistryModel.EnsureBondLength(20, false);
}
if (data.Contains("M END"))
{
var conv = new SdFileConverter();
chemistryModel = conv.Import(data);
chemistryModel.EnsureBondLength(20, false);
}
}
}
else
{
if (Chemistry != null && !(Chemistry is Model))
{
Debugger.Break();
throw new ArgumentException($"Object must be of type {nameof(Model)}.");
}
chemistryModel = Chemistry as Model;
if (chemistryModel != null)
{
chemistryModel.EnsureBondLength(20, false);
}
}
//assuming we've got this far, we should have something we can draw
if (chemistryModel != null)
{
if (chemistryModel.TotalAtomsCount > 0)
{
chemistryModel.RescaleForXaml(true, Constants.StandardBondLength);
CurrentViewModel = new ViewModel(chemistryModel);
CurrentViewModel.SetTextParams(chemistryModel.XamlBondLength);
DrawChemistry(CurrentViewModel);
}
}
}
private void button1_Click(object sender, EventArgs e)
{
StringBuilder sb = new StringBuilder();
sb.Append("All molecule files (*.mol, *.sdf, *.cml)|*.mol;*.sdf;*.cml");
sb.Append("|CML molecule files (*.cml)|*.cml");
sb.Append("|MDL molecule files (*.mol, *.sdf)|*.mol;*.sdf");
openFileDialog1.FileName = "*.*";
openFileDialog1.Filter = sb.ToString();
DialogResult dr = openFileDialog1.ShowDialog();
if (dr == DialogResult.OK)
{
string fileType = Path.GetExtension(openFileDialog1.FileName).ToLower();
string filename = Path.GetFileName(openFileDialog1.FileName);
string mol = File.ReadAllText(openFileDialog1.FileName);
string cml = "";
CMLConverter cmlConvertor = new CMLConverter();
SdFileConverter sdFileConverter = new SdFileConverter();
Model model = null;
switch (fileType)
{
case ".mol":
case ".sdf":
model = sdFileConverter.Import(mol);
model.RefreshMolecules();
model.Relabel();
cml = cmlConvertor.Export(model);
//model.DumpModel("After Import");
break;
case ".cml":
case ".xml":
model = cmlConvertor.Import(mol);
model.RefreshMolecules();
model.Relabel();
cml = cmlConvertor.Export(model);
break;
}
this.Text = filename;
this.display1.Chemistry = cml;
}
}
private void UpdateDisplay()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
ErrorsAndWarnings.Text = "";
using (new WaitCursor())
{
var tag = ResultsListView.SelectedItems[0]?.Tag;
LiteEntity le = (LiteEntity)tag;
var chemStructure = GetChemStructure(le);
if (!string.IsNullOrEmpty(chemStructure))
{
_lastMolfile = ConvertToWindows(chemStructure);
SdFileConverter sdConverter = new SdFileConverter();
_lastModel = sdConverter.Import(chemStructure);
if (_lastModel.AllWarnings.Count > 0 || _lastModel.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", chemStructure);
List <string> lines = new List <string>();
if (_lastModel.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, _lastModel.AllErrors));
lines.Add("Errors(s)");
lines.AddRange(_lastModel.AllErrors);
}
if (_lastModel.AllWarnings.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, _lastModel.AllWarnings));
lines.Add("Warnings(s)");
lines.AddRange(_lastModel.AllWarnings);
}
ErrorsAndWarnings.Text = string.Join(Environment.NewLine, lines);
}
ChebiId = le.chebiId;
flexDisplayControl1.Chemistry = _lastModel;
}
else
{
flexDisplayControl1.Chemistry = null;
ErrorsAndWarnings.Text = "No structure available.";
}
EnableImport();
}
}
public override void Execute(object parameter)
{
CMLConverter cmlConverter = new CMLConverter();
SdFileConverter sdfConverter = new SdFileConverter();
if (Clipboard.ContainsData(Globals.FormatCML))
{
string pastedCML = (string)Clipboard.GetData(Globals.FormatCML);
EditViewModel.PasteCML(pastedCML);
}
else if (Clipboard.ContainsText())
{
bool failedCML = false;
bool failedSDF = false;
string pastedText = Clipboard.GetText();
Model buffer = null;
