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com.daylight
Class Bond

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

public class Bond
extends DaylightObject

Object representing a bond

Field Summary
 
Fields inherited from class com.daylight.DaylightCppObject
ref
 
Constructor Summary
Bond()
           
 
Method Summary
protected  void finalize()
          Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.
 BondType getBondOrder()
          from dt_bondorder.
 BondType getBondType()
          from dt_bondtype.
 DoubleBondOrientation getDoubleBondOrientation()
          from dt_dbo.
 DoubleBondOrientation getDoubleBondOrientation(Bond singleBond1, Bond singleBond2)
          from dt_dbo.
 DoubleBondOrientation getDoubleBondOrientation(Bond singleBond, boolean isFirstSingle)
          from dt_dbo.
 boolean isAromatic()
          from dt_aromatic.
 Sequence permuteToFirstInSequence(Sequence seq, ChiralValue chiralValue)
          from dt_chiperm.
 void remove()
          from dt_dealloc.
 void setBondOrder(BondType order)
          from dt_setbondorder.
 void setBondType(BondType bondType)
          from dt_setbondtype.
 void setDoubleBondOrientation(Bond singleBond1, Bond singleBond2, DoubleBondOrientation orientation)
          from dt_setdbo.
 void setDoubleBondOrientation(Bond singleBond, boolean isFirstSingle, DoubleBondOrientation orientation)
          from dt_setdbo.
 void setDoubleBondOrientation(DoubleBondOrientation orientation)
          from dt_setdbo.
 
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

Bond

public Bond()
Method Detail

remove

public void remove()
            throws DaylightException
from dt_dealloc. Removes the bond. Wrapper object becomes the null object.

Throws:
DaylightException

isAromatic

public boolean isAromatic()
                   throws DaylightException
from dt_aromatic.

Throws:
DaylightException

getBondOrder

public BondType getBondOrder()
                      throws DaylightException
from dt_bondorder.

Throws:
DaylightException

setBondOrder

public void setBondOrder(BondType order)
                  throws DaylightException
from dt_setbondorder.

Throws:
DaylightException

getBondType

public BondType getBondType()
                     throws DaylightException
from dt_bondtype.

Throws:
DaylightException

setBondType

public void setBondType(BondType bondType)
                 throws DaylightException
from dt_setbondtype.

Throws:
DaylightException

getDoubleBondOrientation

public DoubleBondOrientation getDoubleBondOrientation(Bond singleBond1,
                                                      Bond singleBond2)
                                               throws DaylightException
from dt_dbo.

Parameters:
singleBond1 -
singleBond2 -
Returns:
DoubleBondOrientation values are 'Cis', 'Trans' and 'Unspecified' Calculates the double-bond orientation between bonds 'bond1' and 'bond2'. The Bond must be a double bond. Both 'bond1' and 'bond2' are single bonds attached to the atoms at each end of the bond, one to each atom. When an implicit hydrogen atom is bonded to one of the central atoms (see dt_hcount(3)) its cis/trans bond is not represented in the molecule. Use the other forms of getDoubleBondOrientation for this purpose.
Throws:
DaylightException

getDoubleBondOrientation

public DoubleBondOrientation getDoubleBondOrientation(Bond singleBond,
                                                      boolean isFirstSingle)
                                               throws DaylightException
from dt_dbo.

Parameters:
singleBond -
isFirstSingle -
Returns:
DoubleBondOrientation values are 'Cis', 'Trans' and 'Unspecified' Use this form of the method when only one of the single bonds connected to this bond is connected to an atom that is not an implicit hydrogen. If 'isFirstSingle' is true, 'singleBond' is a bond connecting to the first atom of this bond.
Throws:
DaylightException
See Also:
getDoubleBondOrientation(com.daylight.Bond, com.daylight.Bond)

getDoubleBondOrientation

public DoubleBondOrientation getDoubleBondOrientation()
                                               throws DaylightException
from dt_dbo.

Returns:
DoubleBondOrientation values are 'Cis', 'Trans' and 'Unspecified' Use this form of the method when the single bonds connected to this bond are connected to implicit hydrogen atoms.
Throws:
DaylightException
See Also:
getDoubleBondOrientation(com.daylight.Bond, com.daylight.Bond)

setDoubleBondOrientation

public void setDoubleBondOrientation(Bond singleBond1,
                                     Bond singleBond2,
                                     DoubleBondOrientation orientation)
                              throws DaylightException
from dt_setdbo.

Parameters:
singleBond1 -
singleBond2 -
orientation - values are 'Cis', 'Trans' and 'Unspecified' Sets the double-bond orientation between bonds 'bond1' and 'bond2'. The Bond must be a double bond. Both 'bond1' and 'bond2' are single bonds attached to the atoms at each end of 'bond', one to each atom. When an implicit hydrogen atom is bonded to one of the central atoms (see dt_hcount(3)) its cis/trans bond is not represented in the molecule. Use the other forms of getDoubleBondOrientation for this purpose.
Throws:
DaylightException

setDoubleBondOrientation

public void setDoubleBondOrientation(Bond singleBond,
                                     boolean isFirstSingle,
                                     DoubleBondOrientation orientation)
                              throws DaylightException
from dt_setdbo.

Parameters:
singleBond -
isFirstSingle -
orientation - values are 'Cis', 'Trans' and 'Unspecified' Use this form of the method when only one of the single bonds connected to this bond is connected to an atom that is not an implicit hydrogen. If 'isFirstSingle' is true, 'singleBond' is a bond connecting to the first atom of this bond.
Throws:
DaylightException
See Also:
getDoubleBondOrientation(com.daylight.Bond, com.daylight.Bond)

setDoubleBondOrientation

public void setDoubleBondOrientation(DoubleBondOrientation orientation)
                              throws DaylightException
from dt_setdbo.

Parameters:
orientation - values are 'Cis', 'Trans' and 'Unspecified' const Bond& singleBond2, DoubleBondOrientationEnum orientation). Use this form of the method when the single bonds connected to this bond are connected to implicit hydrogen atoms.
Throws:
DaylightException
See Also:
setDoubleBondOrientation(com.daylight.Bond, com.daylight.Bond, com.daylight.enumtype.DoubleBondOrientation)

permuteToFirstInSequence

public Sequence permuteToFirstInSequence(Sequence seq,
                                         ChiralValue chiralValue)
                                  throws DaylightException
from dt_chiperm.

Parameters:
seq -
chiralValue - values are 'None', 'Tetrahedral', 'TetrahedralAl', 'SquarePlanar', 'TrigonalBipyramidal', 'Octahedral', 'TetrahedralAnticlockwise', and 'TetrahedralClockwise'
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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