Reactor (Marvin API documentation (c) 1998-2021 ChemAxon Ltd.)

java.lang.Object
- chemaxon.reaction.Reactor

All Implemented Interfaces:: chemaxon.license.Licensable, java.io.Serializable

@PublicAPI
public class Reactor
extends java.lang.Object
implements chemaxon.license.Licensable, java.io.Serializable

Executes a chemical reaction: creates products from reactants with reaction center data. If the reaction centers have not yet been searched for, uses substructure search to find and (optionally) store them. Provides API to single reaction processing.

See the documentation for details.

An example usage of the API:

 // create Reactor
 Reactor reactor = new Reactor();

 // set the reaction ('rxmol' is the reaction molecule)
 // reaction rules are read from RDF/MRV tags
 reactor.setReaction(rxmol);

 // set the reactants
 reactor.setReactants(reactants);

 // get the results
 Molecule[] products;
 while ((products = reactor.react()) != null) {
     // export result molecules
     for (Molecule product : products) {
         exporter.write(product);
     }
 }

Another example with reaction rules and reaction output:

 // create Reactor
 Reactor reactor = new Reactor();

 // set the reaction
 // ('rxmol' is the reaction molecule,
 // 'rid' is the reaction ID
 // 'reactivity' is the reactivity rule,
 // 'selectivity' is the selectivity rule
 // 'tolerances' is the tolerance string)
 reactor.setReaction(rxmol, rid, reactivity, selectivity, tolerances);

 // set Reactor options
 reactor.setResultType(Reactor.REACTION_OUTPUT);
 reactor.setRatio(new int[] { 1, 2 });

 // set the reactants
 reactor.setReactants(reactants);

 // get the results
 Molecule[] result;
 while ((result = reactor.react()) != null) {
     // export result (reaction molecule)
     for (Molecule rxn : result) {
         exporter.write(rxn);
     }
 };

Since:: JChem 3.0
Version:: JChem 6.4, 06/20/2014
Author:: Nora Mate, Zsolt Mohacsi
See Also:: ConcurrentReactorProcessor, Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static double`	`DEF_TOLERANCE` The default tolerance.
`static int`	`FUSED_REACTION_OUTPUT` Output type: fused reaction output.
`static int`	`IGNORE_REACTIVITY` No-rule type: ignore reactivity rule.
`static int`	`IGNORE_SELECTIVITY` No-rule type: ignore selectivity rule.
`static int`	`IGNORE_TOLERANCE` No-rule type: ignore selectivity tolerance.
`static int`	`MAPPING_STYLE_CHANGING` Output reaction mapping style: changing (ChemAxon).
`static int`	`MAPPING_STYLE_COMPLETE` Output reaction mapping style: complete.
`static int`	`MAPPING_STYLE_MATCHING` Output reaction mapping style: matching (Daylight).
`static int`	`MAPPING_STYLE_NONE` Output reaction mapping style: none.
`static java.lang.String`	`MINOR_PRODUCT_TAG`
`static int`	`NO_DUPLICATE_FILTERING` No duplicate product list filtering
`static int`	`ORDER_INSENSITIVE_DUPLICATE_FILTERING` Order insensitive duplicate product list filtering
`static int`	`ORDER_SENSITIVE_DUPLICATE_FILTERING` Order sensitive duplicate product list filtering
`static int`	`PRODUCT_OUTPUT` Output type: products.
`static int`	`REACTION_OUTPUT` Output type: reaction.

Constructor Summary

Constructors
Constructor and Description

Reactor()
Default constructor.

