/// <summary>
/// Coordinates are written between parenthesis. The z-coord may be omitted '(0,1,),(2,3,)'.
/// </summary>
/// <param name="iter">input characters, iterator is progressed by this method</param>
/// <param name="state">output CXSMILES state</param>
/// <returns>parse was a success (or not)</returns>
private static bool ProcessCoords(CharIter iter, CxSmilesState state)
{
if (state.atomCoords == null)
{
state.atomCoords = new List <double[]>();
}
while (iter.HasNext())
{
// end of coordinate list
if (iter.Curr() == ')')
{
iter.Next();
iter.NextIf(','); // optional
return(true);
}
double x = ReadDouble(iter);
if (!iter.NextIf(','))
{
return(false);
}
double y = ReadDouble(iter);
if (!iter.NextIf(','))
{
return(false);
}
double z = ReadDouble(iter);
iter.NextIf(';');
state.coordFlag = state.coordFlag || z != 0;
state.atomCoords.Add(new double[] { x, y, z });
}
return(false);
}
private static double ReadDouble(CharIter iter)
{
int sign = +1;
if (iter.NextIf('-'))
{
sign = -1;
}
else if (iter.NextIf('+'))
{
sign = +1;
}
double intPart;
double fracPart = 0;
int divisor = 1;
intPart = (double)ProcessUnsignedInt(iter);
if (intPart < 0)
{
intPart = 0;
}
iter.NextIf('.');
char c;
while (iter.HasNext() && IsDigit(c = iter.Curr()))
{
fracPart *= 10;
fracPart += c - '0';
divisor *= 10;
iter.Next();
}
return(sign * (intPart + (fracPart / divisor)));
}
/// <summary>
/// CXSMILES radicals.
/// </summary>
/// <param name="iter">input characters, iterator is progressed by this method</param>
/// <param name="state">output CXSMILES state</param>
/// <returns>parse was a success (or not)</returns>
private static bool ProcessRadicals(CharIter iter, CxSmilesState state)
{
if (state.atomRads == null)
{
state.atomRads = new SortedDictionary <int, Radical>();
}
CxSmilesState.Radical rad;
switch (iter.Next())
{
case '1':
rad = Monovalent;
break;
case '2':
rad = Divalent;
break;
case '3':
rad = DivalentSinglet;
break;
case '4':
rad = DivalentTriplet;
break;
case '5':
rad = Trivalent;
break;
case '6':
rad = TrivalentDoublet;
break;
case '7':
rad = TrivalentQuartet;
break;
default:
return(false);
}
if (!iter.NextIf(':'))
{
return(false);
}
var dest = new List <int>(4);
if (!ProcessIntList(iter, CommaSeparatorChar, dest))
{
return(false);
}
foreach (var atomidx in dest)
{
state.atomRads.Add(atomidx, rad);
}
return(true);
}
private static int ProcessUnsignedInt(CharIter iter)
{
if (!iter.HasNext())
{
return(-1);
}
char c = iter.Curr();
if (!IsDigit(c))
{
return(-1);
}
int res = c - '0';
iter.Next();
while (iter.HasNext() && IsDigit(c = iter.Curr()))
{
res = res * 10 + c - '0';
iter.Next();
}
return(res);
}
private static bool SkipIntMap(CharIter iter)
{
while (iter.HasNext())
{
char c = iter.Curr();
if (Char.IsDigit(c) || c == ',' || c == ':')
{
iter.Next();
}
else
{
return(true);
}
}
// ran of end
return(false);
}
private static bool SkipIntList(CharIter iter, char sep)
{
while (iter.HasNext())
{
char c = iter.Curr();
if (IsDigit(c) || c == sep)
{
iter.Next();
}
else
{
return(true);
}
}
// ran off end
return(false);
}
/// <summary>
/// Process atom labels from extended SMILES in a char iter.
