private static ValidationReport ValidateChargeConservation(IReaction reaction, IAtomContainer reactants, IAtomContainer products)
{
var report = new ValidationReport();
var chargeConservation = new ValidationTest(reaction, "Total formal charge is not preserved during the reaction");
var atoms1 = reactants.Atoms;
int totalCharge1 = 0;
foreach (var atom1 in atoms1)
{
totalCharge1 = +atom1.FormalCharge.Value;
}
var atoms2 = products.Atoms;
int totalCharge2 = 0;
foreach (var atom2 in atoms2)
{
totalCharge2 = +atom2.FormalCharge.Value;
}
if (totalCharge1 != totalCharge2)
{
report.Errors.Add(chargeConservation);
}
else
{
report.OKs.Add(chargeConservation);
}
return(report);
}
// the Molecule tests
private static ValidationReport ValidateBondOrderSum(IAtom atom, IAtomContainer molecule)
{
var report = new ValidationReport();
var checkBondSum = new ValidationTest(atom, "The atom's total bond order is too high.");
try
{
var structgenATF = CDK.CdkAtomTypeFactory;
int bos = (int)molecule.GetBondOrderSum(atom);
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol).ToReadOnlyList();
if (atomTypes.Count == 0)
{
checkBondSum.Details = $"Cannot validate bond order sum for atom not in valency atom type list: {atom.Symbol}";
report.Warnings.Add(checkBondSum);
}
else
{
IAtomType failedOn = null;
bool foundMatchingAtomType = false;
foreach (var type in atomTypes)
{
if (atom.FormalCharge == type.FormalCharge)
{
foundMatchingAtomType = true;
if (bos == type.BondOrderSum)
{
// skip this atom type
}
else
{
failedOn = type;
}
}
}
if (foundMatchingAtomType)
{
report.OKs.Add(checkBondSum);
}
else
{
if (failedOn != null)
{
checkBondSum.Details = $"Bond order exceeds the one allowed for atom {atom.Symbol} for which the total bond order is {failedOn.BondOrderSum}";
}
else
{
}
report.Errors.Add(checkBondSum);
}
}
}
catch (Exception exception)
{
Trace.TraceError($"Error while performing atom bos validation: {exception.Message}");
Debug.WriteLine(exception);
}
return(report);
}
private static ValidationReport ValidateMaxBondOrder(IBond bond)
{
var report = new ValidationReport();
var maxBO = new ValidationTest(bond, "Bond order exceeds the maximum for one of its atoms.");
try
{
var structgenATF = CDK.CdkAtomTypeFactory;
for (int i = 0; i < bond.Atoms.Count; i++)
{
var atom = bond.Atoms[i];
if (atom is IPseudoAtom)
{
// ok, all is fine; we don't know the properties of pseudo atoms
break;
}
var atomTypes = structgenATF.GetAtomTypes(atom.Symbol);
IAtomType failedOn = null;
bool foundMatchingAtomType = false;
foreach (var atomType in atomTypes)
{
if (!BondManipulator.IsHigherOrder(bond.Order, atomType.MaxBondOrder))
{
foundMatchingAtomType = true;
}
else
{
failedOn = atomType;
}
}
if (foundMatchingAtomType)
{
report.OKs.Add(maxBO);
}
else
{
if (failedOn != null)
{
maxBO.Details = $"Bond order exceeds the one allowed for atom {atom.Symbol} for which the maximum bond order is {failedOn.MaxBondOrder}";
}
report.Errors.Add(maxBO);
}
}
}
catch (Exception exception)
{
Trace.TraceError("Error while performing atom bos validation");
Debug.WriteLine(exception);
maxBO.Details = $"Error while performing atom bos validation: {exception.ToString()}";
report.CDKErrors.Add(maxBO);
}
return(report);
}
private static ValidationReport ValidateAtomCountConservation(IReaction reaction, IAtomContainer reactants, IAtomContainer products)
{
var report = new ValidationReport();
