From eed2ed687b9316307c615424ea6c22a8617971df Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Thu, 31 Oct 2024 09:53:19 +0100
Subject: [PATCH 01/24] data models for additional primitives

---
 molviewspec/molviewspec/nodes.py | 89 ++++++++++++++++++++++++++++----
 1 file changed, 78 insertions(+), 11 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index e41aab9..c1c9a77 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -44,6 +44,17 @@
 CustomT = Optional[Mapping[str, Any]]
 RefT = Optional[str]
 
+# TODO: to be used for angle, dihedral
+class LabelCommonProps(BaseModel):
+    label_template: Optional[str] = Field(
+        description="Template used to construct the label. Use {{distance}} as placeholder for the distance."
+    )
+    label_size: Optional[float | Literal["auto"]] = Field(
+        description="Size of the label. Auto scales it by the distance."
+    )
+    label_auto_size_scale: Optional[float] = Field(description="Scaling factor for auto size.")
+    label_auto_size_min: Optional[float] = Field(description="Minimum size for auto size.")
+    label_color: Optional[ColorT] = Field(description="Color of the label.")
 
 class Node(BaseModel):
     """
@@ -725,18 +736,8 @@ class LineParams(_LineParamsBase):
     tooltip: Optional[str] = Field(description="Tooltip to show when hovering on the line.")
 
 
-class DistanceMeasurementParams(_LineParamsBase):
+class DistanceMeasurementParams(_LineParamsBase, LabelCommonProps):
     kind: Literal["distance_measurement"] = "distance_measurement"
-    label_template: Optional[str] = Field(
-        description="Template used to construct the label. Use {{distance}} as placeholder for the distance."
-    )
-    label_size: Optional[float | Literal["auto"]] = Field(
-        description="Size of the label. Auto scales it by the distance."
-    )
-    label_auto_size_scale: Optional[float] = Field(description="Scaling factor for auto size.")
-    label_auto_size_min: Optional[float] = Field(description="Minimum size for auto size.")
-    label_color: Optional[ColorT] = Field(description="Color of the label.")
-
 
 class PrimitiveLabelParams(_LineParamsBase):
     kind: Literal["label"] = "label"
@@ -748,6 +749,7 @@ class PrimitiveLabelParams(_LineParamsBase):
 
 
 class PlaneParams(BaseModel):
+    # TODO: bounding_box?
     kind: Literal["plane"] = "plane"
     point: PrimitivePositionT = Field(description="Point on plane.")
     normal: Vec3[float] = Field(description="Normal vector of plane.")
@@ -769,3 +771,68 @@ def validate_state_tree(json: str) -> None:
     :raises ValidationError if JSON is malformed or state tree type definitions are violated
     """
     State.parse_raw(json)
+
+# TODO: to be discussed
+# class TooltipAndColorProps(BaseModel):
+#     tooltip: Optional[str] = Field(description="Default tooltip for primitives in this group")
+#     color: Optional[ColorT] = Field(
+#         description="Color of the line. If not specified, the primitives group color is used."
+#     )
+
+# TODO: fields instead of plain types
+class CircleParams(BaseModel):
+    center: Vec3 = Field(description="The center of the circle.")
+    # TODO: elaborate names and semantics depending on
+    # how Mol* implements circles
+    # (should be dir_major and dir_minor perhaps as these two here are just Vec3)
+    major_axis: PrimitivePositionT = Field(description="Major axis of this circle.")
+    minor_axis: PrimitivePositionT = Field(description="Minor axis of this circle.")
+
+# TODO: add collection of descriptions for the fields with the same name
+class Polygon(BaseModel):
+    vertices: list[float] = Field(description="3N length array of floats with vertex position (x1, y1, z1, ...)")
+    
+class Star(BaseModel):
+    center: Vec3 = Field(description="The center of the star.")
+    inner_radius: float = Field(description="The inner radius of the star")
+    outer_radius: float = Field(description="The outer radius of the star")
+    # TODO: is this correct meaning?
+    point_count: int = Field(description="The number of points the star contains")
+    # TODO: inherit from TransformParams instead?
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+    
+class Box(TransformParams):
+    center: Vec3 = Field(description="The center of the box")
+    # TODO: is this correct meaning?
+    extent: Vec3 = Field(description="The height and width of the box")
+    # TODO: include in TransformParams instead?
+    scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling")
+    as_edges: Optional[bool] = Field(description="Determine whether to render the box as edges")
+    # TODO: meaning of this? Thickness of edges?
+    edge_radius: Optional[float] = Field(description="The thickness of edges.")
+
+class Cylinder(BaseModel):
+    center: Vec3 = Field(description="The center of the box")
+    radius_top: float = Field(description="The radius of the top of the cylinder top. Radius equal to zero will yield a cone.")
+    radius_bottom: float = Field(description="The radius of the bottom of the cylinder. Radius equal to zero will yield a reversed cone.")
+    height: float = Field(description="The height of the cone.")
+    # TODO: meaning of the following two? Check Sebastian's answers in some of the PRs.
+    theta_start: float = Field(description="TODO")
+    theta_length: float = Field(description="TODO")
+    # TODO: type for rotation as field
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+    bottom_cap: bool = Field(description="Determine whether to cap the top of the cylinder.")
+    top_cap: bool = Field(description="Determine whether to cap the bottom of the cylinder.")
+    
+# class Arrow(BaseModel):
+#     # TODO: better name, "from" is a reserved keyword 
+#     line_from: Vec3 = Field(description="The center of the box")
+#     line_to: 
+#     cylinder_radius:
+#     arrow_radius:
+#     arrow_height:
+#     arrow_from, arrow_to,

From 4fad172e57dbd163c3388e054d39f9023fdea049 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Thu, 31 Oct 2024 13:09:57 +0100
Subject: [PATCH 02/24] more models

---
 molviewspec/molviewspec/nodes.py | 64 ++++++++++++++++++++++++++------
 1 file changed, 53 insertions(+), 11 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index c1c9a77..6a54096 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -615,7 +615,6 @@ class TransformParams(BaseModel):
     )
     translation: Optional[Vec3[float]] = Field(description="3d vector describing the translation")
 
-
 class CameraParams(BaseModel):
     """
     Controls the global camera position.
@@ -808,8 +807,8 @@ class Box(TransformParams):
     # TODO: is this correct meaning?
     extent: Vec3 = Field(description="The height and width of the box")
     # TODO: include in TransformParams instead?
-    scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling")
-    as_edges: Optional[bool] = Field(description="Determine whether to render the box as edges")
+    scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling.")
+    as_edges: Optional[bool] = Field(description="Determine whether to render the box as edges.")
     # TODO: meaning of this? Thickness of edges?
     edge_radius: Optional[float] = Field(description="The thickness of edges.")
 
@@ -828,11 +827,54 @@ class Cylinder(BaseModel):
     bottom_cap: bool = Field(description="Determine whether to cap the top of the cylinder.")
     top_cap: bool = Field(description="Determine whether to cap the bottom of the cylinder.")
     
