J. Cheminf. 2011, 3, 33

Table Of Contents

Previous topic

Image formats

Next topic

PNG2 format (png2)

This Page

PNG 2D depiction (png)

2D depiction of a single molecule, or add/extract a chemical structure from a .png file

The PNG format has several uses. The most common is to generate a .png file for a single structure (which may contain several disconnected components). 2D coordinates are generated if not present:

obabel mymol.smi -O image.png

Chemical structure data can be embedded in the .png file (in a tEXt chunk):

obabel mymol.mol -O image.png -xO molfile

The parameter of the -xO option specifies the format (“file”can be added). Note that if you intend to embed a 2D or 3D format, you may have to call --gen2d or --gen3d to generate the required coordinates if they are not present in the input.

Molecules can also be embedded in an existing PNG file:

obabel existing.png mymol1.smi mymol2.mol -O augmented.png -xO mol

Reading from a PNG file will extract any embedded chemical structure data:

obabel augmented.png -O contents.sdf

Read Options

y <additional chunk ID>
 Look also in chunks with specified ID

Write Options

p <pixels> image size, default 300
O <format ID>

Format of embedded text

For example, molfile or smi.

y <additional chunk ID>
 Write to a chunk with specified ID