//try to convert the pasted text with the CML converter first
try
{
buffer = cmlConverter.Import(pastedText);
}
catch
{
failedCML = true;
}
if (failedCML)
{
buffer = sdfConverter.Import(pastedText);
failedSDF = buffer.GeneralErrors.Any();
}
if (failedCML & failedSDF)
{
if (buffer.GeneralErrors.Any())
{
Chem4Word.Core.UserInteractions.InformUser("Unable to paste text as chemistry: " + buffer.GeneralErrors[0]);
}
else
{
Chem4Word.Core.UserInteractions.InformUser("Unable to paste text as chemistry: unknown error.");
}
}
else
{
EditViewModel.PasteModel(buffer);
}
}
}
public void SdfImportBenzene()
{
SdFileConverter mc = new SdFileConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("Benzene.txt"));
// Basic sanity checks
Assert.True(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
Assert.True(m.TotalAtomsCount == 6, $"Expected 6 Atoms; Got {m.TotalAtomsCount}");
Assert.True(m.TotalBondsCount == 6, $"Expected 6 Bonds; Got {m.TotalBondsCount}");
// Check that names and formulae have not been trashed
Assert.True(m.Molecules.Values.First().Names.Count == 2, $"Expected 2 Chemical Names; Got {m.Molecules.Values.First().Names.Count}");
Assert.True(m.Molecules.Values.First().Formulas.Count == 2, $"Expected 2 Formulae; Got {m.Molecules.Values.First().Formulas.Count }");
// Check that we have one ring
Assert.True(m.Molecules.Values.First().Rings.Count == 1, $"Expected 1 Ring; Got {m.Molecules.Values.First().Rings.Count}");
}
public void SdfImportBenzene()
{
SdFileConverter mc = new SdFileConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("Benzene.txt"));
// Basic sanity checks
Assert.IsTrue(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
Assert.IsTrue(m.AllAtoms.Count == 6, $"Expected 6 Atoms; Got {m.AllAtoms.Count}");
Assert.IsTrue(m.AllBonds.Count == 6, $"Expected 6 Bonds; Got {m.AllBonds.Count}");
// Check that names and formulae have not been trashed
Assert.IsTrue(m.Molecules[0].ChemicalNames.Count == 2, $"Expected 2 Chemical Names; Got {m.Molecules[0].ChemicalNames.Count}");
Assert.IsTrue(m.Molecules[0].Formulas.Count == 2, $"Expected 2 Formulae; Got {m.Molecules[0].Formulas.Count }");
// Check that we have one ring
Assert.IsTrue(m.Molecules.SelectMany(m1 => m1.Rings).Count() == 1, $"Expected 1 Ring; Got {m.Molecules.SelectMany(m1 => m1.Rings).Count()}");
}
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);
}
public Library()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
string libraryTarget = Path.Combine(Globals.Chem4WordV3.AddInInfo.ProgramDataPath, Constants.LibraryFileName);
_sdFileConverter = new SdFileConverter();
_cmlConverter = new CMLConverter();
if (!File.Exists(libraryTarget))
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", "Copying initial Library database");
Stream stream = ResourceHelper.GetBinaryResource(Assembly.GetExecutingAssembly(), "Library.zip");
using (ZipFile zip = ZipFile.Read(stream))
{
zip.ExtractAll(Globals.Chem4WordV3.AddInInfo.ProgramDataPath, ExtractExistingFileAction.OverwriteSilently);
}
}
}
private void btnConvertModel_Click(object sender, EventArgs e)
{
TextBoxFormat format = GetTextBoxFormat(txtStructure);
switch (format)
{
case TextBoxFormat.Json:
JSONConverter converter1 = new JSONConverter();
Model model1 = converter1.Import((object)txtStructure.Text);
model1.RebuildMolecules();
model1.Relabel();
model1.CustomXmlPartGuid = Guid.NewGuid().ToString("N");
CMLConverter converter2 = new CMLConverter();
txtStructure.Text = converter2.Export(model1);
break;
case TextBoxFormat.Cml:
CMLConverter converter3 = new CMLConverter();
Model model2 = converter3.Import((object)txtStructure.Text);