-# class Arrow(BaseModel):
-#     # TODO: better name, "from" is a reserved keyword 
-#     line_from: Vec3 = Field(description="The center of the box")
-#     line_to: 
-#     cylinder_radius:
-#     arrow_radius:
-#     arrow_height:
-#     arrow_from, arrow_to,
+
+# NOTE: arrow should be derived from line perhaps?
+# This allows us to make use of inheritance 
+class Arrow(_LineParamsBase):
+    # TODO: clarify meaning of the following to and modify depending
+    # on frontend implementation
+    arrow_radius: float = Field(description="The radius (extent) of the arrow.")
+    arrow_height: float = Field(description="The height of the arrow.")
+    arrow_from: Vec3 = Field(description="Start of the arrow.")
+    arrow_to: Vec3 = Field(description="End of the arrow.")
+    
+SolidKindTypeT = Literal["tetra", "octa", "dodeca", "icosahedron"]
+
+class PlatonicSolid(BaseModel):
+    solid_kind: SolidKindTypeT
+    center: float = Field(description="The center of the platonic solid.")
+    radius: float = Field(description="The radius of the platonic solid.")
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+    
+class Prism(BaseModel):
+    position: PrimitivePositionT = Field(description="Position of this prism.")
+    # TODO: meaning?
+    base_point_count: int = Field(description="Count of base points")
+    height: float = Field(description="The height of the prism.")
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+    
+class Pyramid(BaseModel):
+    vertices: list[float] = Field(description="3N length array of floats with vertex position (x1, y1, z1, ...)")
+    translation: Optional[Vec3[float]] = Field(description="3d vector describing the translation")
+    scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling")
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+
+class Sphere(BaseModel):
+    center: Vec3 = Field(description="The center of the circle.")
+    radius: float | PrimitivePositionT = Field(description="The radius of the sphere.")
+    
+    # TODO:
+# class Torus(BaseModel): center, outer_radius, tube_radius, theta_start, theta_length, rotation 
+# Wedge: center, width, height, depth, rotation
+# Ellipsoid: direction_major, direction_minor, direction_normal, center, radius_scale
+
+# TODO:
+# Distance: a: PositionT, b, label props (template, color, …), line props
+# Angle:a, b, c, label props (template, color, …), line props, angle visual props
+# Dihedral: a, b, c, d, label props (template, color, …), line props, angle visual props

From 73a41d599b1bb14b6c811f86cee8c6319f5b71f8 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Thu, 31 Oct 2024 13:26:45 +0100
Subject: [PATCH 03/24] more models

---
 molviewspec/molviewspec/nodes.py | 36 ++++++++++++++++++++++++++++----
 1 file changed, 32 insertions(+), 4 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 6a54096..aef4bd3 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -870,11 +870,39 @@ class Sphere(BaseModel):
     radius: float | PrimitivePositionT = Field(description="The radius of the sphere.")
     
     # TODO:
-# class Torus(BaseModel): center, outer_radius, tube_radius, theta_start, theta_length, rotation 
-# Wedge: center, width, height, depth, rotation
-# Ellipsoid: direction_major, direction_minor, direction_normal, center, radius_scale
+class Torus(BaseModel):
+    center: Vec3 = Field(description="The center of the torus.")
+    outer_radius: float = Field(description="The outer radius of the torus")
+    tube_radius: float = Field(description="The tube radius.")
+    # TODO:
+    theta_start: float = Field(description="TODO")
+    # TODO:
+    theta_length: float = Field(description="TODO")
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+
+class Wedge(BaseModel):
+    center: Vec3 = Field(description="The center of the wedge.")
+    width: float = Field(description="The width of the wedge.")
+    height: float = Field(description="The height of the wedge.")
+    depth: float = Field(description="The depth of the wedge.")
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+    
+class Ellipsoid(BaseModel):
+    # TODO: adjust based on frontend implementation
+    direction_major: Vec3[float] = Field(description="Major direction of the ellipsoid.")
+    direction_minor: Vec3[float] = Field(description="Minor direction of the ellipsoid.")
+    direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")
+    center: Vec3 = Field(description="The center of the ellipsoid.")
+    # TODO: is the meaning correct
+    radius_scale: Optional[Vec3[float]] = Field(description="3d vector describing the radius scaling.")
 
 # TODO:
-# Distance: a: PositionT, b, label props (template, color, …), line props
+class Distance(PrimitiveLabelParams):
+    a: PrimitivePositionT = Field(description="The first point.")
+    b: PrimitivePositionT = Field(description="The second point.")
 # Angle:a, b, c, label props (template, color, …), line props, angle visual props
 # Dihedral: a, b, c, d, label props (template, color, …), line props, angle visual props

From 22c43244fee5c2e44936d2e371c2d452ce5fe149 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Fri, 1 Nov 2024 08:57:36 +0100
Subject: [PATCH 04/24] naming fixes

---
 molviewspec/molviewspec/nodes.py | 36 ++++++++++++++++++++------------
 1 file changed, 23 insertions(+), 13 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index aef4bd3..c1c6241 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -802,7 +802,7 @@ class Star(BaseModel):
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
     
-class Box(TransformParams):
+class BoxParams(TransformParams):
     center: Vec3 = Field(description="The center of the box")
     # TODO: is this correct meaning?
     extent: Vec3 = Field(description="The height and width of the box")
@@ -812,7 +812,7 @@ class Box(TransformParams):
     # TODO: meaning of this? Thickness of edges?
     edge_radius: Optional[float] = Field(description="The thickness of edges.")
 
-class Cylinder(BaseModel):
+class CylinderParams(BaseModel):
     center: Vec3 = Field(description="The center of the box")
     radius_top: float = Field(description="The radius of the top of the cylinder top. Radius equal to zero will yield a cone.")
     radius_bottom: float = Field(description="The radius of the bottom of the cylinder. Radius equal to zero will yield a reversed cone.")
@@ -830,7 +830,7 @@ class Cylinder(BaseModel):
 
 # NOTE: arrow should be derived from line perhaps?
 # This allows us to make use of inheritance 
-class Arrow(_LineParamsBase):
+class ArrowParams(_LineParamsBase):
     # TODO: clarify meaning of the following to and modify depending
     # on frontend implementation
     arrow_radius: float = Field(description="The radius (extent) of the arrow.")
@@ -840,7 +840,7 @@ class Arrow(_LineParamsBase):
     
 SolidKindTypeT = Literal["tetra", "octa", "dodeca", "icosahedron"]
 
-class PlatonicSolid(BaseModel):
+class PlatonicSolidParams(BaseModel):
     solid_kind: SolidKindTypeT
     center: float = Field(description="The center of the platonic solid.")
     radius: float = Field(description="The radius of the platonic solid.")
@@ -848,7 +848,7 @@ class PlatonicSolid(BaseModel):
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
     
-class Prism(BaseModel):
+class PrismParams(BaseModel):
     position: PrimitivePositionT = Field(description="Position of this prism.")
     # TODO: meaning?
     base_point_count: int = Field(description="Count of base points")
@@ -857,7 +857,7 @@ class Prism(BaseModel):
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
     
-class Pyramid(BaseModel):
+class PyramidParams(BaseModel):
     vertices: list[float] = Field(description="3N length array of floats with vertex position (x1, y1, z1, ...)")
     translation: Optional[Vec3[float]] = Field(description="3d vector describing the translation")
     scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling")
@@ -865,12 +865,12 @@ class Pyramid(BaseModel):
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
 
-class Sphere(BaseModel):
+class SphereParams(BaseModel):
     center: Vec3 = Field(description="The center of the circle.")
     radius: float | PrimitivePositionT = Field(description="The radius of the sphere.")
     
     # TODO:
-class Torus(BaseModel):
+class TorusParams(BaseModel):
     center: Vec3 = Field(description="The center of the torus.")
     outer_radius: float = Field(description="The outer radius of the torus")
     tube_radius: float = Field(description="The tube radius.")
@@ -882,7 +882,7 @@ class Torus(BaseModel):
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
 
-class Wedge(BaseModel):
+class WedgeParams(BaseModel):
     center: Vec3 = Field(description="The center of the wedge.")
     width: float = Field(description="The width of the wedge.")
     height: float = Field(description="The height of the wedge.")
@@ -891,7 +891,7 @@ class Wedge(BaseModel):
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
     
-class Ellipsoid(BaseModel):
+class EllipsoidParams(BaseModel):
     # TODO: adjust based on frontend implementation
     direction_major: Vec3[float] = Field(description="Major direction of the ellipsoid.")
     direction_minor: Vec3[float] = Field(description="Minor direction of the ellipsoid.")
@@ -901,8 +901,18 @@ class Ellipsoid(BaseModel):
     radius_scale: Optional[Vec3[float]] = Field(description="3d vector describing the radius scaling.")
 
