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);
}
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
}
public static void RefreshAllStructures(Word.Document doc)
{
string module = $"{Product}.{Class}.{MethodBase.GetCurrentMethod().Name}()";
if (Globals.Chem4WordV3.SystemOptions == null)
{
Globals.Chem4WordV3.LoadOptions();
}
IChem4WordRenderer renderer =
Globals.Chem4WordV3.GetRendererPlugIn(
Globals.Chem4WordV3.SystemOptions.SelectedRendererPlugIn);
if (renderer != null)
{
foreach (CustomXMLPart xmlPart in doc.CustomXMLParts)
{
var cml = xmlPart.XML;
var cxmlId = CustomXmlPartHelper.GetCmlId(xmlPart);
CMLConverter cc = new CMLConverter();
var model = cc.Import(cml);
renderer.Properties = new Dictionary <string, string>();
renderer.Properties.Add("Guid", cxmlId);
renderer.Cml = cml;
string tempfileName = renderer.Render();
if (File.Exists(tempfileName))
{
UpdateThisStructure(doc, model, cxmlId, tempfileName);
}
}
}
}
private void HandleDataContextChanged()
{
ChemistryModel chemistryModel = null;
if (Chemistry is string)
{
var data = Chemistry as string;
if (!string.IsNullOrEmpty(data))
{
if (data.StartsWith("<"))
{
var conv = new CMLConverter();
chemistryModel = conv.Import(data);
}
if (data.Contains("M END"))
{
var conv = new SdFileConverter();
chemistryModel = conv.Import(data);
}
}
}
else
{
if (Chemistry != null && !(Chemistry is ChemistryModel))
{
throw new ArgumentException("Object must be of type 'Chem4Word.Model.Model'.");
}
chemistryModel = Chemistry as ChemistryModel;
}
if (chemistryModel != null)
{
if (chemistryModel.AllAtoms.Count > 0)
{
chemistryModel.RescaleForXaml(Constants.StandardBondLength * 2);
Debug.WriteLine($"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;
}
}
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;
}
}
}
/// <summary>
/// Create an OpenXml Word Document from the CML
/// </summary>
/// <param name="cml">Input Chemistry</param>
/// <param name="guid">Bookmark to create</param>
/// <param name="options"></param>
/// <returns></returns>
public static string CreateFromCml(string cml, string guid, Options options, IChem4WordTelemetry telemetry, Point topLeft)
{
CMLConverter cc = new CMLConverter();
Model.Model m = cc.Import(cml);
string fileName = Path.Combine(Path.GetTempPath(), $"Chem4Word-V3-{guid}.docx");
bool canRender = m.AllAtoms.Count > 0 && (m.MeanBondLength > Constants.BondLengthTolerance / 2 || m.AllBonds.Count == 0);
if (canRender)
{
string bookmarkName = "C4W_" + guid;
// Create a Wordprocessing document.
using (WordprocessingDocument package = WordprocessingDocument.Create(fileName, WordprocessingDocumentType.Document))
{
// Add a new main document part.
MainDocumentPart mdp = package.AddMainDocumentPart();
mdp.Document = new Document(new Body());
Body docbody = package.MainDocumentPart.Document.Body;
// This is for test
//AddParagraph(docbody, "Hello World", bookmarkName);
// This will be live
AddPictureFromModel(docbody, m, bookmarkName, options, telemetry, topLeft);
// Save changes to the main document part.