model2.RebuildMolecules();
model2.Relabel();
JSONConverter converter4 = new JSONConverter();
txtStructure.Text = converter4.Export(model2);
break;
case TextBoxFormat.MolFile:
SdFileConverter converter5 = new SdFileConverter();
Model model3 = converter5.Import((object)txtStructure.Text);
model3.RebuildMolecules();
model3.Relabel();
CMLConverter converter6 = new CMLConverter();
txtStructure.Text = converter6.Export(model3);
break;
}
EnableButtons();
}
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);
}
}
private void LoadModel(string fileName)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
if (!string.IsNullOrEmpty(fileName) && File.Exists(fileName))
{
try
{
string contents = string.Empty;
using (var fileStream = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.Read))
{
using (var textReader = new StreamReader(fileStream))
{
contents = textReader.ReadToEnd();
}
}
Model model = null;
string fileType = Path.GetExtension(fileName).ToLower();
switch (fileType)
{
case ".cml":
var cmlConverter = new CMLConverter();
model = cmlConverter.Import(contents);
break;
case ".sdf":
case ".mol":
var sdFileConverter = new SdFileConverter();
model = sdFileConverter.Import(contents);
break;
case ".json":
var jsonConverter = new JSONConverter();
model = jsonConverter.Import(contents);
break;
}
if (model != null)
{
lastModel = model;
// Load model into TreeView
foreach (var modelMolecule in model.Molecules.Values)
{
LoadTreeNode(modelMolecule);
}
model.AtomsChanged += Model_AtomsChanged;
model.BondsChanged += Model_BondsChanged;
model.MoleculesChanged += Model_MoleculesChanged;
model.PropertyChanged += Model_PropertyChanged;
int atoms = model.TotalAtomsCount;
int bonds = model.TotalBondsCount;
textBox1.AppendText($"Total Atoms Count is {atoms}, Total Bonds Count is {bonds}\n");
var list = new List <string>();
list.AddRange(model.GeneralErrors);
list.AddRange(model.AllErrors);
list.AddRange(model.AllWarnings);
textBox1.AppendText(string.Join(Environment.NewLine, list) + "\n");
}
}
catch (Exception exception)
{
_telemetry.Write(module, "Exception", $"Exception: {exception.Message}");
_telemetry.Write(module, "Exception(Data)", $"Exception: {exception}");
MessageBox.Show(exception.StackTrace, exception.Message);
}
}
// Local function to allow recursive calling
void LoadTreeNode(Molecule modelMolecule, TreeNode root = null)
{
TreeNode parentNode;
if (root == null)
{
//FileInfo fi = new FileInfo(fileName);
//parentNode = treeView1.Nodes.Add(modelMolecule.Path, fi.Name + ": " + modelMolecule.ToString());
parentNode = treeView1.Nodes.Add(modelMolecule.Path, modelMolecule.ToString());
textBox1.AppendText($"Molecule {modelMolecule.Path} added.\n");
}
else
{
parentNode = root.Nodes.Add(modelMolecule.Path, modelMolecule.ToString());
textBox1.AppendText($"Molecule {modelMolecule.Path} added.\n");
}
parentNode.Tag = modelMolecule;
if (modelMolecule.Atoms.Any())
{
var atomsNode = parentNode.Nodes.Add(modelMolecule.Path + "/Atoms", $"Atoms: count {modelMolecule.Atoms.Count}");
foreach (Atom atom in modelMolecule.Atoms.Values)
{
var res = atomsNode.Nodes.Add(atom.Path, atom.ToString());
res.Tag = atom;
textBox1.AppendText($"Atom {atom.Path} added.\n");
}
}
if (modelMolecule.Bonds.Any())
{
var bondsNode = parentNode.Nodes.Add(modelMolecule.Path + "/Bonds", $"Bonds: count {modelMolecule.Bonds.Count}");
foreach (Bond bond in modelMolecule.Bonds)
{
var res = bondsNode.Nodes.Add(bond.Path, bond.ToString());
res.Tag = bond;
textBox1.AppendText($"Bond {bond.Path} added.\n");
}
}
if (modelMolecule.Formulas.Any())
{
var formulasNode = parentNode.Nodes.Add(modelMolecule.Path + "/Formulas", $"Formulas: count {modelMolecule.Formulas.Count}");