 # TODO:
-class Distance(PrimitiveLabelParams):
+class DistanceParams(LabelCommonProps):
     a: PrimitivePositionT = Field(description="The first point.")
     b: PrimitivePositionT = Field(description="The second point.")
-# Angle:a, b, c, label props (template, color, …), line props, angle visual props
-# Dihedral: a, b, c, d, label props (template, color, …), line props, angle visual props
+
+class AngleParams(LabelCommonProps):
+    a: PrimitivePositionT = Field(description="The first point.")
+    b: PrimitivePositionT = Field(description="The second point.")
+    c: PrimitivePositionT = Field(description="The third point.")
+        
+class DihedralParams(LabelCommonProps, _LineParamsBase): 
+    a: PrimitivePositionT = Field(description="The first point.")
+    b: PrimitivePositionT = Field(description="The second point.")
+    c: PrimitivePositionT = Field(description="The third point.")
+    d: PrimitivePositionT = Field(description="The fourth point.")
+    # TODO: angle visual props - what does it mean?

From b4af2facb1f59a81c38f0ac244e508a5891669d7 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Fri, 1 Nov 2024 09:02:12 +0100
Subject: [PATCH 05/24] types

---
 molviewspec/molviewspec/nodes.py | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index c1c6241..02ce6b4 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -771,15 +771,9 @@ def validate_state_tree(json: str) -> None:
     """
     State.parse_raw(json)
 
-# TODO: to be discussed
-# class TooltipAndColorProps(BaseModel):
-#     tooltip: Optional[str] = Field(description="Default tooltip for primitives in this group")
-#     color: Optional[ColorT] = Field(
-#         description="Color of the line. If not specified, the primitives group color is used."
-#     )
-
 # TODO: fields instead of plain types
 class CircleParams(BaseModel):
+    kind: Literal["circle"] = "circle"
     center: Vec3 = Field(description="The center of the circle.")
     # TODO: elaborate names and semantics depending on
     # how Mol* implements circles
@@ -789,9 +783,11 @@ class CircleParams(BaseModel):
 
 # TODO: add collection of descriptions for the fields with the same name
 class Polygon(BaseModel):
+    kind: Literal["polygon"] = "polygon"
     vertices: list[float] = Field(description="3N length array of floats with vertex position (x1, y1, z1, ...)")
     
 class Star(BaseModel):
+    kind: Literal["star"] = "star"
     center: Vec3 = Field(description="The center of the star.")
     inner_radius: float = Field(description="The inner radius of the star")
     outer_radius: float = Field(description="The outer radius of the star")
@@ -803,6 +799,7 @@ class Star(BaseModel):
     )
     
 class BoxParams(TransformParams):
+    kind: Literal["box"] = "box"
     center: Vec3 = Field(description="The center of the box")
     # TODO: is this correct meaning?
     extent: Vec3 = Field(description="The height and width of the box")
@@ -813,6 +810,7 @@ class BoxParams(TransformParams):
     edge_radius: Optional[float] = Field(description="The thickness of edges.")
 
 class CylinderParams(BaseModel):
+    kind: Literal["cylinder"] = "cylinder"
     center: Vec3 = Field(description="The center of the box")
     radius_top: float = Field(description="The radius of the top of the cylinder top. Radius equal to zero will yield a cone.")
     radius_bottom: float = Field(description="The radius of the bottom of the cylinder. Radius equal to zero will yield a reversed cone.")
@@ -833,6 +831,7 @@ class CylinderParams(BaseModel):
 class ArrowParams(_LineParamsBase):
     # TODO: clarify meaning of the following to and modify depending
     # on frontend implementation
+    kind: Literal["arrow"] = "arrow"
     arrow_radius: float = Field(description="The radius (extent) of the arrow.")
     arrow_height: float = Field(description="The height of the arrow.")
     arrow_from: Vec3 = Field(description="Start of the arrow.")
@@ -841,6 +840,7 @@ class ArrowParams(_LineParamsBase):
 SolidKindTypeT = Literal["tetra", "octa", "dodeca", "icosahedron"]
 
 class PlatonicSolidParams(BaseModel):
+    kind: Literal["platonic_solid"] = "platonic_solid"
     solid_kind: SolidKindTypeT
     center: float = Field(description="The center of the platonic solid.")
     radius: float = Field(description="The radius of the platonic solid.")
@@ -849,6 +849,7 @@ class PlatonicSolidParams(BaseModel):
     )
     
 class PrismParams(BaseModel):
+    kind: Literal["prism"] = "prism"
     position: PrimitivePositionT = Field(description="Position of this prism.")
     # TODO: meaning?
     base_point_count: int = Field(description="Count of base points")
@@ -858,6 +859,7 @@ class PrismParams(BaseModel):
     )
     
 class PyramidParams(BaseModel):
+    kind: Literal["pyramid"] = "pyramid"
     vertices: list[float] = Field(description="3N length array of floats with vertex position (x1, y1, z1, ...)")
     translation: Optional[Vec3[float]] = Field(description="3d vector describing the translation")
     scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling")
@@ -866,11 +868,13 @@ class PyramidParams(BaseModel):
     )
 
 class SphereParams(BaseModel):
+    kind: Literal["sphere"] = "sphere"
     center: Vec3 = Field(description="The center of the circle.")
     radius: float | PrimitivePositionT = Field(description="The radius of the sphere.")
     
     # TODO:
 class TorusParams(BaseModel):
+    kind: Literal["torus"] = "torus"
     center: Vec3 = Field(description="The center of the torus.")
     outer_radius: float = Field(description="The outer radius of the torus")
     tube_radius: float = Field(description="The tube radius.")
@@ -883,6 +887,7 @@ class TorusParams(BaseModel):
     )
 
 class WedgeParams(BaseModel):
+    kind: Literal["wedge"] = "wedge"
     center: Vec3 = Field(description="The center of the wedge.")
     width: float = Field(description="The width of the wedge.")
     height: float = Field(description="The height of the wedge.")
@@ -893,6 +898,7 @@ class WedgeParams(BaseModel):
     
 class EllipsoidParams(BaseModel):
     # TODO: adjust based on frontend implementation
+    kind: Literal["ellipsoid"] = "ellipsoid"
     direction_major: Vec3[float] = Field(description="Major direction of the ellipsoid.")
     direction_minor: Vec3[float] = Field(description="Minor direction of the ellipsoid.")
     direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")
@@ -902,15 +908,18 @@ class EllipsoidParams(BaseModel):
 
 # TODO:
 class DistanceParams(LabelCommonProps):
+    kind: Literal["disatance"] = "disatance"
     a: PrimitivePositionT = Field(description="The first point.")
     b: PrimitivePositionT = Field(description="The second point.")
 
 class AngleParams(LabelCommonProps):
+    kind: Literal["angle"] = "angle"
     a: PrimitivePositionT = Field(description="The first point.")
     b: PrimitivePositionT = Field(description="The second point.")
     c: PrimitivePositionT = Field(description="The third point.")
         
 class DihedralParams(LabelCommonProps, _LineParamsBase): 
+    kind: Literal["dihedral"] = "dihedral"
     a: PrimitivePositionT = Field(description="The first point.")
     b: PrimitivePositionT = Field(description="The second point.")
     c: PrimitivePositionT = Field(description="The third point.")

From 5605c4e878cc569bbdb0f562a063c5ce9537ab53 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Fri, 1 Nov 2024 09:03:47 +0100
Subject: [PATCH 06/24] box

---
 molviewspec/molviewspec/builder.py | 32 ++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index 1796410..43e3347 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -12,6 +12,7 @@
 from pydantic import BaseModel, PrivateAttr
 
 from molviewspec.nodes import (
+    BoxParams,
     CameraParams,
     CanvasParams,
     ColorFromSourceParams,
@@ -566,6 +567,7 @@ def tooltip_from_source(
     def transform(
         self,
         *,
+        # TODO: given as Optional[Mat3[float]] in nodes.py
         rotation: Sequence[float] | None = None,
         translation: Sequence[float] | None = None,
         custom: CustomT = None,
@@ -935,3 +937,33 @@ def label(
         node = Node(kind="primitive", params=params)
         self._add_child(node)
         return self
+
+    def box(self,
+        *,
+        center: Vec3,
+        extent: Vec3,
+        # TODO: adjust default? 
+        scaling: Vec3[float] | None = 1.0,
+        as_edges: bool | None = False,
+        edge_radius: float | None = None,
+        rotation: Sequence[float] | None = None,
+        translation: Vec3[float] | None = None,    
+        custom: CustomT = None,
+        ref: RefT = None,
+        ) -> Primitives:
+        # TODO annotation
+        # """
+        # Defines a box
+        # :param center: center of the box
+        # :param extent: height and width of the box
+        # :param scaling: scaling
+        # :param as_edges: 3d vector describing the scaling.
+        # :param label_offset: camera-facing offset to prevent overlap with geometry
+        # :param custom: optional, custom data to attach to this node
+        # :param ref: optional, reference that can be used to access this node
+        # :return: this builder
+        # """
+        params = make_params(BoxParams, {"kind": "box", **locals()})
+        node = Node(kind="primitive", params=params)
+        self._add_child(node)
+        return self
\ No newline at end of file

