public ValidationReport ValidateReaction(IReaction subject)
{
Trace.TraceInformation($"Validating {nameof(IReaction)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateReaction(subject));
}
// traverse into super class
report.Add(ValidateChemObject(subject));
// traverse into hierarchy
var reactants = subject.Reactants;
foreach (var reactant in reactants)
{
report.Add(ValidateMolecule(reactant));
}
var products = subject.Products;
foreach (var product in products)
{
report.Add(ValidateMolecule(product));
}
return(report);
}
public ValidationReport ValidateChemModel(IChemModel subject)
{
Trace.TraceInformation($"Validating {nameof(IChemModel)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateChemModel(subject));
}
// traverse into super class
report.Add(ValidateChemObject(subject));
// traverse into hierarchy
ICrystal crystal = subject.Crystal;
if (crystal != null)
{
report.Add(ValidateCrystal(crystal));
}
IReactionSet reactionSet = subject.ReactionSet;
if (reactionSet != null)
{
report.Add(ValidateReactionSet(reactionSet));
}
var moleculeSet = subject.MoleculeSet;
if (moleculeSet != null)
{
report.Add(ValidateMoleculeSet(moleculeSet));
}
return(report);
}
public override ValidationReport ValidateBond(IBond subject)
{
var report = new ValidationReport();
report.Add(ValidateStereoChemistry(subject));
report.Add(ValidateMaxBondOrder(subject));
return(report);
}
public override ValidationReport ValidateAtom(IAtom subject)
{
var report = new ValidationReport();
report.Add(ValidateCharge(subject));
report.Add(ValidateHydrogenCount(subject));
report.Add(ValidatePseudoAtom(subject));
return(report);
}
public ValidationReport ValidateAtom(IAtom subject)
{
Trace.TraceInformation($"Validating {nameof(IAtom)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateAtom(subject));
}
// traverse into super class
report.Add(ValidateAtomType(subject));
// traverse into hierarchy
return(report);
}
public ValidationReport ValidateElectronContainer(IElectronContainer subject)
{
Trace.TraceInformation($"Validating {nameof(IElectronContainer)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateElectronContainer(subject));
}
// traverse into super class
report.Add(ValidateChemObject(subject));
// traverse into hierarchy
return(report);
}
public ValidationReport ValidateReactionSet(IReactionSet subject)
{
Trace.TraceInformation("Validating org.openscience.cdk.ReactionSet");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateReactionSet(subject));
}
// traverse into super class
report.Add(ValidateChemObject(subject));
// traverse into hierarchy
foreach (var reaction in subject)
{
report.Add(ValidateReaction(reaction));
}
return(report);
}
public ValidationReport ValidateMoleculeSet(IChemObjectSet <IAtomContainer> subject)
{
Trace.TraceInformation($"Validating {nameof(IChemObjectSet<IAtomContainer>)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateMoleculeSet(subject));
}
// traverse into super class
report.Add(ValidateChemObject(subject));
// traverse into hierarchy
foreach (var container in subject)
{
report.Add(ValidateMolecule(container));
}
return(report);
}
public ValidationReport ValidateChemSequence(IChemSequence subject)
{
Trace.TraceInformation($"Validating {nameof(IChemSequence)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateChemSequence(subject));
}
// traverse into super class
report.Add(ValidateChemObject(subject));
// traverse into hierarchy
foreach (var model in subject)
{
report.Add(ValidateChemModel(model));
}
return(report);
}
public ValidationReport ValidateBond(IBond subject)
{
Trace.TraceInformation($"Validating {nameof(IBond)}");
var report = new ValidationReport();
// apply validators
foreach (var test in validators.Values)
{
report.Add(test.ValidateBond(subject));
}
// traverse into super class
report.Add(ValidateElectronContainer(subject));
// traverse into hierarchy
foreach (var atom in subject.Atoms)
{
report.Add(ValidateAtom(atom));
}
return(report);
}
public override ValidationReport ValidateReaction(IReaction subject)
{
var report = new ValidationReport();
var container1 = subject.Builder.NewAtomContainer();
var reactants = subject.Reactants;
for (int i = 0; i < reactants.Count; i++)
{
container1.Add(reactants[i]);
}
var container2 = subject.Builder.NewAtomContainer();
var products = subject.Products;
for (int i = 0; i < products.Count; i++)
{
container2.Add(products[i]);
}
report.Add(ValidateAtomCountConservation(subject, container1, container2));
report.Add(ValidateChargeConservation(subject, container1, container2));
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);
}