/// <summary> Method that assign properties to an atom given a particular atomType.
///
/// </summary>
/// <param name="atom"> Atom to configure
/// </param>
/// <param name="atomType"> AtomType
/// </param>
public static void configure(IAtom atom, IAtomType atomType)
{
atom.AtomTypeName = atomType.AtomTypeName;
atom.MaxBondOrder = atomType.MaxBondOrder;
atom.BondOrderSum = atomType.BondOrderSum;
atom.VanderwaalsRadius = atomType.VanderwaalsRadius;
atom.CovalentRadius = atomType.CovalentRadius;
atom.Valency = atomType.Valency;
atom.setFormalCharge(atomType.getFormalCharge());
atom.Hybridization = atomType.Hybridization;
atom.FormalNeighbourCount = atomType.FormalNeighbourCount;
atom.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
atom.setFlag(CDKConstants.IS_HYDROGENBOND_DONOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_DONOR));
System.Object constant = atomType.getProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT);
if (constant != null)
{
atom.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, constant);
}
atom.setFlag(CDKConstants.ISAROMATIC, atomType.getFlag(CDKConstants.ISAROMATIC));
System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color");
if (color != null)
{
atom.setProperty("org.openscience.cdk.renderer.color", color);
}
if (atomType.AtomicNumber != 0)
{
atom.AtomicNumber = atomType.AtomicNumber;
}
if (atomType.getExactMass() > 0.0)
{
atom.setExactMass(atomType.getExactMass());
}
}
/// <summary> Method that assign properties to an atom given a particular atomType.
///
/// </summary>
/// <param name="atom"> Atom to configure
/// </param>
/// <param name="atomType"> AtomType
/// </param>
public static void configure(IAtom atom, IAtomType atomType)
{
atom.AtomTypeName = atomType.AtomTypeName;
atom.MaxBondOrder = atomType.MaxBondOrder;
atom.BondOrderSum = atomType.BondOrderSum;
atom.VanderwaalsRadius = atomType.VanderwaalsRadius;
atom.CovalentRadius = atomType.CovalentRadius;
atom.Valency = atomType.Valency;
atom.setFormalCharge(atomType.getFormalCharge());
atom.Hybridization = atomType.Hybridization;
atom.FormalNeighbourCount = atomType.FormalNeighbourCount;
atom.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
atom.setFlag(CDKConstants.IS_HYDROGENBOND_DONOR, atomType.getFlag(CDKConstants.IS_HYDROGENBOND_DONOR));
System.Object constant = atomType.getProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT);
if (constant != null)
{
atom.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, constant);
}
atom.setFlag(CDKConstants.ISAROMATIC, atomType.getFlag(CDKConstants.ISAROMATIC));
System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color");
if (color != null)
{
atom.setProperty("org.openscience.cdk.renderer.color", color);
}
if (atomType.AtomicNumber != 0)
{
atom.AtomicNumber = atomType.AtomicNumber;
}
if (atomType.getExactMass() > 0.0)
{
atom.setExactMass(atomType.getExactMass());
}
}
/// <summary> Configures an atom to have all the data of the
/// given isotope.
///
/// </summary>
/// <param name="atom"> The atom to be configure
/// </param>
/// <param name="isotope"> The isotope to read the data from
/// </param>
/// <returns> The configured atom
/// </returns>
public virtual IAtom configure(IAtom atom, IIsotope isotope)
{
atom.MassNumber = isotope.MassNumber;
atom.Symbol = isotope.Symbol;
atom.setExactMass(isotope.getExactMass());
atom.AtomicNumber = isotope.AtomicNumber;
atom.NaturalAbundance = isotope.NaturalAbundance;
return(atom);
}
/// <summary> Configures an atom to have all the data of the
/// given isotope.
///
/// </summary>
/// <param name="atom"> The atom to be configure
/// </param>
/// <param name="isotope"> The isotope to read the data from
/// </param>
/// <returns> The configured atom
/// </returns>
public virtual IAtom configure(IAtom atom, IIsotope isotope)
{
atom.MassNumber = isotope.MassNumber;
atom.Symbol = isotope.Symbol;
atom.setExactMass(isotope.getExactMass());
atom.AtomicNumber = isotope.AtomicNumber;
atom.NaturalAbundance = isotope.NaturalAbundance;
return atom;
}
/// <summary> Configures an atom. Finds the correct element type by looking at the Atom's
/// atom type name, and if that fails, picks the first atom type matching
/// the Atom's element symbol..