From 72f2c2c9d5fb42672ddf5fa320c8fadecf09a6ff Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Fri, 1 Nov 2024 11:12:28 +0100
Subject: [PATCH 07/24] cage; fix description;

---
 molviewspec/molviewspec/builder.py | 30 ++++++++++++++++++++++++++++++
 molviewspec/molviewspec/nodes.py   |  5 ++---
 2 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index 43e3347..f251918 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -939,6 +939,36 @@ def label(
         return self
 
     def box(self,
+        *,
+        center: Vec3,
+        extent: Vec3,
+        # TODO: adjust default? 
+        scaling: Vec3[float] | None = 1.0,
+        as_edges: bool | None = False,
+        edge_radius: float | None = None,
+        rotation: Sequence[float] | None = None,
+        translation: Vec3[float] | None = None,    
+        custom: CustomT = None,
+        ref: RefT = None,
+        ) -> Primitives:
+        # TODO annotation
+        # """
+        # Defines a box
+        # :param center: center of the box
+        # :param extent: height and width of the box
+        # :param scaling: scaling
+        # :param as_edges: 3d vector describing the scaling.
+        # :param label_offset: camera-facing offset to prevent overlap with geometry
+        # :param custom: optional, custom data to attach to this node
+        # :param ref: optional, reference that can be used to access this node
+        # :return: this builder
+        # """
+        params = make_params(BoxParams, {"kind": "box", **locals()})
+        node = Node(kind="primitive", params=params)
+        self._add_child(node)
+        return self
+    
+    def cage(self,
         *,
         center: Vec3,
         extent: Vec3,
diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 02ce6b4..4043bd5 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -800,9 +800,8 @@ class Star(BaseModel):
     
 class BoxParams(TransformParams):
     kind: Literal["box"] = "box"
-    center: Vec3 = Field(description="The center of the box")
-    # TODO: is this correct meaning?
-    extent: Vec3 = Field(description="The height and width of the box")
+    center: Vec3 = Field(description="The center of the box.")
+    extent: Vec3 = Field(description="The width, the height, and the depth of the box.")
     # TODO: include in TransformParams instead?
     scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling.")
     as_edges: Optional[bool] = Field(description="Determine whether to render the box as edges.")

From a18e49165d19abb0d4728c46bc245e4e94fe5083 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Tue, 5 Nov 2024 11:12:58 +0100
Subject: [PATCH 08/24] fixes; cylinder;

---
 molviewspec/molviewspec/builder.py | 38 ++++++++++++++++++++++++++++--
 molviewspec/molviewspec/nodes.py   |  7 ++++--
 2 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index f251918..95196f6 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -12,6 +12,7 @@
 from pydantic import BaseModel, PrivateAttr
 
 from molviewspec.nodes import (
+# from molviewspec.molviewspec.nodes import (
     BoxParams,
     CameraParams,
     CanvasParams,
@@ -25,6 +26,7 @@
     ComponentInlineParams,
     ComponentSelectorT,
     CustomT,
+    CylinderParams,
     DescriptionFormatT,
     DistanceMeasurementParams,
     DownloadParams,
@@ -942,8 +944,9 @@ def box(self,
         *,
         center: Vec3,
         extent: Vec3,
+        color: ColorT | None = None,
         # TODO: adjust default? 
-        scaling: Vec3[float] | None = 1.0,
+        scaling: Vec3[float] | None = [1.0, 1.0, 1.0],
         as_edges: bool | None = False,
         edge_radius: float | None = None,
         rotation: Sequence[float] | None = None,
@@ -996,4 +999,35 @@ def cage(self,
         params = make_params(BoxParams, {"kind": "box", **locals()})
         node = Node(kind="primitive", params=params)
         self._add_child(node)
-        return self
\ No newline at end of file
+        return self
+
+    def cylinder(self,
+        *,
+        radius_top: float,
+        radius_bottom: float,
+        height: float,
+        # TODO: theta start/length once clarified
+        bottom_cap: bool,
+        top_cap: bool,
+        color: ColorT | None = None,
+        rotation: Sequence[float] | None = None,
+        custom: CustomT = None,
+        ref: RefT = None,
+        ) -> Primitives:
+        # TODO annotation
+        # """
+        # Defines a box
+        # :param center: center of the box
+        # :param extent: height and width of the box
+        # :param scaling: scaling
+        # :param as_edges: 3d vector describing the scaling.
+        # :param label_offset: camera-facing offset to prevent overlap with geometry
+        # :param custom: optional, custom data to attach to this node
+        # :param ref: optional, reference that can be used to access this node
+        # :return: this builder
+        # """
+        params = make_params(CylinderParams, {"kind": "cylinder", **locals()})
+        node = Node(kind="primitive", params=params)
+        self._add_child(node)
+        return self
+    
\ No newline at end of file
diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 4043bd5..b54ec4b 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -701,7 +701,7 @@ class LinesParams(BaseModel):
     indices: list[int] = Field(
         description="2N length array of indices into vertices that form lines (l1_1, ll1_2, ...)"
     )
-    line_groups: Optional[list[int]] = Field(description="Assign a number to each triangle to group them.")
+    line_groups: Optional[list[int]] = Field(description="Assign a number to each line to group them.")
     group_colors: Optional[Mapping[int, ColorT]] = Field(
         description="Assign a color to each group. If not assigned, default primitives group color is used. Takes precedence over line_colors."
     )
@@ -800,6 +800,9 @@ class Star(BaseModel):
     
 class BoxParams(TransformParams):
     kind: Literal["box"] = "box"
+    # TODO: implement
+    box_groups: Optional[list[int]] = Field(description="Assign a number to each box to group them.")
+    color: Optional[ColorT] = Field(description="Default color for the box.")
     center: Vec3 = Field(description="The center of the box.")
     extent: Vec3 = Field(description="The width, the height, and the depth of the box.")
     # TODO: include in TransformParams instead?
@@ -810,7 +813,7 @@ class BoxParams(TransformParams):
 
 class CylinderParams(BaseModel):
     kind: Literal["cylinder"] = "cylinder"
-    center: Vec3 = Field(description="The center of the box")
+    color: Optional[ColorT] = Field(description="Default color for the box.")
     radius_top: float = Field(description="The radius of the top of the cylinder top. Radius equal to zero will yield a cone.")
     radius_bottom: float = Field(description="The radius of the bottom of the cylinder. Radius equal to zero will yield a reversed cone.")
     height: float = Field(description="The height of the cone.")

From d1e9cb98a61656696b44a5b5a2701463e9236ef8 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Tue, 5 Nov 2024 11:15:03 +0100
Subject: [PATCH 09/24] Vec3 to PrimitivePositionT for all centers

---
 molviewspec/molviewspec/nodes.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index b54ec4b..ede191d 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -774,7 +774,7 @@ def validate_state_tree(json: str) -> None:
 # TODO: fields instead of plain types
 class CircleParams(BaseModel):
     kind: Literal["circle"] = "circle"
-    center: Vec3 = Field(description="The center of the circle.")
+    center: PrimitivePositionT = Field(description="The center of the circle.")
     # TODO: elaborate names and semantics depending on
     # how Mol* implements circles
     # (should be dir_major and dir_minor perhaps as these two here are just Vec3)
@@ -788,7 +788,7 @@ class Polygon(BaseModel):
     
 class Star(BaseModel):
     kind: Literal["star"] = "star"
-    center: Vec3 = Field(description="The center of the star.")
+    center: PrimitivePositionT = Field(description="The center of the star.")
     inner_radius: float = Field(description="The inner radius of the star")
     outer_radius: float = Field(description="The outer radius of the star")
     # TODO: is this correct meaning?
@@ -803,7 +803,7 @@ class BoxParams(TransformParams):
     # TODO: implement
     box_groups: Optional[list[int]] = Field(description="Assign a number to each box to group them.")
     color: Optional[ColorT] = Field(description="Default color for the box.")
-    center: Vec3 = Field(description="The center of the box.")
+    center: PrimitivePositionT = Field(description="The center of the box.")
     extent: Vec3 = Field(description="The width, the height, and the depth of the box.")
     # TODO: include in TransformParams instead?
     scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling.")
@@ -871,13 +871,13 @@ class PyramidParams(BaseModel):
 
 class SphereParams(BaseModel):
     kind: Literal["sphere"] = "sphere"
-    center: Vec3 = Field(description="The center of the circle.")
+    center: PrimitivePositionT = Field(description="The center of the circle.")
     radius: float | PrimitivePositionT = Field(description="The radius of the sphere.")
     
