private void Settings_FormClosing(object sender, FormClosingEventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
if (_dirty)
{
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:
SearcherOptions.Save();
DialogResult = DialogResult.OK;
break;
case DialogResult.No:
DialogResult = DialogResult.Cancel;
break;
}
}
}
catch (Exception ex)
{
new ReportError(Telemetry, TopLeft, module, ex).ShowDialog();
}
}
public static DialogResult UpgradeIsRequired(Word.Document doc)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
DialogResult result = DialogResult.Cancel;
int count = LegacyChemistryCount(doc);
if (count > 0)
{
StringBuilder sb = new StringBuilder();
sb.AppendLine($"We have detected {count} legacy Chemistry objects in this document.");
sb.AppendLine("Would you like them converted to the new format?");
sb.AppendLine("");
sb.AppendLine(" Click Yes to Upgrade then");
sb.AppendLine(" Click No to leave them as they are");
sb.AppendLine("");
sb.AppendLine("This operation can't be undone.");
result = UserInteractions.AskUserYesNo(sb.ToString());
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Detected {count} legacy chemistry ContentControl(s)");
}
return(result);
}
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();
}
}
private void ImportIntoLibrary_OnClick(object sender, RoutedEventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
Globals.Chem4WordV3.Telemetry.Write(module, "Action", "Triggered");
try
{
if (Globals.Chem4WordV3.LibraryNames == null)
{
Globals.Chem4WordV3.LoadNamesFromLibrary();
}
StringBuilder sb;
// Start with V2 Add-In data path
string importFolder = Path.Combine(Globals.Chem4WordV3.AddInInfo.AppDataPath, @"Chemistry Add-In for Word");
if (Directory.Exists(importFolder))
{
if (Directory.Exists(Path.Combine(importFolder, "Chemistry Gallery")))
{
importFolder = Path.Combine(importFolder, "Chemistry Gallery");
}
}
else
{
importFolder = Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments);
}
if (Directory.Exists(importFolder))
{
// Fix scrolling to selected item by using code from https://social.msdn.microsoft.com/Forums/expression/en-US/1257aebc-22a6-44f6-975b-74f5067728bc/autoposition-showfolder-dialog?forum=vbgeneral
VistaFolderBrowserDialog browser = new VistaFolderBrowserDialog();
browser.Description = "Select a folder to import cml files from";
browser.UseDescriptionForTitle = true;
browser.RootFolder = Environment.SpecialFolder.Desktop;
browser.ShowNewFolderButton = false;
browser.SelectedPath = importFolder;
Forms.DialogResult dr = browser.ShowDialog();
if (dr == Forms.DialogResult.OK)
{
string selectedFolder = browser.SelectedPath;
string doneFile = Path.Combine(selectedFolder, "library-import-done.txt");
sb = new StringBuilder();
sb.AppendLine("Do you want to import the Gallery structures into the Library?");
sb.AppendLine("(This cannot be undone.)");
dr = UserInteractions.AskUserYesNo(sb.ToString());
if (dr == Forms.DialogResult.Yes)
{
if (File.Exists(doneFile))
{
sb = new StringBuilder();
sb.AppendLine($"All files have been imported already from '{selectedFolder}'");
sb.AppendLine("Do you want to rerun the import?");
dr = UserInteractions.AskUserYesNo(sb.ToString());
if (dr == Forms.DialogResult.Yes)
{
File.Delete(doneFile);
}
}
}
if (dr == Forms.DialogResult.Yes)
{
int fileCount = 0;
var lib = new Database.Library();
var transaction = lib.StartTransaction();
try
{
var xmlFiles = Directory.GetFiles(selectedFolder, "*.cml").ToList();
xmlFiles.AddRange(Directory.GetFiles(selectedFolder, "*.mol"));
if (xmlFiles.Count > 0)
{
ProgressBar.Maximum = xmlFiles.Count;
ProgressBar.Minimum = 0;
ProgressBarHolder.Visibility = Visibility.Visible;
SetButtonState(false);
int progress = 0;
int total = xmlFiles.Count;
foreach (string cmlFile in xmlFiles)
{
progress++;
ShowProgress(progress, cmlFile.Replace($"{selectedFolder}\\", "") + $" [{progress}/{total}]");
var cml = File.ReadAllText(cmlFile);
// Set second parameter to true if properties are to be calculated on import
if (lib.ImportCml(cml, transaction, false))
{
fileCount++;
}
}
lib.EndTransaction(transaction, false);
}
ProgressBarHolder.Visibility = Visibility.Collapsed;
SetButtonState(true);
