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 Redo_Click(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
Model m = _redoStack.Pop();
Debug.WriteLine(
$"Popped F: {m.ConciseFormula} BL: {m.MeanBondLength.ToString("#,##0.00")} from Redo Stack");
if (!string.IsNullOrEmpty(_lastCml))
{
CMLConverter cc = new CMLConverter();
var clone = cc.Import(_lastCml);
_lastCml = cc.Export(m);
Debug.WriteLine(
$"Pushing F: {clone.ConciseFormula} BL: {clone.MeanBondLength.ToString("#,##0.00")} onto Undo Stack");
_undoStack.Push(clone);
}
ShowChemistry($"Redo -> {m.ConciseFormula}", m);
}
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 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 HandleChangedCml(string cml, string captionPrefix)
{
var cc = new CMLConverter();
if (_lastCml != EmptyCml)
{
var clone = cc.Import(_lastCml);
Debug.WriteLine(
$"Pushing F: {clone.ConciseFormula} BL: {clone.MeanBondLength.ToString("#,##0.00")} onto Stack");
_undoStack.Push(clone);
}
Model m = cc.Import(cml);
m.Relabel(true);
m.EnsureBondLength(20, false);
_lastCml = cc.Export(m);
// Cause re-read of settings (in case they have changed)
_editorOptions = new AcmeOptions(null);
SetDisplayOptions();
RedoStack.SetOptions(_editorOptions);
UndoStack.SetOptions(_editorOptions);
ShowChemistry($"{captionPrefix} {m.ConciseFormula}", m);
}
private void OnWpfButtonClick(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
WpfEventArgs args = (WpfEventArgs)e;
if (args.Button.ToUpper().Equals("OK"))
{
DialogResult = DialogResult.OK;
CMLConverter cc = new CMLConverter();
JSONConverter jc = new JSONConverter();
Model.Model model = jc.Import(args.OutputValue);
OutputValue = cc.Export(model);
}
if (args.Button.ToUpper().Equals("CANCEL"))
{
DialogResult = DialogResult.Cancel;
OutputValue = "";
}
WpfChemDoodle editor = elementHost1.Child as WpfChemDoodle;
if (editor != null)
{
editor.OnButtonClick -= OnWpfButtonClick;
editor = null;
}
Hide();
}
private void ProcessResponse(HttpWebResponse response)
{
LabelInfo.Text = "";
// read data via the response stream
using (Stream resStream = response.GetResponseStream())
{
if (resStream != null)
{
StreamReader sr = new StreamReader(resStream);
string temp = sr.ReadToEnd();
CMLConverter cmlConverter = new CMLConverter();
Model.Model model = cmlConverter.Import(temp);
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);
}
Cml = cmlConverter.Export(model);
display1.Chemistry = Cml;
ImportButton.Enabled = true;
}
}
}
private void EditLabelsHost_FormClosing(object sender, FormClosingEventArgs e)
{
if (!_closedInCode)
{
if (elementHost1.Child is LabelsEditor editor)
{
if (editor.IsDirty)
{
StringBuilder sb = new StringBuilder();
sb.AppendLine("Do you wish to save your changes?");
sb.AppendLine(" Click 'Yes' to save your changes and exit.");
sb.AppendLine(" Click 'No' to discard your changes and exit.");
sb.AppendLine(" Click 'Cancel' to return to the form.");
DialogResult dr = UserInteractions.AskUserYesNoCancel(sb.ToString());
switch (dr)
{
case DialogResult.Cancel:
e.Cancel = true;
break;
case DialogResult.Yes:
var cmlConvertor = new CMLConverter();
Cml = cmlConvertor.Export(editor.EditedModel);
DialogResult = DialogResult.OK;
break;
case DialogResult.No:
DialogResult = DialogResult.Cancel;
break;
}
}
}
}
}
private void EditorHost_FormClosing(object sender, FormClosingEventArgs e)
{
if (DialogResult != DialogResult.OK && e.CloseReason == CloseReason.UserClosing)
{
if (elementHost1.Child is CmlEditor editor &&
editor.IsDirty)
{
StringBuilder sb = new StringBuilder();
sb.AppendLine("Do you wish to save your changes?");
sb.AppendLine(" Click 'Yes' to save your changes and exit.");
sb.AppendLine(" Click 'No' to discard your changes and exit.");
