toxTree.query
Class SimpleReactions
java.lang.Object
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
|
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 |
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
SimpleReactions
public SimpleReactions()
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
Copyright © 2004-2012 Ideaconsult Ltd.. All Rights Reserved.