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com.daylight
Class Atom

java.lang.Object
  extended by com.daylight.DaylightCppObject
      extended by com.daylight.DaylightObject
          extended by com.daylight.Atom

public class Atom
extends DaylightObject

Object representing an Atom

Field Summary
 
Fields inherited from class com.daylight.DaylightCppObject
ref
 
Constructor Summary
Atom()
           
 
Method Summary
 Bond addBond(Atom toAtom, BondType bondType)
          from dt_addbond.
protected  void finalize()
          Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.
 int getArbitraryOrder()
          from dt_arborder.
 int getAtomicNumber()
          from dt_number.
 int getAtomicWeight()
          from dt_weight.
 Bond getBond(Atom toAtom)
          from dt_bond.
 Stream getChiralBonds(ChiralValue chiralValue)
          from dt_chiseq.
 ChiralValue getChiralValue(Sequence sequence)
          from dt_chival.
 Atom getConnectedAtom(Bond connectingBond)
          from dt_xatom.
 int getFormalCharge()
          from dt_charge.
 int getHydrogenCount()
          from dt_hcount.
 int getImplicitHydrogenCount()
          from dt_imp_hcount.
static Atom getIsomericHydrogen()
          from dt_isohydro.
 Substructure getReactionMapSet()
          from dt_getmap.
 java.lang.String getSymbol()
          from dt_symbol.
 int getSymmetryClass(boolean useIsomericSmiles)
          from dt_symclass.
 int getSymmetryOrder(boolean useIsomericSmiles)
          from dt_symorder.
 boolean inSameReactionMap(Atom atom)
          from dt_mapped.
 boolean isAromatic()
          from dt_aromatic.
 boolean isChiral()
          from dt_ischiral.
 void makeReactionMapSeparate()
          from dt_setmap.
 void remove()
           
 void setArbitraryOrder(int value)
          from dt_setarborder.
 void setAromatic(boolean aromatic)
          from dt_setaromatic.
 void setAtomicNumber(int value)
          from dt_setnumber.
 void setAtomicWeight(int value)
          from dt_setweight.
 void setChiralValue(Sequence sequence, ChiralValue chiralValue)
          from dt_setchival.
 void setFormalCharge(int value)
          from dt_setcharge.
 void setImplicitHydrogenCount(int value)
          from dt_setimp_hcount.
 void setSameReactionMap(Atom atom)
          from dt_setmap.
 
Methods inherited from class com.daylight.DaylightObject
appendStringProperty, checkProgramLicense, checkToolkitLicense, clearErrors, disableVirtualHandles, equals, getAdjunct, getAncestor, getBase, getBooleanProperty, getChiralClass, getChiralOrder, getCount, getErrors, getExistingObjectCount, getHandleProperty, getIntegerProperty, getParent, getPropertyNames, getPropertyType, getRealProperty, getRuntimeLibraryCreationDate, getRuntimeLibraryVersion, getStream, getStringProperty, getType, getTypename, getUniqueId, getUniqueIdRange, getWorstErrorType, hashCode, isNullObject, mpInitialize, mpLock, mpTrylock, mpUnlock, saveError, setAdjunct, setBooleanProperty, setHandleProperty, setIntegerProperty, setRealProperty, setStringProperty
 
Methods inherited from class java.lang.Object
clone, getClass, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Atom

public Atom()
Method Detail

addBond

public Bond addBond(Atom toAtom,
                    BondType bondType)
             throws DaylightException
from dt_addbond.

Throws:
DaylightException

remove

public void remove()
            throws DaylightException
Throws:
DaylightException

getBond

public Bond getBond(Atom toAtom)
             throws DaylightException
from dt_bond.

Throws:
DaylightException

getConnectedAtom

public Atom getConnectedAtom(Bond connectingBond)
                      throws DaylightException
from dt_xatom.

Throws:
DaylightException

getChiralBonds

public Stream getChiralBonds(ChiralValue chiralValue)
                      throws DaylightException
from dt_chiseq.

