Package chemaxon.reaction

Class Reactor

  • All Implemented Interfaces:
    chemaxon.license.Licensable
    @PublicAPI
public class Reactor
extends Object
implements chemaxon.license.Licensable
    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
    See Also:
    ConcurrentReactorProcessor

    • 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

    • Constructor Detail

      • Reactor

        public Reactor()
        Default constructor.

    • Method Detail

      • setLicenseEnvironment

        public void setLicenseEnvironment​(String env)
        For internal use only.
        Specified by:
        setLicenseEnvironment in interface chemaxon.license.Licensable
        Parameters:
        env - the license environment

      • getReactionID

        public String getReactionID()
        Returns the reaction ID. For internal use only.
        Returns:
        the reaction ID
        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)

      • 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

      • 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:

        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​(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​(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 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​(String reactantIDProp,
                                        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​(String[] reactantIDProps,
                                        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​(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​(Map<String,​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​(String[][] sourceProperties,
                                      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,
                        String rid,
                        String reactivity,
                        String selectivity,
                        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,
                        String rid,
                        String reactivity,
                        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​(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​(String str,
                              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 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: The map is filled when the ReactionResultEnumerator.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