Let's start with the following basic depiction. Note that information on the SVG output options (e.g. -xC) is available in the docs or via "obabel -H svg", and that you can use the mouse to zoom in, etc.
obabel dataset.sdf -O output1.svg -xC
With some magic, we can convert carboxylic acid groups (and anything else listed in the user-editable superatom.txt) into COOH in the depiction. Let's add thick lines too:
obabel dataset.sdf -O output2.svg -xC --genalias -xA -xt
We can also do some fun stuff with descriptors (see "obabel -L descriptors" for a list). Let's sort by molecular weight and replace the title with the molecular formula and molecular weight:
obabel dataset.sdf -O output3.svg -xC --sort MW --title "" --append "formula MW"
You might have noticed that all of the molecules have a substructure in common. Let's highlight some of this in green, and get rid of the other colours:
obabel dataset.sdf -O output4.svg -xC -xu -s "[#6]~2~[#6]NCCN=C~2 green"
And finally, if the molecules are related, it can be useful to align the depictions using a substructure in order to identify similarities and differences (this has been improved in the development version):
obabel dataset.sdf -O output5.svg -xC -xu -s "[#6]~2~[#6]NCCN=C~2 green" --align
What other depiction features would you find useful?