private void LoadCdw()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
if (!string.IsNullOrEmpty(ProductAppDataPath))
{
_loading = true;
// Allow extra 500ms for form to load
Thread.Sleep(500);
Stopwatch sw = new Stopwatch();
sw.Start();
string htmlfile = "";
if (IsSingleMolecule)
{
htmlfile = ResourceHelper.GetStringResource(Assembly.GetExecutingAssembly(), "ChemDoodleWeb.Single.html");
}
else
{
htmlfile = ResourceHelper.GetStringResource(Assembly.GetExecutingAssembly(), "ChemDoodleWeb.Multi.html");
}
File.WriteAllText(Path.Combine(ProductAppDataPath, "Editor.html"), htmlfile);
Telemetry.Write(module, "Timing", $"Writing resources to disk took {SafeDouble.Duration(sw.ElapsedMilliseconds)}ms");
Telemetry.Write(module, "Information", "Starting browser");
WebBrowser.Navigate(Path.Combine(ProductAppDataPath, "Editor.html"));
}
}
/// <summary>
/// Ensure that bond length is between 5 and 95, and force to default if required
/// </summary>
/// <param name="target">Target bond length (if force true)</param>
/// <param name="force">true to force setting of bond length to target bond length</param>
public string EnsureBondLength(double target, bool force)
{
string result = string.Empty;
if (TotalBondsCount > 0 && MeanBondLength > 0)
{
if (Math.Abs(MeanBondLength - target) < 0.1)
{
result = string.Empty;
}
else
{
if (force)
{
result = $"Forced BondLength from {SafeDouble.AsString(MeanBondLength)} to {SafeDouble.AsString(target)}";
ScaleToAverageBondLength(target);
}
else
{
if (MeanBondLength < Constants.MinimumBondLength - Constants.BondLengthTolerance ||
MeanBondLength > Constants.MaximumBondLength + Constants.BondLengthTolerance)
{
result = $"Adjusted BondLength from {SafeDouble.AsString(MeanBondLength)} to {SafeDouble.AsString(target)}";
ScaleToAverageBondLength(target);
}
else
{
result = $"BondLength of {SafeDouble.AsString(MeanBondLength)} is within tolerance";
}
}
}
}
return(result);
}
private void DeployCdw800()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
if (!string.IsNullOrEmpty(ProductAppDataPath))
{
Stopwatch sw = new Stopwatch();
sw.Start();
string markerFile = Path.Combine(ProductAppDataPath, "ChemDoodle-Web-800.txt");
string otherVersion = Path.Combine(ProductAppDataPath, "ChemDoodle-Web-702.txt");
string refreshFile = Path.Combine(ProductAppDataPath, "ChemDoodle-Web-Refresh.txt");
if (File.Exists(otherVersion))
{
Telemetry.Write(module, "Information", "Deleting CDW 702 resources from disk");
File.Delete(otherVersion);
DelTree(Path.Combine(ProductAppDataPath, "ChemDoodleWeb"));
}
if (File.Exists(refreshFile))
{
Telemetry.Write(module, "Information", "Refreshing CDW 800 resources");
File.Delete(refreshFile);
File.Delete(markerFile);
DelTree(Path.Combine(ProductAppDataPath, "ChemDoodleWeb"));
}
if (!File.Exists(markerFile))
{
Telemetry.Write(module, "Information", "Writing CDW 800 resources to disk");
File.WriteAllText(markerFile, "Delete this file to refresh ChemDoodle Web");
Stream stream = ResourceHelper.GetBinaryResource(Assembly.GetExecutingAssembly(), "ChemDoodleWeb.ChemDoodleWeb_800.zip");
// NB: Top level of zip file must be the folder ChemDoodleWeb
using (ZipFile zip = ZipFile.Read(stream))
