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Structural Frameworks

StreamableChemAxon/Infocom JChem Extensions version 4.3.0.v202000 by Infocom Corporation

The Structural Frameworks Plugin calculates Bemis-Murcko frameworks and other structure-based reduced representations for the input molecule.

Options

Type
  • Bemis-Murcko framework: Bemis-Murcko framework is calculated by removing side chains from the input and generalizing atom/bond types. If Keep single atom for non-empty acyclic structures option is selected, acyclic inputs are not erased completely, but are represented by a single node.
  • Maximum common substructure: calculates MCS for every pairs of input fragments. The input must contain at least two disconnected fragments.
  • Largest ring: returns the largest SSSR ring of the input.
  • All fused ring systems: returns the fused ring systems of the input.
  • Largest fused ring system: returns the largest the fused ring systems of the input.
  • Smallest set of the smallest rings (SSSR): returns the SSSR rings of the input.
  • Complete set of the smallest rings (CSSR): returns the CSSR rings of the input.
  • Only pre/post process, no framework reduction: this option can be used to examine the optional pre- or postprocess functionality. Selecting this option will skip any framework reduction/fragmentation.
Input preprocess
  • Process only the largest fragment of the input structure: if selected then the largest fragment will be processed in the following steps.
  • Prune input the input structure will be generalized by changing all atom types to carbon, all bond types to single and removing all stereo/wedge bond flags.
  • Add explicit hydrogens will invoke hydrogenize on the input.
  • Remove explicit hydrogens will invoke dehydrogenize on the input.
Output postprocess
  • Prune results will generalize the resulting framework after the calculations.
  • Return only the largest fragment of the result will keep only the largest resulting fragment.
  • Remove topologically equivalent output fragments will remove duplicated result fragments.
Structure column
The structure column.

Input Ports

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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains structural frameworks.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install ChemAxon/Infocom JChem Extensions Feature from the following update site:

KNIME 4.3

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