sb.AppendLine(" Click 'Cancel' to return to the form.");
DialogResult dr = UserInteractions.AskUserYesNoCancel(sb.ToString());
switch (dr)
{
case DialogResult.Cancel:
e.Cancel = true;
break;
case DialogResult.Yes:
DialogResult = DialogResult.OK;
CMLConverter cc = new CMLConverter();
OutputValue = cc.Export(editor.EditedModel);
Hide();
break;
case DialogResult.No:
break;
}
}
}
}
private void Save_Click(object sender, EventArgs e)
{
CMLConverter cc = new CMLConverter();
DialogResult = DialogResult.Cancel;
switch (_editorType)
{
case "ACME":
if (elementHost1.Child is Editor acmeEditor &&
acmeEditor.IsDirty)
{
DialogResult = DialogResult.OK;
var model = acmeEditor.EditedModel;
model.RescaleForCml();
// Replace any temporary Ids which are Guids
model.ReLabelGuids();
OutputValue = cc.Export(model);
}
break;
case "LABELS":
if (elementHost1.Child is LabelsEditor labelsEditor &&
labelsEditor.IsDirty)
{
DialogResult = DialogResult.OK;
OutputValue = cc.Export(labelsEditor.EditedModel);
}
break;
default:
if (elementHost1.Child is CmlEditor cmlEditor &&
cmlEditor.IsDirty)
{
DialogResult = DialogResult.OK;
OutputValue = cc.Export(cmlEditor.EditedModel);
}
break;
}
Hide();
}
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 Save_Click(object sender, EventArgs e)
{
DialogResult = DialogResult.OK;
_closedInCode = true;
if (elementHost1.Child is LabelsEditor editor)
{
CMLConverter cc = new CMLConverter();
DialogResult = DialogResult.OK;
Cml = cc.Export(editor.EditedModel);
Hide();
}
}
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);
}
}
}
}
}
// Called by ImportCml(), ImportCml()
private long AddChemistry(SQLiteConnection conn, Model model, string chemistryName, string formula)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
long lastId;
StringBuilder sb = new StringBuilder();
model.RemoveExplicitHydrogens();
Byte[] blob = Encoding.UTF8.GetBytes(_cmlConverter.Export(model, true));
//Byte[] blob = Encoding.UTF8.GetBytes(_sdFileConverter.Export(model));
sb.AppendLine("INSERT INTO GALLERY");
sb.AppendLine(" (Chemistry, Name, Formula)");
sb.AppendLine("VALUES");
sb.AppendLine(" (@blob, @name, @formula)");
SQLiteCommand command = new SQLiteCommand(sb.ToString(), conn);
command.Parameters.Add("@blob", DbType.Binary, blob.Length).Value = blob;
command.Parameters.Add("@name", DbType.String, chemistryName.Length).Value = chemistryName;
command.Parameters.Add("@formula", DbType.String, formula.Length).Value = formula;
command.ExecuteNonQuery();
string sql = "SELECT last_insert_rowid()";
SQLiteCommand cmd = new SQLiteCommand(sql, conn);
lastId = (Int64)cmd.ExecuteScalar();
return(lastId);
}
catch (Exception ex)
{
using (var form = new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex))
{
form.ShowDialog();
}
return(-1);
}
}
public void RefreshPanels()
{
RefreshFormulaePanel();
RefreshNamesPanel();
if (string.IsNullOrEmpty(_cml))
{
Model.Model model = new Model.Model();
model.Molecules.Add(Molecule);
CMLConverter cmlConverter = new CMLConverter();
_cml = cmlConverter.Export(model);
display1.Chemistry = _cml;
}
}
private void Save_Click(object sender, EventArgs e)
{
CMLConverter cc = new CMLConverter();
DialogResult = DialogResult.Cancel;
if (elementHost1.Child is CmlEditor editor &&
editor.IsDirty)
{
DialogResult = DialogResult.OK;
OutputValue = cc.Export(editor.EditedModel);
}
Hide();
}
public void CmlImportExportNested()
{
CMLConverter mc = new CMLConverter();
Model model_1 = mc.Import(ResourceHelper.GetStringResource("NestedMolecules.xml"));
// Basic Sanity Checks
Assert.True(model_1.Molecules.Count == 1, $"Expected 1 Molecule; Got {model_1.Molecules.Count}");
// Check molecule m0 has 4 child molecules and no atoms
