toxTree.query

Class SimpleReactions

java.lang.Object

toxTree.query.SimpleReactions

public class SimpleReactions
extends Object

Handles hydrolysis and couple of metabolic reactions necessary to implement Cramer rules Intended to be a general class to perform reactions on arbitrary molecules ... Preconfigured reactions are stored as CML files in config directory

Author:

Nina Jeliazkova Modified 2005-8-18

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.openscience.cdk.smiles.SmilesGenerator	gen
protected static String[]	hydrolize
protected static String[]	hydrolizePO4
protected static org.openscience.cdk.interfaces.IReaction[]	hydrolysis
protected static org.openscience.cdk.interfaces.IReaction[]	hydrolysisPO4
protected static Logger	logger
protected static org.openscience.cdk.interfaces.IReaction[]	metabolic
protected static String[]	metabolize
protected org.openscience.cdk.interfaces.IReaction	reaction

Constructor Summary

Constructors

Constructor and Description
SimpleReactions()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.interfaces.IAtomContainerSet	canMetabolize(org.openscience.cdk.interfaces.IAtomContainer mol, boolean allPossible)
org.openscience.cdk.interfaces.IAtomContainerSet	canMetabolize(org.openscience.cdk.interfaces.IAtomContainer mol, boolean allPossible, org.openscience.cdk.interfaces.IChemObjectBuilder builder) Checks if 4 predefined metabolic reactions can be applied to Molecule mol
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)
org.openscience.cdk.interfaces.IReaction	getHydrolysisPO4Reaction(int index)
static int	getHydrolysisPO4ReactionCount()
org.openscience.cdk.interfaces.IReaction	getHydrolysisReaction(int index)
static int	getHydrolysisReactionCount()
org.openscience.cdk.interfaces.IReaction	getMetabolicReaction(int index)
static int	getMetabolicReactionCount()
protected static org.openscience.cdk.interfaces.IAtomContainerSet	hydrolize(org.openscience.cdk.interfaces.IAtomContainer a, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q, List list, org.openscience.cdk.interfaces.IChemObjectBuilder builder)
org.openscience.cdk.interfaces.IAtomContainerSet	hydrolizesPO4(org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainerSet	hydrolizesPO4(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IChemObjectBuilder builder)
org.openscience.cdk.interfaces.IAtomContainerSet	isReadilyHydrolised(org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainerSet	isReadilyHydrolised(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IChemObjectBuilder builder) Checks if 6 predefined hydrolysis reactions can be applied to Molecule mol
org.openscience.cdk.interfaces.IAtomContainerSet	isReadilyHydrolisedSimpleEster(org.openscience.cdk.interfaces.IAtomContainer mol) Checks if simple ester hydrolysis can be applied to Molecule mol
org.openscience.cdk.interfaces.IAtomContainerSet	isReadilyHydrolisedSimpleEster(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IChemObjectBuilder builder)
protected org.openscience.cdk.interfaces.IReaction	loadHydrolysisReaction(int index)
protected org.openscience.cdk.interfaces.IReaction	loadMetabolicReaction(int index)
protected org.openscience.cdk.interfaces.IReaction	loadPreconfiguredReaction(String filename)
static org.openscience.cdk.interfaces.IAtomContainerSet	process(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IReaction reaction)
static org.openscience.cdk.interfaces.IAtomContainerSet	process(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IReaction reaction, org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static void	setResidualID(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainerSet r)

Methods inherited from class java.lang.Object

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

Field Detail

gen

protected static org.openscience.cdk.smiles.SmilesGenerator gen

logger

protected static Logger logger

reaction

protected org.openscience.cdk.interfaces.IReaction reaction

hydrolysis

protected static org.openscience.cdk.interfaces.IReaction[] hydrolysis

metabolic

protected static org.openscience.cdk.interfaces.IReaction[] metabolic

hydrolysisPO4

protected static org.openscience.cdk.interfaces.IReaction[] hydrolysisPO4

hydrolize

protected static String[] hydrolize

metabolize

protected static String[] metabolize

hydrolizePO4

protected static String[] hydrolizePO4

Constructor Detail

SimpleReactions

public SimpleReactions()

