Ingredient properties

Default Ingredient

Property name (old schema)	Property name (new schema)	Description	New Location
color		[r, g, b]
coordsystem	coordinate_system	'left' or 'right' depending on generating software	Moved to representations.mesh.coordinate_system
cutoff_boundary
cutoff_surface
distExpression	distance_expression	Used to calculate weights as a function of distance. overwrite_distFunc is always true so this does not get used
distFunction	distance_function	Used to calculate weights as a function of distance. overwrite_distFunc is always true so this does not get used
encapsulatingRadius	removed from input props, calculated instead	radius of the smallest sphere that completely encapsulates the ingredient
excluded_partners_name	excluded_names
force_random
gradient
isAttractor	is_attractor
jitterMax	max_jitter	vector with maximum jitter distance in units of grid spacing
meshFile	path (should just be the file path)		Moved to representations.mesh.path
meshName	name		Moved to representations.mesh.name (should be the file name)
meshObject	removed
meshType	removed		representations.mesh.format is the equivalent but we get it from the file extension
molarity			moved to "composition" info
name	Removed from recipes, the key is the name
nbJitter	jitter_attempts	number of jitter attempts
nbMol	count	discrete number of entities, overrides molarity (?)	moved to "composition" info
offset
orientBiasRotRangeMax	changed to an array orient_bias_range[1]	maximum of the rotation range for orientation bias
orientBiasRotRangeMin	changed to an array orient_bias_range[0]	minimum of the rotation range for orientation bias
overwrite_distFunc	overwrite_distance_function
packing	Old attribute, replaced with packing_mode
packingMode	packing_mode
packingPriority	priority		moved to "composition" info
++ partners	Class Partners, see below
partners_name	name		moved to partners.names
partners_position	position		moved to partners.position
partners_weight	weight		moved to partners.weight
pdb	id		Moved to representations.atomic.id
perturbAxisAmplitude	perturb_axis_amplitude
placeType	place_type
position	Moved to specific subtypes	Need disambiguation between position, positions, positions2
positions	Moved to specific subtypes	Need disambiguation between position, positions, positions2
positions2	Moved to specific subtypes	Need disambiguation between position, positions, positions2
principalVector	principal_vector
proba_binding	probability_binding		moved to partners.probability_binding
proba_not_binding	probability_repelled		moved to partners.probability_repelled
properties	Removed
radii	Removed for general, only in multi_sphere and multi cylindar representations	Need disambiguation between radii, radius
radius	Moved to specific subtypes (single sphere and single cylinder)	Need disambiguation between radii, radius
rejectionThreshold	rejection_threshold
++ representations
resolution_dictionary
rotAxis	rotation_axis
rotRange	rotation_range
source			moved to representations.atomic.translate
sphereFile		url to sphere file	moved to representations.packing.file
Type	type
useOrientBias		should be removed (?)
useRotAxis	use_rotation_axis
weight

            "partners": {
                "names": [],
                "probability_binding": 0.5,
                "positions": [], // what is this used for? is it a relative position?
                "excluded_names": [],
                "probability_repelled": 0.5,
                "weight": 0.2,
            },

            "representations": {
                "mesh": {
                    "path": "",
                    "name": "",
                    "format": "",
                    "coordinate_system": "left"
                },
                "atomic": {
                    "id": "1hbv",
                    "format": "pdb",
                    "transform": { // optional 
                        "center": true,
                        "translate": [
                            55.3107,
                            -0.0190,
                            -50.2087
                        ]
                    }
                },
                // OR 
                "atomic": {
                    "path": "",
                    "name": "",
                    "format": "",
                },
                "packing": {
                    "path": "autoPACKserver/collisionTrees/",
                    "name": "HIV1_VPU_Hyb_0_1_0.sph",
                    "format": "sph",
                }
                // OR 
                "packing": {
                    "radii": [],
                    "positions": []
                }
            },

single_sphere

required attributes: radius: number

Property name (old schema)	Property name (new schema)	Description

Sphere Tree

Property name (old schema)	Property name (new schema)	Description

Grow/Cylinder

Property name (old schema)	Property name (new schema)	Description

Cube

required attributes: bounds: [[number, number, number], [number, number, number]]

Property name (old schema)	Property name (new schema)	Description