     # TODO:
 class TorusParams(BaseModel):
     kind: Literal["torus"] = "torus"
-    center: Vec3 = Field(description="The center of the torus.")
+    center: PrimitivePositionT = Field(description="The center of the torus.")
     outer_radius: float = Field(description="The outer radius of the torus")
     tube_radius: float = Field(description="The tube radius.")
     # TODO:
@@ -890,7 +890,7 @@ class TorusParams(BaseModel):
 
 class WedgeParams(BaseModel):
     kind: Literal["wedge"] = "wedge"
-    center: Vec3 = Field(description="The center of the wedge.")
+    center: PrimitivePositionT = Field(description="The center of the wedge.")
     width: float = Field(description="The width of the wedge.")
     height: float = Field(description="The height of the wedge.")
     depth: float = Field(description="The depth of the wedge.")
@@ -904,7 +904,7 @@ class EllipsoidParams(BaseModel):
     direction_major: Vec3[float] = Field(description="Major direction of the ellipsoid.")
     direction_minor: Vec3[float] = Field(description="Minor direction of the ellipsoid.")
     direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")
-    center: Vec3 = Field(description="The center of the ellipsoid.")
+    center: PrimitivePositionT = Field(description="The center of the ellipsoid.")
     # TODO: is the meaning correct
     radius_scale: Optional[Vec3[float]] = Field(description="3d vector describing the radius scaling.")
 

From 9b72e3c552087937c64b292b5a646616793f42fd Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Tue, 5 Nov 2024 11:18:21 +0100
Subject: [PATCH 10/24] Vec3 to PrimitivePositionT

---
 molviewspec/molviewspec/nodes.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index ede191d..43ead62 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -836,8 +836,8 @@ class ArrowParams(_LineParamsBase):
     kind: Literal["arrow"] = "arrow"
     arrow_radius: float = Field(description="The radius (extent) of the arrow.")
     arrow_height: float = Field(description="The height of the arrow.")
-    arrow_from: Vec3 = Field(description="Start of the arrow.")
-    arrow_to: Vec3 = Field(description="End of the arrow.")
+    arrow_from: PrimitivePositionT = Field(description="Start of the arrow.")
+    arrow_to: PrimitivePositionT = Field(description="End of the arrow.")
     
 SolidKindTypeT = Literal["tetra", "octa", "dodeca", "icosahedron"]
 

From 84e128f56cdcc010e79c89dafbf163060a90c544 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Mon, 11 Nov 2024 06:33:54 +0100
Subject: [PATCH 11/24] Transform mixin

---
 molviewspec/molviewspec/nodes.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 43ead62..64523e9 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -653,7 +653,6 @@ class PrimitiveComponentExpressions(BaseModel):
 a list of expressions within a specific structure.
 """
 
-
 class PrimitivesParams(BaseModel):
     color: Optional[ColorT] = Field(description="Default color for primitives in this group")
     label_color: Optional[ColorT] = Field(description="Default label color for primitives in this group")
@@ -797,8 +796,14 @@ class Star(BaseModel):
     rotation: Optional[Mat3[float]] = Field(
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
-    
-class BoxParams(TransformParams):
+
+class TransformMixin:
+    rotation: Optional[Mat3[float]] = Field(
+        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    )
+    translation: Optional[Vec3[float]] = Field(description="3d vector describing the translation")
+
+class BoxParams(TransformMixin):
     kind: Literal["box"] = "box"
     # TODO: implement
     box_groups: Optional[list[int]] = Field(description="Assign a number to each box to group them.")
@@ -810,6 +815,7 @@ class BoxParams(TransformParams):
     as_edges: Optional[bool] = Field(description="Determine whether to render the box as edges.")
     # TODO: meaning of this? Thickness of edges?
     edge_radius: Optional[float] = Field(description="The thickness of edges.")
+    alignment: Literal["axes", "principal-axes"] = "axes"
 
 class CylinderParams(BaseModel):
     kind: Literal["cylinder"] = "cylinder"

From e89eb17c622c36ed553b53fda97a80b0c5bf8aa8 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Mon, 11 Nov 2024 06:36:59 +0100
Subject: [PATCH 12/24] fix cylinder params

---
 molviewspec/molviewspec/nodes.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 64523e9..dd36325 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -820,9 +820,10 @@ class BoxParams(TransformMixin):
 class CylinderParams(BaseModel):
     kind: Literal["cylinder"] = "cylinder"
     color: Optional[ColorT] = Field(description="Default color for the box.")
+    bottom: PrimitivePositionT = Field(description="Position of the bottom.")
+    up: PrimitivePositionT = Field(description="Position of the top.")
     radius_top: float = Field(description="The radius of the top of the cylinder top. Radius equal to zero will yield a cone.")
     radius_bottom: float = Field(description="The radius of the bottom of the cylinder. Radius equal to zero will yield a reversed cone.")
-    height: float = Field(description="The height of the cone.")
     # TODO: meaning of the following two? Check Sebastian's answers in some of the PRs.
     theta_start: float = Field(description="TODO")
     theta_length: float = Field(description="TODO")

From 99921cb8f7ed30ea4fc8d2732c61114232ec5c22 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Mon, 11 Nov 2024 06:41:18 +0100
Subject: [PATCH 13/24] cage

---
 molviewspec/molviewspec/nodes.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index dd36325..0f87e23 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -797,26 +797,31 @@ class Star(BaseModel):
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
 
-class TransformMixin:
+class TransformMixin(BaseModel):
     rotation: Optional[Mat3[float]] = Field(
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
     )
     translation: Optional[Vec3[float]] = Field(description="3d vector describing the translation")
 
-class BoxParams(TransformMixin):
-    kind: Literal["box"] = "box"
-    # TODO: implement
-    box_groups: Optional[list[int]] = Field(description="Assign a number to each box to group them.")
-    color: Optional[ColorT] = Field(description="Default color for the box.")
+class RectangularPrismMixin(BaseModel):
     center: PrimitivePositionT = Field(description="The center of the box.")
     extent: Vec3 = Field(description="The width, the height, and the depth of the box.")
     # TODO: include in TransformParams instead?
     scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling.")
-    as_edges: Optional[bool] = Field(description="Determine whether to render the box as edges.")
     # TODO: meaning of this? Thickness of edges?
     edge_radius: Optional[float] = Field(description="The thickness of edges.")
     alignment: Literal["axes", "principal-axes"] = "axes"
-
+    groups: Optional[list[int]] = Field(description="Assign a number to each box to group them.")
+    color: Optional[ColorT] = Field(description="Default color for the box.")
+    
+class BoxParams(TransformMixin, RectangularPrismMixin):
+    kind: Literal["box"] = "box"
+    # TODO: implement
+    
+class CageParams(TransformMixin, RectangularPrismMixin):
+    kind: Literal["cage"] = "cage"
+    type: Literal["as_lines", "as_geometry"] = "as_lines"
+    
 class CylinderParams(BaseModel):
     kind: Literal["cylinder"] = "cylinder"
     color: Optional[ColorT] = Field(description="Default color for the box.")

