Generating SVG Pictures with Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Generating SVG Pictures with Open Babel

This chapter provides introductions and tutorial examples on Open Babel 'obabel -o svg' command to generate molecule structure images in SVG format. Topics include '-xi', '-xS', '-xX' and '-xC' options to control elements on the output SVG images; '-xPnnn' to control image size.

"obabel -o svg" - Molecule Picture in SVG

"obabel -:... -o svg" - Generate SVG from SMILES

"obabel ... -o svg -xi" - Show Atom Indices in SVG

"obabel ... -o svg -xS" - Ball/Stick Depiction in SVG

"obabel ... -o svg -xX" - Hide Implicit H in SVG

"obabel ... -o svg -xC" - Hide Terminal C in SVG

"obabel ... -o svg -xP300" - Control Image Size

"obabel ... -o svg" - Two "svg" XML Tag Levels

"obabel ... -o svg -xd" - Hide Molecule Name

"babel ... -o svg -xd -xP300" - Open Babel 2.4 Bug

Scale SVG Images using "viewBox" Attribute

Takeaways:

Open Babel "obabel ... -o svg" command generates molecule structure in SVG format.
"obabel ... -o svg -xi" command displays atom indeces in molecule SVG image.
"obabel ... -o svg -xS" command displays molecule in ball and stick style in molecule SVG image.
"obabel ... -o svg -xX" command removes implicit hydrogen symbols in molecule SVG image.
"obabel ... -o svg -xC" command removes terminal carbon symbols in molecule SVG image.
"obabel ... -o svg -xPnnn" command specifies the size of molecule SVG image.
Open Babel generate molecule SVG images using two levels of <svg ...> tags to be able to include multiple molecules.