Molecule molecule_1 = model_1.Molecules.Values.First();
Assert.True(molecule_1.Molecules.Count == 4, $"Expected 4 Molecule; Got {molecule_1.Molecules.Count}");
Assert.True(molecule_1.Atoms.Count == 0, $"Expected 0 Atoms; Got {molecule_1.Atoms.Count}");
// Check molecule m2 has no child molecules and 6 atoms
molecule_1 = model_1.Molecules.Values.First().Molecules.Values.ToList()[1];
Assert.True(molecule_1.Molecules.Count == 0, $"Expected 0 Molecule; Got {molecule_1.Molecules.Count}");
Assert.True(molecule_1.Atoms.Count == 6, $"Expected 6 Atoms; Got {molecule_1.Atoms.Count}");
// Check molecule m1 has 1 child molecules and no atoms
molecule_1 = model_1.Molecules.Values.First().Molecules.Values.First();
Assert.True(molecule_1.Molecules.Count == 1, $"Expected 1 Molecule; Got {molecule_1.Molecules.Count}");
Assert.True(molecule_1.Atoms.Count == 0, $"Expected 0 Atoms; Got {molecule_1.Atoms.Count}");
// Check molecule m5 has 1 child molecules and 6 atoms
molecule_1 = model_1.Molecules.Values.First().Molecules.Values.First().Molecules.Values.First();
Assert.True(molecule_1.Molecules.Count == 0, $"Expected 0 Molecule; Got {molecule_1.Molecules.Count}");
Assert.True(molecule_1.Atoms.Count == 6, $"Expected 6 Atoms; Got {molecule_1.Atoms.Count}");
var exported = mc.Export(model_1);
Model model_2 = mc.Import(exported);
// Basic Sanity Checks
Assert.True(model_2.Molecules.Count == 1, $"Expected 1 Molecule; Got {model_2.Molecules.Count}");
// Check molecule m0 has 4 child molecules and no atoms
Molecule molecule_2 = model_2.Molecules.Values.First();
Assert.True(molecule_2.Molecules.Count == 4, $"Expected 4 Molecule; Got {molecule_2.Molecules.Count}");
Assert.True(molecule_2.Atoms.Count == 0, $"Expected 0 Atoms; Got {molecule_2.Atoms.Count}");
// Check molecule m2 has no child molecules and 6 atoms
molecule_2 = model_2.Molecules.Values.First().Molecules.Values.ToList()[1];
Assert.True(molecule_2.Molecules.Count == 0, $"Expected 0 Molecule; Got {molecule_2.Molecules.Count}");
Assert.True(molecule_2.Atoms.Count == 6, $"Expected 6 Atoms; Got {molecule_2.Atoms.Count}");
// Check molecule m1 has 1 child molecules and no atoms
molecule_2 = model_2.Molecules.Values.First().Molecules.Values.First();
Assert.True(molecule_2.Molecules.Count == 1, $"Expected 1 Molecule; Got {molecule_2.Molecules.Count}");
Assert.True(molecule_2.Atoms.Count == 0, $"Expected 0 Atoms; Got {molecule_2.Atoms.Count}");
// Check molecule m5 has 1 child molecules and 6 atoms
molecule_2 = model_2.Molecules.Values.First().Molecules.Values.First().Molecules.Values.First();
Assert.True(molecule_2.Molecules.Count == 0, $"Expected 0 Molecule; Got {molecule_2.Molecules.Count}");
Assert.True(molecule_2.Atoms.Count == 6, $"Expected 6 Atoms; Got {molecule_2.Atoms.Count}");
}
private void EditWithAcme_Click(object sender, EventArgs e)
{
#if !DEBUG
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
#endif
if (!string.IsNullOrEmpty(_lastCml))
{
using (EditorHost editorHost = new EditorHost(_lastCml, "ACME"))
{
editorHost.ShowDialog(this);
if (editorHost.DialogResult == DialogResult.OK)
{
CMLConverter cc = new CMLConverter();
var clone = cc.Import(_lastCml);
Debug.WriteLine(
$"Pushing F: {clone.ConciseFormula} BL: {clone.MeanBondLength.ToString("#,##0.00")} onto Stack");
_undoStack.Push(clone);
Model m = cc.Import(editorHost.OutputValue);
m.Relabel(true);
_lastCml = cc.Export(m);
// Cause re-read of settings (in case they have changed)
_editorOptions = new AcmeOptions(null);
SetDisplayOptions();
RedoStack.SetOptions(_editorOptions);
UndoStack.SetOptions(_editorOptions);
ShowChemistry($"Edited {m.ConciseFormula}", m);
}
}
TopMost = true;
TopMost = false;
Activate();
}
#if !DEBUG
}
catch (Exception exception)
