public virtual void TestToStringFractionalCoordinates()
{
IAtom atom = (IAtom)NewChemObject();
atom.FractionalPoint3D = new Vector3(2, 3, 4);
string description = atom.ToString();
Assert.IsTrue(description.Contains("F3D"));
}
public override void TestToString()
{
IAtom atom = (IAtom)NewChemObject();
string description = atom.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
/// <summary> Returns a one line string representation of this SingleElectron.
/// This method is conform RFC #9.
///
/// </summary>
/// <returns> The string representation of this SingleElectron
/// </returns>
public override System.String ToString()
{
System.Text.StringBuilder stringContent = new System.Text.StringBuilder();
stringContent.Append("SingleElectron(");
stringContent.Append(this.GetHashCode());
if (atom != null)
{
stringContent.Append(", ");
//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'"
stringContent.Append(atom.ToString());
}
stringContent.Append(')');
return(stringContent.ToString());
}
/// <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);
}
public override string ToString() => $"Atom: {Atom.ToString()}";
/// <inheritdoc/>
public override string ToString()
{
return($"{nameof(AtomRef)}({atom.ToString()})");
}
/// <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;
}