foreach (var formula in modelMolecule.Formulas)
{
formulasNode.Nodes.Add(formula.Id, $"Formula {formula.Id} {formula.Convention} {formula.Inline}");
}
}
if (modelMolecule.Names.Any())
{
var namesNode = parentNode.Nodes.Add(modelMolecule.Path + "/Names", $"Names: count {modelMolecule.Names.Count}");
foreach (var name in modelMolecule.Names)
{
namesNode.Nodes.Add(name.Id, $"Name {name.Id} {name.DictRef} {name.Name}");
}
}
if (modelMolecule.Rings.Any())
{
var ringsNode = parentNode.Nodes.Add(modelMolecule.Path + "/Rings", $"Rings: count {modelMolecule.Rings.Count}");
int ringCounter = 1;
foreach (Ring r in modelMolecule.Rings)
{
var ringnode = ringsNode.Nodes.Add(r.GetHashCode().ToString(), $"Ring {ringCounter++} - Priority {r.Priority} with {r.Atoms.Count} Atoms");
ringnode.Tag = r;
foreach (Atom a in r.Atoms)
{
ringnode.Nodes.Add(r.GetHashCode() + a.Id, $"{a.Id} - {a.Path}");
}
}
}
foreach (var childMol in modelMolecule.Molecules.Values)
{
LoadTreeNode(childMol, parentNode);
}
}
}
private string FetchStructure()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
string result = lastSelected;
ImportButton.Enabled = false;
ListView.SelectedListViewItemCollection selected = Results.SelectedItems;
if (selected.Count > 0)
{
ListViewItem item = selected[0];
string pubchemId = item.Text;
PubChemId = pubchemId;
if (!pubchemId.Equals(lastSelected))
{
Cursor = Cursors.WaitCursor;
// https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/241/record/SDF
var securityProtocol = ServicePointManager.SecurityProtocol;
ServicePointManager.SecurityProtocol = securityProtocol | SecurityProtocolType.Tls11 | SecurityProtocolType.Tls12;
try
{
var request = (HttpWebRequest)WebRequest.Create(
string.Format(CultureInfo.InvariantCulture, "{0}rest/pug/compound/cid/{1}/record/SDF",
UserOptions.PubChemRestApiUri, pubchemId));
request.Timeout = 30000;
request.UserAgent = "Chem4Word";
HttpWebResponse response;
response = (HttpWebResponse)request.GetResponse();
if (HttpStatusCode.OK.Equals(response.StatusCode))
{
// we will read data via the response stream
using (var resStream = response.GetResponseStream())
{
lastMolfile = new StreamReader(resStream).ReadToEnd();
SdFileConverter sdFileConverter = new SdFileConverter();
Model.Model model = sdFileConverter.Import(lastMolfile);
if (model.MeanBondLength < Core.Helpers.Constants.MinimumBondLength - Core.Helpers.Constants.BondLengthTolerance ||
model.MeanBondLength > Core.Helpers.Constants.MaximumBondLength + Core.Helpers.Constants.BondLengthTolerance)
{
model.ScaleToAverageBondLength(Core.Helpers.Constants.StandardBondLength);
}
this.display1.Chemistry = model;
if (model.AllWarnings.Count > 0 || model.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", lastMolfile);
List <string> lines = new List <string>();
if (model.AllErrors.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, model.AllErrors));
lines.Add("Errors(s)");
lines.AddRange(model.AllErrors);
}
if (model.AllWarnings.Count > 0)
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, model.AllWarnings));
lines.Add("Warnings(s)");
lines.AddRange(model.AllWarnings);
}
ErrorsAndWarnings.Text = string.Join(Environment.NewLine, lines);
}
else
{
CMLConverter cmlConverter = new CMLConverter();
Cml = cmlConverter.Export(model);
ImportButton.Enabled = true;
}
}
result = pubchemId;
}
else
{
result = string.Empty;
lastMolfile = string.Empty;
StringBuilder sb = new StringBuilder();
sb.AppendLine($"Bad request. Status code: {response.StatusCode}");
UserInteractions.AlertUser(sb.ToString());
}
}
catch (Exception ex)
{
if (ex.Message.Equals("The operation has timed out"))