Constructors
Constructor and Description
`Reactor()` Default constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`getProductCount()` Returns the number of products.
`int`	`getReactantCount()` Returns the number of reactants.
`Molecule[]`	`getReactants()` Returns the input reactants.
`RxnMolecule`	`getReaction()` Returns the reaction.
`java.lang.String`	`getReactionID()` Returns the reaction ID.
`java.lang.String`	`getReactionIDPropertyName()` Returns the reaction ID property (RDF/MRV tag) name.
`java.util.Map<MolAtom,AtomIdentifier>`	`getReactionMap()` Gets the mapping for the last performed reaction.
`Molecule`	`getReactionProduct(int i)` Returns a reaction product.
`Molecule`	`getReactionReactant(int i)` Returns a reaction reactant.
`Standardizer`	`getStandardizer()` Returns the reactant standardizer object.
`boolean`	`isGenerateMinorProducts()` Returns `true` if minor products are generated.
`boolean`	`isLicensed()`
`boolean`	`isReverse()` Returns `true` if the reaction is to be processed in reversed direction.
`boolean`	`isSingle()` Returns `true` if single mode is set.
`Molecule[]`	`react()` Performs the reaction.
`void`	`restart()` Restarts the reactor: the following call to `react()` will return the first product set.
`void`	`setComponentIDPropertyNames(java.lang.String[] reactantIDProps, java.lang.String[] productIDProps)` Sets reactant/product ID property (SDF/MRV tag) names.
`void`	`setComponentIDPropertyNames(java.lang.String reactantIDProp, java.lang.String productIDProp)` Sets reactant/product ID property (SDF/MRV tag) names.
`void`	`setCopyAllReactantProperties(boolean c)` Sets to copy all reactant properties to output products/reactions.
`void`	`setCopyReactantProperties(java.util.Map<java.lang.String,java.lang.String> patternBasedProperties)` Sets the reactant properties which should created in output products/reactions, based on a pattern.
`void`	`setCopyReactantProperties(java.lang.String[][] reactantPropertiesToCopy)` Sets the reactant properties which should be copied to output products/reactions.
`void`	`setCopyReactantProperties(java.lang.String[][] sourceProperties, java.lang.String[][] targetProperties)` Sets the reactant properties which should be copied to output products/reactions.
`void`	`setDuplicateFiltering(int duplicateFilteringMethod)` Sets duplicate product list filtering.
`void`	`setGenerateMinorProducts(boolean generateMinorProducts)` If set then products lists are not filtered out by the selectivity rule, but they are tagged as minor products.
`void`	`setIgnoreReactionDefinedStandardizer(boolean ignore)` Sets to ignore the standardization defined in the `STANDARDIZATION` RDF/MRV tag of the reaction molecule.
`void`	`setIgnoreRules(int type)` Ignore reaction rules: `0`: apply both rules (default) `IGNORE_REACTIVITY`: ignore reactivity rule `IGNORE_SELECTIVITY`: ignore selectivity rule `IGNORE_TOLERANCE`: ignore selectivity tolerance `IGNORE_REACTIVITY` \| `IGNORE_SELECTIVITY`: ignore both rules `IGNORE_REACTIVITY` \| `IGNORE_TOLERANCE`: ignore reactivity rule and selectivity tolerance
`void`	`setLicenseEnvironment(java.lang.String env)` For internal use only.
`void`	`setMaxNumberOfProductSets(int pieces)` Sets the maximum number of products sets to be returned for one reactant set.
`void`	`setOutputReactionMappingStyle(int style)` Sets the output reaction's mapping style.
`void`	`setProductIndexes(int[] inds)` Sets the product indexes (1-based) to be returned (default: `null` - all products).
`void`	`setRatio(int[] ratio)` Sets the ratio of the reactants.
`void`	`setReactants(Molecule[] mols)` Sets the reactants.
`void`	`setReaction(Molecule rxmol)` Sets the reaction with reaction rules set in RDF/MRV tags `REACTIVITY`, `EXCLUDE`, `SELECTIVITY`, `TOLERANCE`.
`void`	`setReaction(Molecule rxmol, java.lang.String rid)` Sets the reaction with reaction rules set in RDF/MRV tags `REACTIVITY`, `EXCLUDE`, `SELECTIVITY`, `TOLERANCE`.
`void`	`setReaction(Molecule rxmol, java.lang.String rid, java.lang.String reactivity, java.lang.String selectivity, double[] tolerances)` Sets the reaction and the reaction rules.
`void`	`setReaction(Molecule rxmol, java.lang.String rid, java.lang.String reactivity, java.lang.String selectivity, java.lang.String tolerances)` Sets the reaction and the reaction rules.
`void`	`setReactionCenterMarkEnabled(boolean enabled)` Sets whether the bonds of the reaction center on the output should be marked with the following bond marks: `MolBond.RC_MAKE_OR_BREAK` for bonds that are created or broken during the reaction `MolBond.RC_CHANGE` for bonds that are changed (type and/or one ligand change)
`void`	`setReactionIDPropertyName(java.lang.String reactionIDProp)` Sets the reaction ID property (RDF/MRV tag) name.
`void`	`setReactionString(java.lang.String str)` Sets the reaction and optionally the reaction rules specified in a string.
`void`	`setReactionString(java.lang.String str, java.lang.String rid)` Sets the reaction and optionally the reaction rules specified in a string.
`void`	`setResultType(int type)` Sets the result type.
`void`	`setReverse(boolean reverse)` Sets the "reverse" property: `true` if the reaction is to be processed in reversed direction, that is, the product and reactant sides are swapped.
`void`	`setSearchOptions(java.lang.String searchOptions)` Modifies the default search options used by the Reactor engine.
`void`	`setShowUnsuccessfulReactions(boolean showUnsuccessfulReactions)` Sets if unsuccessful reactions (reactions which do not result products) should be shown in output.
`void`	`setSingle(boolean single)` Process unambiguous reactions only, where each reactant has a single reaction site.
`void`	`setStandardizer(Standardizer standardizer)` Sets the reactant standardizer object.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - PRODUCT_OUTPUT
```
public static final int PRODUCT_OUTPUT
```
    Output type: products.
    
