/// <summary>
/// Generates and assigns abbreviations to a molecule. Abbreviations are first
/// generated with <see cref="Generate(IAtomContainer)"/> and the filtered based on
/// the coverage. Currently only abbreviations that cover 100%, or < 40% of the
/// atoms are assigned.
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>number of new abbreviations</returns>
/// <seealso cref="Generate(IAtomContainer)"/>
public int Apply(IAtomContainer mol)
{
var newSgroups = Generate(mol);
var sgroups = mol.GetCtabSgroups();
if (sgroups == null)
{
sgroups = new List <Sgroup>();
}
else
{
sgroups = new List <Sgroup>(sgroups);
}
var prev = sgroups.Count;
foreach (var sgroup in newSgroups)
{
var coverage = sgroup.Atoms.Count / (double)mol.Atoms.Count;
// update xml comment if changed!
if (!sgroup.Bonds.Any() || coverage < 0.4d)
{
sgroups.Add(sgroup);
}
}
mol.SetCtabSgroups(sgroups);
return(sgroups.Count - prev);
}
public void TestSgroupAtomListWrapping()
{
IAtomContainer mol = TestMoleculeFactory.MakeEthylPropylPhenantren();
Sgroup sgroup = new Sgroup();
foreach (var atom in mol.Atoms)
{
sgroup.Atoms.Add(atom);
}
mol.SetCtabSgroups(new[] { sgroup });
StringWriter sw = new StringWriter();
using (MDLV2000Writer mdlw = new MDLV2000Writer(sw))
{
mdlw.Write(mol);
string output = sw.ToString();
Assert.IsTrue(output.Contains("M SAL 1 15"));
Assert.IsTrue(output.Contains("M SAL 1 4"));
}
}
/// <summary>
/// Reads the bond atoms, order and stereo configuration.
/// </summary>
public void ReadBondBlock(IAtomContainer readData)
{
Trace.TraceInformation("Reading BOND block");
bool foundEND = false;
while (!foundEND)
{
string command = ReadCommand(ReadLine());
if (string.Equals("END BOND", command, StringComparison.Ordinal))
{
foundEND = true;
}
else
{
Debug.WriteLine($"Parsing bond from: {command}");
var tokenizer = Strings.Tokenize(command).GetEnumerator();
IBond bond = readData.Builder.NewBond();
// parse the index
try
{
tokenizer.MoveNext();
string indexString = tokenizer.Current;
bond.Id = indexString;
}
catch (Exception exception)
{
string error = "Error while parsing bond index";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
// parse the order
try
{
tokenizer.MoveNext();
string orderString = tokenizer.Current;
int order = int.Parse(orderString, NumberFormatInfo.InvariantInfo);
if (order >= 4)
{
Trace.TraceWarning("Query order types are not supported (yet). File a bug if you need it");
}
else
{
bond.Order = BondManipulator.CreateBondOrder((double)order);
}
}
catch (Exception exception)
{
string error = "Error while parsing bond index";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
// parse index atom 1
try
{
tokenizer.MoveNext();
string indexAtom1String = tokenizer.Current;
int indexAtom1 = int.Parse(indexAtom1String, NumberFormatInfo.InvariantInfo);
IAtom atom1 = readData.Atoms[indexAtom1 - 1];
bond.Atoms.Add(atom1); // bond.Atoms[0]
}
catch (Exception exception)
{
string error = "Error while parsing index atom 1 in bond";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
// parse index atom 2
try
{
tokenizer.MoveNext();
string indexAtom2String = tokenizer.Current;
int indexAtom2 = int.Parse(indexAtom2String, NumberFormatInfo.InvariantInfo);
IAtom atom2 = readData.Atoms[indexAtom2 - 1];
bond.Atoms.Add(atom2); // bond.Atoms[1]
}
catch (Exception exception)
{
string error = "Error while parsing index atom 2 in bond";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
var endpts = new List <IAtom>();
string attach = null;
// the rest are key=value fields
if (command.IndexOf('=') != -1)
{
var options = ParseOptions(ExhaustStringTokenizer(tokenizer));
foreach (var key in options.Keys)
{
string value = options[key];
try
{
switch (key)
{
case "CFG":
int configuration = int.Parse(value, NumberFormatInfo.InvariantInfo);
if (configuration == 0)
{
bond.Stereo = BondStereo.None;
}
else if (configuration == 1)
{
bond.Stereo = BondStereo.Up;
}
else if (configuration == 2)
{
bond.Stereo = BondStereo.None;
}
else if (configuration == 3)
{
bond.Stereo = BondStereo.Down;
}
break;
case "ENDPTS":
string[] endptStr = value.Split(' ');
// skip first value that is count
for (int i = 1; i < endptStr.Length; i++)
{
endpts.Add(readData.Atoms[int.Parse(endptStr[i], NumberFormatInfo.InvariantInfo) - 1]);
}
break;
case "ATTACH":
attach = value;
break;
default:
Trace.TraceWarning("Not parsing key: " + key);
break;
}
}
catch (Exception exception)
{
string error = "Error while parsing key/value " + key + "=" + value + ": "
+ exception.Message;
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
}
}
// storing bond
readData.Bonds.Add(bond);
// storing positional variation
if (string.Equals("ANY", attach, StringComparison.Ordinal))
{
Sgroup sgroup = new Sgroup {
Type = SgroupType.ExtMulticenter
};
sgroup.Atoms.Add(bond.Begin); // could be other end?
sgroup.Bonds.Add(bond);
foreach (var endpt in endpts)
{
sgroup.Atoms.Add(endpt);
}
var sgroups = readData.GetCtabSgroups();
if (sgroups == null)
{
readData.SetCtabSgroups(sgroups = new List <Sgroup>(4));
}
sgroups.Add(sgroup);
}
Debug.WriteLine($"Added bond: {bond}");
}
}
}