private SdfState ReadCtabFooter(StreamReader reader)
{
SdfState result = SdfState.Error;
while (!reader.EndOfStream)
{
string line = SdFileConverter.GetNextLine(reader); //reader.ReadLine();
if (!string.IsNullOrEmpty(line))
{
if (line.StartsWith(MDLConstants.M_CHG) ||
line.StartsWith(MDLConstants.M_ISO) ||
line.StartsWith(MDLConstants.M_RAD))
{
ReadAtomPropertyLine(line);
}
if (line.Equals(MDLConstants.M_END))
{
result = SdfState.EndOfCtab;
break;
}
}
}
return(result);
}
public override SdfState ImportFromStream(StreamReader reader, Molecule molecule, out string message)
{
message = null;
_molecule = molecule;
SdfState result = SdfState.Null;
try
{
bool isFormula = false;
string internalName = "";
while (!reader.EndOfStream)
{
string line = SdFileConverter.GetNextLine(reader); //reader.ReadLine();;
if (!string.IsNullOrEmpty(line))
{
if (line.Equals(MDLConstants.SDF_END))
{
// End of SDF Section
result = SdfState.EndOfData;
break;
}
if (line.StartsWith(">"))
{
// Clear existing Property Name
internalName = string.Empty;
// See if we can find the property in our translation table
foreach (var property in _propertyTypes)
{
if (line.Equals(property.ExternalName))
{
isFormula = property.IsFormula;
internalName = property.InternalName;
break;
}
}
}
else
{
// Property Data
if (!string.IsNullOrEmpty(internalName))
{
if (isFormula)
{
var formula = new Formula();
formula.Convention = internalName;
formula.Inline = line;
_molecule.Formulas.Add(formula);
}
else
{
var name = new ChemicalName();
name.DictRef = internalName;
name.Name = line;
_molecule.ChemicalNames.Add(name);
}
}
}
}
else
{
internalName = string.Empty;
}
}
}
catch (System.Exception ex)
{
Debug.WriteLine(ex.Message);
result = SdfState.Error;
}
return(result);
}
private Counts ReadCtabHeader(StreamReader reader)
{
Counts result = new Counts();
// Title
string title = SdFileConverter.GetNextLine(reader); //reader.ReadLine();
if (!string.IsNullOrEmpty(title))
{
if (title.StartsWith("$MDL"))
{
_molecule.Errors.Add("RGFiles are currently not supported");
throw new Exception("RGFiles are currently not supported");
}
if (title.StartsWith("$RXN"))
{
_molecule.Errors.Add("RXNFiles are currently not supported");
throw new Exception("RXNFiles are currently not supported");
}
if (title.StartsWith("$RDFILE"))
{
_molecule.Errors.Add("RDFiles are currently not supported");
throw new Exception("RDFiles are currently not supported");
}
if (title.StartsWith("<XDfile>"))
{
_molecule.Errors.Add("XDFiles are currently not supported");
throw new Exception("XDFiles are currently not supported");
}
}
// Header
string header = SdFileConverter.GetNextLine(reader); //reader.ReadLine();
// Comment
string comment = SdFileConverter.GetNextLine(reader); //reader.ReadLine();
// Counts
string counts = SdFileConverter.GetNextLine(reader); //reader.ReadLine();
if (counts.ToLower().Contains("v2000"))
{
try
{
result.Atoms = ParseInteger(counts, 0, 3);
result.Bonds = ParseInteger(counts, 3, 3);
result.Version = GetSubString(counts, 34, 5).ToUpper();
}
catch (Exception ex)
{
result.Message = $"Exception {ex.Message}";
Debug.WriteLine(ex.Message);
}
}
else
{
result.Message = "Line containing atom and bond counts not found!";
}
return(result);
}
private void ReadBonds(StreamReader reader, int bonds)
{
int idx = 0;
while (!reader.EndOfStream && idx < bonds)
{
string line = SdFileConverter.GetNextLine(reader); //reader.ReadLine();
if (!string.IsNullOrEmpty(line))
{
// create bond
int atomNumber1 = ParseInteger(line, 0, 3);
Atom atom1 = atomByNumber[atomNumber1];
if (atom1 == null)
{
//throw new Exception("Cannot resolve atomNumber :" + atomNumber1 + ": in " + line);
_molecule.Warnings.Add($"Cannot resolve atomNumber {atomNumber1} at line {SdFileConverter.LineNumber}");
_molecule.Warnings.Add($"{line}");
}
int atomNumber2 = ParseInteger(line, 3, 3);
Atom atom2 = atomByNumber[atomNumber2];
if (atom2 == null)
{
//throw new Exception("Cannot resolve atomNumber :" + atomNumber2 + ": in " + line);
_molecule.Warnings.Add($"Cannot resolve atomNumber {atomNumber2} at line {SdFileConverter.LineNumber}");
_molecule.Warnings.Add($"{line}");
}
idx++;
Bond thisBond = new Bond()
{
StartAtom = atom1, EndAtom = atom2
};
// Bond Order
String order = GetSubString(line, 6, 3);
if (!string.IsNullOrEmpty(order))
{
int bondOrder = ParseInteger(order);
if (bondOrder <= 4)
{
thisBond.Order = BondOrder(bondOrder);
}
else
{
thisBond.Order = BondOrder(bondOrder);
_molecule.Warnings.Add($"Unsupported Bond Type of {order} at Line {SdFileConverter.LineNumber}");
}
}
// stereo
String stereo = GetSubString(line, 9, 3);
if (!string.IsNullOrEmpty(stereo))
{
thisBond.Stereo = BondStereoFromMolfile(ParseInteger(stereo));
}
// add bond to molecule
_molecule.Bonds.Add(thisBond);
bondByNumber.Add(idx, thisBond);
}
}
}
private void ReadAtoms(StreamReader reader, int atoms)
{
int idx = 0;
while (!reader.EndOfStream && idx < atoms)
{
string line = SdFileConverter.GetNextLine(reader); //reader.ReadLine();
if (!string.IsNullOrEmpty(line))
{
// create atom
Atom thisAtom = new Atom();
double x = Double.Parse(GetSubString(line, 0, 9), CultureInfo.InvariantCulture);
double y = Double.Parse(GetSubString(line, 10, 9), CultureInfo.InvariantCulture);
double z = Double.Parse(GetSubString(line, 20, 9), CultureInfo.InvariantCulture);
// Inverting Y co-ordinate to make it the right way up.
thisAtom.Position = new Point(x, 0 - y);
// element type
String elType = GetSubString(line, 31, 3);
// Hack: Fix Up for R#
elType = elType.Replace("#", "");
if (ElementExists(elType))
{
thisAtom.Element = _pt.Elements[elType];
}
else
{
//throw new Exception(elType + " is not a valid element atomicSymbol");
_molecule.Errors.Add($"{elType} at Line {SdFileConverter.LineNumber} is not a valid Element");
_molecule.Errors.Add($"{line}");
}
// isotope
int delta = ParseInteger(line, 34, 2);
if (delta != 0)
{
thisAtom.IsotopeNumber = delta;
}
// charge
int ch = ParseInteger(line, 36, 3);
thisAtom.FormalCharge = FormalChargeFromMolfile(ch);
thisAtom.DoubletRadical = DoubletRadicalFromMolfile(ch);
// field 3 is atom parity (a *write-only* field, so not used)
// int parity = ParseInteger(line, 39, 3);
// field 4 hydrogen count
// int hCount = ParseInteger(line, 42, 3);
// field 5 stereoCareBox
// int field5 = ParseInteger(line, 45, 3);
// field 6 valency/oxidation state
// int oxState = ParseInteger(line, 48, 3);
// field 7 H0 designator
// int hZero = ParseInteger(line, 51, 3);
// atom-atom mapping
int atomMap = ParseInteger(line, 60, 3);
if (atomMap != 0)
{
// ToDo: What to do here ???
}
// inversion/retention flag
// int hZero = ParseInteger(line, 63, 3);
// exact change flag
// int hZero = ParseInteger(line, 66, 3);
idx++;
// Add atom to molecule
thisAtom.Id = $"a{idx}";
_molecule.Atoms.Add(thisAtom);
atomByNumber.Add(idx, thisAtom);
}
}
}