RDKit MCS

This node is used to find the Maximum Common Substructure (MCS) of a set of compounds using the RDKit MCS code. Such a calculation can be a long running process. Therefore, a timeout must be specified as part of the options. The MCS of an empty list of molecules is undefined and results in empty result cells. The MCS of a single molecule is the molecule itself (as SMARTS value). All other MCS calculations are based on the specified parameters.

Options

RDKit molecule column

Select here the RDKit Molecule column to be used as input.

Threshold

Fraction of molecules that the MCS must cover. Defaults to 1.0. 0.0 < threshold ≤ 1.0.

Ring matches ring only

Determines whether ring bonds only match other ring bonds. Default is unchecked.

Complete rings only

Determines whether only complete rings are included in the MCS. Default is unchecked.

Match valences

Determines whether atom valences are used in the comparison. Default is unchecked.

Atom comparison

Specify here how atoms shall be compared: Compare Any, Compare Elements, Compare Isotopes.

Bond comparison

Specify here how bonds shall be compared: Compare Any, Compare Order, Compare Exact Order.

Timeout (in seconds)

Specify here how long the MCS calculation shall run at a maximum. Default is 300 seconds. There is currently no way to interrupt a long-running MCS calculation. Even if you cancel an executing node the calculation will continue in the background and will occupy system resources until it is either done or the specified timeout occurs. Use longer timeouts with care!

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Workflows

• 01_Clustering_and_Interactive_Compound_SelectionKNIME Hub
• 01_R-Group_DecompositionKNIME Hub
• 01_R-Group_Decomposition_embed_imagesKNIME Hub
• 01_R-Group_Decomposition_embed_imagesKNIME Hub
• 02_R_Group_Decomposition_heatmapKNIME Hub
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