Multiple reactants

These examples demonstrate reaction processing on multiple reactants: a molecule file with possibly more than one molecule structures is specified in place of each reaction reactant. Reactor can process multiple reactants in two modes, sequential or combinatorial (default: sequential). In the examples below, the first reactant file reactant1.smiles contains 2 molecules and the second reactant file reactant2.smiles contains 3 molecules.

1. Process the reaction in sequential mode(default) with reaction output type:

   react -r reaction.rxn reactant1.smiles reactant2.smiles -t reaction

   The result is:

   ClC(=O)N1C2=CC=CC=C2C=CC3=C1C=CC=C3.CCC1=CC=C(O)C=C1>>CCC1=CC=C(OC(=O)N2C3=CC=CC=C3C=CC4=C2C=CC=C4)C=C1.Cl
   
   CCC1=CC=C(CC(Cl)=O)C=C1.CCCO>>CCCOC(=O)CC1=CC=C(CC)C=C1.Cl
   
   CCC1=CC=C(CC(Cl)=O)C=C1.OC1CCCCC1>>CCC1=CC=C(CC(=O)OC2CCCCC2)C=C1.Cl

   Note, that the last (second) molecule in the first reactant file reactant1.smiles is repeatedly paired with both the second and the third molecule in the second reactant file reactant2.smilessince the first reactant file contains less molecules than the second reactant file.

2. Process the reaction in combinatorial modewith reaction output type:

   react -r reaction.rxn reactant1.smiles reactant2.smiles -m comb -t reaction

   The result is:

   ClC(=O)N1C2=CC=CC=C2C=CC3=C1C=CC=C3.CCC1=CC=C(O)C=C1>>CCC1=CC=C(OC(=O)N2C3=CC=CC=C3C=CC4=C2C=CC=C4)C=C1.Cl
   
   ClC(=O)N1C2=CC=CC=C2C=CC3=C1C=CC=C3.CCCO>>CCCOC(=O)N1C2=CC=CC=C2C=CC3=C1C=CC=C3.Cl
   
   ClC(=O)N1C2=CC=CC=C2C=CC3=C1C=CC=C3.OC1CCCCC1>>O=C(OC1CCCCC1)N2C3=CC=CC=C3C=CC4=C2C=CC=C4.Cl
   
   CCC1=CC=C(CC(Cl)=O)C=C1.CCC1=CC=C(O)C=C1>>CCC1=CC=C(CC(=O)OC2=CC=C(CC)C=C2)C=C1.Cl
   
   CCC1=CC=C(CC(Cl)=O)C=C1.CCCO>>CCCOC(=O)CC1=CC=C(CC)C=C1.Cl
   
   CCC1=CC=C(CC(Cl)=O)C=C1.OC1CCCCC1>>CCC1=CC=C(CC(=O)OC2CCCCC2)C=C1.Cl

   Note, that there are 2*3=6 reactions, since all reactant pairs are processed with the first reactant taken from reactant1.smiles and the second from reactant2.smiles.

The use and meaning of command-line options in the above commands: