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joelib.util
Class IsomerismDetection  

java.lang.Object
  joelib.util.IsomerismDetection

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public class IsomerismDetection

extends java.lang.Object

Helper class to detect E/Z isomerism.

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Field Summary
static int	CIS_ISOMERISM
static int	CISTRANS_ISOMERISM_UNDEFINED
static int	E_ISOMERISM
static int	EZ_ISOMERISM_UNDEFINED
private static org.apache.log4j.Category	logger
static int	TRANS_ISOMERISM
static int	Z_ISOMERISM

 

Constructor Summary

IsomerismDetection()

 

Method Summary
static int	getCisTransFrom2D3D(joelib.molecule.JOEBond bond)           Checks bonds for cis/trans isomerism using 2D/3D informations.
static int	getCisTransFrom2D3D(joelib.molecule.JOEBond bond, boolean setSingleBondFlags)           Checks bonds for cis/trans isomerism using 2D/3D informations.
static int	isCisTransBond(joelib.molecule.JOEBond bond)           Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond. Cases: E/trans -- bondUP/doubleBond/bondUP E/trans -- bondDOWN/doubleBond/bondDOWN Z/cis -- bondUP/doubleBond/bondDOWN Z/cis -- bondDOWN/doubleBond/bondUP This method does not check multiple definitions.
static int	isCisTransBond(joelib.molecule.JOEBond bond, boolean setSingleBondFlags)           Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond. Cases: E/trans -- bondUP/doubleBond/bondUP E/trans -- bondDOWN/doubleBond/bondDOWN Z/cis -- bondUP/doubleBond/bondDOWN Z/cis -- bondDOWN/doubleBond/bondUP This method does not check multiple definitions.
static void	setCisTransBond(joelib.molecule.JOEBond bond, int ezType)           Sets up/down informations for cis/trans isomerism of a double bond. Cases: E/trans -- bondUP/doubleBond/bondUP Z/cis -- bondDOWN/doubleBond/bondUP The method gets two heavy atoms with the highest atomic number and sets the corresponding up/down bond flags for cis/trans isomeres.

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

logger

private static org.apache.log4j.Category logger

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EZ_ISOMERISM_UNDEFINED

public static final int EZ_ISOMERISM_UNDEFINED

See Also:

Constant Field Values

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CISTRANS_ISOMERISM_UNDEFINED

public static final int CISTRANS_ISOMERISM_UNDEFINED

See Also:

Constant Field Values

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Z_ISOMERISM

public static final int Z_ISOMERISM

See Also:

Constant Field Values

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E_ISOMERISM

public static final int E_ISOMERISM

See Also:

Constant Field Values

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CIS_ISOMERISM

public static final int CIS_ISOMERISM

See Also:

Constant Field Values

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TRANS_ISOMERISM

public static final int TRANS_ISOMERISM

See Also:

Constant Field Values

Constructor Detail

IsomerismDetection

public IsomerismDetection()

Method Detail

setCisTransBond

public static void setCisTransBond(joelib.molecule.JOEBond bond,
                                   int ezType)

Sets up/down informations for cis/trans isomerism of a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
Z/cis -- bondDOWN/doubleBond/bondUP

The method gets two heavy atoms with the highest atomic number and sets the corresponding up/down bond flags for cis/trans isomeres.

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isCisTransBond

public static int isCisTransBond(joelib.molecule.JOEBond bond)

Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
E/trans -- bondDOWN/doubleBond/bondDOWN
Z/cis -- bondUP/doubleBond/bondDOWN
Z/cis -- bondDOWN/doubleBond/bondUP

This method does not check multiple definitions. If no up/down informations are available, the getCisTransFrom2D3D(JOEBond) 55 method is used also to get cis/trans informations. Single bond flags will be not set if a cis/trans double bond is detected.

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isCisTransBond

public static int isCisTransBond(joelib.molecule.JOEBond bond,
                                 boolean setSingleBondFlags)

Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
E/trans -- bondDOWN/doubleBond/bondDOWN
Z/cis -- bondUP/doubleBond/bondDOWN
Z/cis -- bondDOWN/doubleBond/bondUP

This method does not check multiple definitions. If no up/down informations are available, the getCisTransFrom2D3D(JOEBond) 55 method is used also to get cis/trans informations.

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getCisTransFrom2D3D

public static int getCisTransFrom2D3D(joelib.molecule.JOEBond bond)

Checks bonds for cis/trans isomerism using 2D/3D informations. Single bond flags will be not set if a cis/trans double bond is detected.

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getCisTransFrom2D3D

public static int getCisTransFrom2D3D(joelib.molecule.JOEBond bond,
                                      boolean setSingleBondFlags)

Checks bonds for cis/trans isomerism using 2D/3D informations.

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> joelib >> [ util overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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