chemaxon.reaction
Class Reaction

java.lang.Object
  chemaxon.reaction.Reaction

All Implemented Interfaces:

java.io.Serializable

public class Reaction
extends java.lang.Object
implements java.io.Serializable

Stores reaction data. The reaction data consists of:

• the reaction equation and
• the reaction rules (reactivity, selectivity)

Stores connection data read from the reaction equation.

Since:

JChem 3.0

Version:

5.0.3 03/19/2008

Author:

Nora Mate, Zsolt Mohacsi

See Also:

Serialized Form

Field Summary

static int	ALL_SIDE Reactant and product sides of the reaction molecule
protected int	bcount Number of changed bonds.
static int	DATA_ALL Required data: all.
static int	DATA_ATOMS Required data: atom data.
static int	DATA_BONDS Required data: bond data.
static int	DATA_DOUBLE_BOND_STEREO Required data: double bond stereo.
static int	DATA_PARITY Required data: parity.
protected int[]	emaps End map numbers: bond atom2.
protected static int	LEN Default array length.
protected int[]	map2map Identical maps.
protected int[]	map2pindex Map number -> product index array.
protected int[]	map2rindex Map number -> reactant index array.
protected int[]	map2stereo Map -> reaction stereo info array.
protected static int	MAXMAPS Maximal number of map values.
protected java.util.ArrayList	patomprops Atom objects for storing product atom properties.
protected int[]	pbondtypes Product bond types.
protected java.util.ArrayList	pcistrans Stores double bond stereo info (product-side).
protected int[]	pindex2map Product index -> map number array.
protected java.util.ArrayList	pparities Stores parity info (product-side).
static int	PRODUCT_SIDE Product side of the reaction molecule
protected static int	PROP_CHARGE Constant: charge atom property.
protected static int	PROP_HCOUNT Constant: hydrogen count atom property.
protected static int	PROP_RADICAL Constant: radical atom property.
protected static int	PROP_STGRP Constant: enhanced stereo atom property.
protected int[]	proptypes Property types corresponding to 'ratomprops', 'patomprops'.
protected java.util.ArrayList	ratomprops Atom objects for storing reactant atom properties.
protected int[]	rbondtypes Reactant bond types.
protected java.util.ArrayList	rcistrans Stores double bond stereo info (reactant-side).
static int	REACTANT_SIDE Reactant side of the reaction molecule
protected int[]	rindex2map Reactant index -> map number array.
protected ChemJEP	rjep The JEP object that evaluates the reactivity (acceptance) rule.
protected java.util.ArrayList	rparities Stores parity info (reactant-side).
protected RxnMolecule	rxn The reaction molecule.
protected ChemJEP	sjep The JEP object that evaluates the selectivity (measure) rule.
protected int[]	smaps Start map numbers: bond atom1.
protected double[]	tolerances The tolerance value corresponding to the selectivity rule.

Constructor Summary

Reaction()
Default constructor.

Reaction(java.lang.String id)
Constructor.

