private void ProcessBondAtomIDs(int pos, NewBondInfo newBondInfo)
{
var line = input.ReadLine();
int bondIndex = 0;
while (line != null)
{
if (line.IndexOf('}') != -1)
{
// done
return;
}
else
{
var id = GetValue(line);
var atom = (IAtom)atomIDs[id];
if (atom == null)
{
throw new CDKException($"File is corrupt: atom ID does not exist {id}");
}
newBondInfo.Set(bondIndex, pos, atom);
bondIndex++;
}
line = input.ReadLine();
}
}
private void ProcessBondBlock()
{
string line = input.ReadLine();
var newBondInfo = new NewBondInfo();
while (line != null)
{
if (line.IndexOf('{') != -1)
{
ProcessBondBlockBlock(line, newBondInfo);
}
else if (line.IndexOf('}') != -1)
{
break;
}
else
{
Trace.TraceWarning("Skipping non-block: " + line);
}
line = input.ReadLine();
}
foreach (var info in newBondInfo.IndexToAtoms)
{
SetBondAtoms(info.Key, info.Value[0], info.Value[1]);
}
}
private void ProcessBondBlockBlock(string line, NewBondInfo newBondInfo)
{
var command = GetCommand(line);
if (string.Equals(command, "aid1", StringComparison.Ordinal))
{
// assume this is the first block in the atom block
Debug.WriteLine("ASN bonds aid1 found");
ProcessBondAtomIDs(0, newBondInfo);
}
else if (string.Equals(command, "aid2", StringComparison.Ordinal))
{
// assume this is the first block in the atom block
Debug.WriteLine("ASN bonds aid2 found");
ProcessBondAtomIDs(1, newBondInfo);
}
else
{
Trace.TraceWarning("Skipping atom block block: " + command);
SkipBlock();
}
}
