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Aligning molecule orientation

Life Sciences Molecules Orientation Cheminformatics

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This workflow demonstrates how to align molecules according to a substructure, so they are all shown in the same orientation (in this example accoring to the carbocylic acid). The bit of the molecules according to which they should be aligned is drawn in the sketcher component. The resulting SMARTS is used in the RDKit Generate Coords node to change the 2D coordinates of the atoms (set the rendering to SDF by right-clicking on the column header and check the changed coordinates). Required extension: RDKit

Used extensions & nodes

Created with KNIME Analytics Platform version 4.4.0
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    KNIME Base Chemistry Types & Nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

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    KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

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    KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

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    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

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    RDKit Nodes Feature Trusted extension

    NIBR

    Version 4.3.0

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