tools.moltyping
Class ExtendedAtomAndBondTyper

java.lang.Object
  extended by tools.moltyping.ExtendedAtomAndBondTyper

public class ExtendedAtomAndBondTyper
extends java.lang.Object


Constructor Summary
ExtendedAtomAndBondTyper(EnumerationsAtomTypes.AtomLabelType type)
           
 
Method Summary
 java.lang.String getAtomLabel(org.openscience.cdk.interfaces.IAtom atom)
          Acessor function that returns atom type depending on AtomLabelType chosen.
 EnumerationsAtomTypes.AtomLabelType getAtomLabelType()
           
static java.lang.String getAtomSymbol(org.openscience.cdk.interfaces.IAtom atom)
           
static java.lang.String getAtomType(org.openscience.cdk.interfaces.IAtom atom)
          returns the CDK atom type
static java.lang.String getAtomTypeName(org.openscience.cdk.interfaces.IAtom atom)
           
static java.lang.String getBondSymbol(org.openscience.cdk.interfaces.IBond bond)
          returns the bond symbol for a given bond
static java.lang.String getBondSymbolNoAromatic(org.openscience.cdk.interfaces.IBond bond)
          returns the bond symbol for a given bond
static java.lang.String getDaylightInvariant(org.openscience.cdk.interfaces.IAtom atom)
           
static java.lang.String getDaylightInvariantRing(org.openscience.cdk.interfaces.IAtom atom)
          Daylight Invariant + Ring as Atom Label: Symbol.
static java.lang.String getElementNeighborRingType(org.openscience.cdk.interfaces.IAtom atom)
          returns the element plus neighbor count type plus ring information
static java.lang.String getElementNeighborType(org.openscience.cdk.interfaces.IAtom atom)
          returns the element plus neighbor count type
static java.lang.Integer getFormalneighbourCount(org.openscience.cdk.interfaces.IAtom atom)
           
static java.lang.Integer getHydrogenCount(org.openscience.cdk.interfaces.IAtom atom)
           
static java.lang.String getRingAtomType(org.openscience.cdk.interfaces.IAtom atom)
          returns a cdk atom type flagged with r and aromaticity information
static java.lang.Integer getValency(org.openscience.cdk.interfaces.IAtom atom)
           
static boolean needsAromaticityDetection(EnumerationsAtomTypes.AtomLabelType atomLabelType)
           
 void setAtomLabelType(EnumerationsAtomTypes.AtomLabelType type)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ExtendedAtomAndBondTyper

public ExtendedAtomAndBondTyper(EnumerationsAtomTypes.AtomLabelType type)
Method Detail

getAtomType

public static java.lang.String getAtomType(org.openscience.cdk.interfaces.IAtom atom)
returns the CDK atom type

Parameters:
atom -
Returns:

getBondSymbol

public static java.lang.String getBondSymbol(org.openscience.cdk.interfaces.IBond bond)
returns the bond symbol for a given bond

Parameters:
bond -
Returns:

getBondSymbolNoAromatic

public static java.lang.String getBondSymbolNoAromatic(org.openscience.cdk.interfaces.IBond bond)
returns the bond symbol for a given bond

Parameters:
bond -
Returns:

getDaylightInvariant

public static java.lang.String getDaylightInvariant(org.openscience.cdk.interfaces.IAtom atom)

getDaylightInvariantRing

public static java.lang.String getDaylightInvariantRing(org.openscience.cdk.interfaces.IAtom atom)
Daylight Invariant + Ring as Atom Label: Symbol.#Heavyneighbours.valence-hydrogens.mass.charge.#hydrogens.InRing e.g. 12.2.3.mass.0.1.1


getElementNeighborRingType

public static java.lang.String getElementNeighborRingType(org.openscience.cdk.interfaces.IAtom atom)
returns the element plus neighbor count type plus ring information

Parameters:
atom -
Returns:

getAtomTypeName

public static java.lang.String getAtomTypeName(org.openscience.cdk.interfaces.IAtom atom)

getAtomSymbol

public static java.lang.String getAtomSymbol(org.openscience.cdk.interfaces.IAtom atom)

getFormalneighbourCount

public static java.lang.Integer getFormalneighbourCount(org.openscience.cdk.interfaces.IAtom atom)

getValency

public static java.lang.Integer getValency(org.openscience.cdk.interfaces.IAtom atom)

getHydrogenCount

public static java.lang.Integer getHydrogenCount(org.openscience.cdk.interfaces.IAtom atom)

getElementNeighborType

public static java.lang.String getElementNeighborType(org.openscience.cdk.interfaces.IAtom atom)
returns the element plus neighbor count type

Parameters:
atom -
Returns:

getRingAtomType

public static java.lang.String getRingAtomType(org.openscience.cdk.interfaces.IAtom atom)
returns a cdk atom type flagged with r and aromaticity information

Parameters:
atom -
Returns:

needsAromaticityDetection

public static boolean needsAromaticityDetection(EnumerationsAtomTypes.AtomLabelType atomLabelType)
                                         throws MoltyperException
Throws:
MoltyperException

getAtomLabel

public java.lang.String getAtomLabel(org.openscience.cdk.interfaces.IAtom atom)
                              throws MoltyperException
Acessor function that returns atom type depending on AtomLabelType chosen. This function should be accessed by the fingerprinters.

Parameters:
atom - Atom to be Atomtyped
type - AtomLabelType
Returns:
Throws:
MoltyperException

getAtomLabelType

public EnumerationsAtomTypes.AtomLabelType getAtomLabelType()

setAtomLabelType

public void setAtomLabelType(EnumerationsAtomTypes.AtomLabelType type)