ImmutableAtomType(IAtomType type) { this.element = type.getSymbol(); this.atomicNumber = type.getAtomicNumber(); this.naturalAbundance = type.getNaturalAbundance(); this.exactMass = type.getExactMass(); this.massNumber = type.getMassNumber(); this.formalCharge = type.getFormalCharge(); this.hybridization = type.getHybridization(); this.formalNeighbourCount = type.getFormalNeighbourCount(); this.identifier = type.getAtomTypeName(); this.maxBondOrder = type.getMaxBondOrder(); this.bondOrderSum = type.getBondOrderSum(); this.covalentRadius = type.getCovalentRadius(); this.flags = (short)type.getFlagValue(); this.properties = Collections.unmodifiableMap(type.getProperties()); if (type.getValency() != null) { this.electronValency = type.getValency(); } else { Integer piBondCount = type.getProperty(CDKConstants.PI_BOND_COUNT, Integer.class); if (piBondCount != null && formalNeighbourCount != null) { this.electronValency = piBondCount + formalNeighbourCount; } else { this.electronValency = null; } } }
if (type.getValency() != CDKConstants.UNSET) { double valence = container.getBondOrderSum(atom); if (atom.getImplicitHydrogenCount() != null && atom.getImplicitHydrogenCount() != 0) valence += atom.getImplicitHydrogenCount(); if (valence > type.getValency()) return false;
ImmutableAtomType(IAtomType type) { this.element = type.getSymbol(); this.atomicNumber = type.getAtomicNumber(); this.naturalAbundance = type.getNaturalAbundance(); this.exactMass = type.getExactMass(); this.massNumber = type.getMassNumber(); this.formalCharge = type.getFormalCharge(); this.hybridization = type.getHybridization(); this.formalNeighbourCount = type.getFormalNeighbourCount(); this.identifier = type.getAtomTypeName(); this.maxBondOrder = type.getMaxBondOrder(); this.bondOrderSum = type.getBondOrderSum(); this.covalentRadius = type.getCovalentRadius(); this.flags = (short)type.getFlagValue(); this.properties = Collections.unmodifiableMap(type.getProperties()); if (type.getValency() != null) { this.electronValency = type.getValency(); } else { Integer piBondCount = type.getProperty(CDKConstants.PI_BOND_COUNT, Integer.class); if (piBondCount != null && formalNeighbourCount != null) { this.electronValency = piBondCount + formalNeighbourCount; } else { this.electronValency = null; } } }
/** * Method to test the get/setValency() methods. */ @Test public void testSetValency_Integer() { int valency = 4; IAtomType a = (IAtomType) newChemObject(); a.setValency(valency); Assert.assertEquals(valency, (int) a.getValency()); }
if (type.getValency() != CDKConstants.UNSET) { double valence = container.getBondOrderSum(atom); if (atom.getImplicitHydrogenCount() != null && atom.getImplicitHydrogenCount() != 0) valence += atom.getImplicitHydrogenCount(); if (valence > type.getValency()) return false;
/** * Constructs an isotope by copying the symbol, atomic number, * flags, identifier, exact mass, natural abundance and mass * number from the given IIsotope. It does not copy the * listeners and properties. If the element is an instanceof * IAtomType, then the maximum bond order, bond order sum, * van der Waals and covalent radii, formal charge, hybridization, * electron valency, formal neighbour count and atom type name * are copied too. * * @param element IIsotope to copy information from */ public AtomType(IElement element) { super(element); if (element instanceof IAtomType) { this.maxBondOrder = ((IAtomType) element).getMaxBondOrder(); this.bondOrderSum = ((IAtomType) element).getBondOrderSum(); this.covalentRadius = ((IAtomType) element).getCovalentRadius(); this.formalCharge = ((IAtomType) element).getFormalCharge(); this.hybridization = ((IAtomType) element).getHybridization(); this.electronValency = ((IAtomType) element).getValency(); this.formalNeighbourCount = ((IAtomType) element).getFormalNeighbourCount(); this.identifier = ((IAtomType) element).getAtomTypeName(); } }
