/// <summary>
/// Internal method for parsing charge, to allow concatenated signs (--, ++)
/// the method recursively invokes increment or decrementing an accumulator.
/// </summary>
/// <param name="acc"> accumulator</param>
/// <param name="buffer">a character buffer</param>
/// <returns>the charge value</returns>
private static int ReadCharge(int acc, CharBuffer buffer)
{
if (buffer.GetIf('+'))
{
return(buffer.NextIsDigit() ? acc + buffer.GetNumber()
: ReadCharge(acc + 1, buffer));
}
if (buffer.GetIf('-'))
{
return(buffer.NextIsDigit() ? acc - buffer.GetNumber()
: ReadCharge(acc - 1, buffer));
}
return(acc);
}
/// <summary>
/// Read the hydrogen count and progress the provided buffer. The hydrogen
/// count is specified by a 'H' an 0 or more digits. A 'H' without digits is
/// intercepted as 'H1'. When there is no 'H' or 'H0' is specified then the
/// the hydrogen count is 0.
/// </summary>
/// <param name="buffer">a character buffer</param>
/// <returns>the hydrogen count, 0 if none</returns>
public static int ReadHydrogens(CharBuffer buffer)
{
if (buffer.GetIf('H'))
{
// when no number is specified 'H' then there is 1 hydrogen
int count = buffer.GetNumber();
return(count < 0 ? 1 : count);
}
return(0);
}
/// <summary>
/// Read the atom class of a bracket atom and progress the buffer (if read).
/// The atom class is the last attribute of the bracket atom and is
/// identified by a ':' followed by one or more digits. The atom class may be
/// padded such that ':005' and ':5' are equivalent.
/// </summary>
/// <seealso href="http://www.opensmiles.org/opensmiles.html#atomclass">Atom Class - OpenSMILES Specification</seealso >
/// <param name="buffer">a character buffer</param>
/// <returns>the atom class, or 0</returns>
public static int ReadClass(CharBuffer buffer)
{
if (buffer.GetIf(':'))
{
if (buffer.NextIsDigit())
{
return(buffer.GetNumber());
}
throw new InvalidSmilesException("invalid atom class, <digit>+ must follow ':'", buffer);
}
return(0);
}
/// <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));
}
/// <summary>
/// Read a molecule from the character buffer.
/// </summary>
/// <param name="buffer">a character buffer</param>
/// <exception cref="InvalidSmilesException">invalid grammar</exception>
private void ReadSmiles(CharBuffer buffer)
{
// primary dispatch
while (buffer.HasRemaining())
{
char c = buffer.Get();
switch (c)
{
// aliphatic subset
case '*':
hasAstrix = true;
AddAtom(AtomImpl.AliphaticSubset.Any, buffer);
break;
case 'B':
if (buffer.GetIf('r'))
{
AddAtom(AtomImpl.AliphaticSubset.Bromine, buffer);
}
else
{
AddAtom(AtomImpl.AliphaticSubset.Boron, buffer);
}
break;
case 'C':
if (buffer.GetIf('l'))
{
AddAtom(AtomImpl.AliphaticSubset.Chlorine, buffer);
}
else
{
AddAtom(AtomImpl.AliphaticSubset.Carbon, buffer);
}
break;
case 'N':
AddAtom(AtomImpl.AliphaticSubset.Nitrogen, buffer);
break;
case 'O':
AddAtom(AtomImpl.AliphaticSubset.Oxygen, buffer);
break;
case 'P':
AddAtom(AtomImpl.AliphaticSubset.Phosphorus, buffer);
break;
case 'S':
AddAtom(AtomImpl.AliphaticSubset.Sulfur, buffer);
break;
case 'F':
AddAtom(AtomImpl.AliphaticSubset.Fluorine, buffer);
break;
case 'I':
AddAtom(AtomImpl.AliphaticSubset.Iodine, buffer);
break;
// aromatic subset
case 'b':
AddAtom(AtomImpl.AromaticSubset.Boron, buffer);
g.AddFlags(Graph.HAS_AROM);
break;
case 'c':
AddAtom(AtomImpl.AromaticSubset.Carbon, buffer);
g.AddFlags(Graph.HAS_AROM);
break;
case 'n':
AddAtom(AtomImpl.AromaticSubset.Nitrogen, buffer);
g.AddFlags(Graph.HAS_AROM);
break;
case 'o':
AddAtom(AtomImpl.AromaticSubset.Oxygen, buffer);
g.AddFlags(Graph.HAS_AROM);
break;
case 'p':
AddAtom(AtomImpl.AromaticSubset.Phosphorus, buffer);
g.AddFlags(Graph.HAS_AROM);
break;
case 's':
AddAtom(AtomImpl.AromaticSubset.Sulfur, buffer);
g.AddFlags(Graph.HAS_AROM);
break;
// D/T for hydrogen isotopes - non-standard but OpenSMILES spec
// says it's possible. The D and T here are automatic converted
// to [2H] and [3H].
