Depiction

This node uses the CDK depiction api to render the structure as a PNG or an SVG. A variety of options for formatting are provided as well as the ability to highlight atoms and bonds.

Options

Structure column

The input structure to render, can be any format that is compatible with the CDK adapter cell. When using a format other than a CDK cell you may find the atom numbers update, take this into consideration if highlighting.

Image settings

Configure the settings for the image including rendering size. Although KNIME SVG ignores the height and width it is set in the SVG.

Format

The format of the image: PNG or SVG. SVG images scale better, for improved image quality on PNG increase the size.

Width

The width of the image (ignored for SVG)

Height

The height of the image (ignored for SVG)

Fill to fit?

Whether the render should fill the available canvas. Unlikely to be a reason to uncheck this.

General

With molecule title?

If checked overlays molecule title. Not currently available.

With atom colours?

If checked uses colours atom symbols using typical colours, oxygens are red, nitrogens are blue, etc.

With atom numbers?

If checked overlays atom numbers

With carbon symbols?

If checked renders all carbon symbols.

With terminal carbons?

If checked renders terminal carbons.

Highlights

Highlighting is optional, if a CDK cell is provided the clear existing highlighting option can be used to ensure fresh highlighting

Clear existing highlights?

A CDK cell may already contain highlights, check this option to remove these prior to rendering (and adding new highlights if selected)

Highlight atoms

Check if atoms are to be highlighted

Atom index positions

The index positions to highlight, either provide a single int compatible column or a list of int values. Missing values allowed.

Highlight bonds

Check if bonds are to be highlighted

Bond index positions

The index positions to highlight, either provide a single int compatible column or a list of int values. Missing values allowed.

With out glow?

If selected provides a overlayed highlight surrounding the atom/bond. Otherwise atom/bond is coloured directly.

Outer glow width?

The width for the outer glow overlay/

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Workflows

• EWDD - Workshop_02KNIME Hub

Links

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