Library generation

A program that uses a SMIRKS string or an MDL reaction file to perform reactions on input molecules. The program has a number of flags. OELibraryGen options are: -implicitH, performs the reaction with implicit hydrogens (default false), -relax, ensures unmapped atoms on the reactant side are not deleted during reaction (default false), -valence, applies automatic valence correction (default false). SMILES generation options are: -isomeric, includes atom and bond stereochemistry in the output (default false), -unique, only include unique product canonical SMILES (default false). Input and output options are: -reactants, a molecule file, or files, of reactants, -smirks, a SMIRKS string of the reaction or -rxn, an MDL reaction file of the reaction, and optionally, -product, the output molecule file. The program will output the molecules to stdout as SMILES if no output file is set.


prompt > libgen -smirks '[C:1]c1c([N:2])cccc1>>[C:1]c1cc([N:2])ccc1' -reactants input.smi
prompt > libgen -rxn reaction.rxn -reactants input.smi -product output.smi -valence -isomeric


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See also