{
_telemetry.Write(module, "Exception", $"Exception: {exception.Message}");
_telemetry.Write(module, "Exception(Data)", $"Exception: {exception}");
MessageBox.Show(exception.StackTrace, exception.Message);
}
#endif
}
private void Save_Click(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
CMLConverter cc = new CMLConverter();
DialogResult = DialogResult.Cancel;
if (elementHost1.Child is Chem4Word.ACME.Editor editor &&
editor.IsDirty)
{
DialogResult = DialogResult.OK;
OutputValue = cc.Export(editor.EditedModel);
}
Telemetry.Write(module, "Verbose", $"Result: {DialogResult}");
Hide();
}
public DialogResult Edit()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
DialogResult result = DialogResult.Cancel;
try
{
Telemetry.Write(module, "Verbose", "Called");
if (HasSettings)
{
LoadSettings();
}
CMLConverter cmlConverter = new CMLConverter();
Model.Model model = cmlConverter.Import(Cml);
JSONConverter jsonConverter = new JSONConverter();
string json = jsonConverter.Export(model);
ChemDoodleWeb cdwEditor = new ChemDoodleWeb();
cdwEditor.TopLeft = TopLeft;
cdwEditor.Telemetry = Telemetry;
cdwEditor.ProductAppDataPath = ProductAppDataPath;
cdwEditor.UserOptions = _editorOptions;
cdwEditor.Before_JSON = json;
cdwEditor.IsSingleMolecule = model.Molecules.Count == 1;
cdwEditor.AverageBondLength = model.MeanBondLength;
result = cdwEditor.ShowDialog();
if (result == DialogResult.OK)
{
Properties = new Dictionary <string, string>();
Properties.Add("Before_Formula", cdwEditor.Before_Formula);
Properties.Add("After_Formula", cdwEditor.After_Formula);
json = cdwEditor.After_JSON;
cdwEditor.Close();
model = jsonConverter.Import(json);
Cml = cmlConverter.Export(model);
}
}
catch (Exception ex)
{
new ReportError(Telemetry, TopLeft, module, ex).ShowDialog();
}
return(result);
}
private string CmlFromBytes(byte[] byteArray, long id)
{
string cml = Encoding.UTF8.GetString(byteArray);
CMLConverter cc = new CMLConverter();
Model.Model m = cc.Import(cml);
double before = m.MeanBondLength;
if (before < Constants.MinimumBondLength - Constants.BondLengthTolerance ||
before > Constants.MaximumBondLength + Constants.BondLengthTolerance)
{
m.ScaleToAverageBondLength(Constants.StandardBondLength);
double after = m.MeanBondLength;
Debug.WriteLine($"Structure Id: {id} rescaled from {before.ToString("#0.00")} to {after.ToString("#0.00")}");
}
return(cc.Export(m));
}
private void EditLabels_Click(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
#if !DEBUG
try
#endif
{
if (!string.IsNullOrEmpty(_lastCml))
{
using (EditorHost editorHost = new EditorHost(_lastCml, "LABELS"))
{
editorHost.ShowDialog(this);
if (editorHost.DialogResult == DialogResult.OK)
{
CMLConverter cc = new CMLConverter();
var clone = cc.Import(_lastCml);
Debug.WriteLine(
$"Pushing F: {clone.ConciseFormula} BL: {clone.MeanBondLength.ToString("#,##0.00")} onto Stack");
_undoStack.Push(clone);
Model m = cc.Import(editorHost.OutputValue);
m.Relabel(true);
_lastCml = cc.Export(m);
ShowChemistry($"Edited {m.ConciseFormula}", m);
}
}
TopMost = true;
TopMost = false;
Activate();
}
}
#if !DEBUG
catch (Exception exception)
{
_telemetry.Write(module, "Exception", $"Exception: {exception.Message}");
_telemetry.Write(module, "Exception(Data)", $"Exception: {exception}");
MessageBox.Show(exception.StackTrace, exception.Message);
}
#endif
}
private void ImportStructure()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
using (new WaitCursor())
{
CMLConverter conv = new CMLConverter();
var expModel = (Model.Model)display1.Chemistry;
double before = expModel.MeanBondLength;
expModel.ScaleToAverageBondLength(Core.Helpers.Constants.StandardBondLength);
double after = expModel.MeanBondLength;