///
/// </summary>
/// <param name="atom"> The atom to be configured
/// </param>
/// <returns> The configured atom
/// </returns>
/// <throws> CDKException when it could not recognize and configure the </throws>
/// <summary> IAtom
/// </summary>
public virtual IAtom configure(IAtom atom)
{
if (atom is IPseudoAtom)
{
// do not try to configure PseudoAtom's
return(atom);
}
try
{
IAtomType atomType = null;
System.String atomTypeName = atom.AtomTypeName;
if (atomTypeName == null || atomTypeName.Length == 0)
{
//logger.debug("Using atom symbol because atom type name is empty...");
IAtomType[] types = getAtomTypes(atom.Symbol);
if (types.Length > 0)
{
//logger.warn("Taking first atom type, but other may exist");
atomType = types[0];
}
else
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String message = "Could not configure atom with unknown ID: " + atom.ToString() + " + (id=" + atom.AtomTypeName + ")";
//logger.warn(message);
throw new CDKException(message);
}
}
else
{
atomType = getAtomType(atom.AtomTypeName);
}
//logger.debug("Configuring with atomtype: ", atomType);
atom.Symbol = atomType.Symbol;
atom.MaxBondOrder = atomType.MaxBondOrder;
atom.BondOrderSum = atomType.BondOrderSum;
atom.VanderwaalsRadius = atomType.VanderwaalsRadius;
atom.CovalentRadius = atomType.CovalentRadius;
atom.Hybridization = atomType.Hybridization;
System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color");
if (color != null)
{
atom.setProperty("org.openscience.cdk.renderer.color", color);
}
if (atomType.AtomicNumber != 0)
{
atom.AtomicNumber = atomType.AtomicNumber;
}
else
{
//logger.debug("Did not configure atomic number: AT.an=", atomType.AtomicNumber);
}
if (atomType.getExactMass() > 0.0)
{
atom.setExactMass(atomType.getExactMass());
}
else
{
//logger.debug("Did not configure mass: AT.mass=", atomType.AtomicNumber);
}
}
catch (System.Exception exception)
{
//logger.warn("Could not configure atom with unknown ID: ", atom, " + (id=", atom.AtomTypeName, ")");
//logger.debug(exception);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException(exception.ToString());
}
//logger.debug("Configured: ", atom);
return(atom);
}
/// <summary> Configures an atom. Finds the correct element type by looking at the Atom's
/// atom type name, and if that fails, picks the first atom type matching
/// the Atom's element symbol..
///
/// </summary>
/// <param name="atom"> The atom to be configured
/// </param>
/// <returns> The configured atom
/// </returns>
/// <throws> CDKException when it could not recognize and configure the </throws>
/// <summary> IAtom
/// </summary>
public virtual IAtom configure(IAtom atom)
{
if (atom is IPseudoAtom)
{
// do not try to configure PseudoAtom's
return atom;
}
try
{
IAtomType atomType = null;
System.String atomTypeName = atom.AtomTypeName;
if (atomTypeName == null || atomTypeName.Length == 0)
{
//logger.debug("Using atom symbol because atom type name is empty...");
IAtomType[] types = getAtomTypes(atom.Symbol);
if (types.Length > 0)
{
//logger.warn("Taking first atom type, but other may exist");
atomType = types[0];
}
else
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String message = "Could not configure atom with unknown ID: " + atom.ToString() + " + (id=" + atom.AtomTypeName + ")";
//logger.warn(message);
throw new CDKException(message);
}
}
else
{
atomType = getAtomType(atom.AtomTypeName);
}
//logger.debug("Configuring with atomtype: ", atomType);
atom.Symbol = atomType.Symbol;
atom.MaxBondOrder = atomType.MaxBondOrder;
atom.BondOrderSum = atomType.BondOrderSum;
atom.VanderwaalsRadius = atomType.VanderwaalsRadius;
atom.CovalentRadius = atomType.CovalentRadius;
atom.Hybridization = atomType.Hybridization;
System.Object color = atomType.getProperty("org.openscience.cdk.renderer.color");
if (color != null)
{
atom.setProperty("org.openscience.cdk.renderer.color", color);
}
if (atomType.AtomicNumber != 0)
{
atom.AtomicNumber = atomType.AtomicNumber;
}
else
{
//logger.debug("Did not configure atomic number: AT.an=", atomType.AtomicNumber);
}
if (atomType.getExactMass() > 0.0)
{
atom.setExactMass(atomType.getExactMass());
}
else
{
//logger.debug("Did not configure mass: AT.mass=", atomType.AtomicNumber);
}
}
catch (System.Exception exception)
{
//logger.warn("Could not configure atom with unknown ID: ", atom, " + (id=", atom.AtomTypeName, ")");
//logger.debug(exception);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
throw new CDKException(exception.ToString());
}
//logger.debug("Configured: ", atom);
return atom;
}