public void TestCreateReader_IChemFormat()
{
IChemFormat format = (IChemFormat)XYZFormat.Instance;
ISimpleChemObjectReader reader = factory.CreateReader(format, new StringReader(""));
Assert.IsNotNull(reader);
Assert.AreEqual(format.FormatName, reader.Format.FormatName);
}
/// <summary>
/// Detects the format of the Reader input, and if known, it will return
/// a CDK Reader to read the format, or null when the reader is not
/// implemented.
/// </summary>
/// <param name="input"></param>
/// <returns><see langword="null"/> if CDK does not contain a reader for the detected format.</returns>
/// <seealso cref="CreateReader(TextReader)"/>
public ISimpleChemObjectReader CreateReader(Stream input)
{
IChemFormat format = null;
ISimpleChemObjectReader reader = null;
if (input is GZipStream)
{
var istreamToRead = new ReadSeekableStream(input, 65536);
format = formatFactory.GuessFormat(istreamToRead);
var type = GetReaderType(format);
if (type != null)
{
try
{
reader = (ISimpleChemObjectReader)type.GetConstructor(new Type[] { typeof(Stream) }).Invoke(new object[] { istreamToRead });
}
catch (CDKException e1)
{
var wrapper = new IOException("Exception while setting the Stream: " + e1.Message, e1);
throw wrapper;
}
}
}
else
{
var bistream = input;
var istreamToRead = bistream; // if gzip test fails, then take default
// bistream.Mark(5);
int countRead = 0;
var abMagic = new byte[4];
countRead = bistream.Read(abMagic, 0, 4);
bistream.Seek(0, SeekOrigin.Begin);
if (countRead == 4)
{
if (abMagic[0] == (byte)0x1F && abMagic[1] == (byte)0x8B)
{
istreamToRead = new GZipStream(bistream, CompressionMode.Decompress);
return(CreateReader(istreamToRead));
}
}
format = formatFactory.GuessFormat(istreamToRead);
var type = GetReaderType(format);
if (type != null)
{
try
{
reader = (ISimpleChemObjectReader)type.GetConstructor(new Type[] { typeof(Stream) }).Invoke(new object[] { istreamToRead });
}
catch (CDKException e1)
{
var wrapper = new IOException("Exception while setting the Stream: " + e1.Message, e1);
throw wrapper;
}
}
}
return(reader);
}
public IChemFile GetChemFile(ISimpleChemObjectReader reader, bool useRebond)
{
Assert.IsNotNull(reader);
reader.IOSettings["UseRebondTool"].Setting = useRebond.ToString();
var chemFile = reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
return(chemFile);
}
public void TestReadGzWithGzipDetection()
{
var filename = "NCDK.Data.XYZ.bf3.xyz.gz";
var input = ResourceLoader.GetAsStream(filename);
// ok, if format ok, try instantiating a reader
ISimpleChemObjectReader reader = factory.CreateReader(input);
Assert.IsNotNull(reader);
Assert.AreEqual(((IChemFormat)XYZFormat.Instance).ReaderClassName, reader.GetType().FullName);
// now try reading something from it
var chemFile = reader.Read(builder.NewChemFile());
var molecule = builder.NewAtomContainer();
foreach (var container in ChemFileManipulator.GetAllAtomContainers(chemFile))
{
molecule.Add(container);
}
Assert.IsNotNull(molecule);
Assert.AreEqual(4, molecule.Atoms.Count);
}
public void TestBug2153298()
{
var filename = "NCDK.Data.ASN.PubChem.cid1145.xml";
var ins = ResourceLoader.GetAsStream(filename);
Assert.IsNotNull(ins, "Cannot find file: " + filename);
IChemFormatMatcher realFormat = (IChemFormatMatcher)PubChemCompoundXMLFormat.Instance;
factory.RegisterFormat(realFormat);
// ok, if format ok, try instantiating a reader
ins = ResourceLoader.GetAsStream(filename);
ISimpleChemObjectReader reader = factory.CreateReader(ins);
Assert.IsNotNull(reader);