Method Summary

protected int	getBaseMap(int map) Returns the base map corresponding to the given map.
int[]	getChangingAtoms(boolean all, int side) Returns the indexes of changing atoms.
int[][]	getChangingBondData(boolean all) Returns changing bond data.
protected java.lang.String	getFID() Deprecated. Not used.
java.lang.String	getID() Returns the reaction ID.
protected Molecule	getProduct(int i) Returns the i-th product.
protected MolAtom	getProductAtom(int i) Returns the i-th atom existing only on the product side.
protected int	getProductAtomCount() Returns the number of atoms existing only on the product side.
protected int	getProductCount() Returns the number of products.
protected Molecule[]	getProducts() Returns the reaction products.
Molecule	getReactant(int i) Returns the i-th reactant.
protected MolAtom	getReactantAtom(int i) Returns the i-th atom existing only on the reactant side.
protected int	getReactantAtomCount() Returns the number of atoms existing only on the reactant side.
int	getReactantCount() Returns the number of reactants.
protected Molecule[]	getReactants() Returns the reaction reactants.
static java.lang.String	getReactivity(java.lang.String reactivity, java.lang.String exclude) Returns reactivity combined with exclude condition.
static double[]	getTolerances(java.lang.String tolerances) Returns double[] created from ";" separated list of real numbers.
void	setFID(java.lang.String fid) Deprecated. Not used.
void	setReaction(Molecule mol) Sets the reaction molecule representing the reaction equation.
void	setReaction(Molecule mol, boolean fuse) Sets the reaction molecule representing the reaction equation.
void	setReaction(Molecule mol, boolean fuse, boolean skipMappingCheck) Sets the reaction molecule representing the reaction equation.
void	setReactivityRule(java.lang.String rule, Evaluator evaluator) Sets the reactivity (acceptance) rule.
void	setRequiredData(int data) Sets the required data to be stored.
void	setSelectivityRule(java.lang.String rule, double[] tolerances, Evaluator evaluator) Sets the selectivity rule with tolerance.
void	setSelectivityRule(java.lang.String rule, Evaluator evaluator) Deprecated. Use setSelectivityRule(String, double[], Evaluator) or setSelectivityRule(String, String, Evaluator) and set tolerances parameter to null
void	setSelectivityRule(java.lang.String rule, java.lang.String tolerances, Evaluator evaluator) Sets the selectivity rule with tolerance.

Methods inherited from class java.lang.Object

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

Field Detail

MAXMAPS

protected static final int MAXMAPS

Maximal number of map values.

See Also:

Constant Field Values

LEN

protected static final int LEN

Default array length.

See Also:

Constant Field Values

PROP_CHARGE

protected static final int PROP_CHARGE

Constant: charge atom property.

See Also:

Constant Field Values

PROP_RADICAL

protected static final int PROP_RADICAL

Constant: radical atom property.

See Also:

Constant Field Values

PROP_STGRP

protected static final int PROP_STGRP

Constant: enhanced stereo atom property.

See Also:

Constant Field Values

PROP_HCOUNT

protected static final int PROP_HCOUNT

Constant: hydrogen count atom property.

See Also:

Constant Field Values

REACTANT_SIDE

public static final int REACTANT_SIDE

Reactant side of the reaction molecule

See Also:

Constant Field Values

PRODUCT_SIDE

public static final int PRODUCT_SIDE

Product side of the reaction molecule

See Also:

Constant Field Values

ALL_SIDE

public static final int ALL_SIDE

Reactant and product sides of the reaction molecule

See Also:

Constant Field Values

DATA_ATOMS

public static final int DATA_ATOMS

Required data: atom data.

See Also:

Constant Field Values

DATA_BONDS

public static final int DATA_BONDS

Required data: bond data.

See Also:

Constant Field Values

DATA_PARITY

public static final int DATA_PARITY

Required data: parity.

See Also:

Constant Field Values

DATA_DOUBLE_BOND_STEREO

public static final int DATA_DOUBLE_BOND_STEREO

Required data: double bond stereo.

See Also:

Constant Field Values

DATA_ALL

public static final int DATA_ALL

Required data: all.

See Also:

Constant Field Values

rxn

protected RxnMolecule rxn

The reaction molecule.

rjep

protected ChemJEP rjep

The JEP object that evaluates the reactivity (acceptance) rule.

sjep

protected ChemJEP sjep

The JEP object that evaluates the selectivity (measure) rule.

tolerances

protected double[] tolerances

The tolerance value corresponding to the selectivity rule.

map2map

protected int[] map2map

Identical maps.

smaps

protected int[] smaps

Start map numbers: bond atom1.

emaps

protected int[] emaps

End map numbers: bond atom2.

rbondtypes

protected int[] rbondtypes

Reactant bond types.

pbondtypes

protected int[] pbondtypes

Product bond types.

bcount

protected int bcount

Number of changed bonds.