Telemetry.Write(module, "Information", $"Structure rescaled from {before.ToString("#0.00")} to {after.ToString("#0.00")}");
expModel.Relabel();
using (new WaitCursor())
{
expModel.Molecules[0].ChemicalNames.Clear();
if (_allResults.IupacNames != null)
{
foreach (var di in _allResults.IupacNames)
{
var cn = new Model.ChemicalName();
cn.Name = di.data;
cn.DictRef = "chebi:Iupac";
expModel.Molecules[0].ChemicalNames.Add(cn);
}
}
if (_allResults.Synonyms != null)
{
foreach (var di in _allResults.Synonyms)
{
var cn = new Model.ChemicalName();
cn.Name = di.data;
cn.DictRef = "chebi:Synonym";
expModel.Molecules[0].ChemicalNames.Add(cn);
}
}
Cml = conv.Export(expModel);
}
}
}
private void EditorHost_FormClosing(object sender, FormClosingEventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
if (DialogResult != DialogResult.OK && e.CloseReason == CloseReason.UserClosing)
{
if (elementHost1.Child is Chem4Word.ACME.Editor editor &&
editor.IsDirty)
{
StringBuilder sb = new StringBuilder();
sb.AppendLine("Do you wish to save your changes?");
sb.AppendLine(" Click 'Yes' to save your changes and exit.");
sb.AppendLine(" Click 'No' to discard your changes and exit.");
sb.AppendLine(" Click 'Cancel' to return to the form.");
DialogResult dr = UserInteractions.AskUserYesNoCancel(sb.ToString());
switch (dr)
{
case DialogResult.Cancel:
e.Cancel = true;
break;
case DialogResult.Yes:
DialogResult = DialogResult.OK;
var model = editor.EditedModel;
model.RescaleForCml();
// Replace any temporary Ids which are Guids
model.ReLabelGuids();
CMLConverter cc = new CMLConverter();
OutputValue = cc.Export(model);
Telemetry.Write(module, "Verbose", $"Result: {DialogResult}");
Hide();
editor = null;
break;
case DialogResult.No:
Telemetry.Write(module, "Verbose", $"Result: {DialogResult}");
editor = null;
break;
}
}
}
}
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 DialogResult Edit()
{
DialogResult result = DialogResult.Cancel;
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
Telemetry.Write(module, "Verbose", "Called");
if (HasSettings)
{
LoadSettings();
}
// Strip off Formulae and ChemicalNames as we don't edit them here
CMLConverter cmlConverter = new CMLConverter();
Model.Model model = cmlConverter.Import(Cml);
foreach (Molecule molecule in model.Molecules)
{
molecule.ChemicalNames.Clear();
molecule.Formulas.Clear();
molecule.ConciseFormula = "";
}
EditorHost host = new EditorHost(cmlConverter.Export(model));
host.TopLeft = TopLeft;
host.ShowDialog();
result = host.Result;
Cml = host.OutputValue;
host.Close();
host.Dispose();
}
catch (Exception ex)
{
new ReportError(Telemetry, TopLeft, module, ex).ShowDialog();
}
return(result);
}
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 OnSaveClick(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
Globals.Chem4WordV3.Telemetry.Write(module, "Action", "Triggered");
try
{
if (CanSave())
{
Cml = _cmlConvertor.Export(_model);
DialogResult = DialogResult.OK;
}
else
{
UserInteractions.InformUser("Can't save because at least one user defined label contains an error");
}
}
catch (Exception ex)
{
new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex).ShowDialog();
}
}
public static void DoUpgrade(Word.Document doc)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
int sel = doc.Application.Selection.Range.Start;
Globals.Chem4WordV3.DisableDocumentEvents(doc);
try
{
string extension = doc.FullName.Split('.').Last();
string guid = Guid.NewGuid().ToString("N");
string timestamp = DateTime.Now.ToString("yyyyMMdd-HHmmss", CultureInfo.InvariantCulture);
string destination = Path.Combine(Globals.Chem4WordV3.AddInInfo.ProductAppDataPath, "Backups", $"Chem4Word-{timestamp}-{guid}.{extension}");
File.Copy(doc.FullName, destination);
