Reaction Space Generator

For each reaction a chemical space will be created.


Reaction column
Name of the column that defines your reaction, either in rxn or smirks format. If given as smirks, the column type is required as basic string type.
Name column
Column that provides the reaction name.
Configure CoLibri
The CoLibri plugin allows using labels for functional groups instead of writing long SMARTS terms. These labels you can use in rxn reaction definitions. Second, the CoLibri plugin comes with a set of SMARTS-patterns for protecting groups that should be removed in the final reaction product. Here you may view, edit and extend these lists. They are global settings for all generator and enumerator nodes.
Remove protecting groups
Uncheck this switch to leave the input unmodified, not removing protecting groups as defined in the CoLibri settings (see above). The default is to check for removal.
Molecule column
Name of the column that serves as input for your reagents. The molecule fragments may be given in mol2, sdf or smiles format.
Reagent specifier column
The content in this (optional) integer column is either 1, 2, 3, 4 or empty. If a number is given, the molecule in this row may only be used for the corresponding reagent, otherwise on empty or any other content this molecule will be used for all reagents. If a molecule should be used for multiple but not all reagents, it has to be duplicated in multiple rows each with one of the desired reagent numbers.
If a molecule is specified in this way as described above for one or multiple reagents, but not for all, it may not match for the specified reagents. In this case, and if the statistics option to check unmatched molecules is chosen, this non matching molecule will be listed in the non matching reagents table.
Root output directory
Specify an existing directory, where the chemical spaces will be created.
Statistics and non matching reagents
  • Create full statistics with all matching molecules and open in external editor. The matching molecules won't be displayed in the console.
  • Check for unmatched molecules with specified reagents.
  • Basic matching statistics on console.
  • Basic info. This is much faster than the other options that generate matching statistics!
Statistics will appear in the KNIME console at info level - set level in menu File > Preferences > KNIME > KNIME GUI > Console View Log Level to INFO.
Keep debug files and show the log after the run
This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

Input Ports

Reaction definition: Accepted column types are either rxn or string for smirks.
Reagents: Accepted column types are mol2, sdf or smiles.
Optionally this table may contain a reagent specifier column, see description above for option "reagent specifier column".

Output Ports

Chemical spaces: Paths to the generated chemical spaces. The path is composed by two components:
  1. The reaction name
  2. The node number
Non matching reagents: Input molecules with specified reagents, that don't match in these places.
Please note that this table will only be available if at least the statistics option to check unmatched molecules is chosen.


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