private static void WriteHeader(
TextWriter writer, Molecule molecule)
{
writer.Write('\n');
writer.Write(" Written by signature package");
writer.Write('\n');
writer.Write('\n');
int a = molecule.GetAtomCount();
int b = molecule.GetBondCount();
writer.Write($"{a,3:D}{b,3:D} 0 0 0 0 0 0 0 0999 V2000");
writer.Write('\n');
}
public void AddRing(int atomToAttachTo, int ringSize, Molecule molecule)
{
var numberOfAtoms = molecule.GetAtomCount();
var previous = atomToAttachTo;
for (int i = 0; i < ringSize; i++)
{
molecule.AddAtom("C");
int current = numberOfAtoms + i;
molecule.AddSingleBond(previous, current);
previous = current;
}
molecule.AddSingleBond(numberOfAtoms, numberOfAtoms + (ringSize - 1));
}
public static void WriteToStream(Stream stream, Molecule molecule)
{
try
{
using (var writer = new StreamWriter(stream))
{
WriteHeader(writer, molecule);
for (int i = 0; i < molecule.GetAtomCount(); i++)
{
WriteAtom(writer, molecule, i);
}
for (int i = 0; i < molecule.GetBondCount(); i++)
{
WriteBond(writer, molecule, i);
}
writer.Write("M END");
writer.Write('\n');
}
}
catch (IOException)
{
}
}
public static List <int> FindTetrahedralChiralCenters(Molecule molecule)
{
List <int> chiralCenterIndices = new List <int>();
MoleculeSignature molSig = new MoleculeSignature(molecule);
List <string> signatureStrings = molSig.GetVertexSignatureStrings();
for (int i = 0; i < molecule.GetAtomCount(); i++)
{
int[] connected = molecule.GetConnected(i);
if (connected.Length < 4)
{
continue;
}
else
{
string s0 = signatureStrings[connected[0]];
string s1 = signatureStrings[connected[1]];
string s2 = signatureStrings[connected[2]];
string s3 = signatureStrings[connected[3]];
if (string.Equals(s0, s1, StringComparison.Ordinal) ||
string.Equals(s0, s2, StringComparison.Ordinal) ||
string.Equals(s0, s3, StringComparison.Ordinal) ||
string.Equals(s1, s2, StringComparison.Ordinal) ||
string.Equals(s1, s3, StringComparison.Ordinal) ||
string.Equals(s2, s3, StringComparison.Ordinal))
{
continue;
}
else
{
chiralCenterIndices.Add(i);
}
}
}
return(chiralCenterIndices);
}