From 3959aaf3236617fb437bbf8a169a29d683c70b3e Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Thu, 14 Nov 2024 10:32:52 +0100
Subject: [PATCH 14/24] fix center param type; remove as_edges param; remove
 outdated comment;

---
 molviewspec/molviewspec/builder.py | 5 ++---
 molviewspec/molviewspec/nodes.py   | 1 -
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index 95196f6..5b8ae95 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -942,12 +942,11 @@ def label(
 
     def box(self,
         *,
-        center: Vec3,
+        center: PrimitivePositionT,
         extent: Vec3,
         color: ColorT | None = None,
         # TODO: adjust default? 
         scaling: Vec3[float] | None = [1.0, 1.0, 1.0],
-        as_edges: bool | None = False,
         edge_radius: float | None = None,
         rotation: Sequence[float] | None = None,
         translation: Vec3[float] | None = None,    
@@ -973,7 +972,7 @@ def box(self,
     
     def cage(self,
         *,
-        center: Vec3,
+        center: PrimitivePositionT,
         extent: Vec3,
         # TODO: adjust default? 
         scaling: Vec3[float] | None = 1.0,
diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 0f87e23..5e94fd1 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -816,7 +816,6 @@ class RectangularPrismMixin(BaseModel):
     
 class BoxParams(TransformMixin, RectangularPrismMixin):
     kind: Literal["box"] = "box"
-    # TODO: implement
     
 class CageParams(TransformMixin, RectangularPrismMixin):
     kind: Literal["cage"] = "cage"

From c0b83c612bde09bbe350d2b7a63addf32cd3fb0c Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Fri, 15 Nov 2024 09:55:07 +0100
Subject: [PATCH 15/24] change rotation implementation from 9d matrix to angle
 and axis

---
 molviewspec/molviewspec/nodes.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 5e94fd1..523c45f 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -793,13 +793,20 @@ class Star(BaseModel):
     # TODO: is this correct meaning?
     point_count: int = Field(description="The number of points the star contains")
     # TODO: inherit from TransformParams instead?
-    rotation: Optional[Mat3[float]] = Field(
-        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
-    )
+    # rotation: Optional[Mat3[float]] = Field(
+    #     description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    # )
 
 class TransformMixin(BaseModel):
-    rotation: Optional[Mat3[float]] = Field(
-        description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    # rotation: Optional[Mat3[float]] = Field(
+    #     description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
+    # )
+    rotation_axis: Optional[Vec3] = Field(
+        # TODO: better description
+        description="Rotation axis"
+    )
+    rotation_radians: Optional[int] = Field(
+        description="Rotation angle in radians"
     )
     translation: Optional[Vec3[float]] = Field(description="3d vector describing the translation")
 

From 16db139a18d8de9fef3c35d17e5d2582bdef725f Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Fri, 15 Nov 2024 11:10:13 +0100
Subject: [PATCH 16/24] cage support; fix params;

---
 molviewspec/molviewspec/builder.py | 23 ++++++++++++-----------
 molviewspec/molviewspec/nodes.py   |  2 --
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index 5b8ae95..9a28383 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -14,6 +14,7 @@
 from molviewspec.nodes import (
 # from molviewspec.molviewspec.nodes import (
     BoxParams,
+    CageParams,
     CameraParams,
     CanvasParams,
     ColorFromSourceParams,
@@ -60,7 +61,7 @@
     TransparencyInlineParams,
     Vec3,
 )
-from molviewspec.utils import get_major_version_tag, make_params
+from molviewspec.molviewspec.utils import get_major_version_tag, make_params
 
 
 def create_builder() -> Root:
@@ -945,15 +946,14 @@ def box(self,
         center: PrimitivePositionT,
         extent: Vec3,
         color: ColorT | None = None,
-        # TODO: adjust default? 
         scaling: Vec3[float] | None = [1.0, 1.0, 1.0],
-        edge_radius: float | None = None,
-        rotation: Sequence[float] | None = None,
+        rotation_axis: Vec3[float] | None = None,
+        rotation_radians: float | None = None,
         translation: Vec3[float] | None = None,    
         custom: CustomT = None,
         ref: RefT = None,
         ) -> Primitives:
-        # TODO annotation
+        # TODO: annotation
         # """
         # Defines a box
         # :param center: center of the box
@@ -974,12 +974,13 @@ def cage(self,
         *,
         center: PrimitivePositionT,
         extent: Vec3,
-        # TODO: adjust default? 
-        scaling: Vec3[float] | None = 1.0,
-        as_edges: bool | None = False,
+        color: ColorT | None = None,
+        scaling: Vec3[float] | None = [1.0, 1.0, 1.0],
         edge_radius: float | None = None,
-        rotation: Sequence[float] | None = None,
-        translation: Vec3[float] | None = None,    
+        rotation_axis: Vec3[float] | None = None,
+        rotation_radians: float | None = None,
+        translation: Vec3[float] | None = None,  
+        type: Literal["as_lines", "as_geometry"] = "as_lines", 
         custom: CustomT = None,
         ref: RefT = None,
         ) -> Primitives:
@@ -995,7 +996,7 @@ def cage(self,
         # :param ref: optional, reference that can be used to access this node
         # :return: this builder
         # """
-        params = make_params(BoxParams, {"kind": "box", **locals()})
+        params = make_params(CageParams, {"kind": "cage", **locals()})
         node = Node(kind="primitive", params=params)
         self._add_child(node)
         return self
diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 523c45f..b9e47bd 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -815,8 +815,6 @@ class RectangularPrismMixin(BaseModel):
     extent: Vec3 = Field(description="The width, the height, and the depth of the box.")
     # TODO: include in TransformParams instead?
     scaling: Optional[Vec3[float]] = Field(description="3d vector describing the scaling.")
-    # TODO: meaning of this? Thickness of edges?
-    edge_radius: Optional[float] = Field(description="The thickness of edges.")
     alignment: Literal["axes", "principal-axes"] = "axes"
     groups: Optional[list[int]] = Field(description="Assign a number to each box to group them.")
     color: Optional[ColorT] = Field(description="Default color for the box.")

From 9a298e2571abe0921e4564251491720076894342 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Sat, 16 Nov 2024 06:50:18 +0100
Subject: [PATCH 17/24] cylinder fix params

---
 molviewspec/molviewspec/builder.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index 9a28383..fbf58e5 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -1003,14 +1003,15 @@ def cage(self,
 
     def cylinder(self,
         *,
+        bottom: Vec3[float],
+        up: Vec3[float],
         radius_top: float,
         radius_bottom: float,
-        height: float,
-        # TODO: theta start/length once clarified
         bottom_cap: bool,
         top_cap: bool,
         color: ColorT | None = None,
-        rotation: Sequence[float] | None = None,
+        rotation_axis: Vec3[float] | None = None,
+        rotation_radians: float | None = None,
         custom: CustomT = None,
         ref: RefT = None,
         ) -> Primitives:

From e2d1ba824b11cb41b10e26850f38c321719a532d Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Sat, 16 Nov 2024 07:04:57 +0100
Subject: [PATCH 18/24] cylinder to cone; no theta

---
 molviewspec/molviewspec/builder.py |  2 +-
 molviewspec/molviewspec/nodes.py   | 11 ++++++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index fbf58e5..762ed22 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -1001,7 +1001,7 @@ def cage(self,
         self._add_child(node)
         return self
 
-    def cylinder(self,
+    def cone(self,
         *,
         bottom: Vec3[float],
         up: Vec3[float],
diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index b9e47bd..29c8961 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -833,9 +833,9 @@ class CylinderParams(BaseModel):
     up: PrimitivePositionT = Field(description="Position of the top.")
     radius_top: float = Field(description="The radius of the top of the cylinder top. Radius equal to zero will yield a cone.")
     radius_bottom: float = Field(description="The radius of the bottom of the cylinder. Radius equal to zero will yield a reversed cone.")
-    # TODO: meaning of the following two? Check Sebastian's answers in some of the PRs.
-    theta_start: float = Field(description="TODO")
-    theta_length: float = Field(description="TODO")
+    # TODO: Implement start end of the arc (theta start end)
+    # theta_start: float = Field(description="TODO")
+    # theta_length: float = Field(description="TODO")
     # TODO: type for rotation as field
     rotation: Optional[Mat3[float]] = Field(
         description="9d vector describing the rotation, in a column major (j * 3 + i indexing) format, this is equivalent to Fortran-order in numpy, to be multiplied from the left",
@@ -843,6 +843,11 @@ class CylinderParams(BaseModel):
     bottom_cap: bool = Field(description="Determine whether to cap the top of the cylinder.")
     top_cap: bool = Field(description="Determine whether to cap the bottom of the cylinder.")
     