    See Also:
    
    Constant Field Values
  - REACTION_OUTPUT
```
public static final int REACTION_OUTPUT
```
    Output type: reaction.
    
    See Also:
    
    Constant Field Values
  - FUSED_REACTION_OUTPUT
```
public static final int FUSED_REACTION_OUTPUT
```
    Output type: fused reaction output.
    
    See Also:
    
    Constant Field Values
  - NO_DUPLICATE_FILTERING
```
public static final int NO_DUPLICATE_FILTERING
```
    No duplicate product list filtering
    
    See Also:
    
    Constant Field Values
  - ORDER_SENSITIVE_DUPLICATE_FILTERING
```
public static final int ORDER_SENSITIVE_DUPLICATE_FILTERING
```
    Order sensitive duplicate product list filtering
    
    See Also:
    
    Constant Field Values
  - ORDER_INSENSITIVE_DUPLICATE_FILTERING
```
public static final int ORDER_INSENSITIVE_DUPLICATE_FILTERING
```
    Order insensitive duplicate product list filtering
    
    See Also:
    
    Constant Field Values
  - MAPPING_STYLE_NONE
```
public static final int MAPPING_STYLE_NONE
```
    Output reaction mapping style: none.
    
    See Also:
    
    Constant Field Values
  - MAPPING_STYLE_CHANGING
```
public static final int MAPPING_STYLE_CHANGING
```
    Output reaction mapping style: changing (ChemAxon).
    
    See Also:
    
    Constant Field Values
  - MAPPING_STYLE_COMPLETE
```
public static final int MAPPING_STYLE_COMPLETE
```
    Output reaction mapping style: complete.
    
    See Also:
    
    Constant Field Values
  - MAPPING_STYLE_MATCHING
```
public static final int MAPPING_STYLE_MATCHING
```
    Output reaction mapping style: matching (Daylight).
    
    See Also:
    
    Constant Field Values
  - IGNORE_REACTIVITY
```
public static final int IGNORE_REACTIVITY
```
    No-rule type: ignore reactivity rule.
    
    See Also:
    
    Constant Field Values
  - IGNORE_SELECTIVITY
```
public static final int IGNORE_SELECTIVITY
```
    No-rule type: ignore selectivity rule.
    
    See Also:
    
    Constant Field Values
  - IGNORE_TOLERANCE
```
public static final int IGNORE_TOLERANCE
```
    No-rule type: ignore selectivity tolerance.
    
    See Also:
    
    Constant Field Values
  - DEF_TOLERANCE
```
public static final double DEF_TOLERANCE
```
    The default tolerance.
    
    See Also:
    