proptypes

protected int[] proptypes

Property types corresponding to 'ratomprops', 'patomprops'.

ratomprops

protected java.util.ArrayList ratomprops

Atom objects for storing reactant atom properties.

patomprops

protected java.util.ArrayList patomprops

Atom objects for storing product atom properties.

map2stereo

protected int[] map2stereo

Map -> reaction stereo info array.

map2rindex

protected int[] map2rindex

Map number -> reactant index array. Shows which reactant a given atom map belongs to. The product index is set to -1 if the mapped atom exists only on the product side.

map2pindex

protected int[] map2pindex

Map number -> product index array. Shows which product a given atom map belongs to. The product index is set to -1 if the mapped atom exists only on the reactant side.

rindex2map

protected int[] rindex2map

Reactant index -> map number array. Shows a representative map number from the reactant.

pindex2map

protected int[] pindex2map

Product index -> map number array. Shows a representative map number from the product.

rparities

protected java.util.ArrayList rparities

Stores parity info (reactant-side). Stores reactant-side parity-info in int[7] arrays. 0: central atom map 1-4: ligand atom maps 5: parity sign 6: parity

pparities

protected java.util.ArrayList pparities

Stores parity info (product-side). Stores product-side parity-info in int[7] arrays. 0: central atom map 1-4: ligand atom maps 5: parity sign 6: parity

rcistrans

protected java.util.ArrayList rcistrans

Stores double bond stereo info (reactant-side). Stores reactant-side reaction stereo2 (cis/trans) info in int[5] arrays. 0-3: the A1-A2=A3-A4 atom maps 4: the cis/trans constant

See Also:

StereoConstants.CIS, StereoConstants.TRANS, StereoConstants.CTUNSPEC

pcistrans

protected java.util.ArrayList pcistrans

Stores double bond stereo info (product-side). Stores product-side reaction stereo2 (cis/trans) info in int[5] arrays. 0-3: the A1-A2=A3-A4 atom maps 4: the cis/trans constant

See Also:

StereoConstants.CIS, StereoConstants.TRANS, StereoConstants.CTUNSPEC

Constructor Detail

Reaction

public Reaction()

Default constructor.

Reaction

public Reaction(java.lang.String id)

Constructor.

Parameters:

id - is the reaction ID

Method Detail

setRequiredData

public void setRequiredData(int data)

Sets the required data to be stored. Default: DATA_ALL.

Parameters:

data - is the required data, an OR-ed combination of the DATA_ constants (e.g. DATA_ATOMS | DATA_BONDS)

Since:

JChem 3.2

See Also:

DATA_ATOMS, DATA_BONDS, DATA_PARITY, DATA_DOUBLE_BOND_STEREO

getChangingBondData

public int[][] getChangingBondData(boolean all)

Returns changing bond data. The DATA_BONDS flag should be set to get this result (see setRequiredData(int)). By default, all flags are set. Format: an array of int[6] elements. If we denote one such int[6] element by 'b' then:

• b[0] is the reactant side bond index, -1 if bond exists only on the product side
• b[1] is the first endpoint atom index on the reactant side, -1 if atom exists only on the product side
• b[2] is the second endpoint atom index on the reactant side, -1 if atom exists only on the product side
• b[3] is the product side bond index, -1 if bond exists only on the reactant side
• b[4] is the first endpoint atom index on the product side, -1 if atom exists only on the reactant side
• b[5] is the second endpoint atom index on the product side -1 if atom exists only on the reactant side

Parameters:

all - is true if all changing bonds should be returned, false if bonds between orphan/widow atoms should be excluded

Returns:

the changing bond data

Since:

JChem 3.2

getChangingAtoms

public int[] getChangingAtoms(boolean all,
                              int side)

Returns the indexes of changing atoms. Changing atoms: atom existing only on the reactant or the product side, atoms having changing bonds, and atoms having changing properties (e.g. charge). The DATA_BONDS flag should be set to include atoms having changing bonds and the DATA_ATOMS flag should be set to include atoms having changing atom properties (see setRequiredData(int)). By default, all flags are set.