package.MainDocumentPart.Document.Save();
}
}
return(fileName);
}
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 EditorHost_Load(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
Cursor.Current = Cursors.WaitCursor;
if (TopLeft.X != 0 && TopLeft.Y != 0)
{
Left = (int)TopLeft.X;
Top = (int)TopLeft.Y;
}
CMLConverter cc = new CMLConverter();
JSONConverter jc = new JSONConverter();
Model.Model model = cc.Import(_cml);
WpfChemDoodle editor = new WpfChemDoodle();
editor.Telemetry = Telemetry;
editor.ProductAppDataPath = ProductAppDataPath;
editor.UserOptions = UserOptions;
editor.TopLeft = TopLeft;
editor.StructureJson = jc.Export(model);
editor.IsSingleMolecule = model.Molecules.Count == 1;
editor.AverageBondLength = model.MeanBondLength;
editor.InitializeComponent();
elementHost1.Child = editor;
editor.OnButtonClick += OnWpfButtonClick;
this.Show();
Application.DoEvents();
}
/// <summary>
/// Occurs after a new custom XMl part is loaded into the document
/// Useful for updating the Navigator
/// </summary>
/// <param name="NewPart"></param>
private void OnPartAfterLoad(CustomXMLPart NewPart)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
var converter = new CMLConverter();
//get the chemistry
var chemModel = converter.Import(NewPart.XML);
//find out which content control macthes the custom XML part
try
{
// ReSharper disable once InconsistentNaming
var matchingCC = (from ContentControl cc in _doc.ContentControls
orderby cc.Range.Start
where CustomXmlPartHelper.GuidFromTag(cc?.Tag) == CustomXmlPartHelper.GetCmlId(NewPart)
select cc).First();
//get the ordinal position of the content control
int start = 0;
foreach (ContentControl cc in _doc.ContentControls)
{
if (cc.ID == matchingCC.ID)
{
break;
}
start += 1;
}
//insert the new navigator item at the ordinal position
var newNavItem = new NavigatorItem()
{
CMLId = matchingCC?.Tag,
ChemicalStructure = NewPart.XML,
XMLPart = NewPart,
Name = chemModel.ConciseFormula
};
try
{
NavigatorItems.Insert(start, newNavItem);
}
catch (ArgumentOutOfRangeException) //can happen when there are more content controls than navigator items
{
//so simply insert the new navigator item at the end
NavigatorItems.Add(newNavItem);
}
}
catch (InvalidOperationException)
{
//sequence contains no elements - thrown on close
//just ignore
}
}
catch (Exception ex)
{
new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex).ShowDialog();
}
}
private void ClearChemistry_Click(object sender, EventArgs e)
{
var cc = new CMLConverter();
_undoStack.Push(cc.Import(_lastCml));
_lastCml = "<cml></cml>";
Display.Clear();
EnableUndoRedoButtons();
}
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
}
public void SetProperties(string cml, List <string> used1DProperties, AcmeOptions options)
{
CMLConverter cc = new CMLConverter();
_model = cc.Import(cml, used1DProperties);
_used1DProperties = used1DProperties;
EditorOptions = options;
InitialiseEditor();
}
private void MainWindow_OnLoaded(object sender, RoutedEventArgs e)
{
CMLConverter conv = new CMLConverter();
ComboBoxItem cb1 = new ComboBoxItem();
cb1.Tag = conv.Import(ChemistryValues.TESTOSTERONE);
cb1.Content = "testosterone";
SelectStructureCombo.Items.Add(cb1);
ComboBoxItem cb2 = new ComboBoxItem();
cb2.Tag = ChemistryValues.PARAFUCHSIN_CARBOL;
cb2.Content = "parafuchsin carbol";
SelectStructureCombo.Items.Add(cb2);
ComboBoxItem cb3 = new ComboBoxItem();
cb3.Tag = conv.Import(ChemistryValues.PHTHALOCYANINE);
cb3.Content = "phthalocyanine";
SelectStructureCombo.Items.Add(cb3);
ComboBoxItem cb4 = new ComboBoxItem();
cb4.Tag = conv.Import(ChemistryValues.THEMONSTER);
cb4.Content = "The Monster";
SelectStructureCombo.Items.Add(cb4);
ComboBoxItem cb5 = new ComboBoxItem();
cb5.Tag = conv.Import(ChemistryValues.INSULIN);
cb5.Content = "insulin";
SelectStructureCombo.Items.Add(cb5);
ComboBoxItem cb6 = new ComboBoxItem();
cb6.Tag = conv.Import(ChemistryValues.CHARGESPLUS);
cb6.Content = "lots of charges";
SelectStructureCombo.Items.Add(cb6);
}
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 FormEditLabels_Load(object sender, EventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