    Constant Field Values
  - MINOR_PRODUCT_TAG
```
public static final java.lang.String MINOR_PRODUCT_TAG
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Reactor
```
public Reactor()
```
    Default constructor.
- Method Detail
  - setLicenseEnvironment
```
public void setLicenseEnvironment(java.lang.String env)
```
    For internal use only.
    
    Specified by:
    
    setLicenseEnvironment in interface chemaxon.license.Licensable
    
    Parameters:
    
    env - the license environment
  - getReactionID
```
public java.lang.String getReactionID()
```
    Returns the reaction ID. For internal use only.
    
    Returns:
    
    the reaction ID
    
    Since:
    
    JChem 2.3
  - setIgnoreRules
```
public void setIgnoreRules(int type)
```
    Ignore reaction rules:
    - 0: apply both rules (default)
    - IGNORE_REACTIVITY: ignore reactivity rule
    - IGNORE_SELECTIVITY: ignore selectivity rule
    - IGNORE_TOLERANCE: ignore selectivity tolerance
    - IGNORE_REACTIVITY | IGNORE_SELECTIVITY: ignore both rules
    - IGNORE_REACTIVITY | IGNORE_TOLERANCE: ignore reactivity rule and selectivity tolerance
    Parameters:
    
    type - is the rule type(s) to be ignored (see above)
    
    Since:
    
    JChem 2.3
  - setSingle
```
public void setSingle(boolean single)
```
    Process unambiguous reactions only, where each reactant has a single reaction site. If there is more than one reaction site in a reactant then null is returned by react() method. The default is false (non-single mode).
    
    Parameters:
    
    single - is true if single mode
    
    Since:
    
    JChem 2.3
  - isSingle
```
public boolean isSingle()
```
    Returns true if single mode is set.
    
    Returns:
    
    true if single mode
    
    Since:
    
    JChem 2.3
    
    See Also:
    
    setSingle(boolean)
  - setShowUnsuccessfulReactions
```
public void setShowUnsuccessfulReactions(boolean showUnsuccessfulReactions)
```
    Sets if unsuccessful reactions (reactions which do not result products) should be shown in output. If true, then unsuccessful reactions will be shown with empty products side in the output. This options works only in case of REACTION_OUTPUT.
    
    Parameters:
    
    showUnsuccessfulReactions - if true, then unsuccessful reactions will be shown with empty products side in the output
    
    Since:
    
    JChem 5.3.2
    
    See Also:
    
    setResultType(int)
  - setDuplicateFiltering
```
public void setDuplicateFiltering(int duplicateFilteringMethod)
```
    Sets duplicate product list filtering. Available filtering methods:
    - NO_DUPLICATE_FILTERING: no duplicate filtering
    - ORDER_SENSITIVE_DUPLICATE_FILTERING: order sensitive duplicate filtering
    - ORDER_INSENSITIVE_DUPLICATE_FILTERING: order insensitive duplicate filtering
    The default is ORDER_SENSITIVE_DUPLICATE_FILTERING. Note that skipping duplicate product list filtering increases efficiency therefore it is wise to set this parameter to NO_DUPLICATE_FILTERING if duplicates do not matter (e.g. if only the first product list is queried by calling react() only once).
    Parameters:
    
    duplicateFilteringMethod - is the filtering method
    
    Since:
    
    JChem 5.0.1
  - setMaxNumberOfProductSets
```
public void setMaxNumberOfProductSets(int pieces)
```
    Sets the maximum number of products sets to be returned for one reactant set. Set -1 to return all product sets. (default: return all product sets)
    
    Parameters:
    
    pieces - is the maximum number of products set to be returned for one reactant set
    
    Since:
    
    JChem 5.0
  - setProductIndexes
```
public void setProductIndexes(int[] inds)
```
    Sets the product indexes (1-based) to be returned (default: null - all products).
    
    Parameters:
    
    inds - is the 1-based product index array, null for all products
    
    Since:
    
    JChem 2.2
  - setResultType
```
public void setResultType(int type)
```
    Sets the result type.
    Available types:
    - PRODUCT_OUTPUT: products molecules are returned. Each call to react() method returns the next product set.
    - REACTION_OUTPUT: reactants -> products reaction is returned. Each call to react() method returns a reaction containing the next product set.
    - FUSED_REACTION_OUTPUT: reactants -> products reaction is returned, with all possible products on the right side. react() method should only be called once; further react() calls will return null.
    In case of REACTION_OUTPUT and FUSED_REACTION_OUTPUT the Molecule[] array returned by react() method will contain the reactants -> products reaction as RxnMolecule.