{
zip.ExtractAll(ProductAppDataPath, ExtractExistingFileAction.OverwriteSilently);
}
string cssfile = ResourceHelper.GetStringResource(Assembly.GetExecutingAssembly(), "ChemDoodleWeb.Chem4Word.css");
File.WriteAllText(Path.Combine(ProductAppDataPath, "Chem4Word.css"), cssfile);
string jsfile = ResourceHelper.GetStringResource(Assembly.GetExecutingAssembly(), "ChemDoodleWeb.Chem4Word.js");
File.WriteAllText(Path.Combine(ProductAppDataPath, "Chem4Word.js"), jsfile);
}
sw.Stop();
Telemetry.Write(module, "Timing", $"Writing resources to disk took {SafeDouble.Duration(sw.ElapsedMilliseconds)}ms");
}
}
public override string ToString()
{
StringBuilder sb = new StringBuilder();
sb.Append($"{Text}");
sb.Append(" ");
sb.Append($"at {PointHelper.AsString(BoundingBox.Location)}");
sb.Append(" ");
sb.Append($"size {SafeDouble.AsString4(BoundingBox.Size.Width)}x{SafeDouble.AsString4(BoundingBox.Size.Height)}");
return(sb.ToString());
}
private void GetWin32ProcessorData()
{
ManagementObjectSearcher searcher = new ManagementObjectSearcher(QueryProcessor);
ManagementObjectCollection objCol = searcher.Get();
foreach (var o in objCol)
{
var mgtObject = (ManagementObject)o;
try
{
string temp = mgtObject["Name"].ToString();
// Replace tab with space
temp = temp.Replace("\t", " ");
// Replace up to 15 double spaces with single space
int i = 0;
while (temp.IndexOf(" ", StringComparison.InvariantCulture) != -1)
{
temp = temp.Replace(" ", " ");
i++;
if (i > 15)
{
break;
}
}
_cpuName = temp;
}
catch
{
_cpuName = "?";
}
try
{
_logicalProcessors = mgtObject["NumberOfLogicalProcessors"].ToString();
}
catch
{
_logicalProcessors = "?";
}
try
{
double speed = double.Parse(mgtObject["CurrentClockSpeed"].ToString()) / 1024;
_cpuSpeed = SafeDouble.AsString(speed) + "GHz";
}
catch
{
_cpuSpeed = "?";
}
}
}
private void WebBrowser_OnLoadCompleted(object sender, NavigationEventArgs e)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
try
{
// Allow extra 500ms for document to load
Thread.Sleep(500);
if (!string.IsNullOrEmpty(StructureJson))
{
var version = ExecuteJavaScript("GetVersion");
if (version != null)
{
var source = (HwndSource)PresentationSource.FromDependencyObject(WebBrowser);
if (source != null)
{
var host = (System.Windows.Forms.Integration.ElementHost)Control.FromChildHandle(source.Handle);
var form = (Form)host?.TopLevelControl;
if (form != null)
{
form.Text = AppTitle + version;
}
}
}
// Send JSON to ChemDoodle before we do anything else
ExecuteJavaScript("SetJSON", StructureJson, AverageBondLength);
ExecuteJavaScript("ShowHydrogens", UserOptions.ShowHydrogens);
ExecuteJavaScript("AtomsInColour", UserOptions.ColouredAtoms);
ExecuteJavaScript("ShowCarbons", UserOptions.ShowCarbons);
ExecuteJavaScript("ReScale", BondLength.Text);
Mouse.OverrideCursor = System.Windows.Input.Cursors.Arrow;
_sw.Stop();
Telemetry.Write(module, "Timing", $"ChemDoodle Web ready in {SafeDouble.Duration(_sw.ElapsedMilliseconds)}ms");
_loading = false;
}
}
catch (Exception ex)
{
new ReportError(Telemetry, TopLeft, module, ex).ShowDialog();
Mouse.OverrideCursor = System.Windows.Input.Cursors.Arrow;
}
}
private void GetWin32PhysicalMemoryData()
{
