Atom type:

This is where you select which atom you would like to create. Selecting one of the options will automatically change the covalence and color so that it matches with the atom (expect for "Custom"). Use "Custom" if it's not on the list and manually select which covalence and color the atom must have.

Bond:

This is where you select which bond type you would like to use. The configuration of the empties will automatically change. If some atoms end up with no empties around them, it means that it is not possible to add this specific bond for that atom.

Create Atom:

With one empty selected, clicking this button will add a new atom where the empty is. The bond in between is decided by "Bond", the color is decided by "Color" and the covalence by "Covalence".

Covalence:

This is where you select how many empties you would like to have around your next atom, but depending on the "Atom type", this option will automatically change.

Color (Color):

This is where you select which color you would like for this specific atom, but depending on the "Atom type", this option will automatically change.

Reset to Default (Color):

This button will reset the color input to the default value for the "Atom type".

Rotation:

This input will effect how much the atom will rotate clock-wise once you click on "Rotate Atom" (in degrees).

Rotate Atom:

With one icosphere selected, that is attached to one other atom, clicking on this button will cause the atom to rotate around its Y-axis, with a value of "Rotation".

Delete Atom:

With one icosphere selected, that is attached to one other atom (expect for cyclic atoms), clicking this button will cause the atom to be deleted.

Delete Everything:

This button will delete the entire molecule you were working on and hopefully fixes any errors.

Amount of Atoms:

This input will effect how many atoms the cyclic compound will contain.

Create Cyclic Compound:

With two icospheres selected, clicking on this button will cause two new empties to be placed on the icospheres. By selecting on of the two empties and by clicking "Create Atom" (like you normally would), the atoms placed will form the ring. The final ring will contain the amount of atoms from "Amount of Atoms".

Note: The two icospheres will form the "base" of the ring and can no longer be deleted with "Delete Atom".

Hydrogen to Empty Slots:

Clicking this button will add hydrogen atoms to all the "empty slots".

Prepare for Animation:

With this option checked, when clicking on "Complete Molecule", the cylinders will split and receive "Shape Keys", so you can easily detach two atoms from one another for animation.

Complete Molecule:

Clicking this button will add a box around the molecule which will be the parent of all the icospheres and cylinders. It also removes any remaining empties. Only once this button is pressed, can a new molecule be created.

Start Frame:

This input refers to when the atom should still be attached to the molecule.

End Frame:

This input refers to when the atom should let go of the molecule.

Frame Step:

This input correlated to how often a key frame should be placed when "Bake to Keyframes" is pressed. (If set to 1, a key frame gets placed every frame, if set to 2, a key frame gets placed every two frames, et cetera.

Bake to Keyframes:

With one icosphere selected, that is part of a completed molecule, this button will make the atom let go of the molecule at frame "End Frame", by baking the animation to key frames.

Icosphere Subdivisions:

This input corresponds to the amount of subdivisions the icospheres have.

Cilinder Vertices:

This input corresponds to the amount of vertices the cylinders have on their bases.

Hydrogen Size:

This input correspond to the sizes of the hydrogen atoms in comparison to the other atoms. (1 is the same size, 0 is no size at all.)

Cilinder Radius:

This input corresponds to the radius of the cylinders.

Cilinder Distance:

This input corresponds to the distance between cylinders for double and triple bonds.

Reset to Default (Display):

This input resets all the values under "Display" to their default values.

Smooth Shading (Icosphere Material):

This input enables/disables smooth shading for the icospheres.

Icosphere Roughness:

This input corresponds to the roughness value that the materials of the icospheres have.

Icosphere Metallic:

This input corresponds to the metallic value that the materials of the icospheres have.

Reset to Default (Icosphere Material):

This input resets all the values under "Icosphere Material" to their default values.

Smooth Shading (Cilinder Material):

This input enables/disables smooth shading for the cylinders.

Color (Cilinder Material):

This input controls the color of the cylinders.

Cilinder Roughness:

This input corresponds to the rougness value that the material of the cylinders has.

Cilinder Metallic:

This input corresponds to the metallic value that the material of the cylinders has.

Reset to Default (Cilinder Material):

This input resets all the values under "Cilinder Material" to their default values.

Version 1.0:

Standard version

Version 1.0.1:

• Changed the name of the "properties", so it won't interfere with other add-ons.
• Works for Blender 3.4.1.
• Slight changes in the code, but the outcome is still the same