cosmol-viewer 0.1.4.dev2__cp37-abi3-manylinux_2_17_i686.manylinux2014_i686.whl → 0.1.5.dev7__cp37-abi3-manylinux_2_17_i686.manylinux2014_i686.whl

cosmol_viewer/__init__.pyi

@@ -1,16 +1,16 @@
-from typing import Optional, Union, List 
+from typing import Optional, Union, List
 
 def parse_sdf(
     sdf: str,
     keep_h: bool = True,
     multimodel: bool = True,
     onemol: bool = False
-) -> "MoleculeData":
+) -> MoleculeData:
     """
-    Parse an SDF file or string into molecule data.
+    Parse an SDF string into molecule data.
 
     # Args
-      - sdf: Path to an SDF file or a string containing SDF content.
+      - sdf: Path to an SD string containing SDF content.
       - keep_h: Whether to keep explicit hydrogen atoms (default: True).
       - multimodel: Whether to allow multiple models in one file (default: True).
       - onemol: Whether to merge multiple models into one molecule (default: False).
@@ -21,11 +21,30 @@ def parse_sdf(
     # Example
     ```python
     from cosmol_viewer import parse_sdf
-    mol = parse_sdf("molecule.sdf")
+    mol = parse_sdf(open("./molecule.sdf", "r", encoding="utf-8").read())
     ```
     """
     ...
 
+def parse_mmcif(
+    mmcif: str
+) -> ProteinData:
+    """
+    Parse an MMCIF string into protein data.
+
+    # Args
+      - mmcif: Path to an MMCIF string containing MMCIF content.
+
+    # Returns
+      - ProteinData: Parsed protein data object.
+
+    # Example
+    ```python
+    from cosmol_viewer import parse_mmcif
+    prot = parse_mmcif(open("./protein.cif", "r", encoding="utf-8").read())
+    ```
+    """
+    ...
 
 class Scene:
     """
@@ -54,12 +73,12 @@ class Scene:
         """
         ...
 
-    def add_shape(self, shape: Union["Sphere", "Stick", "Molecules"], id: Optional[str] = None) -> None:
+    def add_shape(self, shape: Union["Sphere", "Stick", "Molecules", "Protein"], id: Optional[str] = None) -> None:
         """
         Add a shape to the scene.
 
         # Args
-          - shape: A shape instance (PySphere, PyStick, or PyMolecules).
+          - shape: A shape instance (Sphere, Stick, Molecules, or Protein).
           - id: Optional string ID to associate with the shape.
 
         If the `id` is provided and a shape with the same ID exists,
@@ -73,7 +92,7 @@ class Scene:
         """
         ...
 
-    def update_shape(self, id: str, shape: Union["Sphere", "Stick", "Molecules"]) -> None:
+    def update_shape(self, id: str, shape: Union["Sphere", "Stick", "Molecules", "Protein"]) -> None:
         """
         Update an existing shape in the scene by its ID.
 
@@ -102,6 +121,20 @@ class Scene:
         """
         ...
 
+    def recenter(self, center: List[float]) -> None:
+        """
+        Recenter the scene at a given point.
+
+        # Args
+          - center: An XYZ array of 3 float values representing the new center.
+
+        # Example
+        ```python
+        scene.recenter([0.0, 0.0, 0.0])
+        ```
+        """
+        ...
+
     def scale(self, scale: float) -> None:
         """
         Set the global scale factor of the scene.
@@ -132,6 +165,17 @@ class Scene:
         """
         ...
 
+    def use_black_background(self) -> None:
+        """
+        Set the background color of the scene to black.
+
+        # Example
+        ```python
+        scene.use_black_background()
+        ```
+        """
+        ...
+
 class Viewer:
     """
     A viewer that renders 3D scenes in different runtime environments
@@ -201,7 +245,7 @@ class Viewer:
           - loops: Number of loops to repeat (-1 for infinite).
           - width: The viewport width in pixels.
           - height: The viewport height in pixels.
-          - smooth: Whether to smooth the animation by 
+          - smooth: Whether to smooth the animation by
             interpolating between frames.
 
         # Returns
@@ -296,23 +340,50 @@ class Stick:
 
 class Molecules:
     """
-    A molecular shape object parsed from SDF data.
+    A molecular shape object.
 
     # Example
     ```python
-    mol = parse_sdf("molecule.sdf")
+    mol = parse_sdf(open("molecule.sdf", "r", encoding="utf-8").read())
     molecules = Molecules(mol).centered().color([0,1,0])
     ```
     """
 
     def __init__(self, molecule_data: "MoleculeData") -> None: ...
+    def get_center(self) -> List[float]: ...
     def centered(self) -> "Molecules": ...
     def color(self, color: List[float]) -> "Molecules": ...
     def color_rgba(self, color: List[float]) -> "Molecules": ...
     def opacity(self, opacity: float) -> "Molecules": ...
+    def reset_color(self) -> "Molecules": ...
 
