.. _section_example_oechem_libgen: 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. Example -------------------------------------------------------------------------------- .. oe:language:: c++ .. code-block:: console 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 .. oe:language:: python .. code-block:: console prompt > libgen.py -smirks '[C:1]c1c([N:2])cccc1>>[C:1]c1cc([N:2])ccc1' -reactants input.smi prompt > libgen.py -rxn reaction.rxn -reactants input.smi -product output.smi -valence -isomeric .. oe:language:: java .. code-block:: console 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 .. oe:language:: csharp .. code-block:: console 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 Code -------------------------------------------------------------------------------- .. oe:language:: c++ .. only:: oehtml .. admonition:: Download code :download:`libgen.cpp <../../../../sublibs/oechem/examples/libgen.cpp>` .. only:: oepdf .. oe:source:: libgen.cpp :language: c++ .. oe:language:: python .. only:: oehtml .. admonition:: Download code :download:`libgen.py <../../../../wrappers/python/examples/oechem/libgen.py>` .. only:: oepdf .. oe:source:: libgen.py :language: python .. oe:language:: java .. only:: oehtml .. admonition:: Download code :download:`LibGen.java <../../../../wrappers/java/examples/openeye/examples/oechem/LibGen.java>` .. only:: oepdf .. oe:source:: LibGen.java :language: java .. oe:language:: csharp .. only:: oehtml .. admonition:: Download code :download:`LibGen.cs <../../../../wrappers/csharp/Csharp-Examples/OEChem/LibGen.cs>` .. only:: oepdf .. oe:source:: LibGen.cs :language: csharp .. seealso:: * :oe:cls:`OELibraryGen` class * :oe:func:`OEChem::OEParseSmirks` function * :oe:func:`OEReadMDLReactionQueryFile` function