public static bool Read([NotNull] this WebResponse thisValue, [NotNull] IOSettings settings)
{
IIOOnRead ioOnRead = settings as IIOOnRead ?? throw new ArgumentException("Argument must provide an OnRead implementation.", nameof(settings));
Stream stream = null;
StreamReader reader = null;
try
{
stream = GetStream(thisValue);
if (stream == null)
{
return(false);
}
reader = new StreamReader(stream, settings.Encoding, true);
int length;
char[] chars = new char[settings.BufferSize];
do
{
length = reader.Read(chars);
}while (length > 0 && ioOnRead.OnRead(chars, length));
return(true);
}
catch (Exception ex) when(settings.OnError != null)
{
settings.OnError(ex);
return(false);
}
finally
{
ObjectHelper.Dispose(ref reader);
ObjectHelper.Dispose(ref stream);
}
}
public static string ReadToEnd([NotNull] this WebResponse thisValue, IOSettings settings = null)
{
settings ??= new IOSettings();
Stream stream = null;
StreamReader reader = null;
string result;
try
{
stream = GetStream(thisValue);
if (stream == null)
{
return(null);
}
reader = new StreamReader(stream, settings.Encoding, true, settings.BufferSize);
result = reader.ReadToEnd();
}
catch (Exception ex) when(settings.OnError != null)
{
result = null;
settings.OnError(ex);
}
finally
{
ObjectHelper.Dispose(ref reader);
ObjectHelper.Dispose(ref stream);
}
return(result);
}
/// <inheritdoc />
public IOHttpDownloadFileWebRequestSettings(IOSettings settings)
: base(settings)
{
if (settings is not IOHttpDownloadFileWebRequestSettings ioHttpDownloadFileWebRequestSettings)
{
return;
}
Overwrite = ioHttpDownloadFileWebRequestSettings.Overwrite;
}
private void InitIOSettings()
{
useRebondTool = IOSettings.Add(new BooleanIOSetting("UseRebondTool", Importance.Low,
"Should the PDBReader deduce bonding patterns?", "false"));
readConnect = IOSettings.Add(new BooleanIOSetting("ReadConnectSection", Importance.Low,
"Should the CONECT be read?", "true"));
useHetDictionary = IOSettings.Add(new BooleanIOSetting("UseHetDictionary", Importance.Low,
"Should the PDBReader use the HETATM dictionary for atom types?", "false"));
}
private void InitIOSettings()
{
write2DCoordinates = IOSettings.Add(new BooleanIOSetting("write2DCoordinates", Importance.Low,
"Should 2D coordinates be added?", "true"));
write3DCoordinates = IOSettings.Add(new BooleanIOSetting("write3DCoordinates", Importance.Low,
"Should 3D coordinates be added?", "true"));
builder = IOSettings.Add(new StringIOSetting("builder", Importance.Low,
$"Which {nameof(IChemObjectBuilder)} should be used?",
"NCDK.Silent.ChemObjectBuilder"));
}
private void InitIOSettings()
{
var basisOptions = new List <string>
{
"6-31g",
"6-31g*",
"6-31g(d)",
"6-311g",
"6-311+g**"
};
basis = new OptionIOSetting("Basis", Importance.Medium, "Which basis set do you want to use?",
basisOptions, "6-31g");
var methodOptions = new List <string>
{
"rb3lyp",
"b3lyp",
"rhf"
};
method = new OptionIOSetting("Method", Importance.Medium, "Which method do you want to use?",
methodOptions, "b3lyp");
var commandOptions = new List <string>
{
"energy calculation",
"geometry optimization",
"IR frequency calculation",
"IR frequency calculation (with Raman)"
};
command = IOSettings.Add(new OptionIOSetting("Command", Importance.High,
"What kind of job do you want to perform?", commandOptions, "energy calculation"));
comment = IOSettings.Add(new StringIOSetting("Comment", Importance.Low,
"What comment should be put in the file?", "Created with CDK (http://cdk.sf.net/)"));
memory = IOSettings.Add(new StringIOSetting("Memory", Importance.Low,
"How much memory do you want to use?", "unset"));
shell = IOSettings.Add(new BooleanIOSetting("OpenShell", Importance.Medium,
"Should the calculation be open shell?", "false"));
proccount = IOSettings.Add(new IntegerIOSetting("ProcessorCount", Importance.Low,
"How many processors should be used by Gaussian?", "1"));
usecheckpoint = new BooleanIOSetting("UseCheckPointFile", Importance.Low,
"Should a check point file be saved?", "false");
}
/// <summary>
/// Creates a PDB writer.
