MolViewSpec tree schema v1

This is the exhaustive list of MolViewSpec node kinds, their parameters, and parent-child relationships. Parameters with ?: are optional, i.e. they may be omitted, meaning that the default value should be used. Parameters with : are required, i.e. omitting them will result in an invalid MolViewSpec tree.

This specification is formalized by the OpenAPI JSON schema.

(This document was auto-generated by node lib/commonjs/cli/mvs/mvs-print-schema --markdown in Mol*.)

`root`

[Root of the tree must be of this kind]

Auxiliary node kind that only appears as the tree root.

Parent: none

Params:

`download`

This node instructs to retrieve a data resource.

Parent: root

Params:

url:string

URL of the data resource.

`parse`

This node instructs to parse a data resource.

Parent: download

Params:

format:"mmcif" | "bcif" | "pdb" | "map"

Format of the input data resource.

`structure`

This node instructs to create a structure from a parsed data resource. "Structure" refers to an internal representation of molecular coordinates without any visual representation.

Parent: parse

Params:

type:"model" | "assembly" | "symmetry" | "symmetry_mates"

Type of structure to be created ("model" for original model coordinates, "assembly" for assembly structure, "symmetry" for a set of crystal unit cells based on Miller indices, "symmetry_mates" for a set of asymmetric units within a radius from the original model).

block_header?:string | null

Header of the CIF block to read coordinates from (only applies when the input data are from CIF or BinaryCIF). If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read coordinates from (only applies when the input data are from CIF or BinaryCIF and block_header is null).

Default: 0

model_index?:Integer

0-based index of model in case the input data contain multiple models.

Default: 0

assembly_id?:string | null

Assembly identifier (only applies when kind is "assembly"). If null, the first assembly is selected.

Default: null

radius?:number

Distance (in Angstroms) from the original model in which asymmetric units should be included (only applies when kind is "symmetry_mates").

Default: 5

ijk_min?:[Integer, Integer, Integer]

Miller indices of the bottom-left unit cell to be included (only applies when kind is "symmetry").

Default: [-1, -1, -1]

ijk_max?:[Integer, Integer, Integer]

Miller indices of the top-right unit cell to be included (only applies when kind is "symmetry").

Default: [1, 1, 1]

`transform`

This node instructs to rotate and/or translate structure coordinates.

Parent: structure

Params:

rotation?:Array<number>

Rotation matrix (3x3 matrix flattened in column major format (j*3+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. The default value is the identity matrix (corresponds to no rotation).

Default: [1, 0, 0, 0, 1, 0, 0, 0, 1]

translation?:[number, number, number]

Translation vector, applied to the structure coordinates after rotation. The default value is the zero vector (corresponds to no translation).

Default: [0, 0, 0]

`component`

This node instructs to create a component (i.e. a subset of the parent structure).

Parent: structure

Params:

selector:("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water" | "coarse") | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>>

Defines what part of the parent structure should be included in this component.

`component_from_uri`

This node instructs to create a component defined by an external annotation resource.

Parent: structure

Params:

uri:string

URL of the annotation resource.

format:"cif" | "bcif" | "json"

Format of the annotation resource.

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the component identifier.

Default: "component"

field_values?:Array<string> | null

List of component identifiers (i.e. values in the field given by field_name) which should be included in this component. If null, component identifiers are ignored (all annotation rows are included), and field_name field can be dropped from the annotation.

Default: null

`component_from_source`

This node instructs to create a component defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: structure

Params:

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from. If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from. If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the component identifier.

Default: "component"

field_values?:Array<string> | null

List of component identifiers (i.e. values in the field given by field_name) which should be included in this component. If null, component identifiers are ignored (all annotation rows are included), and field_name field can be dropped from the annotation.

Default: null

`representation`

This node instructs to create a visual representation of a component.

Parent: component or component_from_uri or component_from_source

Params:

type:cartoon | ball_and_stick | spacefill | carbohydrate | surface

Representation type

[This parameter determines the rest of parameters]

Case type: "cartoon":

size_factor?:number

Scales the corresponding visuals.

Default: 1
tubular_helices?:boolean

Simplify corkscrew helices to tubes.