/// </summary>
/// <param name="iter">char iteration</param>
/// <param name="dest">destination of labels (atomidx->label)</param>
/// <returns>parse success/failure</returns>
private static bool ProcessAtomLabels(CharIter iter, SortedDictionary <int, string> dest)
{
int atomIdx = 0;
while (iter.HasNext())
{
// fast forward through empty labels
while (iter.NextIf(';'))
{
atomIdx++;
}
char c = iter.Next();
if (c == '$')
{
iter.NextIf(','); // optional
// end of atom label
return(true);
}
else
{
iter.pos--; // push back
var beg = iter.pos;
var rollback = beg;
while (iter.HasNext())
{
if (iter.pos == beg && iter.Curr() == '_' && iter.Peek() == 'R')
{
++beg;
}
// correct step over of escaped label
if (iter.Curr() == '&')
{
rollback = iter.pos;
if (iter.NextIf('&') && iter.NextIf('#') && iter.NextIfDigit())
{
while (iter.NextIfDigit())
{
} // more digits
if (!iter.NextIf(';'))
{
iter.pos = rollback;
}
else
{
}
}
else
{
iter.pos = rollback;
}
}
else if (iter.Curr() == ';')
{
break;
}
else if (iter.Curr() == '$')
{
break;
}
else
{
iter.Next();
}
}
dest.Add(atomIdx, Unescape(iter.Substr(beg, iter.pos)));
atomIdx++;
if (iter.NextIf('$'))
{
iter.NextIf(','); // optional
return(true);
}
if (!iter.NextIf(';'))
{
return(false);
}
}
}
return(false);
}
/// <summary>
/// Parse an string possibly containing CXSMILES into an intermediate state
/// (<see cref="CxSmilesState"/>) representation.
/// </summary>
/// <param name="str">input character string (SMILES title field)</param>
/// <param name="state">output CXSMILES state</param>
/// <returns>position where CXSMILES ends (below 0 means no CXSMILES)</returns>
public static int ProcessCx(string str, CxSmilesState state)
{
CharIter iter = new CharIter(str);
if (!iter.NextIf('|'))
{
return(-1);
}
while (iter.HasNext())
{
switch (iter.Next())
{
case '$': // atom labels and values
// dest is atom labels by default
SortedDictionary <int, string> dest;
// check for atom values
if (iter.NextIf("_AV:"))
{
dest = state.atomValues = new SortedDictionary <int, string>();
}
else
{
dest = state.atomLabels = new SortedDictionary <int, string>();
}
if (!ProcessAtomLabels(iter, dest))
{
return(-1);
}
break;
case '(': // coordinates
if (!ProcessCoords(iter, state))
{
return(-1);
}
break;
case 'c': // cis/trans/unspec ignored
case 't':
// c/t:
if (iter.NextIf(':'))
{
if (!SkipIntList(iter, CommaSeparatorChar))
{
return(-1);
}
}
// ctu:
else if (iter.NextIf("tu:"))
{
if (!SkipIntList(iter, CommaSeparatorChar))
{
return(-1);
}
}
break;
case 'r': // relative stereochemistry ignored
if (iter.NextIf(':'))
{
if (!SkipIntList(iter, CommaSeparatorChar))
{
return(-1);
}
}
else
{
if (!iter.NextIf(',') && iter.Curr() != '|')
{
return(-1);
}
}
break;
case 'l': // lone pairs ignored
if (!iter.NextIf("p:"))
{
return(-1);
}
if (!SkipIntMap(iter))
{
return(-1);
}
break;
case 'f': // fragment grouping
if (!iter.NextIf(':'))
{
return(-1);
}
if (!ProcessFragmentGrouping(iter, state))
{
return(-1);
}
break;
case 'S': // Sgroup polymers
if (iter.NextIf("g:"))
{
if (!ProcessPolymerSgroups(iter, state))
{
return(-1);
}
}
else if (iter.NextIf("gD:"))
{
if (!ProcessDataSgroups(iter, state))
{
return(-1);
}
}
else
{
return(-1);
}
break;
case 'm': // positional variation
if (!iter.NextIf(':'))
{
return(-1);
}
if (!ProcessPositionalVariation(iter, state))
{
return(-1);
}
break;
case '^': // Radicals
if (!ProcessRadicals(iter, state))
{
return(-1);
}
break;
case 'C':
case 'H': // coordination and hydrogen bonding ignored
if (!iter.NextIf(':'))
{
return(-1);
}
while (iter.HasNext() && IsDigit(iter.Curr()))
{
if (!SkipIntList(iter, DotSeparatorChar))
{
return(-1);
}
iter.NextIf(',');
}
break;
case '|': // end of CX
// consume optional separators
if (!iter.NextIf(' '))
{
iter.NextIf('\t');
}
return(iter.pos);
default:
return(-1);
}
}
return(-1);
}
/// <summary>
/// Polymer Sgroups describe variations of repeating units. Only the atoms and not crossing bonds are written.
