File formats/Chemical Structure
Some formats do not specify the 3D or 2D coordinates of atoms in a molecule, but just the chemical structure, that is a list of atoms and of connections (bonds) between them.
They can be put into text files or be just a text string.
SMILES
JME
This is the native format used by the JME Molecular Editor by Peter Ertl.
Jmol can read this format, both from file or from a text string, and make a flat 2D model out of it; then, using the built-in UFF force field minimization, Jmol generates a 3D model for the molecule, with added hydrogens (the JME format usually does not include hydrogens).
Example, for isopentane:
load inline "5 4 C 7.05 -5.74 C 8.27 -7.84 C 4.63 -7.14 C 5.84 -7.84 C 7.05 -7.14 1 5 1 2 5 1 3 4 1 4 5 1"
or
load isopentane.jme
where 
isopentane.jme is a plain-text file with this content (a single line):
5 4 C 7.05 -5.74 C 8.27 -7.84 C 4.63 -7.14 C 5.84 -7.84 C 7.05 -7.14 1 5 1 2 5 1 3 4 1 4 5 1
By default, Jmol will produce the 3D optimized model. Using the filter "noMin" parameter avoids that and so you will get the model, with atoms adjusted to 3D in preparation for minimization, but without added hydrogens and without the minimization.
Example, for isopentane:
load isopentane.jme filter "noMin"