Default: false

Case type: "ball_and_stick":

size_factor?:number

Scales the corresponding visuals.

Default: 1
ignore_hydrogens?:boolean

Controls whether hydrogen atoms are drawn.

Default: false

Case type: "spacefill":

size_factor?:number

Scales the corresponding visuals.

Default: 1
ignore_hydrogens?:boolean

Controls whether hydrogen atoms are drawn.

Default: false

Case type: "carbohydrate":

size_factor?:number

Scales the corresponding visuals.

Default: 1

Case type: "surface":

size_factor?:number

Scales the corresponding visuals.

Default: 1
ignore_hydrogens?:boolean

Controls whether hydrogen atoms are drawn.

Default: false

`volume`

This node instructs to create a volume from a parsed data resource. "Volume" refers to an internal representation of volumetric data without any visual representation.

Parent: parse

Params:

channel_id?:string | null

Channel identifier (only applies when the input data contain multiple channels).

Default: null

`volume_representation`

This node instructs to create a visual representation of a volume.

Parent: volume

Params:

type:isosurface

Representation type

[This parameter determines the rest of parameters]

Case type: "isosurface":

relative_isovalue?:number | null

Relative isovalue.

Default: null
absolute_isovalue?:number | null

Absolute isovalue. Overrides relative_isovalue.

Default: null
show_wireframe?:boolean

Show mesh wireframe. Defaults to false.

Default: false
show_faces?:boolean

Show mesh faces. Defaults to true.

Default: true

`color`

This node instructs to apply color to a visual representation.

Parent: representation or volume_representation

Params:

color?:ColorName | HexColor

Color to apply to the representation. Can be either an X11 color name (e.g. "red") or a hexadecimal code (e.g. "#FF0011").

Default: "white"

selector?:("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water" | "coarse") | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>>

Defines to what part of the representation this color should be applied.

Default: "all"

`color_from_uri`

This node instructs to apply colors to a visual representation. The colors are defined by an external annotation resource.

Parent: representation

Params:

uri:string

URL of the annotation resource.

format:"cif" | "bcif" | "json"

Format of the annotation resource.

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the color.

Default: "color"

`color_from_source`

This node instructs to apply colors to a visual representation. The colors are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: representation

Params:

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from. If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from. If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the color.

Default: "color"

`opacity`

This node instructs to apply opacity/transparency to a visual representation.

Parent: representation or volume_representation

Params:

opacity:number

Opacity of a representation. 0.0: fully transparent, 1.0: fully opaque.

`label`

This node instructs to add a label (textual visual representation) to a component.

Parent: component or component_from_uri or component_from_source

Params:

text:string

Content of the shown label.

`label_from_uri`

This node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an external annotation resource.

Parent: structure

Params:

uri:string

URL of the annotation resource.

format:"cif" | "bcif" | "json"

Format of the annotation resource.

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the label text.

Default: "label"

`label_from_source`

This node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: structure

Params:

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from. If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from. If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the label text.

Default: "label"

`tooltip`

This node instructs to add a tooltip to a component. "Tooltip" is a text which is not a part of the visualization but should be presented to the users when they interact with the component (typically, the tooltip will be shown somewhere on the screen when the user hovers over a visual representation of the component).

Parent: component or component_from_uri or component_from_source

Params:

text:string

Content of the shown tooltip.

`tooltip_from_uri`

This node instructs to add tooltips to parts of a structure. The tooltips are defined by an external annotation resource.

Parent: structure

Params:

uri:string

URL of the annotation resource.

format:"cif" | "bcif" | "json"

Format of the annotation resource.

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the tooltip text.

Default: "tooltip"

`tooltip_from_source`

This node instructs to add tooltips to parts of a structure. The tooltips are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: structure

Params:

schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

Annotation schema defines what fields in the annotation will be taken into account.

block_header?:string | null

Header of the CIF block to read annotation from. If null, block is selected based on block_index.

Default: null

block_index?:Integer

0-based index of the CIF block to read annotation from (only applies when block_header is null).

Default: 0

category_name?:string | null

Name of the CIF category to read annotation from. If null, the first category in the block is used.

Default: null

field_name?:string

Name of the column in CIF or field name (key) in JSON that contains the tooltip text.

Default: "tooltip"

`focus`

This node instructs to set the camera focus to a component (zoom in).

Parent: root or component or component_from_uri or component_from_source or primitives or primitives_from_uri or volume or volume_representation

Params:

direction?:[number, number, number]

Vector describing the direction of the view (camera position -> focused target).

Default: [0, 0, -1]

up?:[number, number, number]

Vector which will be aligned with the screen Y axis.

Default: [0, 1, 0]

radius?:number | null

Radius of the focused sphere (overrides radius_factor and radius_extra).

Default: null

radius_factor?:number

Radius of the focused sphere relative to the radius of parent component (default: 1). Focused radius = component_radius * radius_factor + radius_extent.

Default: 1

radius_extent?:number

Addition to the radius of the focused sphere, if computed from the radius of parent component (default: 0). Focused radius = component_radius * radius_factor + radius_extent.

Default: 0

`camera`

This node instructs to set the camera position and orientation.

Parent: root

Params:

target:[number, number, number]

Coordinates of the point in space at which the camera is pointing.

position:[number, number, number]

Coordinates of the camera.

up?:[number, number, number]

Vector which will be aligned with the screen Y axis.

Default: [0, 1, 0]

`canvas`

This node sets canvas properties.

Parent: root

Params:

background_color:ColorName | HexColor

Color of the canvas background. Can be either an X11 color name (e.g. "red") or a hexadecimal code (e.g. "#FF0011").

`primitives`

This node groups a list of geometrical primitives

Parent: structure or root

Params:

color?:ColorName | HexColor

Default color for primitives in this group.

Default: "white"

label_color?:ColorName | HexColor

Default label color for primitives in this group.

Default: "white"

tooltip?:string | null

Default tooltip for primitives in this group.

Default: null

opacity?:number

Opacity of primitive geometry in this group.

Default: 1

label_opacity?:number

Opacity of primitive labels in this group.

Default: 1

instances?:Array<Array<number>> | null

Instances of this primitive group defined as 4x4 column major (j * 4 + i indexing) transformation matrices.

Default: null

`primitives_from_uri`

This node loads a list of primitives from URI

Parent: structure or root

Params:

uri:string

Location of the resource.

format:"mvs-node-json"

Format of the data.

references?:Array<string>

List of nodes the data are referencing.

Default: []

`primitive`

This node represents a geometrical primitive

Parent: primitives

Params:

kind:mesh | lines | tube | arrow | distance_measurement | angle_measurement | label | ellipse | ellipsoid | box

Kind of geometrical primitive

[This parameter determines the rest of parameters]

Case kind: "mesh":

vertices:Array<number>

3*n_vertices length array of floats with vertex position (x1, y1, z1, ...).
indices:Array<Integer>

3*n_triangles length array of indices into vertices that form triangles (t1_1, t1_2, t1_3, ...).
triangle_groups?:Array<Integer> | null

Assign a number to each triangle to group them. If not specified, each triangle is considered a separate group (triangle i = group i).

Default: null
group_colors?:{ [K in Integer]: (ColorName | HexColor) }

Assign a color to each group. Where not assigned, uses color.

Default: {}
group_tooltips?:{ [K in Integer]: string }

Assign a tooltip to each group. Where not assigned, uses tooltip.

Default: {}
color?:(ColorName | HexColor) | null

Color of the triangles and wireframe. Can be overwritten by group_colors. If not specified, uses the parent primitives group color.

Default: null
tooltip?:string | null

Tooltip shown when hovering over the mesh. Can be overwritten by group_tooltips. If not specified, uses the parent primitives group tooltip.

Default: null
show_triangles?:boolean

Determine whether to render triangles of the mesh.

Default: true
show_wireframe?:boolean

Determine whether to render wireframe of the mesh.

Default: false
wireframe_width?:number

Wireframe line width (in screen-space units).

Default: 1
wireframe_color?:(ColorName | HexColor) | null

Wireframe color. If not specified, uses group_colors.

