Additional primitives

_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=399) 
+)  
+
+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')

molviewspec/molviewspec/builder.py

@@ -12,8 +12,12 @@
 from pydantic import BaseModel, PrivateAttr
 
 from molviewspec.nodes import (
+# from molviewspec.molviewspec.nodes import (
+    BoxParams,
+    CageParams,
     CameraParams,
     CanvasParams,
+    EllipsisParams,
     ColorFromSourceParams,
     ColorFromUriParams,
     ColorInlineParams,
@@ -24,9 +28,11 @@
     ComponentInlineParams,
     ComponentSelectorT,
     CustomT,
+    CylinderParams,
     DescriptionFormatT,
     DistanceMeasurementParams,
     DownloadParams,
+    EllipsoidParams,
     FocusInlineParams,
     LabelFromSourceParams,
     LabelFromUriParams,
@@ -57,7 +63,7 @@
     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:
@@ -566,6 +572,7 @@ 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 +942,147 @@ def label(
         node = Node(kind="primitive", params=params)
         self._add_child(node)
         return self
+
+    def box(self,
+        *,
+        center: PrimitivePositionT,
+        extent: Vec3,
+        color: ColorT | None = None,
+        scaling: Vec3[float] | None = [1.0, 1.0, 1.0],
+        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
+        # """
+        # 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: PrimitivePositionT,
+        extent: Vec3,
+        color: ColorT | None = None,
+        scaling: Vec3[float] | None = [1.0, 1.0, 1.0],
+        edge_radius: 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:
+        # 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(CageParams, {"kind": "cage", **locals()})
+        node = Node(kind="primitive", params=params)
+        self._add_child(node)
+        return self
+
+    # 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 ellipsis(self,
+        *,
+        center: PrimitivePositionT,
+        color: ColorT | None = None,
+        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(EllipsisParams, {"kind": "circle", **locals()})
+        node = Node(kind="primitive", params=params)
+        self._add_child(node)
+        return self
+
+    # TODO: cone
+    def cylinder(self,
+        *,
+        bottom: Vec3[float],
+        up: Vec3[float],
+        radius_top: float,
+        radius_bottom: float,
+        bottom_cap: bool,
+        top_cap: bool,
+        color: ColorT | None = None,
+        rotation_axis: Vec3[float] | None = None,
+        rotation_radians: 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
+