The input JSON

Key	JSON data type	Value	Feature types	Applicable
config	object	The user’s stored configuration of the plugin	All	user-config is specified
cjson	object	The current CJSON file in full	All except file-formats	input-cjson = true or input-format = "cjson"
xyz, cml, pdb, cif, sdf, mdl, mol, etc.	string	The contents of a file in the respective format	All except file-formats	input-format = <fmt>
file	string	A path to a file in the filesystem	file-formats	Always
options	object	Key/value pairs for each option requested in user-options	menu-commands, input-generators	Always
points	array of number	The coordinates of the requested points	electrostatic-models	Called with --potentials
selectedAtoms	array of number	The indices of the atoms that are currently selected	menu-commands	Always

The output JSON

Key	JSON data type	Value	Feature types	Applicable
message	string	A message to display to the user in a pop-up dialog	All	Always
error	string	Similar, but displays an error, and the plugin is stopped	All	Always
config	object	The user’s configuration of the plugin as it should be saved	All	user-config is specified
cjson	object	A CJSON file to be loaded	All?	output-format = "cjson"
xyz, cml, pdb, cif, sdf, mdl, mol, etc.	string	The contents of a file in the respective format	All?	output-format = <fmt>
charges	array of number	The partial charges on each atom	electrostatic-models	Called with --charges
potentials	array of number	The electrostatic potential at each requested point	electrostatic-models	Called with --potentials
bond	bool	Whether Avogadro should run automatic bond perception	menu-commands	Always
selectedAtoms	array of number	The indices of the atoms that Avogadro should select	menu-commands	Always
warnings	array of string	Non-fatal warnings to be shown in the generator’s dialog	input-generators	Always
generatedFiles	object	Details of several files	input-generators	Always
mainFile	string	The primary input file for a calculation	input-generators	Always