Default: null

Case kind: "lines":

vertices:Array<number>

3*n_vertices length array of floats with vertex position (x1, y1, z1, ...).
indices:Array<Integer>

2*n_lines length array of indices into vertices that form lines (l1_1, l1_2, ...).
line_groups?:Array<Integer> | null

Assign a number to each triangle to group them. If not specified, each line is considered a separate group (line i = group i).

Default: null
group_colors?:{ [K in Integer]: (ColorName | HexColor) }

Assign a color to each group. Where not assigned, uses color.

Default: {}
group_tooltips?:{ [K in Integer]: string }

Assign a tooltip to each group. Where not assigned, uses tooltip.

Default: {}
group_widths?:{ [K in Integer]: number }

Assign a line width to each group. Where not assigned, uses width.

Default: {}
color?:(ColorName | HexColor) | null

Color of the lines. Can be overwritten by group_colors. If not specified, uses the parent primitives group color.

Default: null
tooltip?:string | null

Tooltip shown when hovering over the lines. Can be overwritten by group_tooltips. If not specified, uses the parent primitives group tooltip.

Default: null
width?:number

Line width (in screen-space units). Can be overwritten by group_widths.

Default: 1

Case kind: "tube":

start:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

Start point of the tube.
end:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

End point of the tube.
radius?:number

Tube radius (in Angstroms).

Default: 0.05
dash_length?:number | null

Length of each dash and gap between dashes. If not specified (null), draw full line.

Default: null
color?:(ColorName | HexColor) | null

Color of the tube. If not specified, uses the parent primitives group color.

Default: null
tooltip?:string | null

Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

Default: null

Case kind: "arrow":

start:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

Start point of the arrow.
end?:([number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>) | null

End point of the arrow.

Default: null
direction?:[number, number, number] | null

If specified, the endpoint is computed as start + direction.

Default: null
length?:number | null

Length of the arrow. If unset, the distance between start and end is used.

Default: null
show_start_cap?:boolean

Draw a cap at the start of the arrow.

Default: false
start_cap_length?:number

Length of the start cap.

Default: 0.1
start_cap_radius?:number

Radius of the start cap.

Default: 0.1
show_end_cap?:boolean

Draw a cap at the end of the arrow.

Default: false
end_cap_length?:number

Length of the end cap.

Default: 0.1
end_cap_radius?:number

Radius of the end cap.

Default: 0.1
show_tube?:boolean

Draw a tube connecting the start and end points.

Default: true
tube_radius?:number

Tube radius (in Angstroms).

Default: 0.05
tube_dash_length?:number | null

Length of each dash and gap between dashes. If not specified (null), draw full line.

Default: null
color?:(ColorName | HexColor) | null

Color of the tube. If not specified, uses the parent primitives group color.

Default: null
tooltip?:string | null

Tooltip to show when hovering over the arrow. If not specified, uses the parent primitives group tooltip.

Default: null

Case kind: "distance_measurement":

start:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

Start point of the tube.
end:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

End point of the tube.
radius?:number

Tube radius (in Angstroms).

Default: 0.05
dash_length?:number | null

Length of each dash and gap between dashes. If not specified (null), draw full line.

Default: null
color?:(ColorName | HexColor) | null

Color of the tube. If not specified, uses the parent primitives group color.

Default: null
label_template?:string

Template used to construct the label. Use {{distance}} as placeholder for the distance.

Default: "{{distance}}"
label_size?:number | null

Size of the label (text height in Angstroms). If not specified, size will be relative to the distance (see label_auto_size_scale, label_auto_size_min).

Default: null
label_auto_size_scale?:number

Scaling factor for relative size.

Default: 0.1
label_auto_size_min?:number

Minimum size for relative size.

Default: 0
label_color?:(ColorName | HexColor) | null

Color of the label. If not specified, uses the parent primitives group label_color.

Default: null

Case kind: "angle_measurement":

a:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

Point A.
b:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

Point B.
c:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

Point C.
label_template?:string

Template used to construct the label. Use {{angle}} as placeholder for the angle in radians.