Assert.AreEqual(((IChemFormat)PubChemCompoundXMLFormat.Instance).ReaderClassName, reader.GetType().FullName);
// now try reading something from it
IAtomContainer molecule = (IAtomContainer)reader.Read(builder.NewAtomContainer());
Assert.IsNotNull(molecule);
Assert.AreNotSame(0, molecule.Atoms.Count);
Assert.AreNotSame(0, molecule.Bonds.Count);
}
internal void ExpectReader(string filename, IResourceFormat expectedFormat, int expectedAtomCount, int expectedBondCount)
{
var ins = ResourceLoader.GetAsStream(filename);
Assert.IsNotNull(ins, "Cannot find file: " + filename);
if (expectedFormat is IChemFormatMatcher)
{
factory.RegisterFormat((IChemFormatMatcher)expectedFormat);
}
ISimpleChemObjectReader reader = factory.CreateReader(ins);
Assert.IsNotNull(reader);
Assert.AreEqual(((IChemFormat)expectedFormat).ReaderClassName, reader.GetType().FullName);
// now try reading something from it
IChemObject[] objects = { new ChemFile(), new ChemModel(), new AtomContainer(), new Reaction() };
bool read = false;
for (int i = 0; (i < objects.Length && !read); i++)
{
if (reader.Accepts(objects[i].GetType()))
{
IChemObject chemObject = reader.Read(objects[i]);
Assert.IsNotNull(chemObject, "Reader accepted a " + objects[i].GetType().Name + " but failed to read it");
AssertAtomCount(expectedAtomCount, chemObject);
AssertBondCount(expectedBondCount, chemObject);
read = true;
}
}
if (read)
{
// ok, reseting worked
}
else
{
Assert.Fail("Reading an IChemObject from the Reader did not work properly.");
}
}
public IChemFile GetChemFile(ISimpleChemObjectReader reader)
{
return(GetChemFile(reader, false));
}
public override IEnumerator <IAtomContainer> GetEnumerator()
{
// buffer to store pre-read Mol records in
var buffer = new StringBuilder(10000);
// now try to parse the next Molecule
currentFormat = (IChemFormat)MDLFormat.Instance;
int lineNum = 0;
buffer.Length = 0;
while ((currentLine = input.ReadLine()) != null)
{
// still in a molecule
buffer.Append(currentLine).Append('\n');
lineNum++;
// do MDL molfile version checking
if (lineNum == 4)
{
var versionMatcher = MDL_Version.Match(currentLine);
if (versionMatcher.Success)
{
currentFormat = string.Equals("2000", versionMatcher.Groups[1].Value, StringComparison.Ordinal)
? (IChemFormat)MDLV2000Format.Instance
: (IChemFormat)MDLV3000Format.Instance;
}
}
if (currentLine.StartsWith(M_END, StringComparison.Ordinal))
{
Debug.WriteLine($"MDL file part read: {buffer}");
IAtomContainer molecule = null;
try
{
ISimpleChemObjectReader reader = GetReader(currentFormat, new StringReader(buffer.ToString()));
molecule = reader.Read(builder.NewAtomContainer());
}
catch (Exception exception)
{
Trace.TraceError($"Error while reading next molecule: {exception.Message}");
Debug.WriteLine(exception);
}
if (molecule != null)
{
ReadDataBlockInto(molecule);
yield return(molecule);
}
else if (Skip)
{
// null molecule and skip = true, eat up the rest of the entry until '$$$$'
string line;
while ((line = input.ReadLine()) != null)
{
if (line.StartsWith(SDF_RECORD_SEPARATOR, StringComparison.Ordinal))
{
break;
}
}
}
else
{
// don't yield
}
// empty the buffer
buffer.Clear();
lineNum = 0;
}
// found SDF record separator ($$$$) without parsing a molecule (separator is detected
// in ReadDataBlockInto()) the buffer is cleared and the iterator continues reading
if (currentLine == null)
{
break;
}
if (currentLine.StartsWith(SDF_RECORD_SEPARATOR, StringComparison.Ordinal))
{
buffer.Clear();
lineNum = 0;
}
}
yield break;
}