var atomCount = new ValidationTest(reaction, "Atom count mismatch for reaction: the product side has a different atom count than the reactant side.");
if (reactants.Atoms.Count != products.Atoms.Count)
{
report.Errors.Add(atomCount);
}
else
{
report.OKs.Add(atomCount);
}
return(report);
}
// the Bond tests
private static ValidationReport ValidateStereoChemistry(IBond bond)
{
var report = new ValidationReport();
var bondStereo = new ValidationTest(bond, "Defining stereochemistry on bonds is not safe.", "Use atom based stereochemistry.");
if (bond.Stereo != BondStereo.None)
{
report.Warnings.Add(bondStereo);
}
else
{
report.OKs.Add(bondStereo);
}
return(report);
}
// assumes 1 unit in the coordinate system is one angstrom
public override ValidationReport ValidateBond(IBond subject)
{
var report = new ValidationReport();
// only consider two atom bonds
if (subject.Atoms.Count == 2)
{
var distance = Vector3.Distance(subject.Begin.Point3D.Value, subject.End.Point3D.Value);
if (distance > 3.0)
{ // should really depend on the elements
var badBondLengthError = new ValidationTest(subject,
"Bond length cannot exceed 3 Angstroms.",
"A bond length typically is between 0.5 and 3.0 Angstroms.");
report.Errors.Add(badBondLengthError);
}
}
return(report);
}
private static ValidationReport ValidateHydrogenCount(IAtom atom)
{
var report = new ValidationReport();
var negativeHydrogenCount = new ValidationTest(atom, "An Atom cannot have a negative number of hydrogens attached.");
if (atom.ImplicitHydrogenCount == null)
{
report.Warnings.Add(new ValidationTest(atom, "An atom had unset (null) implicit hydrogen count"));
}
else if (atom.ImplicitHydrogenCount < 0)
{
negativeHydrogenCount.Details = $"Atom has {atom.ImplicitHydrogenCount} hydrogens.";
report.Errors.Add(negativeHydrogenCount);
}
else
{
report.OKs.Add(negativeHydrogenCount);
}
return(report);
}
public override ValidationReport ValidateMolecule(IAtomContainer subject)
{
var report = new ValidationReport();
var emptyMolecule = new ValidationTest(subject, "Molecule does not contain any atom");
if (subject.Atoms.Count == 0)
{
report.Errors.Add(emptyMolecule);
}
else
{
report.OKs.Add(emptyMolecule);
var massCalcProblem = new ValidationTest(subject, "Molecule contains PseudoAtom's. Won't be able to calculate some properties, like molecular mass.");
bool foundMassCalcProblem = false;
for (int i = 0; i < subject.Atoms.Count; i++)
{
if (subject.Atoms[i] is IPseudoAtom)
{
foundMassCalcProblem = true;
}
else
{
report.Add(ValidateBondOrderSum(subject.Atoms[i], subject));
}
}
if (foundMassCalcProblem)
{
report.Warnings.Add(massCalcProblem);
}
else
{
report.OKs.Add(massCalcProblem);
}
}
return(report);
}
// the Isotope tests
public static ValidationReport ValidateIsotopeExistence(IIsotope isotope)
{
var report = new ValidationReport();
var isotopeExists = new ValidationTest(isotope, "Isotope with this mass number is not known for this element.");
try
{
var isotopeFac = CDK.IsotopeFactory;
var isotopes = isotopeFac.GetIsotopes(isotope.Symbol);
bool foundKnownIsotope = false;
if (isotope.MassNumber != null && isotope.MassNumber != 0)
{
foreach (var facIsotope in isotopes)
{
if (facIsotope.MassNumber == isotope.MassNumber)
{
foundKnownIsotope = true;
}
}
}
if (!foundKnownIsotope)
{
report.Errors.Add(isotopeExists);
}
else
{
// isotopic is unspecified
report.OKs.Add(isotopeExists);
}
}
catch (Exception)
{
// too bad...