    Setting the result type restarts processing of the current reactant set - next call to react() will return the first product set.
    Default: PRODUCT_OUTPUT
    Parameters:
    
    type - is the result type
    
    Since:
    
    JChem 5.0
  - setOutputReactionMappingStyle
```
public void setOutputReactionMappingStyle(int style)
```
    Sets the output reaction's mapping style. Available styles:
    Default: MAPPING_STYLE_NONE
    Parameters:
    
    style - is the output reaction's mapping style
    
    Since:
    
    JChem 3.2
  - setReactionCenterMarkEnabled
```
public void setReactionCenterMarkEnabled(boolean enabled)
```
    Sets whether the bonds of the reaction center on the output should be marked with the following bond marks:
    - MolBond.RC_MAKE_OR_BREAK for bonds that are created or broken during the reaction
    - MolBond.RC_CHANGE for bonds that are changed (type and/or one ligand change)
    NOTE: Only works for reaction output! Fused reaction and product output does not support reaction center mark.
    Parameters:
    
    enabled - whether the reaction center on the output should be marked
    
    Since:
    
    5.12
  - setStandardizer
```
public void setStandardizer(Standardizer standardizer)
```
    Sets the reactant standardizer object.
    
    Parameters:
    
    standardizer - is the reactant standardizer object
  - getStandardizer
```
public Standardizer getStandardizer()
```
    Returns the reactant standardizer object.
    
    Returns:
    
    the reactant standardizer object
  - setIgnoreReactionDefinedStandardizer
```
public void setIgnoreReactionDefinedStandardizer(boolean ignore)
```
    Sets to ignore the standardization defined in the STANDARDIZATION RDF/MRV tag of the reaction molecule.
    
    Parameters:
    
    ignore - if true reaction defined standardization is ignored
    
    Since:
    
    JChem 3.2
  - setReverse
```
public void setReverse(boolean reverse)
```
    Sets the "reverse" property: true if the reaction is to be processed in reversed direction, that is, the product and reactant sides are swapped. Default: false. Should be called before calling setReactants(Molecule[]).
    
    Parameters:
    
    reverse - is true if reversed reaction
  - isReverse
```
public boolean isReverse()
```
    Returns true if the reaction is to be processed in reversed direction.
    
    Returns:
    
    whether the reaction is to be processed in reversed direction
  - setSearchOptions
```
public void setSearchOptions(java.lang.String searchOptions)
```
    Modifies the default search options used by the Reactor engine. Only the specified search options will be modified, others will remain default. Note: modifying the default search options is required in very special cases only. Do not modify the search options, unless you are absolutely aware what you are doing!
    
    Parameters:
    
    searchOptions - is the search options string
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    SearchOptions.setOptions(String)
  - setGenerateMinorProducts
```
public void setGenerateMinorProducts(boolean generateMinorProducts)
```
    If set then products lists are not filtered out by the selectivity rule, but they are tagged as minor products. The added SDF property (tag) in minor products is named MINOR_PRODUCT_TAG, its value is "true". In case of product output the generated products are tagged, in case of reaction output the output reaction is tagged. The option has no effect in fused reaction output mode.
    For internal use only.
    
    Parameters:
    
    generateMinorProducts - if true then minor products are generated
    
    Since:
    
    JChem 5.10
  - isGenerateMinorProducts
```
public boolean isGenerateMinorProducts()
```
    Returns true if minor products are generated.
    
    Returns:
    
    true if minor products are generated
    
    Since:
    
    JChem 5.10
    
    See Also:
    
    setGenerateMinorProducts(boolean)
  - setReactionIDPropertyName
```
public void setReactionIDPropertyName(java.lang.String reactionIDProp)
```
    Sets the reaction ID property (RDF/MRV tag) name.
    
    Parameters:
    
    reactionIDProp - is the reaction ID property name
    
    Since:
    
    JChem 3.1.6
  - getReactionIDPropertyName
```
public java.lang.String getReactionIDPropertyName()
```
    Returns the reaction ID property (RDF/MRV tag) name.
    
    Returns:
    
    the reaction ID property (RDF/MRV tag) name
    
    Since:
    
    JChem 5.5
  - setComponentIDPropertyNames
```
public void setComponentIDPropertyNames(java.lang.String reactantIDProp,