File.WriteAllText(doneFile, $"{fileCount} cml files imported into library");
FileInfo fi = new FileInfo(doneFile);
fi.Attributes = FileAttributes.Hidden;
Globals.Chem4WordV3.LoadNamesFromLibrary();
UserInteractions.InformUser($"Successfully imported {fileCount} structures from '{selectedFolder}'.");
}
catch (Exception ex)
{
lib.EndTransaction(transaction, true);
ProgressBarHolder.Visibility = Visibility.Collapsed;
SetButtonState(true);
new ReportError(Globals.Chem4WordV3.Telemetry, TopLeft, module, ex).ShowDialog();
}
}
}
}
}
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");
}
}
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 GetData(string idlist)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
var request = (HttpWebRequest)
WebRequest.Create(
string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esummary.fcgi?db=pccompound&id={1}&retmode=xml",
UserOptions.PubChemWebServiceUri, idlist));
request.Timeout = 30000;
request.UserAgent = "Chem4Word";
var securityProtocol = ServicePointManager.SecurityProtocol;
ServicePointManager.SecurityProtocol = securityProtocol | SecurityProtocolType.Tls11 | SecurityProtocolType.Tls12;
HttpWebResponse response;
try
{
response = (HttpWebResponse)request.GetResponse();
if (HttpStatusCode.OK.Equals(response.StatusCode))
{
Results.Enabled = true;
// we will read data via the response stream
using (var resStream = response.GetResponseStream())
{
var resultDocument = XDocument.Load(new StreamReader(resStream));
var compounds = resultDocument.XPathSelectElements("//DocSum");
if (compounds.Any())
{
foreach (var compound in compounds)
{
var id = compound.XPathSelectElement("./Id");
var name = compound.XPathSelectElement("./Item[@Name='IUPACName']");
//var smiles = compound.XPathSelectElement("./Item[@Name='CanonicalSmile']")
var formula = compound.XPathSelectElement("./Item[@Name='MolecularFormula']");
ListViewItem lvi = new ListViewItem(id.Value);
lvi.SubItems.Add(new ListViewItem.ListViewSubItem(lvi, name.Value));
//lvi.SubItems.Add(new ListViewItem.ListViewSubItem(lvi, smiles.ToString()))
lvi.SubItems.Add(new ListViewItem.ListViewSubItem(lvi, formula.Value));
Results.Items.Add(lvi);
// Add to a list view ...
}
}
else
{
Debug.WriteLine("Something went wrong");
}
}
}
else
{
StringBuilder sb = new StringBuilder();
sb.AppendLine($"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;
}
}
private void ExecuteSearch(int direction)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
if (!string.IsNullOrEmpty(SearchFor.Text))
{
Cursor = Cursors.WaitCursor;
string webCall;
if (direction == 0)
{
webCall = string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esearch.fcgi?db=pccompound&term={1}&retmode=xml&relevanceorder=on&usehistory=y&retmax={2}",
UserOptions.PubChemWebServiceUri, SearchFor.Text, UserOptions.ResultsPerCall);
}
else
{
if (direction == 1)
{
int startFrom = firstResult + numResults;
webCall = string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esearch.fcgi?db=pccompound&term={1}&retmode=xml&relevanceorder=on&usehistory=y&retmax={2}&WebEnv={3}&RetStart={4}",
UserOptions.PubChemWebServiceUri, SearchFor.Text, UserOptions.ResultsPerCall, webEnv, startFrom);
}
else
{
int startFrom = firstResult - numResults;
webCall = string.Format(CultureInfo.InvariantCulture,
"{0}entrez/eutils/esearch.fcgi?db=pccompound&term={1}&retmode=xml&relevanceorder=on&usehistory=y&retmax={2}&WebEnv={3}&RetStart={4}",
UserOptions.PubChemWebServiceUri, SearchFor.Text, UserOptions.ResultsPerCall, webEnv, startFrom);
}
}
var securityProtocol = ServicePointManager.SecurityProtocol;
ServicePointManager.SecurityProtocol = securityProtocol | SecurityProtocolType.Tls11 | SecurityProtocolType.Tls12;
var request = (HttpWebRequest)WebRequest.Create(webCall);
request.Timeout = 30000;
request.UserAgent = "Chem4Word";
HttpWebResponse response;
try
{
response = (HttpWebResponse)request.GetResponse();
if (HttpStatusCode.OK.Equals(response.StatusCode))
{
using (var resStream = response.GetResponseStream())
{
var resultDocument = XDocument.Load(new StreamReader(resStream));
// Get the count of results
resultsCount = int.Parse(resultDocument.XPathSelectElement("//Count").Value);
