Class Reaction

Add a new Molecule in the catalysts.

Add a new Molecule in the catalysts at index.

Add a new Molecule in the products.

Add a new Molecule in the products at index.

Add a new Molecule in the reactants.

Add a new Molecule in the reactants at index.

Empty the Reaction.

Returns a new copy of the Reaction.

Returns the average bond length among reactants and products.

Returns the catalyst Molecule at index.

Returns the number of catalysts.

Merges all reactants into one Molecule and all products into another and creates a new Reaction object from those.

Returns the reactant or product at index (starting with reactants).

Returns the total number of reactants and products.

Returns the name of the Reaction.

Returns the product Molecule at index.

Returns the number of products.

Returns the reactant Molecule at index.

Returns the number of reactants.

This method determines the largest mapping number in use (maxMapNo), creates a boolean array[maxMapNo+1], and within this array flags every mapping number that refers to atoms, which change bonds in the course of the reaction. Mapped atoms that are connected to unpammed atoms are also considered being part of the reaction center. If the reaction is unmapped or has no reactants or products, then null is returned.

Returns whether the reaction is empty.

Returns whether the Reaction is a fragment.

Returns whether all non-hydrogen atoms are mapped and whether every reactant atom has exactly one assigned product atom.

Returns whether the molecules` atom coordinate bounds touch or overlap.

Remove all catalysts from the Reaction.

Mark the Reaction as isFragment.

Sets the name of the Reaction.

Serialize the Reaction to a MDL V2000 Reaction file.

Serialize the Reaction to a MDL V3000 Reaction file.

Serialize the Reaction to a reaction SMILES string.

Removes mapping numbers that are only used on one side of the reaction. Throws an exception if duplicate mapping numbers occur in reactants or products.

Create a new empty Reaction.

Create a new Reaction filled with the provided molecules.

Create a new Reaction based on a MDL Reaction file (V2000 or V3000).

Create a new Reaction based on a reaction SMILES string. The Reaction will contain at most one Molecule for each component.