/// </summary>
/// <param name="output">the stream to write the PDB file to.</param>
public PDBWriter(TextWriter output)
{
writer = output;
writeAsHET = IOSettings.Add(new BooleanIOSetting("WriteAsHET", Importance.Low,
"Should the output file use HETATM", "false"));
useElementSymbolAsAtomName = IOSettings.Add(new BooleanIOSetting("UseElementSymbolAsAtomName", Importance.Low,
"Should the element symbol be written as the atom name", "false"));
writeCONECTRecords = IOSettings.Add(new BooleanIOSetting("WriteCONECT", Importance.Low,
"Should the bonds be written as CONECT records?", "true"));
writeTERRecord = IOSettings.Add(new BooleanIOSetting("WriteTER", Importance.Low,
"Should a TER record be put at the end of the atoms?", "false"));
writeENDRecord = IOSettings.Add(new BooleanIOSetting("WriteEND", Importance.Low,
"Should an END record be put at the end of the file?", "true"));
}
public static string GetString([NotNull] this WebResponse thisValue, IOSettings settings = null)
{
bool bufferFilled = false;
int bufferSize = settings?.BufferSize ?? IOSettings.BUFFER_DEFAULT;
StringBuilder sb = new StringBuilder(bufferSize);
IOReadSettings readSettings = new IOReadSettings(settings, (buf, _) =>
{
if (bufferFilled)
{
return(!bufferFilled);
}
sb.Append(buf);
bufferFilled = sb.Length >= bufferSize;
return(!bufferFilled);
});
return(Read(thisValue, readSettings) && sb.Length > 0
? sb.ToString()
: null);
}
public static Task <bool> ReadAsync([NotNull] this WebResponse thisValue, [NotNull] IOSettings settings, CancellationToken token = default(CancellationToken))
{
token.ThrowIfCancellationRequested();
IIOOnRead ioOnRead = settings as IIOOnRead ?? throw new ArgumentException("Argument must provide an OnRead implementation.", nameof(settings));
Stream stream = null;
StreamReader reader = null;
try
{
stream = GetStream(thisValue);
token.ThrowIfCancellationRequested();
if (stream == null)
{
return(Task.FromResult(false));
}
reader = new StreamReader(stream, settings.Encoding, true);
int length;
char[] chars = new char[settings.BufferSize];
do
{
length = reader.ReadAsync(chars).Execute();
}while (!token.IsCancellationRequested && length > 0 && ioOnRead.OnRead(chars, length));
token.ThrowIfCancellationRequested();
return(Task.FromResult(true));
}
catch (Exception ex) when(settings.OnError != null)
{
settings.OnError(ex);
return(Task.FromResult(false));
}
finally
{
ObjectHelper.Dispose(ref reader);
ObjectHelper.Dispose(ref stream);
}
}
public static string GetTitle([NotNull] this WebResponse thisValue, IOSettings settings = null)
{
string result = null;
StringBuilder sb = new StringBuilder();
IOReadSettings readSettings = new IOReadSettings(settings, (bf, _) =>
{
sb.Append(bf);
string contents = sb.ToString();
Match m = WebResponseHelper.TitleCheckExpression.Match(contents);
if (m.Success)
{
// we found a <title></title> match =]
result = m.Groups[1].Value;
return(false);
}
// reached end of head-block; no title found =[
return(!contents.Contains("</head>", StringComparison.OrdinalIgnoreCase));
});
return(Read(thisValue, readSettings) ? result : null);
}
public static Task <UrlSearchResult> SearchAsync([NotNull] this WebResponse thisValue, string searchFor, UrlSearchFlags flags, IOSettings settings = null, CancellationToken token = default(CancellationToken))
{
token.ThrowIfCancellationRequested();
bool hasTitleFlag = flags.FastHasFlag(UrlSearchFlags.Title);
bool hasBufferFlag = flags.FastHasFlag(UrlSearchFlags.Buffer);
bool hasSearchFlag = !string.IsNullOrEmpty(searchFor);
UrlSearchResult result = new UrlSearchResult();
try
{
Func <char[], int, bool> onRead;
if (hasTitleFlag || hasBufferFlag || hasSearchFlag)
{
StringBuilder sb = new StringBuilder();
StringComparison comparison = flags.FastHasFlag(UrlSearchFlags.IgnoreCase)
? StringComparison.InvariantCultureIgnoreCase
