Creating a reaction molecule programatically

I have 2 Molecule objects that I want to use to for the left and right hand side of a reaction.


How can I programatically create a new Molecule object from these 2 Molecules so that the new Molecule is the reaction?





Thanks





Tim

Basically you should create an RxnMolecule and then add structures by addStructure(Molecule, int). This method will be renamed to addComponent(Molecule, int) in Marvin 4.1.





I attach some sample code with the new method name. It produces 2D output in MRV and therefore performs full clean if the reactant / product are in 0D while arranges components with the help of CleanUtil if reactant / product are in 2D (will be in the API in Marvin 4.1 - if you have an earlier version then just run full clean in all cases).





R-groups are not handles in the example, that is more complicated but I can also send some sample code if you need that (e.g. merge R-group defs from reactant / product into the reaction).





Example runs in 0D and 2D:

Code:

java RxnmolTest reactant.smiles product.smiles java RxnmolTest reactant.mrv product.mrv