Default: "{{angle}}"
label_size?:number | null

Size of the label (text height in Angstroms). If not specified, size will be relative to the distance (see label_auto_size_scale, label_auto_size_min).

Default: null
label_auto_size_scale?:number

Scaling factor for relative size.

Default: 0.33
label_auto_size_min?:number

Minimum size for relative size.

Default: 0
label_color?:(ColorName | HexColor) | null

Color of the label. If not specified, uses the parent primitives group label_color.

Default: null
show_vector?:boolean

Draw vectors between (a, b) and (b, c).

Default: true
vector_color?:(ColorName | HexColor) | null

Color of the vectors.

Default: null
show_section?:boolean

Draw a filled circle section representing the angle.

Default: true
section_color?:(ColorName | HexColor) | null

Color of the angle section. If not specified, the primitives group color is used.

Default: null
section_radius?:number | null

Radius of the angle section. In angstroms.

Default: null
section_radius_scale?:number

Factor to scale the radius of the angle section. Ignored if section_radius is set.

Default: 0.33

Case kind: "label":

position:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

Position of this label.
text:string

The label.
label_size?:number

Size of the label (text height in Angstroms).

Default: 1
label_color?:(ColorName | HexColor) | null

Color of the label. If not specified, uses the parent primitives group label_color.

Default: null
label_offset?:number

Camera-facing offset to prevent overlap with geometry.

Default: 0

Case kind: "ellipse":

color?:(ColorName | HexColor) | null

Color of the ellipse. If not specified, uses the parent primitives group color.

Default: null
as_circle?:boolean

If true, ignores radius_minor/magnitude of the minor axis.

Default: false
center:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

The center of the ellipse.
major_axis?:[number, number, number] | null

Major axis of this ellipse.

Default: null
minor_axis?:[number, number, number] | null

Minor axis of this ellipse.

Default: null
major_axis_endpoint?:([number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>) | null

Major axis endpoint. If specified, overrides major axis to be major_axis_endpoint - center.

Default: null
minor_axis_endpoint?:([number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>) | null

Minor axis endpoint. If specified, overrides minor axis to be minor_axis_endpoint - center.

Default: null
radius_major?:number | null

Radius of the major axis. If unset, the length of the major axis is used.

Default: null
radius_minor?:number | null

Radius of the minor axis. If unset, the length of the minor axis is used.

Default: null
theta_start?:number

Start of the arc. In radians

Default: 0
theta_end?:number

End of the arc. In radians

Default: 6.283185307179586
tooltip?:string | null

Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

Default: null

Case kind: "ellipsoid":

color?:(ColorName | HexColor) | null

Color of the ellipsoid. If not specified, uses the parent primitives group color.

Default: null
center:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

The center of the ellipsoid.
major_axis?:[number, number, number] | null

Major axis of this ellipsoid.

Default: null
minor_axis?:[number, number, number] | null

Minor axis of this ellipsoid.

Default: null
major_axis_endpoint?:([number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>) | null

Major axis endpoint. If specified, overrides major axis to be major_axis_endpoint - center.

Default: null
minor_axis_endpoint?:([number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>) | null

Minor axis endpoint. If specified, overrides minor axis to be minor_axis_endpoint - center.

Default: null
radius?:([number, number, number] | number) | null

Radii of the ellipsoid along each axis.

Default: null
radius_extent?:([number, number, number] | number) | null

Added to the radii of the ellipsoid along each axis.

Default: null
tooltip?:string | null

Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

Default: null

Case kind: "box":

center:[number, number, number] | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ structure_ref: string, expression_schema: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions: Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>> }>>

The center of the box.
extent?:[number, number, number] | null

The width, the height, and the depth of the box. Added to the bounding box determined by the center.

Default: null
show_faces?:boolean

Determine whether to render the faces of the box.

Default: true
face_color?:(ColorName | HexColor) | null

Color of the box faces.

Default: null
show_edges?:boolean

Determine whether to render the edges of the box.

Default: false
edge_radius?:number

Radius of the box edges. In angstroms.

Default: 0.1
edge_color?:(ColorName | HexColor) | null

Color of the edges.

Default: null
tooltip?:string | null

Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

Default: null