}
catch (Exception ex)
{
// Nothing much we can do here :-(
Debug.WriteLine(ex.Message);
}
List <UpgradeTarget> targets = CollectData(doc);
int upgradedCCs = 0;
int upgradedXml = 0;
foreach (var target in targets)
{
if (target.ContentControls.Count > 0)
{
upgradedXml++;
upgradedCCs += target.ContentControls.Count;
}
foreach (var cci in target.ContentControls)
{
foreach (Word.ContentControl cc in doc.ContentControls)
{
if (cc.ID.Equals(cci.Id))
{
if (cci.Type.Equals("2D"))
{
cc.LockContents = false;
cc.Title = Constants.ContentControlTitle;
cc.Tag = target.Model.CustomXmlPartGuid;
cc.LockContents = true;
}
else
{
cc.LockContents = false;
cc.Range.Delete();
int start = cc.Range.Start;
cc.Delete();
doc.Application.Selection.SetRange(start - 1, start - 1);
bool isFormula = false;
string source;
string text = CustomRibbon.GetInlineText(target.Model, cci.Type, ref isFormula, out source);
Word.ContentControl ccn = CustomRibbon.Insert1D(doc.Application, doc, text, isFormula, $"{cci.Type}:{target.Model.CustomXmlPartGuid}");
ccn.LockContents = true;
}
}
}
}
CMLConverter converter = new CMLConverter();
CustomXMLPart cxml = doc.CustomXMLParts.SelectByID(target.CxmlPartId);
cxml.Delete();
doc.CustomXMLParts.Add(converter.Export(target.Model));
}
EraseChemistryZones(doc);
Globals.Chem4WordV3.EnableDocumentEvents(doc);
doc.Application.Selection.SetRange(sel, sel);
if (upgradedCCs + upgradedXml > 0)
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
UserInteractions.AlertUser($"Upgrade Completed{Environment.NewLine}{Environment.NewLine}Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
}
}
private void ExportFromLibrary_OnClick(object sender, RoutedEventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
Globals.Chem4WordV3.Telemetry.Write(module, "Action", "Triggered");
try
{
string exportFolder = Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments);
VistaFolderBrowserDialog browser = new VistaFolderBrowserDialog();
browser.Description = "Select a folder to export your Library's structures as cml files";
browser.UseDescriptionForTitle = true;
browser.RootFolder = Environment.SpecialFolder.Desktop;
browser.ShowNewFolderButton = false;
browser.SelectedPath = exportFolder;
Forms.DialogResult dr = browser.ShowDialog();
if (dr == Forms.DialogResult.OK)
{
exportFolder = browser.SelectedPath;
if (Directory.Exists(exportFolder))
{
Forms.DialogResult doExport = Forms.DialogResult.Yes;
string[] existingCmlFiles = Directory.GetFiles(exportFolder, "*.cml");
if (existingCmlFiles.Length > 0)
{
StringBuilder sb = new StringBuilder();
sb.AppendLine($"This folder contains {existingCmlFiles.Length} cml files.");
sb.AppendLine("Do you wish to continue?");
doExport = UserInteractions.AskUserYesNo(sb.ToString(), Forms.MessageBoxDefaultButton.Button2);
}
if (doExport == Forms.DialogResult.Yes)
{
Database.Library lib = new Database.Library();
int exported = 0;
int progress = 0;
List <ChemistryDTO> dto = lib.GetAllChemistry(null);
int total = dto.Count;
if (total > 0)
{
ProgressBar.Maximum = dto.Count;
ProgressBar.Minimum = 0;
ProgressBarHolder.Visibility = Visibility.Visible;
SetButtonState(false);
var converter = new CMLConverter();
foreach (var obj in dto)
{
progress++;
ShowProgress(progress, $"Structure #{obj.Id} [{progress}/{total}]");
var filename = Path.Combine(browser.SelectedPath, $"Chem4Word-{obj.Id:000000000}.cml");
Model model = converter.Import(obj.Cml);
var outcome = model.EnsureBondLength(Globals.Chem4WordV3.SystemOptions.BondLength, false);
if (!string.IsNullOrEmpty(outcome))
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", outcome);
}
File.WriteAllText(filename, converter.Export(model));
exported++;
}
}