 class MoleculeData:
     """
     Internal representation of molecule data returned by `parse_sdf`.
     """
     ...
+
+class Protein:
+    """
+    A protein shape object.
+
+    # Example
+    ```python
+    mmcif_data  = parse_mmcif(open("2AMD.cif", "r", encoding="utf-8").read())
+    prot = Protein(mmcif_data).centered().color([0,1,0])
+    ```
+    """
+
+    def __init__(self, molecule_data: "MoleculeData") -> None: ...
+    def get_center(self) -> List[float]: ...
+    def centered(self) -> "Molecules": ...
+    def color(self, color: List[float]) -> "Molecules": ...
+    def color_rgba(self, color: List[float]) -> "Molecules": ...
+    def opacity(self, opacity: float) -> "Molecules": ...
+    def reset_color(self) -> "Molecules": ...
+
+class ProteinData:
+    """
+    Internal representation of protein data returned by `parse_mmcif`.
+    """
+    ...

{cosmol_viewer-0.1.4.dev2.dist-info → cosmol_viewer-0.1.5.dev7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.1.4.dev2
+Version: 0.1.5.dev7
 Summary: Molecular visualization tools
 Author-email: 95028 <wjt@cosmol.org>
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
@@ -20,8 +20,8 @@ Project-URL: Repository, https://github.com/COSMol-repl/COSMol-viewer
   </a>
 </div>
 
-A high-performance molecular viewer for `Python` and `Rust`, backed by `Rust`.  
-Supports both static rendering and smooth animation playback — including inside Jupyter notebooks. 
+A high-performance molecular viewer for `Python` and `Rust`, backed by `Rust`.
+Supports both static rendering and smooth animation playback — including inside Jupyter notebooks.
 
 
 A compact, high-performance renderer for molecular and scientific shapes with two usage patterns:
@@ -57,7 +57,7 @@ pip install cosmol-viewer
 ---
 
 ## Quick Start
-
+See examples in [Google Colab](https://colab.research.google.com/drive/1Sw72QWjQh_sbbY43jGyBOfF1AQCycmIx?usp=sharing).
 ### 1. Static molecular rendering
 
 ```python
@@ -103,5 +103,5 @@ Viewer.play(frames, interval=interval, loops=1, width=600, height=400, smooth=Tr
 
 ## Documentation
 
-For API reference and advanced usage, please see the [latest documentation](https://cosmol-repl.github.io/COSMol-viewer).  
+For API reference and advanced usage, please see the [latest documentation](https://cosmol-repl.github.io/COSMol-viewer).
 

cosmol_viewer-0.1.5.dev7.dist-info/RECORD

@@ -0,0 +1,7 @@
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+cosmol_viewer-0.1.5.dev7.dist-info/WHEEL,sha256=oB91FzNpC-hO8c8ewOPvbQZBthpYN_59_Trh5rKisIg,139
+cosmol_viewer/__init__.py,sha256=K33zoYpHqUVvpFdMVxmCtw4uKj9ZXrGuQD4D4DuUmjk,135
+cosmol_viewer/__init__.pyi,sha256=fNOQlMLuOiY6IJxHG8hmdJxeaSbaz4Vn45f3oi17Gyg,10220
+cosmol_viewer/cosmol_viewer.abi3.so,sha256=v5k_up9PYWf9jccaRx54yW8qwVIxrG_ISXYUeSzNOf0,29500808
+cosmol_viewer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+cosmol_viewer-0.1.5.dev7.dist-info/RECORD,,

cosmol_viewer-0.1.5.dev7.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: maturin (1.10.2)
+Root-Is-Purelib: false
+Tag: cp37-abi3-manylinux_2_17_i686
+Tag: cp37-abi3-manylinux2014_i686

cosmol_viewer-0.1.4.dev2.dist-info/RECORD

@@ -1,7 +0,0 @@
-cosmol_viewer-0.1.4.dev2.dist-info/METADATA,sha256=ntIjMLqgxfDlGAyBDKLqv7yYLjx_iSvEtdwizEyrPqU,3466
-cosmol_viewer-0.1.4.dev2.dist-info/WHEEL,sha256=GiWFiSsWOslMBN41z1mfBeDroO-c1QlctGEFpKcYtJE,123
-cosmol_viewer/__init__.py,sha256=K33zoYpHqUVvpFdMVxmCtw4uKj9ZXrGuQD4D4DuUmjk,135
-cosmol_viewer/__init__.pyi,sha256=haGIhR4cKSfwOsni4Vk9dG4r9ApSfDN0Z2Zui-BD3e0,8384
-cosmol_viewer/cosmol_viewer.abi3.so,sha256=SerZm9h3s6aLbm0qQUhV623jq-ci3otUR-vvj2nKv30,26447488
-cosmol_viewer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cosmol_viewer-0.1.4.dev2.dist-info/RECORD,,

cosmol_viewer-0.1.4.dev2.dist-info/WHEEL

@@ -1,4 +0,0 @@
-Wheel-Version: 1.0
-Generator: maturin (1.9.6)
-Root-Is-Purelib: false
-Tag: cp37-abi3-manylinux_2_17_i686.manylinux2014_i686