Method Detail

loadPreconfiguredReaction

protected org.openscience.cdk.interfaces.IReaction loadPreconfiguredReaction(String filename)
                                                                      throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

loadHydrolysisReaction

protected org.openscience.cdk.interfaces.IReaction loadHydrolysisReaction(int index)
                                                                   throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

loadMetabolicReaction

protected org.openscience.cdk.interfaces.IReaction loadMetabolicReaction(int index)
                                                                  throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getHydrolysisReaction

public org.openscience.cdk.interfaces.IReaction getHydrolysisReaction(int index)
                                                               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getMetabolicReaction

public org.openscience.cdk.interfaces.IReaction getMetabolicReaction(int index)
                                                              throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getHydrolysisPO4Reaction

public org.openscience.cdk.interfaces.IReaction getHydrolysisPO4Reaction(int index)
                                                                  throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getHydrolysisReactionCount

public static int getHydrolysisReactionCount()

getMetabolicReactionCount

public static int getMetabolicReactionCount()

getHydrolysisPO4ReactionCount

public static int getHydrolysisPO4ReactionCount()

process

public static org.openscience.cdk.interfaces.IAtomContainerSet process(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                       org.openscience.cdk.interfaces.IReaction reaction)
                                                                throws ReactionException

Throws:

ReactionException

process

public static org.openscience.cdk.interfaces.IAtomContainerSet process(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                       org.openscience.cdk.interfaces.IReaction reaction,
                                                                       org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                                                                throws ReactionException

Throws:

ReactionException

hydrolize

protected static org.openscience.cdk.interfaces.IAtomContainerSet hydrolize(org.openscience.cdk.interfaces.IAtomContainer a,
                                                                            org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q,
                                                                            List list,
                                                                            org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                                                                     throws ReactionException

Throws:

ReactionException

setResidualID

public static void setResidualID(org.openscience.cdk.interfaces.IAtomContainer mol,
                                 org.openscience.cdk.interfaces.IAtomContainerSet r)

createQueryContainer

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createQueryContainer(org.openscience.cdk.interfaces.IAtomContainer container)

hydrolizesPO4

public org.openscience.cdk.interfaces.IAtomContainerSet hydrolizesPO4(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                               throws ReactionException

Throws:

ReactionException

hydrolizesPO4

public org.openscience.cdk.interfaces.IAtomContainerSet hydrolizesPO4(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                      org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                                                               throws ReactionException

Throws:

ReactionException

isReadilyHydrolised

public org.openscience.cdk.interfaces.IAtomContainerSet isReadilyHydrolised(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                     throws ReactionException

Throws:

ReactionException

isReadilyHydrolised

public org.openscience.cdk.interfaces.IAtomContainerSet isReadilyHydrolised(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                            org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                                                                     throws ReactionException

Checks if 6 predefined hydrolysis reactions can be applied to Molecule mol

Parameters:

mol -

Returns:

null if not readily hydrolised, otherwise returns hydrolysis products

Throws:

ReactionException

isReadilyHydrolisedSimpleEster

public org.openscience.cdk.interfaces.IAtomContainerSet isReadilyHydrolisedSimpleEster(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                                throws ReactionException

Checks if simple ester hydrolysis can be applied to Molecule mol

Parameters:

mol -

Returns:

null if not readily hydrolised, otherwise returns hydrolysis products

Throws:

ReactionException

isReadilyHydrolisedSimpleEster

public org.openscience.cdk.interfaces.IAtomContainerSet isReadilyHydrolisedSimpleEster(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                                       org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                                                                                throws ReactionException

Throws:

ReactionException

canMetabolize

public org.openscience.cdk.interfaces.IAtomContainerSet canMetabolize(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                      boolean allPossible)
                                                               throws ReactionException

Throws:

ReactionException

canMetabolize

public org.openscience.cdk.interfaces.IAtomContainerSet canMetabolize(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                      boolean allPossible,
                                                                      org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                                                               throws ReactionException

Checks if 4 predefined metabolic reactions can be applied to Molecule mol

Parameters:

mol -

Returns:

null if not metabolized by these, otherwise returns metabolic products

Throws:

ReactionException