// Current position
firstResult = int.Parse(resultDocument.XPathSelectElement("//RetStart").Value);
int fetched = int.Parse(resultDocument.XPathSelectElement("//RetMax").Value);
lastResult = firstResult + fetched;
// WebEnv for history
webEnv = resultDocument.XPathSelectElement("//WebEnv").Value;
// Set flags for More/Prev buttons
if (lastResult > numResults)
{
PreviousButton.Enabled = true;
}
else
{
PreviousButton.Enabled = false;
}
if (lastResult < resultsCount)
{
NextButton.Enabled = true;
}
else
{
NextButton.Enabled = false;
}
var ids = resultDocument.XPathSelectElements("//Id");
var count = ids.Count();
Results.Items.Clear();
if (count > 0)
{
// Set form title
Text = $"Search PubChem - Showing {firstResult + 1} to {lastResult} [of {resultsCount}]";
Refresh();
var sb = new StringBuilder();
for (var i = 0; i < count; i++)
{
var id = ids.ElementAt(i);
if (i > 0)
{
sb.Append(",");
}
sb.Append(id.Value);
}
GetData(sb.ToString());
}
else
{
// Set error box
ErrorsAndWarnings.Text = "Sorry, no results were found.";
}
}
}
else
{
StringBuilder sb = new StringBuilder();
sb.AppendLine($"Status code {response.StatusCode} was returned by the server");
Telemetry.Write(module, "Warning", sb.ToString());
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;
}
}
}
/// <summary>
/// Add this to the OnMouseLeftButtonDown attribute
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void UIElementOnMouseLeftButtonDown(object sender, MouseButtonEventArgs e)
{
dynamic clobberedElement = sender;
UserInteractions.InformUser(clobberedElement.ID);
}
private void EditorHost_FormClosing(object sender, FormClosingEventArgs e)
{
if (DialogResult != DialogResult.OK && e.CloseReason == CloseReason.UserClosing)
{
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.");
CMLConverter cc = new CMLConverter();
switch (_editorType)
{
case "ACME":
if (elementHost1.Child is Editor acmeEditor &&
acmeEditor.IsDirty)
{
DialogResult dr = UserInteractions.AskUserYesNoCancel(sb.ToString());
switch (dr)
{
case DialogResult.Cancel:
e.Cancel = true;
break;
case DialogResult.Yes:
DialogResult = DialogResult.OK;
var model = acmeEditor.EditedModel;
model.RescaleForCml();
// Replace any temporary Ids which are Guids
model.ReLabelGuids();
OutputValue = cc.Export(model);
Hide();
break;
case DialogResult.No:
break;
}
}
break;
case "LABELS":
if (elementHost1.Child is LabelsEditor labelsEditor &&
labelsEditor.IsDirty)
{
DialogResult dr = UserInteractions.AskUserYesNoCancel(sb.ToString());
switch (dr)
{
case DialogResult.Cancel:
e.Cancel = true;
break;
case DialogResult.Yes:
DialogResult = DialogResult.OK;
OutputValue = cc.Export(labelsEditor.EditedModel);
Hide();
break;
case DialogResult.No:
break;
}
}
break;
default:
if (elementHost1.Child is CmlEditor editor &&
editor.IsDirty)
{
DialogResult dr = UserInteractions.AskUserYesNoCancel(sb.ToString());
switch (dr)
{
case DialogResult.Cancel:
e.Cancel = true;
break;
case DialogResult.Yes:
DialogResult = DialogResult.OK;
OutputValue = cc.Export(editor.EditedModel);
Hide();
break;
case DialogResult.No:
break;
}
}
break;
}
}
}
public static void InsertChemistry(bool isCopy, Application app, FlexDisplay flexDisplay)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
Document doc = app.ActiveDocument;
Selection sel = app.Selection;
ContentControl cc = null;
if (Globals.Chem4WordV3.SystemOptions == null)
{
Globals.Chem4WordV3.LoadOptions();
}
bool allowed = true;
string reason = "";
if (Globals.Chem4WordV3.ChemistryAllowed)
{
if (sel.ContentControls.Count > 0)
{
cc = sel.ContentControls[1];
if (cc.Title != null && cc.Title.Equals(Constants.ContentControlTitle))
{
reason = "a chemistry object is selected";
allowed = false;
}
}
}
else
{
reason = Globals.Chem4WordV3.ChemistryProhibitedReason;
allowed = false;
}
if (allowed)
{
app.ScreenUpdating = false;
Globals.Chem4WordV3.DisableDocumentEvents(doc);
try
{
CMLConverter cmlConverter = new CMLConverter();
Model.Model chem = cmlConverter.Import(flexDisplay.Chemistry);
double before = chem.MeanBondLength;
if (before < Constants.MinimumBondLength - Constants.BondLengthTolerance ||
before > Constants.MaximumBondLength + Constants.BondLengthTolerance)