Parameters:
chiralValue - values are 'None', 'Tetrahedral', 'TetrahedralAl', 'SquarePlanar', 'TrigonalBipyramidal', 'Octahedral', 'TetrahedralAnticlockwise', and 'TetrahedralClockwise'
Returns:
Stream
Throws:
DaylightException

getChiralValue

public ChiralValue getChiralValue(Sequence sequence)
                           throws DaylightException
from dt_chival.

Parameters:
sequence -
Returns:
ChiralValue values are 'None', 'Tetrahedral', 'TetrahedralAl', 'SquarePlanar', 'TrigonalBipyramidal', 'Octahedral', 'TetrahedralAnticlockwise', and 'TetrahedralClockwise'
Throws:
DaylightException

setChiralValue

public void setChiralValue(Sequence sequence,
                           ChiralValue chiralValue)
                    throws DaylightException
from dt_setchival.

Throws:
DaylightException

getArbitraryOrder

public int getArbitraryOrder()
                      throws DaylightException
from dt_arborder.

Throws:
DaylightException

setArbitraryOrder

public void setArbitraryOrder(int value)
                       throws DaylightException
from dt_setarborder.

Throws:
DaylightException

getAtomicNumber

public int getAtomicNumber()
                    throws DaylightException
from dt_number.

Throws:
DaylightException

setAtomicNumber

public void setAtomicNumber(int value)
                     throws DaylightException
from dt_setnumber.

Throws:
DaylightException

getAtomicWeight

public int getAtomicWeight()
                    throws DaylightException
from dt_weight.

Throws:
DaylightException

setAtomicWeight

public void setAtomicWeight(int value)
                     throws DaylightException
from dt_setweight.

Throws:
DaylightException

getFormalCharge

public int getFormalCharge()
                    throws DaylightException
from dt_charge.

Throws:
DaylightException

setFormalCharge

public void setFormalCharge(int value)
                     throws DaylightException
from dt_setcharge.

Throws:
DaylightException

getHydrogenCount

public int getHydrogenCount()
                     throws DaylightException
from dt_hcount.

Throws:
DaylightException

getImplicitHydrogenCount

public int getImplicitHydrogenCount()
                             throws DaylightException
from dt_imp_hcount.

Throws:
DaylightException

setImplicitHydrogenCount

public void setImplicitHydrogenCount(int value)
                              throws DaylightException
from dt_setimp_hcount.

Throws:
DaylightException

getSymbol

public java.lang.String getSymbol()
                           throws DaylightException
from dt_symbol.

Throws:
DaylightException

getSymmetryClass

public int getSymmetryClass(boolean useIsomericSmiles)
                     throws DaylightException
from dt_symclass.

Throws:
DaylightException

getSymmetryOrder

public int getSymmetryOrder(boolean useIsomericSmiles)
                     throws DaylightException
from dt_symorder.

Throws:
DaylightException

isChiral

public boolean isChiral()
                 throws DaylightException
from dt_ischiral.

Throws:
DaylightException

isAromatic

public boolean isAromatic()
                   throws DaylightException
from dt_aromatic.

Throws:
DaylightException

setAromatic

public void setAromatic(boolean aromatic)
                 throws DaylightException
from dt_setaromatic.

Throws:
DaylightException

getReactionMapSet

public Substructure getReactionMapSet()
                               throws DaylightException
from dt_getmap.

Throws:
DaylightException

inSameReactionMap

public boolean inSameReactionMap(Atom atom)
                          throws DaylightException
from dt_mapped.

Throws:
DaylightException

setSameReactionMap

public void setSameReactionMap(Atom atom)
                        throws DaylightException
from dt_setmap.

Throws:
DaylightException

makeReactionMapSeparate

public void makeReactionMapSeparate()
                             throws DaylightException
from dt_setmap. The atom is removed from the current set to which it belongs and is placed in a set by itself.

Throws:
DaylightException

getIsomericHydrogen

public static Atom getIsomericHydrogen()
                                throws DaylightException
from dt_isohydro.

Throws:
DaylightException

finalize

protected void finalize()
                 throws java.lang.Throwable
Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

Overrides:
finalize in class DaylightObject
Throws:
java.lang.Throwable
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