}
return(report);
}
private static ValidationReport ValidatePseudoAtom(IAtom atom)
{
var report = new ValidationReport();
var isElementOrPseudo = new ValidationTest(atom, "Non-element atom must be of class PseudoAtom.");
if (atom is IPseudoAtom)
{
// that's fine
report.OKs.Add(isElementOrPseudo);
}
else
{
// check whether atom is really an element
try
{
var isotopeFactory = CDK.IsotopeFactory;
var element = isotopeFactory.GetElement(atom.Symbol);
if (element == null)
{
isElementOrPseudo.Details = $"Element {atom.Symbol} does not exist.";
report.Errors.Add(isElementOrPseudo);
}
else
{
report.OKs.Add(isElementOrPseudo);
}
}
catch (Exception exception)
{
// well... don't throw an error then.
isElementOrPseudo.Details = exception.ToString();
report.CDKErrors.Add(isElementOrPseudo);
}
}
return(report);
}
// the Atom tests
private static ValidationReport ValidateCharge(IAtom atom)
{
var report = new ValidationReport();
var tooCharged = new ValidationTest(atom, "Atom has an unlikely large positive or negative charge");
switch (atom.AtomicNumber)
{
case AtomicNumbers.O:
case AtomicNumbers.N:
case AtomicNumbers.C:
case AtomicNumbers.H:
if (atom.FormalCharge == 0)
{
report.OKs.Add(tooCharged);
}
else
{
tooCharged.Details = $"Atom {atom.Symbol} has charge {atom.FormalCharge}";
if (atom.FormalCharge < -3)
{
report.Errors.Add(tooCharged);
}
else if (atom.FormalCharge < -1)
{
report.Warnings.Add(tooCharged);
}
else if (atom.FormalCharge > 3)
{
report.Errors.Add(tooCharged);
}
else if (atom.FormalCharge > 1)
{
report.Warnings.Add(tooCharged);
}
}
break;
default:
if (atom.FormalCharge == 0)
{
report.OKs.Add(tooCharged);
}
else
{
tooCharged.Details = $"Atom {atom.Symbol} has charge {atom.FormalCharge}";
if (atom.FormalCharge < -4)
{
report.Errors.Add(tooCharged);
}
else if (atom.FormalCharge < -3)
{
report.Warnings.Add(tooCharged);
}
else if (atom.FormalCharge > 4)
{
report.Errors.Add(tooCharged);
}
else if (atom.FormalCharge > 3)
{
report.Warnings.Add(tooCharged);
}
}
break;
}
return(report);
}
public override ValidationReport ValidateChemObject(IChemObject subject)
{
var report = new ValidationReport();
var properties = subject.GetProperties();
var iter = properties.Keys;
var noNamespace = new ValidationTest(subject,"Dictionary Reference lacks a namespace indicating the dictionary.");
var noDict = new ValidationTest(subject, "The referenced dictionary does not exist.");
var noEntry = new ValidationTest(subject, "The referenced entry does not exist in the dictionary.");
foreach (var key in iter)
{
if (key is string keyName)
{
if (keyName.StartsWith(DictionaryDatabase.DictRefPropertyName, StringComparison.Ordinal))
{
string dictRef = (string)properties[keyName];
string details = "Dictref being anaylyzed: " + dictRef + ". ";
noNamespace.Details = details;
noDict.Details = details;
noEntry.Details = details;
int index = dictRef.IndexOf(':');
if (index != -1)
{
report.OKs.Add(noNamespace);
string dict = dictRef.Substring(0, index);
Debug.WriteLine($"Looking for dictionary:{dict}");
if (db.HasDictionary(dict))
{
report.OKs.Add(noDict);
if (dictRef.Length > index + 1)
{
string entry = dictRef.Substring(index + 1);
Debug.WriteLine($"Looking for entry:{entry}");
if (db.HasEntry(dict, entry))
{
report.OKs.Add(noEntry);
}
else
{
report.Errors.Add(noEntry);
}
}
else
{
report.Errors.Add(noEntry);
}
}
else
{
details += "The dictionary searched: " + dict + ".";
noDict.Details = details;
report.Errors.Add(noDict);
report.Errors.Add(noEntry);
}
}
else
{
// The dictRef has no namespace
details += "There is not a namespace given.";
noNamespace.Details = details;
report.Errors.Add(noNamespace);
report.Errors.Add(noDict);
report.Errors.Add(noEntry);
}
}
else
{
// not a dictref
}
}
else
{
// not a dictref
}
}
return report;
}