ManagementObjectSearcher searcher = new ManagementObjectSearcher(QueryPhysicalMemory);
ManagementObjectCollection objCol = searcher.Get();
try
{
UInt64 capacity = 0;
foreach (var o in objCol)
{
var mgtObject = (ManagementObject)o;
capacity += (UInt64)mgtObject["Capacity"];
}
_physicalMemory = SafeDouble.AsString0((double)capacity / (1024 * 1024 * 1024)) + "GB";
}
catch
{
_physicalMemory = "?";
}
}
public ChemicalServicesResult GetChemicalServicesResult(string molfile)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
DateTime started = DateTime.Now;
ChemicalServicesResult data = null;
try
{
using (HttpClient httpClient = new HttpClient())
{
var formData = new List <KeyValuePair <string, string> >();
formData.Add(new KeyValuePair <string, string>("mol", molfile));
formData.Add(new KeyValuePair <string, string>("machine", SystemHelper.GetMachineId()));
formData.Add(new KeyValuePair <string, string>("version", Globals.Chem4WordV3.AddInInfo.AssemblyVersionNumber));
var content = new FormUrlEncodedContent(formData);
httpClient.Timeout = TimeSpan.FromSeconds(15);
httpClient.DefaultRequestHeaders.Add("user-agent", "Chem4Word");
try
{
var response = httpClient.PostAsync(Constants.Chem4WordWebServiceUri, content).Result;
if (response.Content != null)
{
var responseContent = response.Content;
var jsonContent = responseContent.ReadAsStringAsync().Result;
try
{
data = JsonConvert.DeserializeObject <ChemicalServicesResult>(jsonContent);
}
catch (Exception e3)
{
Telemetry.Write(module, "Exception", e3.Message);
Telemetry.Write(module, "Exception(Data)", jsonContent);
}
if (data != null)
{
if (data.Messages.Any())
{
Telemetry.Write(module, "Timing", string.Join(Environment.NewLine, data.Messages));
}
if (data.Errors.Any())
{
Telemetry.Write(module, "Exception(Data)", string.Join(Environment.NewLine, data.Errors));
}
}
}
}
catch (Exception e2)
{
Telemetry.Write(module, "Exception", e2.Message);
Telemetry.Write(module, "Exception", e2.ToString());
}
}
}
catch (Exception e1)
{
Telemetry.Write(module, "Exception", e1.Message);
Telemetry.Write(module, "Exception", e1.ToString());
}
DateTime ended = DateTime.Now;
TimeSpan duration = ended - started;
Telemetry.Write(module, "Timing", $"Calling Azure http Function Took {SafeDouble.Duration(duration.TotalMilliseconds)}ms");
return(data);
}
private string ToJsonSingle()
{
// Need to store atomIds in dictionary as id of 1st atom not always a0
Dictionary <String, int> atomIds = new Dictionary <string, int>();
JObject jsonOut = new JObject();
List <XmlNode> atoms = GetAtoms();
if (atoms.Count > 0)
{
JArray jAtomsArray = new JArray();
JProperty jAtomsProperty = new JProperty("a", jAtomsArray);
jsonOut.Add(jAtomsProperty);
int atomCount = 0;
foreach (XmlNode atom in atoms)
{
// Fetch or generate atom id
string atomId = GetAttribute(atom, "id");
if (string.IsNullOrEmpty(atomId))
{
atomId = "a" + atomCount;
}
atomIds.Add(atomId, atomCount);
atomCount++;
string atomLabel = GetAttribute(atom, "elementType");
// 2D co-ordinates (if present)
string x2 = GetAttribute(atom, "x2");
string y2 = GetAttribute(atom, "y2");
// 3D co-ordinates (if present)
string x3 = GetAttribute(atom, "x3");
string y3 = GetAttribute(atom, "y3");