case 'H':
if (strict)
{
throw new InvalidSmilesException("hydrogens should be specified in square brackets - '[H]'",
buffer);
}
AddAtom(AtomImpl.EXPLICIT_HYDROGEN, buffer);
break;
case 'D':
if (strict)
{
throw new InvalidSmilesException("deuterium should be specified as a hydrogen isotope - '[2H]'",
buffer);
}
AddAtom(AtomImpl.DEUTERIUM, buffer);
break;
case 'T':
if (strict)
{
throw new InvalidSmilesException("tritium should be specified as a hydrogen isotope - '[3H]'",
buffer);
}
AddAtom(AtomImpl.TRITIUM, buffer);
break;
// bracket atom
case '[':
AddAtom(ReadBracketAtom(buffer), buffer);
break;
// ring bonds
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
Ring(c - '0', buffer);
break;
case '%':
int num = buffer.GetNumber(2);
if (num < 0)
{
throw new InvalidSmilesException("a number (<digit>+) must follow '%':", buffer);
}
if (strict && num < 10)
{
throw new InvalidSmilesException("two digits must follow '%'", buffer);
}
Ring(num, buffer);
lastBondPos = buffer.Position;
break;
// bond/dot
case '-':
if (bond != Bond.Implicit)
{
throw new InvalidSmilesException("Multiple bonds specified:", buffer);
}
bond = Bond.Single;
lastBondPos = buffer.Position;
break;
case '=':
if (bond != Bond.Implicit)
{
throw new InvalidSmilesException("Multiple bonds specified:", buffer);
}
bond = Bond.Double;
lastBondPos = buffer.Position;
break;
case '#':
if (bond != Bond.Implicit)
{
throw new InvalidSmilesException("Multiple bonds specified:", buffer);
}
bond = Bond.Triple;
lastBondPos = buffer.Position;
break;
case '$':
if (bond != Bond.Implicit)
{
throw new InvalidSmilesException("Multiple bonds specified:", buffer);
}
bond = Bond.Quadruple;
lastBondPos = buffer.Position;
break;
case ':':
if (bond != Bond.Implicit)
{
throw new InvalidSmilesException("Multiple bonds specified:", buffer);
}
g.AddFlags(Graph.HAS_AROM);
bond = Bond.Aromatic;
lastBondPos = buffer.Position;
break;
case '/':
if (bond != Bond.Implicit)
{
throw new InvalidSmilesException("Multiple bonds specified:", buffer);
}
bond = Bond.Up;
lastBondPos = buffer.Position;
g.AddFlags(Graph.HAS_BND_STRO);
break;
case '\\':
// we allow C\\C=C/C since it could be an escaping error
if (bond != Bond.Implicit && bond != Bond.Down)
{
throw new InvalidSmilesException("Multiple bonds specified:", buffer);
}
bond = Bond.Down;
lastBondPos = buffer.Position;
g.AddFlags(Graph.HAS_BND_STRO);
break;
case '.':
if (bond != Bond.Implicit)
{
throw new InvalidSmilesException("Bond specified before disconnection:", buffer);
}
bond = Bond.Dot;
break;
// branching
case '(':
if (stack.IsEmpty)
{
throw new InvalidSmilesException("Cannot open branch at this position, SMILES may be truncated:", buffer);
}
stack.Push(stack.Peek());
break;
case ')':
if (stack.Count < 2)
{
throw new InvalidSmilesException("Closing of an unopened branch, SMILES may be truncated:", buffer);
}
stack.Pop();
break;
// termination
case '\t':
case ' ':
// String suffix is title
var sb = new StringBuilder();
while (buffer.HasRemaining())
{
c = buffer.Get();
if (c == '\n' || c == '\r')
{
break;
}
sb.Append(c);
}
g.Title = sb.ToString();
return;
case '\n':
case '\r':
return;
default:
throw new InvalidSmilesException("unexpected character:", buffer);
}
}
}
