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Maximum Common Substructure Search

Finds maximum common substructure among a given set of molecules.

Backend implementation

utilities/canvasMCS
canvasMCS is used to implement this node.

Options

Column containing molecules

Choose the input column.

Column containing titles for smiles

For Smiles input molecules, choose the column that has the molecules' titles.

Minimum number of molecules that must match MCS

Minimum number of molecules that must match the MCS (-min). Default is all. If minMatch exceeds the number of inputs it is perceived as requiring all to match.

Maximum number of molecules that must match MCS

Maximum number of molecules that must match the MCS (-max). Default is all. If maxMatch exceeds the number of inputs it is perceived as requiring all to match. When -max is different than -min, a series of solutions spanning this range is produced.

Stop searching when atom and bond count go below

Stop processing when MCS Atom and Bond Count falls below this threshold.

Mark ring atoms in output SMARTS

In output SMARTS patterns, based on each molecule, marks each atom as cyclic (R) or acyclic (R0).

Restrict compound membership to at most a single MCS group

Limits each input molecule to at most one MCS, the largest.

Atom typing scheme to use

Atom typing scheme. Must be an integer value between 1 and 10 or C

Atom Type Definition File

Atom Type Definition File (only with Custom Atom Type "C")

Output Type

Output Type
Valid types:

CSV (default)

output columns:

    SMILES (input molecule)
    Name
    i_canvas_MCS_Match_Count
    i_canvas_MCS_Size
    i_canvas_MCS_Group
    i_canvas_MCS_Atom_Count
    i_canvas_MCS_Bond_Count
    s_canvas_MCS_SMARTS

Each of these columns contain information about the part of the input molecule that is the maximum common substructure.

Sd
Maestro

Maximum number of molecules to process

Maximum number of molecules to process (default=750). Submitting larger sets may exceed available memory.

Input Ports

: Input can either be Maestro, Smiles, or Sd. If Smiles, then the Title column is selected as well.

Output Ports

: Output can either be CSV, Sd, or Maestro type

Popular Predecessors

Popular Successors

Views

Std output/error of Maximum Common Substructure Search: Std output/error of Maximum Common Substructure Search

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-12-18

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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