string z3 = GetAttribute(atom, "z3");
JObject jAtom = new JObject();
if (string.IsNullOrEmpty(z3))
{
// 2D co-ordinates supplied
jAtom.Add(new JProperty("x", SafeDouble.Parse(x2)));
jAtom.Add(new JProperty("y", SafeDouble.Parse(y2)));
}
else
{
// 3D co-ordinates supplied
jAtom.Add(new JProperty("x", SafeDouble.Parse(x3)));
jAtom.Add(new JProperty("y", SafeDouble.Parse(y3)));
jAtom.Add(new JProperty("z", SafeDouble.Parse(z3)));
}
jAtom.Add(new JProperty("i", atomId));
if (!atomLabel.Equals("C"))
{
jAtom.Add(new JProperty("l", atomLabel));
}
string charge = GetAttribute(atom, "formalCharge");
if (!string.IsNullOrEmpty(charge))
{
jAtom.Add(new JProperty("c", Int32.Parse(charge)));
}
jAtomsArray.Add(jAtom);
}
}
List <XmlNode> bonds = GetBonds();
if (bonds.Count > 0)
{
JArray jBondsArray = new JArray();
JProperty jBondsProperty = new JProperty("b", jBondsArray);
jsonOut.Add(jBondsProperty);
int bondCount = 0;
foreach (XmlNode bond in bonds)
{
// Fetch or generate bond id
string bondId = GetAttribute(bond, "id");
if (string.IsNullOrEmpty(bondId))
{
bondId = "b" + bondCount;
}
string atomRefs2 = GetAttribute(bond, "atomRefs2");
string[] bondStartEnd = atomRefs2.Split(' ');
string bondOrder = GetAttribute(bond, "order");
string bondStereo = "";
if (bond.ChildNodes.Count > 0)
{
XmlNode stereoNode = bond.FirstChild;
bondStereo = stereoNode.InnerText;
}
JObject jBond = new JObject();
jBond.Add(new JProperty("i", bondId));
int atomId0 = atomIds[bondStartEnd[0]];
int atomId1 = atomIds[bondStartEnd[1]];
jBond.Add(new JProperty("b", atomId0));
jBond.Add(new JProperty("e", atomId1));
if (!string.IsNullOrEmpty(bondOrder))
{
Single order = OrderToNumber(bondOrder);
if (order != 1)
{
jBond.Add(new JProperty("o", order));
}
}
if (!string.IsNullOrEmpty(bondStereo))
{
jBond.Add(new JProperty("s", CmlStereoToJson(bondStereo)));
}
jBondsArray.Add(jBond);
bondCount++;
}
}
return(jsonOut.ToString());
}
public Dictionary <string, int> GetLibraryNames()
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}()";
var allNames = new Dictionary <string, int>();
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
using (SQLiteConnection conn = LibraryConnection())
{
using (SQLiteDataReader names = GetAllNames(conn))
{
while (names.Read())
{
string name = names["Name"] as string;
if (!string.IsNullOrEmpty(name) && name.Length > 3)
{
// Exclude any purely numeric names
long numeric = -1;
if (!long.TryParse(name, out numeric))
{
int id = int.Parse(names["ChemistryId"].ToString());
if (!allNames.ContainsKey(name))
{
allNames.Add(name, id);
}
}
}
}
}
}
}
catch (Exception ex)
{
using (var form = new ReportError(Globals.Chem4WordV3.Telemetry, Globals.Chem4WordV3.WordTopLeft, module, ex))
{
form.ShowDialog();
}
}
sw.Stop();
#if DEBUG
// Task 810
Globals.Chem4WordV3.Telemetry.Write(module, "Timing", $"Reading {allNames.Count} Chemical names took {SafeDouble.AsString(sw.ElapsedMilliseconds)}ms");
#endif
return(allNames);
}
/// <summary>
/// This is called via Microsoft.Office.Tools.CustomTaskPanel.OnVisibleChanged and Chem4Word.CustomRibbon.OnShowLibraryClick
/// </summary>
/// <param name="filter"></param>
/// <returns></returns>
