Class Reactor
- java.lang.Object
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- com.actelion.research.chem.reaction.Reactor
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public class Reactor extends java.lang.Object
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Constructor Summary
Constructors Constructor Description Reactor(Reaction reaction)
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.Reactor(Reaction reaction, boolean retainCoordinates)
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.Reactor(Reaction reaction, boolean retainCoordinates, boolean fullyMapReactions, int maxProducts, boolean uniqueOnly)
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Reaction[]
getFullyMappedReactions()
After instantiating the Reactor with fullyMappedReaction==true and after supplying real reactants, this method may be used to construct the fully mapped reaction.java.lang.String[][]
getProductIDCodes()
StereoMolecule[][]
getProducts()
void
setReactant(int no, StereoMolecule reactant)
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Constructor Detail
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Reactor
public Reactor(Reaction reaction)
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants. Reactors built with this constructor will not use product atom coordinates from the generic products, nor will they be able to generate fully mapped reactions. They will produce and return all unique products or reactions.- Parameters:
reaction
- generic reactions consisting of reactant substructures with optional query features
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Reactor
public Reactor(Reaction reaction, boolean retainCoordinates)
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants. Reactors built with this constructor will be able to generate fully mapped reactions, They will produce and return all unique products or reactions.- Parameters:
reaction
- generic reactions consisting of reactant substructures with optional query featuresretainCoordinates
- if true, then atom coordinates from the generic products are taken into the real world products
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Reactor
public Reactor(Reaction reaction, boolean retainCoordinates, boolean fullyMapReactions, int maxProducts, boolean uniqueOnly)
Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants. The reactor may or may not use atoms coordinates from the generic products, when generating clean product atom coordinates.- Parameters:
reaction
- generic reactions consisting of reactant substructures with optional query featuresretainCoordinates
- if true, then atom coordinates from the generic products are taken into the real world productsfullyMapReactions
- if true, then real world reactants and products will have valid mapping numbers after product generationmaxProducts
- maximum number of products/reactions to be enumerateduniqueOnly
- whether to skip duplicate products/reactions because of starting material symmetry
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Method Detail
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setReactant
public void setReactant(int no, StereoMolecule reactant)
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getProducts
public StereoMolecule[][] getProducts()
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getProductIDCodes
public java.lang.String[][] getProductIDCodes()
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getFullyMappedReactions
public Reaction[] getFullyMappedReactions()
After instantiating the Reactor with fullyMappedReaction==true and after supplying real reactants, this method may be used to construct the fully mapped reaction. If one or more reactants have multiple matches of their generic reactants, then multiple reactions leading to isomeric products are returned. After calling this method, one or more new real reactants may provided with setReactant() before calling this method again.- Returns:
- array with one or more reactions
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