bin-start
bin-width
bin-end
output-file
bin-output-file
periodic
elements
position
molecule-by-id
add-atom
domain-position
change-element
rotate-around-origin
save-selected-atoms
translate-atoms
bond-table
element-db
fastparsing
actionname
set-random-number-distribution
random-number-distribution-parameters
set-random-number-engine
random-number-engine-parameters
verbose
fragment-molecule
distance
order
depth-first-search
bond-file
skiplines
offset
change-molname
copy-molecule
fill-void
distances
distance-to-molecule
random-atom-displacement
random-molecule-displacement
distance-to-boundary
DoRotate
fill-molecule
MaxDistance
start-step
interpolation-steps
end-step
id-mapping
load
rotate-around-self
axis
rotate-to-principal-axis-system
save-adjacency
save-bonds
save-selected-molecules
save-temperature
suspend-in-water
verlet-integration
deltat
MDSteps
keep-fixed-CenterOfMass
parse-tremolo-potentials
set-mpqc-parameters
set-output
set-tremolo-atomdata
select-atoms-inside-cuboid
angle-x
angle-y
angle-z
select-atoms-inside-sphere
select-atom-by-element
select-atom-by-id
select-molecules-by-formula
select-molecule-by-id
select-molecules-by-name
select-molecule-by-order
unselect-atoms-inside-cuboid
unselect-atoms-inside-sphere
unselect-atom-by-element
unselect-atom-by-id
unselect-molecules-by-formula
unselect-molecule-by-id
unselect-molecules-by-name
unselect-molecule-by-order
convex-file
nonconvex-file
nonconvex-envelope
add-empty-boundary
center-in-box
change-box
input
output
repeat-box
scale-box
default-molname
set-world-time