/// <summary>
/// Method will return an appropriate reader for the provided format. Each reader is stored
/// in a map, if no reader is available for the specified format a new reader is created. The
/// <see cref="IChemObjectReader.ErrorHandler"/> and
/// <see cref="IChemObjectReader.ReaderMode"/> are set.
/// </summary>
/// <param name="format">The format to obtain a reader for</param>
/// <returns>instance of a reader appropriate for the provided format</returns>
private ISimpleChemObjectReader GetReader(IChemFormat format, TextReader input)
{
ISimpleChemObjectReader reader;
if (format is MDLV2000Format)
{
reader = new MDLV2000Reader(input);
}
else if (format is MDLV3000Format)
{
reader = new MDLV3000Reader(input);
}
else if (format is MDLFormat)
{
reader = new MDLReader(input);
}
else
{
throw new ArgumentException("Unexpected format: " + format);
}
reader.ErrorHandler = this.ErrorHandler;
reader.ReaderMode = this.ReaderMode;
if (currentFormat is MDLV2000Format)
{
reader.AddSettings(IOSettings.Settings);
}
return(reader);
}
/// <summary>
/// MolfileV3000ToAtomContainer
/// </summary>
/// <param name="molfile"></param>
/// <returns></returns>
public static IAtomContainer MolfileV3000ToAtomContainer(string molfile)
{
// Extract any mass info before conversion to avoid losing our custom info in conversion
Dictionary <int, int> map = new Dictionary <int, int>();
if (molfile.Contains(" MASS="))
{
map = ExtractMassAttributes(ref molfile);
}
cdk.io.DefaultChemObjectReader cor;
java.io.StringReader sr = new java.io.StringReader(molfile);
cor = new MDLV3000Reader(sr);
cor.setReaderMode(IChemObjectReader.Mode.RELAXED);
IAtomContainer mol = (IAtomContainer)cor.read(new AtomContainer());
cor.close();
for (int ai = 0; ai < mol.getAtomCount(); ai++)
{
IAtom a = mol.getAtom(ai);
if (map.ContainsKey(ai + 1))
{
a.setMassNumber(new java.lang.Integer(map[ai + 1]));
}
else
{
a.setMassNumber(null);
}
}
ConfigureAtomContainer(mol);
return(mol);
}
/// <summary>
/// Method will return an appropriate reader for the provided format. Each reader is stored
/// in a map, if no reader is available for the specified format a new reader is created. The
/// <see cref="IChemObjectReader.ErrorHandler"/> and
/// <see cref="IChemObjectReader.ReaderMode"/> are set.
/// </summary>
/// <param name="format">The format to obtain a reader for</param>
/// <returns>instance of a reader appropriate for the provided format</returns>
private ISimpleChemObjectReader GetReader(IChemFormat format, TextReader input)
{
ISimpleChemObjectReader reader;
switch (format)
{
case MDLV2000Format _:
reader = new MDLV2000Reader(input);
break;
case MDLV3000Format _:
reader = new MDLV3000Reader(input);
break;
case MDLFormat _:
reader = new MDLReader(input);
break;
default:
throw new ArgumentException($"Unexpected format: {format}");
}
reader.ErrorHandler = this.ErrorHandler;
reader.ReaderMode = this.ReaderMode;
if (currentFormat is MDLV2000Format)
{
reader.AddSettings(IOSettings.Settings);
}
return(reader);
}
/// <summary>
/// MolfileV3000ToAtomContainer
/// </summary>
/// <param name="molfile"></param>
/// <returns></returns>
public static IAtomContainer MolfileV3000ToAtomContainer(string molfile)
{
// Extract any mass info before conversion to avoid losing our custom info in conversion
Dictionary <int, int> map = new Dictionary <int, int>();
if (molfile.Contains(" MASS="))
{
map = ExtractMassAttributes(ref molfile);
}
DefaultChemObjectReader cor;
StringReader sr = new StringReader(molfile);
cor = new MDLV3000Reader(sr);
cor.ReaderMode = ChemObjectReaderMode.Relaxed;
IAtomContainer mol = cor.Read(new AtomContainer());
cor.Close();
for (int ai = 0; ai < mol.Atoms.Count; ai++)
{
IAtom a = mol.Atoms[ai];
if (map.ContainsKey(ai + 1))
{
a.MassNumber = map[ai + 1];
}
//a.setMassNumber(new java.lang.Integer(map[ai + 1]));
else
{
a.MassNumber = null;
}
}
ConfigureAtomContainer(mol);
return(mol);
}
static IAtomContainer RawParse(string text, out string notationType)
{
IAtomContainer mol = null;
if (text == null)
{
notationType = "None";
return(null);
}
if (text.IndexOf('\r') >= 0)
{
goto Go_Mol;
}
if (text.IndexOf('\n') >= 0)
{
goto Go_Mol;
}
mol = ParseSmiles(text);
if (mol != null)
{
notationType = "SMILES";
return(mol);
}
mol = ParseInChI(text);
if (mol != null)
{
notationType = "InChI";
return(mol);
}
Go_Mol:
using (var r = new MDLV2000Reader(new StringReader(text)))
{
var m = CDK.Builder.NewAtomContainer();
try
{
r.Read(m);
mol = m;
}
catch (Exception)
{ }
}
if (mol != null)
{
notationType = "MolBlock";
return(mol);
}
using (var r = new MDLV3000Reader(new StringReader(text)))
{
var m = CDK.Builder.NewAtomContainer();
try
{
r.Read(m);
mol = m;
}
catch (Exception)
{ }
}
if (mol != null)
{
notationType = "MolBlock";
return(mol);
}
notationType = "None";
return(null);
}