ProgressBarHolder.Visibility = Visibility.Collapsed;
SetButtonState(true);
if (exported > 0)
{
UserInteractions.InformUser($"Exported {exported} structures to {browser.SelectedPath}");
}
}
}
}
}
catch (Exception ex)
{
ProgressBarHolder.Visibility = Visibility.Collapsed;
SetButtonState(true);
new ReportError(Globals.Chem4WordV3.Telemetry, TopLeft, module, ex).ShowDialog();
}
}
public static void DoUpgrade(Word.Document doc)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
int sel = doc.Application.Selection.Range.Start;
Globals.Chem4WordV3.DisableDocumentEvents(doc);
try
{
string extension = doc.FullName.Split('.').Last();
string guid = Guid.NewGuid().ToString("N");
string timestamp = DateTime.Now.ToString("yyyyMMdd-HHmmss", CultureInfo.InvariantCulture);
string destination = Path.Combine(Globals.Chem4WordV3.AddInInfo.ProductAppDataPath, "Backups", $"Chem4Word-{timestamp}-{guid}.{extension}");
File.Copy(doc.FullName, destination);
}
catch (Exception ex)
{
// Nothing much we can do here :-(
Debug.WriteLine(ex.Message);
}
Dictionary <string, CustomXMLPart> customXmlParts = new Dictionary <string, CustomXMLPart>();
List <UpgradeTarget> targets = CollectData(doc);
int upgradedCCs = 0;
int upgradedXml = 0;
foreach (var target in targets)
{
if (target.ContentControls.Count > 0)
{
upgradedXml++;
upgradedCCs += target.ContentControls.Count;
}
foreach (var cci in target.ContentControls)
{
foreach (Word.ContentControl cc in doc.ContentControls)
{
if (cc.ID.Equals(cci.Id))
{
int start;
bool isFormula;
string source;
string text;
switch (cci.Type)
{
case "2D":
cc.LockContents = false;
cc.Title = Constants.ContentControlTitle;
cc.Tag = target.Model.CustomXmlPartGuid;
cc.LockContents = true;
// ToDo: Regenerate converted 2D structures
break;
case "new":
cc.LockContents = false;
cc.Range.Delete();
start = cc.Range.Start;
cc.Delete();
doc.Application.Selection.SetRange(start - 1, start - 1);
var model = new Model.Model();
var molecule = new Molecule();
molecule.ChemicalNames.Add(new ChemicalName {
Id = "m1.n1", Name = cci.Text, DictRef = Constants.Chem4WordUserSynonym
});
model.Molecules.Add(molecule);
model.CustomXmlPartGuid = Guid.NewGuid().ToString("N");
var cmlConvertor = new CMLConverter();
doc.CustomXMLParts.Add(cmlConvertor.Export(model));
Word.ContentControl ccn = doc.ContentControls.Add(Word.WdContentControlType.wdContentControlRichText, ref _missing);
ChemistryHelper.Insert1D(ccn, cci.Text, false, $"m1.n1:{model.CustomXmlPartGuid}");
ccn.LockContents = true;
break;
default:
cc.LockContents = false;
cc.Range.Delete();
start = cc.Range.Start;
cc.Delete();
doc.Application.Selection.SetRange(start - 1, start - 1);
isFormula = false;
text = ChemistryHelper.GetInlineText(target.Model, cci.Type, ref isFormula, out source);
Word.ContentControl ccr = doc.ContentControls.Add(Word.WdContentControlType.wdContentControlRichText, ref _missing);
ChemistryHelper.Insert1D(ccr, text, isFormula, $"{cci.Type}:{target.Model.CustomXmlPartGuid}");
ccr.LockContents = true;
break;
}
}
}
}
CMLConverter converter = new CMLConverter();
CustomXMLPart cxml = doc.CustomXMLParts.SelectByID(target.CxmlPartId);
if (customXmlParts.ContainsKey(cxml.Id))
{
customXmlParts.Add(cxml.Id, cxml);
}
doc.CustomXMLParts.Add(converter.Export(target.Model));
}
EraseChemistryZones(doc);
foreach (var kvp in customXmlParts.ToList())
{
kvp.Value.Delete();
}
Globals.Chem4WordV3.EnableDocumentEvents(doc);
doc.Application.Selection.SetRange(sel, sel);
if (upgradedCCs + upgradedXml > 0)
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
UserInteractions.AlertUser($"Upgrade Completed{Environment.NewLine}{Environment.NewLine}Upgraded {upgradedCCs} Chemistry Objects for {upgradedXml} Structures");
}
}