if (TopLeft.X != 0 && TopLeft.Y != 0)
{
Left = (int)TopLeft.X;
Top = (int)TopLeft.Y;
}
// Load Cml into model
_model = _cmlConvertor.Import(Cml);
#region Display Overall Concise Formula
rtbConcise.SelectionFont = new Font("Tahoma", 10);
rtbConcise.Text = "Overall Concise formula for this structure is ";
rtbConcise.SelectionStart = rtbConcise.TextLength;
List <FormulaPart> parts = FormulaHelper.Parts(_model.ConciseFormula);
foreach (var part in parts)
{
switch (part.Count)
{
case 0: // Seperator or multiplier
case 1: // No Subscript
rtbConcise.SelectionFont = new Font("Tahoma", 10);
rtbConcise.SelectionCharOffset = 0;
rtbConcise.AppendText(part.Atom);
break;
default: // With Subscript
rtbConcise.SelectionFont = new Font("Tahoma", 10);
rtbConcise.SelectionCharOffset = 0;
rtbConcise.AppendText(part.Atom);
rtbConcise.SelectionFont = new Font("Tahoma", 7);
rtbConcise.SelectionCharOffset = -5;
rtbConcise.AppendText($"{part.Count}");
break;
}
}
#endregion Display Overall Concise Formula
LoadTabsControls();
}
catch (Exception ex)
{
new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex).ShowDialog();
}
}
public void CmlImportNoAtoms()
{
CMLConverter mc = new CMLConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("NoAtoms.xml"));
// Basic sanity checks
Assert.True(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
Assert.True(m.TotalAtomsCount == 0, $"Expected 0 Atoms; Got {m.TotalAtomsCount}");
Assert.True(m.TotalBondsCount == 0, $"Expected 0 Bonds; Got {m.TotalBondsCount}");
// Check that names and formulae have not been trashed
Assert.True(m.Molecules.Values.First().Names.Count == 1, $"Expected 1 Chemical Names; Got {m.Molecules.Values.First().Names.Count}");
}
private void HandleDataContextChanged()
{
Model chemistryModel = null;
if (Chemistry is string)
{
var data = Chemistry as string;
if (!string.IsNullOrEmpty(data))
{
if (data.StartsWith("<"))
{
var conv = new CMLConverter();
chemistryModel = conv.Import(data);
chemistryModel.EnsureBondLength(20, false);
}
if (data.Contains("M END"))
{
var conv = new SdFileConverter();
chemistryModel = conv.Import(data);
chemistryModel.EnsureBondLength(20, false);
}
}
}
else
{
if (Chemistry != null && !(Chemistry is Model))
{
Debugger.Break();
throw new ArgumentException($"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);
}
}
}
/// <summary>
/// Create an OpenXml Word Document from the CML
/// </summary>
/// <param name="cml">Input Chemistry</param>
/// <param name="guid">Bookmark to create</param>
/// <param name="options"></param>
/// <param name="telemetry"></param>
/// <param name="topLeft"></param>
/// <returns></returns>
public static string CreateFromCml(string cml, string guid, OoXmlV4Options options, IChem4WordTelemetry telemetry, Point topLeft)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
CMLConverter cc = new CMLConverter();
Model model = cc.Import(cml);
if (model.AllErrors.Count > 0 || model.AllWarnings.Count > 0)
{
if (model.AllErrors.Count > 0)
{
telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, model.AllErrors));
}
if (model.AllWarnings.Count > 0)
{
telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, model.AllWarnings));
}
}
string fileName = string.Empty;
bool canRender = model.TotalAtomsCount > 0 &&
(model.TotalBondsCount == 0 ||
model.MeanBondLength > Core.Helpers.Constants.BondLengthTolerance / 2);
if (canRender)
{
fileName = Path.Combine(Path.GetTempPath(), $"Chem4Word-V3-{guid}.docx");
string bookmarkName = Core.Helpers.Constants.OoXmlBookmarkPrefix + guid;
// Create a Wordprocessing document.
using (WordprocessingDocument package = WordprocessingDocument.Create(fileName, WordprocessingDocumentType.Document))
{
// Add a new main document part.
MainDocumentPart mdp = package.AddMainDocumentPart();
mdp.Document = new Document(new Body());
Body docbody = package.MainDocumentPart.Document.Body;
// This will be live
AddPictureFromModel(docbody, model, bookmarkName, options, telemetry, topLeft);
// Save changes to the main document part.
