/// <summary>
/// Read a bracket atom from the buffer. A bracket atom optionally defines
/// isotope, chirality, hydrogen count, formal charge and the atom class.
/// <para>
/// bracket_atom ::= '[' isotope? symbol chiral? hcount? charge? class? ']'
/// </para>
/// </summary>
/// <param name="buffer">a character buffer</param>
/// <returns>a bracket atom</returns>
/// <exception cref="InvalidSmilesException">if the bracket atom did not match the grammar, invalid symbol, missing closing bracket or invalid chiral specification.</exception>
public IAtom ReadBracketAtom(CharBuffer buffer)
{
int start = buffer.Position;
bool arbitraryLabel = false;
if (!buffer.HasRemaining())
{
throw new InvalidSmilesException("Unclosed bracket atom, SMILES may be truncated", buffer);
}
var isotope = buffer.GetNumber();
var aromatic = buffer.NextChar >= 'a' && buffer.NextChar <= 'z';
var element = Element.Read(buffer);
if (element == Element.Unknown)
{
hasAstrix = true;
}
if (strict && element == null)
{
throw new InvalidSmilesException("unrecognised element symbol, SMILES may be truncated: ", buffer);
}
if (element != null && aromatic)
{
g.AddFlags(Graph.HAS_AROM);
}
// element isn't aromatic as per the OpenSMILES specification
if (strict && aromatic && !element.IsAromatic(Element.AromaticSpecification.OpenSmiles))
{
throw new InvalidSmilesException("abnormal aromatic element", buffer);
}
if (element == null)
{
arbitraryLabel = true;
}
configuration = Configuration.Read(buffer);
var hCount = ReadHydrogens(buffer);
var charge = ReadCharge(buffer);
var atomClass = ReadClass(buffer);
if (!arbitraryLabel && !buffer.GetIf(']'))
{
if (strict)
{
throw InvalidSmilesException.InvalidBracketAtom(buffer);
}
else
{
arbitraryLabel = true;
}
}
if (arbitraryLabel)
{
var end = buffer.Position;
int depth = 1;
while (buffer.HasRemaining())
{
char c = buffer.Get();
if (c == '[')
{
depth++;
}
else if (c == ']')
{
depth--;
if (depth == 0)
{
break;
}
}
end++;
}
if (depth != 0)
{
throw new InvalidSmilesException("unparsable label in bracket atom",
buffer,
buffer.Position - 1);
}
var label = buffer.Substr(start, end);
hasAstrix = true;
return(new AtomImpl.BracketAtom(label));
}
return(new AtomImpl.BracketAtom(isotope,
element,
hCount,
charge,
atomClass,
aromatic));
}