public List <ChemistryDTO> GetAllChemistry(string filter)
{
string module = $"{_product}.{_class}.{MethodBase.GetCurrentMethod().Name}({filter})";
var results = new List <ChemistryDTO>();
Stopwatch sw = new Stopwatch();
sw.Start();
using (SQLiteConnection conn = LibraryConnection())
{
SQLiteDataReader chemistry = GetAllChemistry(conn, filter);
while (chemistry.Read())
{
var dto = new ChemistryDTO();
dto.Id = (long)chemistry["ID"];
dto.Cml = CmlFromBytes(chemistry["Chemistry"] as Byte[]);
dto.Name = chemistry["name"] as string;
dto.Formula = chemistry["formula"] as string;
results.Add(dto);
}
chemistry.Close();
chemistry.Dispose();
}
sw.Stop();
Globals.Chem4WordV3.Telemetry.Write(module, "Timing", $"Reading {results.Count} structures took {SafeDouble.AsString(sw.ElapsedMilliseconds)}ms");
return(results);
}
private void GetExternalIpAddress(object o)
{
string module = $"{MethodBase.GetCurrentMethod().Name}()";
try
{
string message;
IpAddress = "0.0.0.0";
for (int i = 0; i < 2; i++)
{
foreach (string place in _placesToTry)
{
_attempts++;
try
{
message = $"Attempt #{_attempts} using '{place}'";
StartUpTimings.Add(message);
Debug.WriteLine(message);
if (place.Contains("chem4word"))
{
GetInternalVersion(place);
}
else
{
GetExternalVersion(place);
}
// Exit out of inner loop
if (!IpAddress.Contains("0.0.0.0"))
{
break;
}
}
catch (Exception exception)
{
Debug.WriteLine(exception.Message);
StartUpTimings.Add(exception.Message);
}
}
// Exit out of outer loop
if (!IpAddress.Contains("0.0.0.0"))
{
break;
}
}
if (IpAddress.Contains("0.0.0.0"))
{
// Handle failure
IpAddress = "8.8.8.8";
}
_ipStopwatch.Stop();
message = $"{module} took {SafeDouble.AsString0(_ipStopwatch.ElapsedMilliseconds)}ms";
StartUpTimings.Add(message);
Debug.WriteLine(message);
}
catch (ThreadAbortException threadAbortException)
{
// Do Nothing
Debug.WriteLine(threadAbortException.Message);
}
catch (Exception exception)
{
Debug.WriteLine(exception.Message);
StartUpTimings.Add(exception.Message);
}
}
private List <string> Initialise()
{
try
{
List <string> timings = new List <string>();
string message = $"SystemHelper.Initialise() started at {SafeDate.ToLongDate(DateTime.Now)}";
timings.Add(message);
Debug.WriteLine(message);
Stopwatch sw = new Stopwatch();
sw.Start();
WordVersion = -1;
#region Get Machine Guid
MachineId = GetMachineId();
ProcessId = Process.GetCurrentProcess().Id;
#endregion Get Machine Guid
#region Get OS Version
// The current code returns 6.2.* for Windows 8.1 and Windows 10 on some systems
// https://msdn.microsoft.com/en-gb/library/windows/desktop/ms724832(v=vs.85).aspx
// https://msdn.microsoft.com/en-gb/library/windows/desktop/dn481241(v=vs.85).aspx
// However as we do not NEED the exact version number,
// I am not going to implement the above as they are too risky
try
{
OperatingSystem operatingSystem = Environment.OSVersion;
string ProductName = HKLM_GetString(@"SOFTWARE\Microsoft\Windows NT\CurrentVersion", "ProductName");
string CsdVersion = HKLM_GetString(@"SOFTWARE\Microsoft\Windows NT\CurrentVersion", "CSDVersion");
if (!string.IsNullOrEmpty(ProductName))
{
StringBuilder sb = new StringBuilder();
if (!ProductName.StartsWith("Microsoft"))
{