{
chem.ScaleToAverageBondLength(Constants.StandardBondLength);
double after = chem.MeanBondLength;
Globals.Chem4WordV3.Telemetry.Write(module, "Information", $"Structure rescaled from {before.ToString("#0.00")} to {after.ToString("#0.00")}");
}
if (isCopy)
{
// Always generate new Guid on Import
chem.CustomXmlPartGuid = Guid.NewGuid().ToString("N");
}
string guidString = chem.CustomXmlPartGuid;
string bookmarkName = "C4W_" + guidString;
if (Globals.Chem4WordV3.SystemOptions == null)
{
Globals.Chem4WordV3.LoadOptions();
}
Globals.Chem4WordV3.SystemOptions.WordTopLeft = Globals.Chem4WordV3.WordTopLeft;
IChem4WordRenderer renderer =
Globals.Chem4WordV3.GetRendererPlugIn(
Globals.Chem4WordV3.SystemOptions.SelectedRendererPlugIn);
if (renderer == null)
{
UserInteractions.WarnUser("Unable to find a Renderer Plug-In");
}
else
{
// Export just incase the CustomXmlPartGuid has been changed
string cml = cmlConverter.Export(chem);
renderer.Properties = new Dictionary <string, string>();
renderer.Properties.Add("Guid", guidString);
renderer.Cml = cml;
string tempfileName = renderer.Render();
if (File.Exists(tempfileName))
{
cc = CustomRibbon.Insert2D(doc, tempfileName, bookmarkName, guidString);
if (isCopy)
{
doc.CustomXMLParts.Add(cml);
}
try
{
// Delete the temporary file now we are finished with it
File.Delete(tempfileName);
}
catch
{
// Not much we can do here
}
}
}
}
catch (Exception ex)
{
new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex)
.ShowDialog();
}
finally
{
// Tidy Up - Resume Screen Updating and Enable Document Event Handlers
app.ScreenUpdating = true;
Globals.Chem4WordV3.EnableDocumentEvents(doc);
if (cc != null)
{
// Move selection point into the Content Control which was just edited or added
app.Selection.SetRange(cc.Range.Start, cc.Range.End);
}
}
}
else
{
UserInteractions.WarnUser($"You can't insert a chemistry object because {reason}");
}
}
static void Main(string[] args)
{
UserInteractions displayer = new UserInteractions();
displayer.Run();
}
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);
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");
}
}
public abstract void Configure(UserInteractions ui);
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);
}
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");
}
}
public static void InsertChemistry(bool isCopy, Application app, Display display, bool fromLibrary)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
Document doc = app.ActiveDocument;
Selection sel = app.Selection;
ContentControl cc = null;
if (Globals.Chem4WordV3.SystemOptions == null)
{
Globals.Chem4WordV3.LoadOptions();
}
bool allowed = true;
string reason = "";
if (Globals.Chem4WordV3.ChemistryAllowed)
{
if (sel.ContentControls.Count > 0)
{
cc = sel.ContentControls[1];
if (cc.Title != null && cc.Title.Equals(Constants.ContentControlTitle))
{
reason = "a chemistry object is selected";
allowed = false;
}
}
}
else
{
reason = Globals.Chem4WordV3.ChemistryProhibitedReason;
allowed = false;
}
if (allowed)
{
try
{
CMLConverter cmlConverter = new CMLConverter();
var model = cmlConverter.Import(display.Chemistry.ToString());
if (fromLibrary)
{
if (Globals.Chem4WordV3.SystemOptions.RemoveExplicitHydrogensOnImportFromLibrary)
{
var targets = model.GetHydrogenTargets();
if (targets.Atoms.Any())
{
foreach (var bond in targets.Bonds)
{
bond.Parent.RemoveBond(bond);
}
foreach (var atom in targets.Atoms)
{
atom.Parent.RemoveAtom(atom);
}
}
}
var outcome = model.EnsureBondLength(Globals.Chem4WordV3.SystemOptions.BondLength,
Globals.Chem4WordV3.SystemOptions.SetBondLengthOnImportFromLibrary);
if (!string.IsNullOrEmpty(outcome))
{
Globals.Chem4WordV3.Telemetry.Write(module, "Information", outcome);
}
}
cc = ChemistryHelper.Insert2DChemistry(doc, cmlConverter.Export(model), isCopy);
}
catch (Exception ex)
{
new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex).ShowDialog();
}
finally
{
if (cc != null)
{
// Move selection point into the Content Control which was just edited or added
app.Selection.SetRange(cc.Range.Start, cc.Range.End);
}
}
}
else
{
UserInteractions.WarnUser($"You can't insert a chemistry object because {reason}");
}
}