package.MainDocumentPart.Document.Save();
}
}
return(fileName);
}
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;
}
}
/// <summary>
/// Loads up the model initially from the document
/// </summary>
private void LoadModel()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
var converter = new CMLConverter();
if (NavigatorItems.Any())
{
NavigatorItems.Clear();
}
if (_doc != null)
{
Dictionary <string, int> added = new Dictionary <string, int>();
var navItems = from ContentControl ccs in _doc.ContentControls
join CustomXMLPart part in _parts
on CustomXmlPartHelper.GuidFromTag(ccs?.Tag) equals CustomXmlPartHelper.GetCmlId(part)
orderby ccs.Range.Start
let chemModel = converter.Import(part.XML)
select new NavigatorItem
{
CMLId = ccs?.Tag, ChemicalStructure = part.XML, XMLPart = part, Name = chemModel.ConciseFormula
};
foreach (NavigatorItem navigatorItem in navItems)
{
string guid = CustomXmlPartHelper.GuidFromTag(navigatorItem.CMLId);
if (!string.IsNullOrEmpty(guid))
{
if (!added.ContainsKey(guid))
{
NavigatorItems.Add(navigatorItem);
added.Add(guid, 1);
}
}
}
Debug.WriteLine("Number of items loaded = {0}", NavigatorItems.Count);
}
}
catch (Exception ex)
{
using (var form = new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex))
{
form.ShowDialog();
}
}
}
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 CmlImportCopperPhthalocyanine()
{
CMLConverter mc = new CMLConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("CopperPhthalocyanine.xml"));
// Basic Sanity Checks
Assert.True(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
Assert.True(m.TotalAtomsCount == 57, $"Expected 57 Atoms; Got {m.TotalAtomsCount}");
Assert.True(m.TotalBondsCount == 68, $"Expected 68 Bonds; Got {m.TotalBondsCount}");
Assert.True(m.Molecules.Values.First().Rings.Count == 12, $"Expected 12 Rings; Got {m.Molecules.Values.First().Rings.Count}");
var list = m.Molecules.Values.First().SortRingsForDBPlacement();
Assert.True(list.Count == 12, $"Expected 12 Rings; Got {list.Count}");
}
public void CmlImportPhthalocyanineThenRefresh()
{
CMLConverter mc = new CMLConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("Phthalocyanine.xml"));
// Basic Sanity Checks
Assert.True(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
Assert.True(m.TotalAtomsCount == 58, $"Expected 58 Atoms; Got {m.TotalAtomsCount}");
Assert.True(m.TotalBondsCount == 66, $"Expected 66 Bonds; Got {m.TotalBondsCount}");
Assert.True(m.Molecules.Values.First().Rings.Count == 9, $"Expected 9 Rings; Got {m.Molecules.Values.First().Rings.Count}");
var list = m.Molecules.Values.First().SortRingsForDBPlacement();
Assert.True(list.Count == 8, $"Expected 8 Rings; Got {list.Count}");
}
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);
}
public void CmlImportCopperPhthalocyanineThenRefresh()
{
CMLConverter mc = new CMLConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("CopperPhthalocyanine.xml"));
m.RefreshMolecules();
// Basic Sanity Checks
Assert.IsTrue(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
Assert.IsTrue(m.AllAtoms.Count == 57, $"Expected 57 Atoms; Got {m.AllAtoms.Count}");
Assert.IsTrue(m.AllBonds.Count == 68, $"Expected 68 Bonds; Got {m.AllBonds.Count}");
Assert.IsTrue(m.Molecules[0].Rings.Count == 12, $"Expected 12 Rings; Got {m.Molecules[0].Rings.Count}");
var list = m.Molecules[0].SortRingsForDBPlacement();
Assert.IsTrue(list.Count == 12, $"Expected 12 Rings; Got {list.Count}");
}
public void CmlImportBenzene()
{
CMLConverter mc = new CMLConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("Benzene.xml"));
// 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 == 3, $"Expected 3 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 CmlImportBenzene()
{
CMLConverter mc = new CMLConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("Benzene.xml"));
// 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, $"Expected 1 Ring; Got {m.Molecules.SelectMany(m1 => m1.Rings).Count()}");
}
private string CmlFromBytes(byte[] byteArray, long id)
{
string cml = Encoding.UTF8.GetString(byteArray);
CMLConverter cc = new CMLConverter();
Model.Model m = cc.Import(cml);
double before = m.MeanBondLength;
if (before < Constants.MinimumBondLength - Constants.BondLengthTolerance ||
before > Constants.MaximumBondLength + Constants.BondLengthTolerance)
{
m.ScaleToAverageBondLength(Constants.StandardBondLength);
double after = m.MeanBondLength;
Debug.WriteLine($"Structure Id: {id} rescaled from {before.ToString("#0.00")} to {after.ToString("#0.00")}");
}
return(cc.Export(m));
}
public void CmlImportTestosteroneThenRefresh()
{
CMLConverter mc = new CMLConverter();
Model m = mc.Import(ResourceHelper.GetStringResource("Testosterone.xml"));
// Basic Sanity Checks
Assert.True(m.Molecules.Count == 1, $"Expected 1 Molecule; Got {m.Molecules.Count}");
Assert.True(m.TotalAtomsCount == 25, $"Expected 25 Atoms; Got {m.TotalAtomsCount}");
Assert.True(m.TotalBondsCount == 28, $"Expected 28 Bonds; Got {m.TotalBondsCount}");
// Check that names and formulae have not been trashed
Assert.True(m.Molecules.Values.First().Names.Count == 4, $"Expected 4 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 }");
Assert.True(m.Molecules.Values.First().Rings.Count == 4, $"Expected 4 Rings; Got {m.Molecules.Values.First().Rings.Count}");
var list = m.Molecules.Values.First().SortRingsForDBPlacement();
Assert.True(list.Count == 4, $"Expected 4 Rings; Got {list.Count}");
}