                                        java.lang.String productIDProp)
```
    Sets reactant/product ID property (SDF/MRV tag) names.
    
    Parameters:
    
    reactantIDProp - is the reactant ID property name
    
    productIDProp - is the product ID property name
    
    Since:
    
    JChem 3.1.6
  - setComponentIDPropertyNames
```
public void setComponentIDPropertyNames(java.lang.String[] reactantIDProps,
                                        java.lang.String[] productIDProps)
```
    Sets reactant/product ID property (SDF/MRV tag) names.
    
    Parameters:
    
    reactantIDProps - is the reactant ID property name array
    
    productIDProps - is the product ID property name array
    
    Since:
    
    JChem 3.1.6
  - setCopyAllReactantProperties
```
public void setCopyAllReactantProperties(boolean c)
```
    Sets to copy all reactant properties to output products/reactions.
    
    Parameters:
    
    c - if true then all properties will be copied
    
    Since:
    
    JChem 5.5
  - setCopyReactantProperties
```
public void setCopyReactantProperties(java.lang.String[][] reactantPropertiesToCopy)
```
    Sets the reactant properties which should be copied to output products/reactions.
    - reactantPropertiesToCopy[i][j]: the j-th property name of the i-th reactant
    Parameters:
    
    reactantPropertiesToCopy - the properties to be copied
    
    Since:
    
    JChem 5.5
  - setCopyReactantProperties
```
public void setCopyReactantProperties(java.util.Map<java.lang.String,java.lang.String> patternBasedProperties)
```
    Sets the reactant properties which should created in output products/reactions, based on a pattern. Contains
    pairs, where the property pattern is an instance of ((*#{.})+)* where
    
    text may contain any string except "#{" and ".." tokens
    
    moleculeID is a string that has a numeric postfix optionally:
    
    Non-numeric postfix: The reaction is the selected molecule
    
    Numeric postfix: index of a reactant (indexing starts from 1)
    
    propertyID a property of the molecule identified by the moleculeID (Case sensitive)
    
    Examples of pattern:
    
    Name list: #{R1.NAME}, #{R2.NAME}, #{R3.NAME}
    
    LogP values of reactants: 1st: #{reactant1.LOGP}, 2nd: #{reactant2.LOGP}
    
    #{Reaction.ID}(#{mol1.ID}, #{mol2.ID}, #{mol3.ID})
    
    #{Reaction.ID}(#{R1.corp_ID}, #{R2.NAME}, #{R3.corp_ID}, #{R4.ID})
    Parameters:
    
    patternBasedProperties - pairs
    
    Since:
    
    JChem 5.7
  - setCopyReactantProperties
```
public void setCopyReactantProperties(java.lang.String[][] sourceProperties,
                                      java.lang.String[][] targetProperties)
```
    Sets the reactant properties which should be copied to output products/reactions.
    - sourceProperties[i][j]: the j-th property name of the i-th reactant
    - targetProperties[i][j]: the j-th property name of the i-th product
    Parameters:
    
    sourceProperties - the properties to be copied
    
    targetProperties - the target properties
    
    Since:
    
    JChem 5.5
  - setRatio
```
public void setRatio(int[] ratio)
```
    Sets the ratio of the reactants. The length of the ratio array should be equal with the number of reactants in the reaction. If there are more than one reactants in the reaction, then one of the reactant ratios should be 1.
    Setting the ratio restarts processing of the current reactant set - next call to react() will return the first product set.
    
    Parameters:
    
    ratio - is the ratio array
    
    Since:
    
    JChem 5.3
  - setReaction
```
public void setReaction(Molecule rxmol)
                 throws ReactionException
```
    Sets the reaction with reaction rules set in RDF/MRV tags REACTIVITY, EXCLUDE, SELECTIVITY, TOLERANCE. Also sets the reactant standardizer defined in the STANDARDIZATION RDF/MRV tag.
    
    Parameters:
    
    rxmol - is the reaction molecule
    
    Throws:
    
    ReactionException - on error
    
    Since:
    
    JChem 2.3
    
    See Also:
    
    setIgnoreReactionDefinedStandardizer(boolean)
  - setReaction
```
public void setReaction(Molecule rxmol,
                        java.lang.String rid)
                 throws ReactionException
```
    Sets the reaction with reaction rules set in RDF/MRV tags REACTIVITY, EXCLUDE, SELECTIVITY, TOLERANCE. Also sets the reactant standardizer defined in the STANDARDIZATION RDF/MRV tag.
    
    Parameters:
    
    rxmol - is the reaction molecule
    
    rid - is the reaction ID
    
    Throws:
    
    ReactionException - on error
    
    Since:
    
