/// <summary> Determines if the atom can be of type AtomType. That is, it sees if this
/// AtomType only differs in bond orders, or implicit hydrogen count.
/// </summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
//logger.debug("couldMatchAtomType: formal charge matches...");
if (atom.Hybridization == type.Hybridization)
{
//logger.debug("couldMatchAtomType: hybridization is OK...");
if (bondOrderSum + hcount <= type.BondOrderSum)
{
//logger.debug("couldMatchAtomType: bond order sum is OK...");
if (maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("couldMatchAtomType: max bond order is OK... We have a match!");
return(true);
}
}
else
{
//logger.debug("couldMatchAtomType: no match", "" + (bondOrderSum + hcount), " > ", "" + type.BondOrderSum);
}
}
}
else
{
//logger.debug("couldMatchAtomType: formal charge does NOT match...");
}
//logger.debug("couldMatchAtomType: No Match");
return(false);
}
/// <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> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
if (bondOrderSum + hcount <= type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug(" We have a match!");
return(true);
}
}
//logger.debug(" No Match");
return(false);
}
/// <summary> Determines if the atom can be of type AtomType. That is, it sees if this
/// AtomType only differs in bond orders, or implicit hydrogen count.
/// </summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
//logger.debug("couldMatchAtomType: formal charge matches...");
if (atom.Hybridization == type.Hybridization)
{
//logger.debug("couldMatchAtomType: hybridization is OK...");
if (bondOrderSum + hcount <= type.BondOrderSum)
{
//logger.debug("couldMatchAtomType: bond order sum is OK...");
if (maxBondOrder <= type.MaxBondOrder)
{
//logger.debug("couldMatchAtomType: max bond order is OK... We have a match!");
return true;
}
}
else
{
//logger.debug("couldMatchAtomType: no match", "" + (bondOrderSum + hcount), " > ", "" + type.BondOrderSum);
}
}
}
else
{
//logger.debug("couldMatchAtomType: formal charge does NOT match...");
}
//logger.debug("couldMatchAtomType: No Match");
return false;
}
/// <summary> Determines if the atom can be of type AtomType.</summary>
public virtual bool couldMatchAtomType(IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
{
//logger.debug(" ... matching atom ", atom.Symbol, " vs ", type);
int hcount = atom.getHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge())
{
if (bondOrderSum + hcount <= type.BondOrderSum && maxBondOrder <= type.MaxBondOrder)
{
//logger.debug(" We have a match!");
return true;
}
}
//logger.debug(" No Match");
return false;
}