: StringComparison.InvariantCulture;
onRead = (c, _) =>
{
if (result.Status == UrlSearchStatus.Unknown)
{
result.Status = UrlSearchStatus.Success;
}
sb.Append(c);
if (hasBufferFlag)
{
result.Buffer = sb.ToString();
hasBufferFlag = false;
}
token.ThrowIfCancellationRequested();
if (!hasTitleFlag && !hasSearchFlag)
{
return(false);
}
string contents = sb.ToString();
if (hasTitleFlag)
{
Match m = WebResponseHelper.TitleCheckExpression.Match(contents);
if (m.Success)
{
result.Title = m.Groups[1].Value;
hasTitleFlag = false;
}
if (hasTitleFlag && contents.Contains("</head>", StringComparison.OrdinalIgnoreCase))
{
hasTitleFlag = false;
}
}
if (hasSearchFlag)
{
// ReSharper disable once AssignNullToNotNullAttribute
if (contents.Contains(searchFor, comparison))
{
result.Status = UrlSearchStatus.Found;
hasSearchFlag = false;
}
}
token.ThrowIfCancellationRequested();
return(hasTitleFlag || hasSearchFlag || hasBufferFlag);
};
}
else
{
onRead = (_, _) =>
{
token.ThrowIfCancellationRequested();
if (result.Status == UrlSearchStatus.Unknown)
{
result.Status = UrlSearchStatus.Success;
}
return(false);
};
}
IOReadSettings readSettings = new IOReadSettings(settings, onRead);
if (!ReadAsync(thisValue, readSettings, token).Execute())
{
result.Status = UrlSearchStatus.Failed;
}
}
catch (WebException wex)
{
result.Status = UrlSearchStatus.Unauthorized;
result.Exception = wex;
}
catch (Exception ex)
{
result.Status = UrlSearchStatus.Error;
result.Exception = ex;
}
return(Task.FromResult(result));
}
public static Task <string> ReadToEndAsync([NotNull] this WebResponse thisValue, IOSettings settings = null, CancellationToken token = default(CancellationToken))
{
token.ThrowIfCancellationRequested();
settings ??= new IOSettings();
Stream stream = null;
StreamReader reader = null;
string result;
try
{
stream = GetStream(thisValue);
token.ThrowIfCancellationRequested();
if (stream == null)
{
return(null);
}
reader = new StreamReader(stream, settings.Encoding, true, settings.BufferSize);
result = reader.ReadToEndAsync().Execute();
token.ThrowIfCancellationRequested();
}
catch (Exception ex) when(settings.OnError != null)
{
result = null;
settings.OnError(ex);
}
finally
{
ObjectHelper.Dispose(ref reader);
ObjectHelper.Dispose(ref stream);
}
return(Task.FromResult(result));
}
//**********************************************************************************************
public override void Edit()
{
IOSettings form = new IOSettings(this);
form.ShowDialog();
}
public static Task <string> GetTitleAsync([NotNull] this WebResponse thisValue, IOSettings settings = null, CancellationToken token = default(CancellationToken))
{
token.ThrowIfCancellationRequested();
string result = null;
StringBuilder sb = new StringBuilder();
IOReadSettings readSettings = new IOReadSettings(settings, (bf, _) =>
{
token.ThrowIfCancellationRequested();
sb.Append(bf);
string contents = sb.ToString();
Match m = WebResponseHelper.TitleCheckExpression.Match(contents);
if (m.Success)
{
// we found a <title></title> match =]
result = m.Groups[1].Value;
return(false);
}
// reached end of head-block; no title found =[
return(!contents.Contains("</head>", StringComparison.OrdinalIgnoreCase));
});
return(ReadAsync(thisValue, readSettings, token)
.ContinueWith(_ => result, token, TaskContinuationOptions.OnlyOnRanToCompletion, TaskScheduler.Default));
}
public static (string Title, string Buffer) Peek([NotNull] this WebResponse thisValue, IOSettings settings = null)
{
bool titleFound = false;
bool bufferFilled = false;
string title = null;
int bufferSize = settings?.BufferSize ?? IOSettings.BUFFER_DEFAULT;
StringBuilder bufferFetch = new StringBuilder(bufferSize);
StringBuilder sb = new StringBuilder(bufferSize);
IOReadSettings readSettings = new IOReadSettings(settings, (buf, _) =>
{
sb.Append(buf);
string contents = sb.ToString();
