// FIXME move to tools
private string NormalizeConciseAndFormalCharge(string conciseS, int formalCharge)
{
if (conciseS != null)
{
CMLAtomArray atomArray = CreateAndAddAtomArrayAndFormalChargeFromConcise(conciseS);
if (atomArray != null)
{
atomArray.Sort(SortType.CHFirst);
conciseS = atomArray.GenerateConcise(formalCharge);
}
}
return(conciseS);
}
// element: formula
// element: atomArray
public void Normalize()
{
// create all possible renderings of formula
// any or all may be present
// concise
var conciseAtt = this.Attribute(Attribute_concise);
// formal charge
int formalCharge = 0;
if (this.Attribute(Attribute_formalCharge) != null)
{
formalCharge = int.Parse(this.Attribute(Attribute_formalCharge).Value, NumberFormatInfo.InvariantInfo);
}
string conciseS = conciseAtt?.Value;
// convention
string convention = this.Convention;
// inline formula (might be SMILES)
string inline = this.Inline;
if (inline != null)
{
inline = inline.Trim();
}
// atomArray
CMLAtomArray atomArray = null;
string atomArray2Concise = null;
var atomArrays = this.Elements(XName_CML_atomArray).Cast <CMLAtomArray>().ToReadOnlyList();
if (atomArrays.Count > 1)
{
throw new ApplicationException($"Only one atomArray child allowed for formula; found: {atomArrays.Count}");
}
else if (atomArrays.Count == 1)
{
atomArray = atomArrays.First();
atomArray.Sort(SortType.CHFirst);
atomArray2Concise = atomArray.GenerateConcise(formalCharge);
}
// concise from inline
if (inline != null)
{
if (SMILES.Equals(convention, StringComparison.Ordinal) ||
SMILES1.Equals(convention, StringComparison.Ordinal))
{
}
}
if (conciseS == null)
{
if (atomArray2Concise != null)
{
conciseS = atomArray2Concise;
}
}
if (conciseS != null)
{
conciseS = NormalizeConciseAndFormalCharge(conciseS, formalCharge);
}
// if no atomArray, create
if (atomArray == null)
{
// causes problems with Jmol
}
else
{
CheckAtomArrayFormat(atomArray);
}
if (atomArray != null)
{
atomArray.Sort(SortType.CHFirst);
}
// check consistency
if (atomArray2Concise != null &&
!atomArray2Concise.Equals(conciseS, StringComparison.Ordinal))
{
throw new ApplicationException($"concise ({conciseS}) and atomArray ({atomArray2Concise}) differ");
}
if (conciseS != null)
{
// by this time we may have generated a non-zero formal charge, so normalize it into concise
conciseS = NormalizeConciseAndFormalCharge(conciseS, this.FormalCharge);
ForceConcise(conciseS);
}
}