+    
+# TODO: instead of theta - tube?
+# addTube in mol*, params accordingly   
+
+
 
 # NOTE: arrow should be derived from line perhaps?
 # This allows us to make use of inheritance 

From b7712ac6f2d725f2dc0322a57f9a3a4f9c7ff4c6 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Sat, 16 Nov 2024 09:33:21 +0100
Subject: [PATCH 19/24] draft for circle

---
 molviewspec/molviewspec/builder.py | 37 ++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index 762ed22..34f7bae 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -17,6 +17,7 @@
     CageParams,
     CameraParams,
     CanvasParams,
+    CircleParams,
     ColorFromSourceParams,
     ColorFromUriParams,
     ColorInlineParams,
@@ -1001,6 +1002,42 @@ def cage(self,
         self._add_child(node)
         return self
 
+    # def ellipsoid(
+    #     self,
+    #     *,
+    #     direction_major: Vec3[float],
+    #     direction_minor: Vec3[float],
+    #     direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")
+    #     center: PrimitivePositionT = Field(description="The center of the ellipsoid.")
+    #     # TODO: is the meaning correct
+    #     radius_scale: Optional[Vec3[float]] = Field(description="3d vector describing the radius scaling.")
+
+        
+    # )
+    
+    def circle(self,
+        *,
+        center: PrimitivePositionT,
+        major_axis: PrimitivePositionT,
+        minor_axis: PrimitivePositionT
+        ):
+        # TODO annotation
+        # """
+        # Defines a box
+        # :param center: center of the box
+        # :param extent: height and width of the box
+        # :param scaling: scaling
+        # :param as_edges: 3d vector describing the scaling.
+        # :param label_offset: camera-facing offset to prevent overlap with geometry
+        # :param custom: optional, custom data to attach to this node
+        # :param ref: optional, reference that can be used to access this node
+        # :return: this builder
+        # """
+        params = make_params(CircleParams, {"kind": "circle", **locals()})
+        node = Node(kind="primitive", params=params)
+        self._add_child(node)
+        return self
+    
     def cone(self,
         *,
         bottom: Vec3[float],

From 6c53d6245f2107fdf97251b3351d7ec980ae8d38 Mon Sep 17 00:00:00 2001
From: Aliaksei <52605565+aliaksei-chareshneu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 09:33:53 +0100
Subject: [PATCH 20/24] Update molviewspec/molviewspec/nodes.py

Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
---
 molviewspec/molviewspec/nodes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 29c8961..0c73b01 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -824,7 +824,7 @@ class BoxParams(TransformMixin, RectangularPrismMixin):
     
 class CageParams(TransformMixin, RectangularPrismMixin):
     kind: Literal["cage"] = "cage"
-    type: Literal["as_lines", "as_geometry"] = "as_lines"
+    render_style: Literal["lines", "geometry"] = "lines"
     
 class CylinderParams(BaseModel):
     kind: Literal["cylinder"] = "cylinder"

From b7e191c3e6892765db4f4fb3e903317e57dc9591 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Sat, 16 Nov 2024 10:18:50 +0100
Subject: [PATCH 21/24] examples

---
 _examples/build_example.py | 113 +++++++++++++++++++++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 _examples/build_example.py

diff --git a/_examples/build_example.py b/_examples/build_example.py
new file mode 100644
index 0000000..9263813
--- /dev/null
+++ b/_examples/build_example.py
@@ -0,0 +1,113 @@
+from molviewspec.molviewspec.builder import create_builder
+from molviewspec.molviewspec.nodes import ComponentExpression
+
+
+builder = create_builder()
+
+download = builder.download(url="https://www.ebi.ac.uk/pdbe/entry-files/download/1tqn_updated.cif")
+structure = download.parse(format="mmcif").model_structure()
+
+component1 = structure.component(selector="ligand").representation(type="ball_and_stick")
+structure.component(selector="polymer").representation(type="cartoon")
+structure.primitives().box(center=ComponentExpression(auth_seq_id=508), extent=[5,5,5], color="green")  # or .cage
+
+# TODO: debug at frontend then try these params
+builder.primitives().box(
+    center=[0.1, 0.1, 0.1],
+    extent=[1.0, 1.0, 1.0],
+    color="red",
+    scaling=[10.0, 1.0, 1.0],
+    translation=[10.0, 10.0, 10.0],
+    rotation_axis=[0.0, 1.0, 0.0],
+    rotation_radians=1.0
+)
+
+structure.primitives().cage(
+    # center=[0.5, 0.5, 0.5],
+    center=ComponentExpression(auth_seq_id=508),
+    extent=[5.0, 3.0, 18.0],
+    color="orange",
+    scaling=[10.0, 1.0, 1.0],
+    translation=[10.0, 10.0, 10.0],
+    rotation_axis=[0.0, 1.0, 0.0],
+    rotation_radians=1.0,
+    edge_radius=7.5,
+    # TODO: as geometry
+    type="as_lines"
+)
+
+structure.primitives().cone(
+    radius_bottom=1.5,
+    radius_top=2.5,
+    bottom_cap=True,
+    top_cap=False,
+    color="magenta",
+    bottom=[1, 1, 1],
+    up=[2,5,10]
+    # bottom=ComponentExpression(auth_seq_id=508),
+    # up=ComponentExpression(auth_seq_id=507) 
+)  
+
+builder.primitives().box(
+    center=[10, 10, 10],
+    extent=[2.0, 3.0, 10.0],
+    color="blue"
+)
+
+
+# let's throw in some lines and labels that intersect each face in the middle
+# (
+#     builder.primitives(color="blue", label_color="blue", tooltip="Generic Axis", transparency=0.5)
+#     # chain primitives to create desired visuals
+#     .line(start=(-0.5, 0.5, 0.5), end=(1.5, 0.5, 0.5), thickness=0.05, color="red", tooltip="### Axis\nX")
+#     # .label(position=(-0.5, 0.5, 0.5), text="X", label_size=0.33, label_color="orange")
+#     .line(start=(0.5, -0.5, 0.5), end=(0.5, 1.5, 0.5), thickness=0.05, color="green", tooltip="### Axis\nY")
+#     # .label(position=(0.5, -0.5, 0.5), text="Y", label_size=0.33, label_color="blue")
+#     .line(start=(0.5, 0.5, -0.5), end=(0.5, 0.5, 1.5), thickness=0.05, color="magenta")
+#     # .label(position=(0.5, 0.5, -0.5), text="Z", label_size=0.33, color="yellow")
+# )
+# builder.primitives().mesh(
+#     vertices=[
+#         0.0, 0.0, 0.0,
+#         1.0, 0.0, 0.0,
+#         1.0, 1.0, 0.0,
+#         0.0, 1.0, 0.0,
+#         0.0, 0.0, 1.0,
+#         1.0, 0.0, 1.0,
+#         1.0, 1.0, 1.0,
+#         0.0, 1.0, 1.0,
+#     ],
+#     indices=[
+#         # bottom
+#         0, 2, 1, 0, 3, 2,
+#         # top
+#         4, 5, 6, 4, 6, 7,
+#         # front
+#         0, 1, 5, 0, 5, 4,
+#         # back
+#         2, 3, 7, 2, 7, 6,
+#         # left
+#         0, 7, 3, 0, 4, 7,
+#         # right
+#         1, 2, 6, 1, 6, 5,
+#     ],
+#     triangle_groups=[0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5],
+#     group_colors={0: "red", 1: "green", 2: "blue", 3: "yellow", 4: "magenta", 5: "cyan"},
+#     group_tooltips={0: "### Side\nbottom", 1: "### Side\ntop", 2: "### Side\nfront", 3: "### Side\nback", 4: "### Side\nleft", 5: "### Side\nright"},
+#     show_wireframe=True,
+#     wireframe_radius=2,
+#     wireframe_color="black",
+# )
+# # let's throw in some lines and labels that intersect each face in the middle
+# (
+#     builder.primitives(color="blue", label_color="blue", tooltip="Generic Axis", transparency=0.5)
+#     # chain primitives to create desired visuals
+#     .line(start=(-0.5, 0.5, 0.5), end=(1.5, 0.5, 0.5), thickness=0.05, color="red", tooltip="### Axis\nX")
+#     .label(position=(-0.5, 0.5, 0.5), text="X", label_size=0.33, label_color="red")
+#     .line(start=(0.5, -0.5, 0.5), end=(0.5, 1.5, 0.5), thickness=0.05, color="green", tooltip="### Axis\nY")
+#     .label(position=(0.5, -0.5, 0.5), text="Y", label_size=0.33, label_color="green")
+#     .line(start=(0.5, 0.5, -0.5), end=(0.5, 0.5, 1.5), thickness=0.05)
+#     .label(position=(0.5, 0.5, -0.5), text="Z", label_size=0.33)
+# )
+
+builder.save_state(destination='./_examples/state.mvsj')
\ No newline at end of file

