RDKit Molecule to SVG

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


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.

Input Ports

Table with an RDKit Molecules.

Output Ports

The input table with an additional column that shows the SVG molecule graphic.


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