public void SetCellParameters(double[] parameters, double[] error)
{
if (parameters == null || parameters.Length != 6)
{
throw new ApplicationException("Must have 6 cell parameters");
}
var cellParamVector = this.Elements(XName_CML_scalar);
var count = cellParamVector.Count();
if (count == 0)
{
for (int i = 0; i < 6; i++)
{
CMLScalar cellParam = CMLCrystal.CreateScalar(
CRYSTAL_DICT_REFS[i], parameters[i], CRYSTAL_DICT_UNITS[i],
double.NaN);
this.Add(cellParam);
}
}
else if (count == 6)
{
int i = 0;
foreach (var e in cellParamVector)
{
CMLScalar cellParam = (CMLScalar)e;
cellParam.SetValue(parameters[i]);
if (error != null)
{
cellParam.ErrorValue = parameters[i];
}
cellParam.DictRef = CRYSTAL_DICT_REFS[i];
i++;
}
}
else
{
throw new ApplicationException(
"Corrupted cell parameters: must be exactly 6 (found: "
+ cellParamVector.Count());
}
}
private CMLMolecule CDKCrystalToCMLMolecule(ICrystal crystal, bool setIDs)
{
var molecule = CDKAtomContainerToCMLMolecule(crystal, false, false);
var cmlCrystal = new CMLCrystal();
if (useCMLIDs && setIDs)
{
IDCreator.CreateIDs(crystal);
}
if (!string.IsNullOrEmpty(crystal.Id))
{
cmlCrystal.Id = crystal.Id;
}
this.CheckPrefix(cmlCrystal);
cmlCrystal.Z = crystal.Z.Value;
var params_ = CrystalGeometryTools.CartesianToNotional(crystal.A, crystal.B, crystal.C);
Debug.WriteLine($"Number of cell params: {params_.Length}");
cmlCrystal.SetCellParameters(params_);
molecule.Add(cmlCrystal);
return(molecule);
}