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java.lang.Objecttools.moltyping.ExtendedAtomAndBondTyper
public class ExtendedAtomAndBondTyper
Constructor Summary | |
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ExtendedAtomAndBondTyper(EnumerationsAtomTypes.AtomLabelType type)
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Method Summary | |
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java.lang.String |
getAtomLabel(org.openscience.cdk.interfaces.IAtom atom)
Acessor function that returns atom type depending on AtomLabelType chosen. |
EnumerationsAtomTypes.AtomLabelType |
getAtomLabelType()
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static java.lang.String |
getAtomSymbol(org.openscience.cdk.interfaces.IAtom atom)
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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)
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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)
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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)
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static java.lang.Integer |
getHydrogenCount(org.openscience.cdk.interfaces.IAtom atom)
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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)
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static boolean |
needsAromaticityDetection(EnumerationsAtomTypes.AtomLabelType atomLabelType)
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void |
setAtomLabelType(EnumerationsAtomTypes.AtomLabelType type)
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Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ExtendedAtomAndBondTyper(EnumerationsAtomTypes.AtomLabelType type)
Method Detail |
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public static java.lang.String getAtomType(org.openscience.cdk.interfaces.IAtom atom)
atom
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public static java.lang.String getBondSymbol(org.openscience.cdk.interfaces.IBond bond)
bond
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public static java.lang.String getBondSymbolNoAromatic(org.openscience.cdk.interfaces.IBond bond)
bond
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public static java.lang.String getDaylightInvariant(org.openscience.cdk.interfaces.IAtom atom)
public static java.lang.String getDaylightInvariantRing(org.openscience.cdk.interfaces.IAtom atom)
public static java.lang.String getElementNeighborRingType(org.openscience.cdk.interfaces.IAtom atom)
atom
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public static java.lang.String getAtomTypeName(org.openscience.cdk.interfaces.IAtom atom)
public static java.lang.String getAtomSymbol(org.openscience.cdk.interfaces.IAtom atom)
public static java.lang.Integer getFormalneighbourCount(org.openscience.cdk.interfaces.IAtom atom)
public static java.lang.Integer getValency(org.openscience.cdk.interfaces.IAtom atom)
public static java.lang.Integer getHydrogenCount(org.openscience.cdk.interfaces.IAtom atom)
public static java.lang.String getElementNeighborType(org.openscience.cdk.interfaces.IAtom atom)
atom
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public static java.lang.String getRingAtomType(org.openscience.cdk.interfaces.IAtom atom)
atom
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public static boolean needsAromaticityDetection(EnumerationsAtomTypes.AtomLabelType atomLabelType) throws MoltyperException
MoltyperException
public java.lang.String getAtomLabel(org.openscience.cdk.interfaces.IAtom atom) throws MoltyperException
atom
- Atom to be Atomtypedtype
- AtomLabelType
MoltyperException
public EnumerationsAtomTypes.AtomLabelType getAtomLabelType()
public void setAtomLabelType(EnumerationsAtomTypes.AtomLabelType type)
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