toxTree.query
Class SimpleReactions

java.lang.Object
  extended by toxTree.query.SimpleReactions

public class SimpleReactions
extends java.lang.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
protected static org.openscience.cdk.smiles.SmilesGenerator gen
           
protected static java.lang.String[] hydrolize
           
protected static java.lang.String[] hydrolizePO4
           
protected static org.openscience.cdk.interfaces.IReaction[] hydrolysis
           
protected static org.openscience.cdk.interfaces.IReaction[] hydrolysisPO4
           
protected static TTLogger logger
           
protected static org.openscience.cdk.interfaces.IReaction[] metabolic
           
protected static java.lang.String[] metabolize
           
protected  org.openscience.cdk.interfaces.IReaction reaction
           
 
Constructor Summary
SimpleReactions()
           
 
Method Summary
 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.IMoleculeSet hydrolize(org.openscience.cdk.interfaces.IAtomContainer a, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q, java.util.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.IMoleculeSet isReadilyHydrolisedSimpleEster(org.openscience.cdk.interfaces.IAtomContainer mol)
          Checks if simple ester hydrolysis can be applied to Molecule mol
 org.openscience.cdk.interfaces.IMoleculeSet 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(java.lang.String filename)
           
static org.openscience.cdk.interfaces.IMoleculeSet process(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IReaction reaction)
           
static org.openscience.cdk.interfaces.IMoleculeSet 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 TTLogger 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 java.lang.String[] hydrolize

metabolize

protected static java.lang.String[] metabolize

hydrolizePO4

protected static java.lang.String[] hydrolizePO4
Constructor Detail

SimpleReactions

public SimpleReactions()
Method Detail

loadPreconfiguredReaction

protected org.openscience.cdk.interfaces.IReaction loadPreconfiguredReaction(java.lang.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.IMoleculeSet process(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                  org.openscience.cdk.interfaces.IReaction reaction)
                                                           throws ReactionException
Throws:
ReactionException

process

public static org.openscience.cdk.interfaces.IMoleculeSet 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.IMoleculeSet hydrolize(org.openscience.cdk.interfaces.IAtomContainer a,
                                                                       org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q,
                                                                       java.util.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.IMoleculeSet 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.IMoleculeSet 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


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