/** * Constructs an isotope by copying the symbol, atomic number, * flags, identifier, exact mass, natural abundance and mass * number from the given IIsotope. It does not copy the * listeners and properties. If the element is an instance of * IAtomType, then the maximum bond order, bond order sum, * van der Waals and covalent radii, formal charge, hybridization, * electron valency, formal neighbour count and atom type name * are copied too. * * @param element IIsotope to copy information from */ public AtomType(IElement element) { super(element); if (element instanceof IAtomType) { this.maxBondOrder = ((IAtomType) element).getMaxBondOrder(); this.bondOrderSum = ((IAtomType) element).getBondOrderSum(); this.covalentRadius = ((IAtomType) element).getCovalentRadius(); this.formalCharge = ((IAtomType) element).getFormalCharge(); this.hybridization = ((IAtomType) element).getHybridization(); this.electronValency = ((IAtomType) element).getValency(); this.formalNeighbourCount = ((IAtomType) element).getFormalNeighbourCount(); this.identifier = ((IAtomType) element).getAtomTypeName(); } }
/** * Constructs an isotope by copying the symbol, atomic number, * flags, identifier, exact mass, natural abundance and mass * number from the given IIsotope. It does not copy the * listeners and properties. If the element is an instance of * IAtomType, then the maximum bond order, bond order sum, * van der Waals and covalent radii, formal charge, hybridization, * electron valency, formal neighbour count and atom type name * are copied too. * * @param element IIsotope to copy information from */ public AtomType(IElement element) { super(element); if (element instanceof IAtomType) { this.maxBondOrder = ((IAtomType) element).getMaxBondOrder(); this.bondOrderSum = ((IAtomType) element).getBondOrderSum(); this.covalentRadius = ((IAtomType) element).getCovalentRadius(); this.formalCharge = ((IAtomType) element).getFormalCharge(); this.hybridization = ((IAtomType) element).getHybridization(); this.electronValency = ((IAtomType) element).getValency(); this.formalNeighbourCount = ((IAtomType) element).getFormalNeighbourCount(); this.identifier = ((IAtomType) element).getAtomTypeName(); } }
/** * Constructs an isotope by copying the symbol, atomic number, * flags, identifier, exact mass, natural abundance and mass * number from the given IIsotope. It does not copy the * listeners and properties. If the element is an instanceof * IAtomType, then the maximum bond order, bond order sum, * van der Waals and covalent radii, formal charge, hybridization, * electron valency, formal neighbour count and atom type name * are copied too. * * @param element IIsotope to copy information from */ public AtomType(IElement element) { super(element); if (element instanceof IAtomType) { this.maxBondOrder = ((IAtomType) element).getMaxBondOrder(); this.bondOrderSum = ((IAtomType) element).getBondOrderSum(); this.covalentRadius = ((IAtomType) element).getCovalentRadius(); this.formalCharge = ((IAtomType) element).getFormalCharge(); this.hybridization = ((IAtomType) element).getHybridization(); this.electronValency = ((IAtomType) element).getValency(); this.formalNeighbourCount = ((IAtomType) element).getFormalNeighbourCount(); this.identifier = ((IAtomType) element).getAtomTypeName(); } }
if (atom.getCovalentRadius() == CDKConstants.UNSET && atomType.getCovalentRadius() != CDKConstants.UNSET) atom.setCovalentRadius(atomType.getCovalentRadius()); if (atom.getValency() == CDKConstants.UNSET && atomType.getValency() != CDKConstants.UNSET) atom.setValency(atomType.getValency()); if (atom.getFormalCharge() == CDKConstants.UNSET && atomType.getFormalCharge() != CDKConstants.UNSET) atom.setFormalCharge(atomType.getFormalCharge());
totalDiff.addChild(DoubleDifference.construct("CR", firstElem.getCovalentRadius(), secondElem.getCovalentRadius())); totalDiff.addChild(IntegerDifference.construct("V", firstElem.getValency(), secondElem.getValency())); totalDiff.addChild(IsotopeDiff.difference(first, second)); if (totalDiff.childCount() > 0) {
atom.setBondOrderSum(atomType.getBondOrderSum()); atom.setCovalentRadius(atomType.getCovalentRadius()); atom.setValency(atomType.getValency()); atom.setFormalCharge(atomType.getFormalCharge()); atom.setHybridization(atomType.getHybridization());