    JChem 5.3
    
    See Also:
    
    setIgnoreReactionDefinedStandardizer(boolean)
  - setReaction
```
public void setReaction(Molecule rxmol,
                        java.lang.String rid,
                        java.lang.String reactivity,
                        java.lang.String selectivity,
                        java.lang.String tolerances)
                 throws ReactionException
```
    Sets the reaction and the reaction rules. Rules can be set to null which means that the rule is not set. Selectivity tolerance is set to the default value: DEF_TOLERANCE if not specified in the Tolerance property. Also sets the reactant standardizer defined in the STANDARDIZATION RDF/MRV tag of the reaction molecule.
    
    Parameters:
    
    rxmol - is the reaction molecule
    
    rid - is the reaction ID
    
    reactivity - is the reactivity rule
    
    selectivity - is the selectivity rule
    
    tolerances - is the tolerance string
    
    Throws:
    
    ReactionException - on error
    
    Since:
    
    JChem 3.1.6
    
    See Also:
    
    setIgnoreReactionDefinedStandardizer(boolean)
  - setReaction
```
public void setReaction(Molecule rxmol,
                        java.lang.String rid,
                        java.lang.String reactivity,
                        java.lang.String selectivity,
                        double[] tolerances)
                 throws ReactionException
```
    Sets the reaction and the reaction rules. Rules can be set to null which means that the rule is not set. Also sets the reactant standardizer defined in the STANDARDIZATION RDF/MRV tag of the reaction molecule.
    
    Parameters:
    
    rxmol - is the reaction molecule
    
    rid - is the reaction ID
    
    reactivity - is the reactivity rule
    
    selectivity - is the selectivity rule
    
    tolerances - is the selectivity tolerance array (one for each selectivity rule, null for taking the default tolerance DEF_TOLERANCE for each rule)
    
    Throws:
    
    ReactionException - on error
    
    Since:
    
    JChem 3.1.6
    
    See Also:
    
    setIgnoreReactionDefinedStandardizer(boolean)
  - getReaction
```
public RxnMolecule getReaction()
```
    Returns the reaction. The returned reaction is the reaction used internally for reaction processing, it can be different from the input reaction (different reaction maps, R-groups, etc).
    
    Returns:
    
    the reaction
    
    Since:
    
    JChem 5.5
  - setReactionString
```
public void setReactionString(java.lang.String str)
                       throws ReactionException
```
    Sets the reaction and optionally the reaction rules specified in a string. The reaction is specified in reaction SMARTS format, the reaction rules are preceded by a prefix denoting the rule type:
    - r: denotes the reactivity rule
    - s: denotes the selectivity rule(s) separated by ";"
    - t: denotes the selectivity tolerance(s) separated by ";"
    In the simplest case the string is the reaction SMARTS string itself and no reaction rules are specified. Example:
```
 [Cl:4][C:3]=O.[#7:2][H:1]>>[#7:2][C:3]=O.[Cl:4][H:1]
 
```
    Rules can be added with the type prefixes described above, items separated by "..". Example:
```
 [Cl:4][C:3]=O.[#7:2][H:1]>>[#7:2][C:3]=O.[Cl:4][H:1]..r:charge(ratom(4)) > 1.2..s:tpsa(product(0))..t:0.5
 
```
    Parameters:
    
    str - is the reaction configuration string described above
    
    Throws:
    
    ReactionException - on configuration error
    
    Since:
    
    JChem 2.3
  - setReactionString
```
public void setReactionString(java.lang.String str,
                              java.lang.String rid)
                       throws ReactionException
```
    Sets the reaction and optionally the reaction rules specified in a string. The reaction is specified in reaction SMARTS format, the reaction rules are preceded by a prefix denoting the rule type:
    - r: denotes the reactivity rule
    - s: denotes the selectivity rule(s) separated by ";"
    - t: denotes the selectivity tolerance(s) separated by ";"
    In the simplest case the string is the reaction SMARTS string itself and no reaction rules are specified. Example:
```
 [Cl:4][C:3]=O.[#7:2][H:1]>>[#7:2][C:3]=O.[Cl:4][H:1]
 
```
    Rules can be added with the type prefixes described above, items separated by "..". Example:
```
 [Cl:4][C:3]=O.[#7:2][H:1]>>[#7:2][C:3]=O.[Cl:4][H:1]..r:charge(ratom(4)) > 1.2..s:tpsa(product(0))..t:0.5
 
```
    Parameters:
    
    str - is the reaction configuration string described above
    
    rid - is the reaction ID
    
    Throws:
    