Parameters:

all - is true if all changing atoms should be returned, false if orphan/widow atoms with only orphan/widow neighbours should be excluded

side -

• REACTANT_SIDE to get changing atoms from the reactant side
• PRODUCT_SIDE to get changing atoms from the product side
• ALL_SIDE to get all changing atoms

Returns:

the changing atom indexes

Since:

JChem 3.2

getReactivity

public static java.lang.String getReactivity(java.lang.String reactivity,
                                             java.lang.String exclude)

Returns reactivity combined with exclude condition. Example:

 reactivity && !exclude

Parameters:

reactivity - is the reactivity rule

exclude - is the exclude rule

Returns:

the combined rectivity rule

getTolerances

public static double[] getTolerances(java.lang.String tolerances)
                              throws ReactionException

Returns double[] created from ";" separated list of real numbers. Empty string in the list is converted to Reactor.DEF_TOLERANCE.

Parameters:

tolerances - is the string: ";" separated list of real numbers

Returns:

the corresponding double[]

Throws:

ReactionException - on format error

setReactivityRule

public void setReactivityRule(java.lang.String rule,
                              Evaluator evaluator)
                       throws ReactionException

Sets the reactivity (acceptance) rule. This is a boolean condition which evaluates to true precisely if the products should be accepted. Evaluation of the reactivity rule precedes the evaluation of the selectivity rule set by setSelectivityRule(String, Evaluator).

Parameters:

rule - is the rule chemical terms string

evaluator - is the evaluator object

Throws:

ReactionException - on parse error

Since:

JChem 2.3

setSelectivityRule

public void setSelectivityRule(java.lang.String rule,
                               Evaluator evaluator)
                        throws ReactionException

Deprecated. Use setSelectivityRule(String, double[], Evaluator) or setSelectivityRule(String, String, Evaluator) and set tolerances parameter to null

Sets the selectivity rule with default tolerance Reactor.DEF_TOLERANCE. This rule is used to sort product sets by decreasing evaluation order, that is, the product set with the largest evaluation result will be returned first by Reactor.react(). The tolerance value is used to filter product sets based on their selectivity compared to the maximal selectivity: a product set is accepted only if the difference between the maximum selectivity and its selectivity is not greater than the specified tolerance. The default tolerance is set such that only values that are approximately equal to the maximum are accepted.

Parameters:

rule - is the rule chemical terms string

evaluator - is the evaluator object

Throws:

ReactionException - on parse error

Since:

JChem 2.3

setSelectivityRule

public void setSelectivityRule(java.lang.String rule,
                               java.lang.String tolerances,
                               Evaluator evaluator)
                        throws ReactionException

Sets the selectivity rule with tolerance. If tolerances parameter is null then default tolerance (Reactor.DEF_TOLERANCE) is used. This rule is used to sort product sets by decreasing evaluation order, that is, the product set with the largest evaluation result will be returned first by Reactor.react(). The tolerance value is used to filter product sets based on their selectivity compared to the maximal selectivity: a product set is accepted only if the difference between the maximum selectivity and its selectivity is not greater than the specified tolerance.

Parameters:

rule - is the rule chemical terms string, items separated by ";"

evaluator - is the evaluator object

tolerances - is the selectivity acceptance tolerance string, items separated by ";". If null then Reactor.DEF_TOLERANCE is used.

Throws:

ReactionException - on parse error

Since:

JChem 2.3

setSelectivityRule

public void setSelectivityRule(java.lang.String rule,
                               double[] tolerances,
                               Evaluator evaluator)
                        throws ReactionException

Sets the selectivity rule with tolerance. If tolerances parameter is null then default tolerance (Reactor.DEF_TOLERANCE) is used. This rule is used to sort product sets by decreasing evaluation order, that is, the product set with the largest evaluation result will be returned first by Reactor.react(). The tolerance value is used to filter product sets based on their selectivity compared to the maximal selectivity: a product set is accepted only if the difference between the maximum selectivity and its selectivity is not greater than the specified tolerance.