From 4ae6e3117bbe661a16b2facbbc725e4b497c430f Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Sat, 16 Nov 2024 10:21:16 +0100
Subject: [PATCH 22/24] upd example

---
 _examples/build_example.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/_examples/build_example.py b/_examples/build_example.py
index 9263813..856a534 100644
--- a/_examples/build_example.py
+++ b/_examples/build_example.py
@@ -42,10 +42,10 @@
     bottom_cap=True,
     top_cap=False,
     color="magenta",
-    bottom=[1, 1, 1],
-    up=[2,5,10]
-    # bottom=ComponentExpression(auth_seq_id=508),
-    # up=ComponentExpression(auth_seq_id=507) 
+    # bottom=[1, 1, 1],
+    # up=[2,5,10]
+    bottom=ComponentExpression(auth_seq_id=508),
+    up=ComponentExpression(auth_seq_id=399) 
 )  
 
 builder.primitives().box(

From a20d3bd4a02e0f9f0001d4afbcaa96c55bb6e052 Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Wed, 20 Nov 2024 07:14:18 +0100
Subject: [PATCH 23/24] ellipsoid prototype (tested, color TODO); ellipsis
 draft (WIP);

---
 molviewspec/molviewspec/builder.py | 49 ++++++++++++++++++++----------
 molviewspec/molviewspec/nodes.py   |  6 ++--
 2 files changed, 35 insertions(+), 20 deletions(-)

diff --git a/molviewspec/molviewspec/builder.py b/molviewspec/molviewspec/builder.py
index 34f7bae..3087784 100644
--- a/molviewspec/molviewspec/builder.py
+++ b/molviewspec/molviewspec/builder.py
@@ -17,7 +17,7 @@
     CageParams,
     CameraParams,
     CanvasParams,
-    CircleParams,
+    EllipsisParams,
     ColorFromSourceParams,
     ColorFromUriParams,
     ColorInlineParams,
@@ -32,6 +32,7 @@
     DescriptionFormatT,
     DistanceMeasurementParams,
     DownloadParams,
+    EllipsoidParams,
     FocusInlineParams,
     LabelFromSourceParams,
     LabelFromUriParams,
@@ -1002,22 +1003,37 @@ def cage(self,
         self._add_child(node)
         return self
 
-    # def ellipsoid(
-    #     self,
-    #     *,
-    #     direction_major: Vec3[float],
-    #     direction_minor: Vec3[float],
-    #     direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")
-    #     center: PrimitivePositionT = Field(description="The center of the ellipsoid.")
-    #     # TODO: is the meaning correct
-    #     radius_scale: Optional[Vec3[float]] = Field(description="3d vector describing the radius scaling.")
-
-        
-    # )
+    # TODO: sphere
+    def ellipsoid(
+        self,
+        *,
+        color: ColorT | None = None,
+        direction_major: Vec3[float],
+        direction_minor: Vec3[float],
+        center: PrimitivePositionT,
+        radius_scale: Vec3[float] | None = None
+        ):
+        # TODO annotation
+        # """
+        # Defines a box
+        # :param center: center of the box
+        # :param extent: height and width of the box
+        # :param scaling: scaling
+        # :param as_edges: 3d vector describing the scaling.
+        # :param label_offset: camera-facing offset to prevent overlap with geometry
+        # :param custom: optional, custom data to attach to this node
+        # :param ref: optional, reference that can be used to access this node
+        # :return: this builder
+        # """
+        params = make_params(EllipsoidParams, {"kind": "ellipsoid", **locals()})
+        node = Node(kind="primitive", params=params)
+        self._add_child(node)
+        return self
     
-    def circle(self,
+    def ellipsis(self,
         *,
         center: PrimitivePositionT,
+        color: ColorT | None = None,
         major_axis: PrimitivePositionT,
         minor_axis: PrimitivePositionT
         ):
@@ -1033,12 +1049,13 @@ def circle(self,
         # :param ref: optional, reference that can be used to access this node
         # :return: this builder
         # """
-        params = make_params(CircleParams, {"kind": "circle", **locals()})
+        params = make_params(EllipsisParams, {"kind": "circle", **locals()})
         node = Node(kind="primitive", params=params)
         self._add_child(node)
         return self
     
-    def cone(self,
+    # TODO: cone
+    def cylinder(self,
         *,
         bottom: Vec3[float],
         up: Vec3[float],
diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index 0c73b01..a942f61 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -771,7 +771,7 @@ def validate_state_tree(json: str) -> None:
     State.parse_raw(json)
 
 # TODO: fields instead of plain types
-class CircleParams(BaseModel):
+class EllipsisParams(BaseModel):
     kind: Literal["circle"] = "circle"
     center: PrimitivePositionT = Field(description="The center of the circle.")
     # TODO: elaborate names and semantics depending on
@@ -920,13 +920,11 @@ class WedgeParams(BaseModel):
     )
     
 class EllipsoidParams(BaseModel):
-    # TODO: adjust based on frontend implementation
     kind: Literal["ellipsoid"] = "ellipsoid"
     direction_major: Vec3[float] = Field(description="Major direction of the ellipsoid.")
     direction_minor: Vec3[float] = Field(description="Minor direction of the ellipsoid.")
-    direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")
+    # direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")
     center: PrimitivePositionT = Field(description="The center of the ellipsoid.")
-    # TODO: is the meaning correct
     radius_scale: Optional[Vec3[float]] = Field(description="3d vector describing the radius scaling.")
 
 # TODO:

From 617a8f3a3c7c412dfaea8cad0b2969d82a87482f Mon Sep 17 00:00:00 2001
From: Aliaksei Chareshneu <chareshneu.tech@gmail.com>
Date: Wed, 20 Nov 2024 07:16:34 +0100
Subject: [PATCH 24/24] fix: add missing color params

---
 molviewspec/molviewspec/nodes.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/molviewspec/molviewspec/nodes.py b/molviewspec/molviewspec/nodes.py
index a942f61..06458dc 100644
--- a/molviewspec/molviewspec/nodes.py
+++ b/molviewspec/molviewspec/nodes.py
@@ -773,6 +773,7 @@ def validate_state_tree(json: str) -> None:
 # TODO: fields instead of plain types
 class EllipsisParams(BaseModel):
     kind: Literal["circle"] = "circle"
+    color: Optional[ColorT] = Field(description="Default color for the circle.")
     center: PrimitivePositionT = Field(description="The center of the circle.")
     # TODO: elaborate names and semantics depending on
     # how Mol* implements circles
@@ -921,6 +922,7 @@ class WedgeParams(BaseModel):
     
 class EllipsoidParams(BaseModel):
     kind: Literal["ellipsoid"] = "ellipsoid"
+    color: Optional[ColorT] = Field(description="Default color for the box.")
     direction_major: Vec3[float] = Field(description="Major direction of the ellipsoid.")
     direction_minor: Vec3[float] = Field(description="Minor direction of the ellipsoid.")
     # direction_normal: Vec3[float] = Field(description="Normal direction of the ellipsoid.")