    ReactionException - on configuration error
    
    Since:
    
    JChem 3.1.6
  - getReactantCount
```
public int getReactantCount()
```
    Returns the number of reactants.
    
    Returns:
    
    the number of reactants
  - getProductCount
```
public int getProductCount()
```
    Returns the number of products.
    
    Returns:
    
    the number of products
  - getReactionReactant
```
public Molecule getReactionReactant(int i)
```
    Returns a reaction reactant.
    
    Parameters:
    
    i - is the reactant index
    
    Returns:
    
    a reaction reactant
    
    Since:
    
    JChem 3.1
  - getReactionProduct
```
public Molecule getReactionProduct(int i)
```
    Returns a reaction product.
    
    Parameters:
    
    i - is the reactant index
    
    Returns:
    
    a reaction product
    
    Since:
    
    JChem 3.1
  - getReactants
```
public Molecule[] getReactants()
```
    Returns the input reactants.
    
    Returns:
    
    the input reactants
    
    Since:
    
    JChem 5.5
  - restart
```
public void restart()
```
    Restarts the reactor: the following call to react() will return the first product set.
  - setReactants
```
public void setReactants(Molecule[] mols)
                  throws ReactionException
```
    Sets the reactants. The reaction should be set before calling this method.
    
    Parameters:
    
    mols - is the reactant array
    
    Throws:
    
    ReactionException - if setting the reactants fails
  - react
```
public Molecule[] react()
                 throws ReactionException
```
    Performs the reaction. Returns the next product list, or null if there are no more product lists. Product lists are ordered according to priority if a selectivity rule is specified.
    In single mode, returns only single results, that is, returns null if here are more than one product lists (see setSingle(boolean)).
    The reaction should be set beforehand.
    The reactants should be set beforehand by setReactants(Molecule[]).
    
    Returns:
    
    the next product list, or null if there are no more product lists
    
    Throws:
    
    ReactionException - on reaction processing error
  - isLicensed
```
public boolean isLicensed()
```
    Specified by:
    
    isLicensed in interface chemaxon.license.Licensable
  - getReactionMap
```
public java.util.Map<MolAtom,AtomIdentifier> getReactionMap()
```
    Gets the mapping for the last performed reaction. For each atoms of the output molecules, that has a map in the input molecules' atoms there is an entry in this map.
    For each entry atom the is an AtomIdentifier containing information on the:
    - origin molecule AtomIdentifier.getMoleculeIndex(), meaninig the index of the molecule in the provided reactans
    - origin atom AtomIdentifier.getAtomIndex(), meaninig the index of atom in the origin molecule
    - reaction schema mapping AtomIdentifier.getReactionSchemaMap() , meaninig the map identifier of atom in the reaction map
    The map is filled when the ReactionPerformer.react() method is called.
    NOTE: If the map does not contain an atom of the result as key, the atom is added to the result during the reaction process
    Returns:
    
    the mapping for the last performed reaction
    
    Since:
    
    5.11

Class Reactor

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

PRODUCT_OUTPUT

REACTION_OUTPUT

FUSED_REACTION_OUTPUT

NO_DUPLICATE_FILTERING

ORDER_SENSITIVE_DUPLICATE_FILTERING

ORDER_INSENSITIVE_DUPLICATE_FILTERING

MAPPING_STYLE_NONE

MAPPING_STYLE_CHANGING

MAPPING_STYLE_COMPLETE

MAPPING_STYLE_MATCHING

IGNORE_REACTIVITY

IGNORE_SELECTIVITY

IGNORE_TOLERANCE

DEF_TOLERANCE

MINOR_PRODUCT_TAG

Constructor Detail

Reactor

Method Detail

setLicenseEnvironment

getReactionID

setIgnoreRules

setSingle

isSingle

setShowUnsuccessfulReactions

setDuplicateFiltering

setMaxNumberOfProductSets

setProductIndexes

setResultType

setOutputReactionMappingStyle

setReactionCenterMarkEnabled

setStandardizer

getStandardizer

setIgnoreReactionDefinedStandardizer

setReverse

isReverse

setSearchOptions

setGenerateMinorProducts

isGenerateMinorProducts

setReactionIDPropertyName

getReactionIDPropertyName

setComponentIDPropertyNames

setComponentIDPropertyNames

setCopyAllReactantProperties

setCopyReactantProperties

setCopyReactantProperties

setCopyReactantProperties

setRatio

setReaction

setReaction

setReaction

setReaction

getReaction

setReactionString

setReactionString

getReactantCount

getProductCount

getReactionReactant

getReactionProduct

getReactants

restart

setReactants

react

isLicensed

getReactionMap