/// </summary>
/// <param name="iter">input characters, iterator is progressed by this method</param>
/// <param name="state">output CXSMILES state</param>
/// <returns>parse was a success (or not)</returns>
private static bool ProcessPolymerSgroups(CharIter iter, CxSmilesState state)
{
if (state.sgroups == null)
{
state.sgroups = new List <PolymerSgroup>();
}
var beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
var keyword = iter.Substr(beg, iter.pos);
if (!iter.NextIf(':'))
{
return(false);
}
var atomset = new List <int>();
if (!ProcessIntList(iter, CommaSeparatorChar, atomset))
{
return(false);
}
string subscript;
string supscript;
if (!iter.NextIf(':'))
{
return(false);
}
// "If the subscript equals the keyword of the Sgroup this field can be empty", ergo
// if omitted it equals the keyword
beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
subscript = Unescape(iter.Substr(beg, iter.pos));
if (string.IsNullOrEmpty(subscript))
{
subscript = keyword;
}
// "In the superscript only connectivity and flip information is allowed.", default
// appears to be "eu" either/unspecified
if (!iter.NextIf(':'))
{
return(false);
}
beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
supscript = Unescape(iter.Substr(beg, iter.pos));
if (string.IsNullOrEmpty(supscript))
{
supscript = "eu";
}
if (iter.NextIf(',') || iter.Curr() == '|')
{
state.sgroups.Add(new CxSmilesState.PolymerSgroup(keyword, atomset, subscript, supscript));
return(true);
}
// not supported: crossing bond info (difficult to work out from doc) and bracket orientation
return(false);
}
private static bool ProcessDataSgroups(CharIter iter, CxSmilesState state)
{
if (state.dataSgroups == null)
{
state.dataSgroups = new List <DataSgroup>(4);
}
var atomset = new List <int>();
if (!ProcessIntList(iter, CommaSeparatorChar, atomset))
{
return(false);
}
if (!iter.NextIf(':'))
{
return(false);
}
var beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
string field = Unescape(iter.Substr(beg, iter.pos));
if (!iter.NextIf(':'))
{
return(false);
}
beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
string value = Unescape(iter.Substr(beg, iter.pos));
if (!iter.NextIf(':'))
{
state.dataSgroups.Add(new CxSmilesState.DataSgroup(atomset, field, value, "", "", ""));
return(true);
}
beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
var operator_ = Unescape(iter.Substr(beg, iter.pos));
if (!iter.NextIf(':'))
{
state.dataSgroups.Add(new CxSmilesState.DataSgroup(atomset, field, value, operator_, "", ""));
return(true);
}
beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
var unit = Unescape(iter.Substr(beg, iter.pos));
if (!iter.NextIf(':'))
{
state.dataSgroups.Add(new CxSmilesState.DataSgroup(atomset, field, value, operator_, unit, ""));
return(true);
}
beg = iter.pos;
while (iter.HasNext() && !IsSgroupDelim(iter.Curr()))
{
iter.Next();
}
string tag = Unescape(iter.Substr(beg, iter.pos));
state.dataSgroups.Add(new CxSmilesState.DataSgroup(atomset, field, value, operator_, unit, tag));
return(true);
}
