RDKit Molecule to SVG

Creates an SVG column showing a molecule A molecule column needs to be provided.

Options

RDKit Mol column

The input column with RDKit Molecules.

New column name

The name of the new column which will contain the SVG.

Remove source column

Set to true to remove the specified source column from the result table.

Drawing Options

Prepare before drawing

Perform a number of cleanup operations on the molecule before drawing it. The operations performed are:

1. Kekulization
2. Adding chiral Hs
3. Generating 2D coordinates (if necessary)
4. Wedging bonds around chiral centers
5. Adding wavy bonds around chiral centers which have been marked as unspecified

Center before drawing

Centers the molecule at the origin before drawing

Clear background

Clears the background with the current background color before drawing

Add atom indices

Includes atom indices in the drawing

Add bond indices

Includes bond indices in the drawing

Add stereo annotations

Adds R/S labels and enhanced stereo annotations to the drawing

Include chiral flag

Adds the chiral flag if set on the molecule

Use simplified stereo groups

Simplifies the drawing of molecules where all specified chiral centers are in one stereo group.

Single color wedge bonds

Draws wedge bonds as single color

Draw explicit methyl groups

Draws terminal methyl groups as CH3

Dummies are attachment points

Draws dummies as attachment points - wavy lines perpendicular to the bond

Draw radicals

Draws radical dots

No atom labels

If set, no atom labels will be drawn

Include isotope labels

Includes information about isotopes

Include isotope labels on dummies

Includes information about isotopes on dummy atoms

Comic mode

Activates "comic mode" - this simulates hand-drawn structures

Black&White mode

Activates black and white mode. No atom/bond coloring is used

Line width for bonds

The line width to be used when drawing bonds

Min font size

The minimum font size

Max font size

The maximum font size

Annotation font scale

The annotation font size is set as a fraction of the symbol font size. This determines that fraction.

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Workflows

• 01_Chemistry_basicsKNIME Hub
• 01_Chemistry_basicsKNIME Hub
• 01_Chemistry_basicsKNIME Hub
• 01_Chemistry_basicsKNIME Hub
• 01_Chemistry_basicsKNIME Hub
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