sb.Append("Microsoft ");
}
sb.Append(ProductName);
if (!string.IsNullOrEmpty(CsdVersion))
{
sb.AppendLine($" {CsdVersion}");
}
else
{
if (!string.IsNullOrEmpty(operatingSystem.ServicePack))
{
sb.Append($" {operatingSystem.ServicePack}");
}
}
sb.Append($" {OsBits}");
sb.Append($" [{operatingSystem.Version}]");
sb.Append($" {CultureInfo.CurrentCulture.Name}");
SystemOs = sb.ToString().Replace(Environment.NewLine, "").Replace("Service Pack ", "SP");
}
}
catch (Exception ex)
{
Debug.WriteLine(ex.Message);
SystemOs = "Exception " + ex.Message;
}
#endregion Get OS Version
#region Get Office/Word Version
try
{
Click2RunProductIds = OfficeHelper.GetClick2RunProductIds();
WordVersion = OfficeHelper.GetWinWordVersionNumber();
WordProduct = OfficeHelper.GetWordProduct(Click2RunProductIds);
}
catch (Exception ex)
{
Debug.WriteLine(ex.Message);
WordProduct = "Exception " + ex.Message;
}
#endregion Get Office/Word Version
#region Get Product Version and Location using reflection
Assembly assembly = Assembly.GetExecutingAssembly();
// CodeBase is the location of the installed files
Uri uriCodeBase = new Uri(assembly.CodeBase);
AddInLocation = Path.GetDirectoryName(uriCodeBase.LocalPath);
Version productVersion = assembly.GetName().Version;
AssemblyVersionNumber = productVersion.ToString();
AddInVersion = "Chem4Word V" + productVersion;
#endregion Get Product Version and Location using reflection
#region Get IpAddress on Thread
// These can be tested via http://www.ipv6proxy.net/
// Our locations
_placesToTry.Add($"https://www.chem4word.co.uk/{Constants.Chem4WordVersionFiles}/client-ip-date.php");
_placesToTry.Add($"http://www.chem4word.com/{Constants.Chem4WordVersionFiles}/client-ip-date.php");
_placesToTry.Add($"https://chem4word.azurewebsites.net/{Constants.Chem4WordVersionFiles}/client-ip-date.php");
// Other Locations
_placesToTry.Add("https://api.my-ip.io/ip");
_placesToTry.Add("https://ip.seeip.org");
_placesToTry.Add("https://ipapi.co/ip");
_placesToTry.Add("https://ident.me/");
_placesToTry.Add("https://api6.ipify.org/");
_placesToTry.Add("https://v4v6.ipv6-test.com/api/myip.php");
message = $"GetIpAddress started at {SafeDate.ToLongDate(DateTime.Now)}";
StartUpTimings.Add(message);
Debug.WriteLine(message);
_ipStopwatch = new Stopwatch();
_ipStopwatch.Start();
Thread thread1 = new Thread(GetExternalIpAddress);
thread1.SetApartmentState(ApartmentState.STA);
thread1.Start(null);
#endregion Get IpAddress on Thread
GetDotNetVersionFromRegistry();
GatherBootUpTimeEtc();
try
{
BrowserVersion = new WebBrowser().Version.ToString();
}
catch
{
BrowserVersion = "?";
}
GetScreens();
#if DEBUG
message = $"GetGitStatus started at {SafeDate.ToLongDate(DateTime.Now)}";
StartUpTimings.Add(message);
Debug.WriteLine(message);
Thread thread2 = new Thread(GetGitStatus);
thread2.SetApartmentState(ApartmentState.STA);
thread2.Start(null);
#endif
sw.Stop();
message = $"SystemHelper.Initialise() took {SafeDouble.AsString0(sw.ElapsedMilliseconds)}ms";
timings.Add(message);
Debug.WriteLine(message);
return(timings);
}
catch (ThreadAbortException threadAbortException)
{
// Do Nothing
Debug.WriteLine(threadAbortException.Message);
}
return(new List <string>());
}