{
ErrorsAndWarnings.Text = "Please try again later - the service has timed out";
}
else
{
ErrorsAndWarnings.Text = ex.Message;
Telemetry.Write(module, "Exception", ex.Message);
Telemetry.Write(module, "Exception", ex.StackTrace);
}
}
finally
{
ServicePointManager.SecurityProtocol = securityProtocol;
Cursor = Cursors.Default;
}
}
}
return(result);
}
private void button1_Click(object sender, EventArgs e)
{
StringBuilder sb = new StringBuilder();
sb.Append("All molecule files (*.mol, *.cml)|*.mol;*.cml");
sb.Append("|CML molecule files (*.cml)|*.cml");
sb.Append("|MDL molecule files (*.mol)|*.mol");
openFileDialog1.Filter = sb.ToString();
DialogResult dr = openFileDialog1.ShowDialog();
if (dr == DialogResult.OK)
{
string fileType = Path.GetExtension(openFileDialog1.FileName).ToLower();
string filename = Path.GetFileName(openFileDialog1.FileName);
string mol = File.ReadAllText(openFileDialog1.FileName);
Model model = null;
switch (fileType)
{
case ".cml":
CMLConverter cmlConverter = new CMLConverter();
model = cmlConverter.Import(mol);
break;
case ".mol":
SdFileConverter molfileConverter = new SdFileConverter();
model = molfileConverter.Import(mol);
break;
}
string fCml = "";
string fCalc = "";
if (model != null)
{
this.Text = filename;
foreach (var molecule in model.Molecules)
{
if (!string.IsNullOrEmpty(molecule.ConciseFormula))
{
fCml += $"{molecule.ConciseFormula} . ";
}
fCalc += $"{molecule.CalculatedFormula()} . ";
}
if (fCalc.EndsWith(" . "))
{
fCalc = fCalc.Substring(0, fCalc.Length - 3);
}
if (fCml.EndsWith(" . "))
{
fCml = fCml.Substring(0, fCml.Length - 3);
}
lblCalculated.Text = $"{fCalc}";
lblFromCml.Text = $"{fCml}";
lblOverall.Text = $"{model.ConciseFormula}";
display1.Chemistry = mol;
}
}
}
private void LoadStructure_Click(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
Model model = null;
StringBuilder sb = new StringBuilder();
sb.Append("All molecule files (*.mol, *.sdf, *.cml)|*.mol;*.sdf;*.cml");
sb.Append("|CML molecule files (*.cml)|*.cml");
sb.Append("|MDL molecule files (*.mol, *.sdf)|*.mol;*.sdf");
openFileDialog1.Title = "Open Structure";
openFileDialog1.InitialDirectory = Environment.SpecialFolder.MyDocuments.ToString();
openFileDialog1.Filter = sb.ToString();
openFileDialog1.FileName = "";
openFileDialog1.ShowHelp = false;
DialogResult dr = openFileDialog1.ShowDialog();
if (dr == DialogResult.OK)
{
string fileType = Path.GetExtension(openFileDialog1.FileName).ToLower();
string filename = Path.GetFileName(openFileDialog1.FileName);
string mol = File.ReadAllText(openFileDialog1.FileName);
CMLConverter cmlConvertor = new CMLConverter();
SdFileConverter sdFileConverter = new SdFileConverter();
switch (fileType)
{
case ".mol":
case ".sdf":
model = sdFileConverter.Import(mol);
break;
case ".cml":
case ".xml":
model = cmlConvertor.Import(mol);
break;
}
if (model != null)
{
model.EnsureBondLength(20, false);
if (string.IsNullOrEmpty(model.CustomXmlPartGuid))
{
model.CustomXmlPartGuid = Guid.NewGuid().ToString("N");
}
if (!string.IsNullOrEmpty(_lastCml))
{
var clone = cmlConvertor.Import(_lastCml);
Debug.WriteLine(
$"Pushing F: {clone.ConciseFormula} BL: {clone.MeanBondLength.ToString("#,##0.00")} onto Stack");
_undoStack.Push(clone);
}
_lastCml = cmlConvertor.Export(model);
_telemetry.Write(module, "Information", $"File: {filename}");
ShowChemistry(filename, model);
}
}
}
catch (Exception exception)
{
_telemetry.Write(module, "Exception", $"Exception: {exception.Message}");
_telemetry.Write(module, "Exception(Data)", $"Exception: {exception}");
MessageBox.Show(exception.StackTrace, exception.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);
}