Parameters:

rule - is the rule chemical terms string, items separated by ";"

evaluator - is the evaluator object

tolerances - is the selectivity acceptance tolerance array. If null then Reactor.DEF_TOLERANCE is used.

Throws:

ReactionException - on parse error

Since:

JChem 2.3

getID

public java.lang.String getID()

Returns the reaction ID.

Returns:

the reaction ID

setFID

public void setFID(java.lang.String fid)

Deprecated. Not used.

Sets the fragmentation ID.

Parameters:

fid - is the fragmentation ID

getFID

protected java.lang.String getFID()

Deprecated. Not used.

Returns fragmentation ID.

Returns:

fragmentation ID

getReactant

public Molecule getReactant(int i)

Returns the i-th reactant.

Parameters:

i - is the reactant index

Returns:

the i-th reactant

getReactants

protected Molecule[] getReactants()

Returns the reaction reactants.

Returns:

the reaction reactants

getReactantCount

public int getReactantCount()

Returns the number of reactants.

Returns:

the number of reactants

getProduct

protected Molecule getProduct(int i)

Returns the i-th product.

Parameters:

i - is the product index

Returns:

the i-th product

getProducts

protected Molecule[] getProducts()

Returns the reaction products.

Returns:

the reaction products

getProductCount

protected int getProductCount()

Returns the number of products.

Returns:

the number of products

getProductAtomCount

protected int getProductAtomCount()

Returns the number of atoms existing only on the product side.

Returns:

the number of atoms existing only on the product side

getProductAtom

protected MolAtom getProductAtom(int i)

Returns the i-th atom existing only on the product side.

Parameters:

i - is the atom index

Returns:

the i-th atom existing only on the product side

getReactantAtomCount

protected int getReactantAtomCount()

Returns the number of atoms existing only on the reactant side.

Returns:

the number of atoms existing only on the reactant side

getReactantAtom

protected MolAtom getReactantAtom(int i)

Returns the i-th atom existing only on the reactant side.

Parameters:

i - is the atom index

Returns:

the i-th atom existing only on the reactant side

setReaction

public void setReaction(Molecule mol)
                 throws ReactionException

Sets the reaction molecule representing the reaction equation. Reaction has to be mapped in changing style.

Parameters:

mol - is the reaction molecule

Throws:

ReactionException - on error (standardization, mapping, ...)

setReaction

public void setReaction(Molecule mol,
                        boolean fuse)
                 throws ReactionException

Sets the reaction molecule representing the reaction equation. Reaction has to be mapped in changing style.

Parameters:

mol - is the reaction molecule

fuse - is true if reaction reactants / products should be fused to form a 1-reactant 1-product molecule used in Standardizer and Reactor transform mode (see Reactor.setTransform(boolean))

Throws:

ReactionException - on error (standardization, mapping, ...)

setReaction

public void setReaction(Molecule mol,
                        boolean fuse,
                        boolean skipMappingCheck)
                 throws ReactionException

Sets the reaction molecule representing the reaction equation. Reaction has to be mapped in changing style.

Parameters:

mol - is the reaction molecule

fuse - is true if reaction reactants / products should be fused to form a 1-reactant 1-product molecule used in Standardizer and Reactor transform mode (see Reactor.setTransform(boolean))

skipMappingCheck - if true reaction mapping will not be checked

Throws:

ReactionException - on error (standardization, mapping, ...)

Since:

JChem 5.0

getBaseMap

protected int getBaseMap(int map)

Returns the base map corresponding to the given map. This is the map itself for unique maps, the original map in the reaction corresponding to the map otherwise.

Parameters:

map - is the map

Returns:

the base map, -1 for non-existing reaction maps