if (!bufferFilled)
{
bufferFetch.Append(buf);
bufferFilled = bufferFetch.Length >= bufferSize;
}
if (!titleFound)
{
Match m = WebResponseHelper.TitleCheckExpression.Match(contents);
if (m.Success)
{
// we found a <title></title> match =]
title = m.Groups[1].Value;
titleFound = true;
}
else
{
// reached end of head-block; no title found =[
titleFound = contents.Contains("</head>", StringComparison.OrdinalIgnoreCase);
}
}
return(!titleFound || !bufferFilled);
});
return(Read(thisValue, readSettings)
? (title, bufferFetch.ToString())
: (null, null));
}
public static Task <string> GetStringAsync([NotNull] this WebResponse thisValue, IOSettings settings = null, CancellationToken token = default(CancellationToken))
{
token.ThrowIfCancellationRequested();
bool bufferFilled = false;
int bufferSize = settings?.BufferSize ?? IOSettings.BUFFER_DEFAULT;
StringBuilder sb = new StringBuilder(bufferSize);
IOReadSettings readSettings = new IOReadSettings(settings, (buf, _) =>
{
if (!bufferFilled)
{
sb.Append(buf);
bufferFilled = sb.Length >= bufferSize;
}
token.ThrowIfCancellationRequested();
return(!bufferFilled);
});
return(ReadAsync(thisValue, readSettings, token)
.ContinueWith(_ => sb.ToString(), token, TaskContinuationOptions.OnlyOnRanToCompletion, TaskScheduler.Default));
}
public static Task <(string Title, string Buffer)> PeekAsync([NotNull] this WebResponse thisValue, IOSettings settings = null, CancellationToken token = default(CancellationToken))
{
token.ThrowIfCancellationRequested();
bool titleFound = false;
bool bufferFilled = false;
string title = null;
int bufferSize = settings?.BufferSize ?? IOSettings.BUFFER_DEFAULT;
StringBuilder bufferFetch = new StringBuilder(bufferSize);
StringBuilder sb = new StringBuilder(bufferSize);
IOReadSettings readSettings = new IOReadSettings(settings, (buf, _) =>
{
token.ThrowIfCancellationRequested();
sb.Append(buf);
string contents = sb.ToString();
if (!bufferFilled)
{
bufferFetch.Append(buf);
bufferFilled = bufferFetch.Length >= bufferSize;
}
if (!titleFound)
{
Match m = WebResponseHelper.TitleCheckExpression.Match(contents);
if (m.Success)
{
// we found a <title></title> match =]
title = m.Groups[1].Value;
titleFound = true;
}
else
{
// reached end of head-block; no title found =[
titleFound = contents.Contains("</head>", StringComparison.OrdinalIgnoreCase);
}
}
token.ThrowIfCancellationRequested();
return(!titleFound || !bufferFilled);
});
return(ReadAsync(thisValue, readSettings, token)
.ContinueWith(_ => (title, bufferFetch.ToString()), token, TaskContinuationOptions.OnlyOnRanToCompletion, TaskScheduler.Default));
}
private void InitIOSettings()
{
forceReadAs3DCoords = IOSettings.Add(new BooleanIOSetting("ForceReadAs3DCoordinates", Importance.Low,
"Should coordinates always be read as 3D?", "false"));
}
public static Task <UrlSearchResult> SearchAsync([NotNull] this WebResponse thisValue, UrlSearchFlags flags, IOSettings settings = null, CancellationToken token = default(CancellationToken))
{
return(SearchAsync(thisValue, null, flags, settings, token));
}
public static UrlSearchResult Search([NotNull] this WebResponse thisValue, UrlSearchFlags flags, IOSettings settings = null)
{
return(Search(thisValue, null, flags, settings));
}
/// <summary>
/// Initializes IO settings.
/// </summary>
/// <remarks>
/// Please note with regards to "writeAromaticBondTypes": bond type values 4 through 8 are for SSS queries only,
/// so a 'query file' is created if the container has aromatic bonds and this settings is true.
/// </remarks>
private void InitIOSettings()
{
programNameOpt = IOSettings.Add(
new StringIOSetting(OptProgramName, Importance.Low,
"Program name to write at the top of the molfile header, should be exactly 8 characters long", "CDK"));
}
public Settings(IOSettings ioSettings, string path = "")
{
Path = path;
IO = ioSettings;
}
