Structural Frameworks

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.

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