cosmol-viewer 0.1.4.dev2__cp37-abi3-manylinux_2_17_i686.manylinux2014_i686.whl → 0.1.7__cp37-abi3-manylinux_2_17_i686.manylinux2014_i686.whl

cosmol_viewer/__init__.pyi

@@ -1,4 +1,4 @@
-from typing import Optional, Union, List 
+from typing import Optional, Union, List
 
 def parse_sdf(
     sdf: str,
@@ -7,10 +7,10 @@ def parse_sdf(
     onemol: bool = False
 ) -> "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, mmcif_data: "ProteinData") -> None: ...
+    def get_center(self) -> List[float]: ...
+    def centered(self) -> "Protein": ...
+    def color(self, color: List[float]) -> "Protein": ...
+    def color_rgba(self, color: List[float]) -> "Protein": ...
+    def opacity(self, opacity: float) -> "Protein": ...
+    def reset_color(self) -> "Protein": ...
+
+class ProteinData:
+    """
+    Internal representation of protein data returned by `parse_mmcif`.
+    """
+    ...

{cosmol_viewer-0.1.4.dev2.dist-info → cosmol_viewer-0.1.7.dist-info}/METADATA

@@ -1,41 +1,43 @@
 Metadata-Version: 2.4
 Name: cosmol-viewer
-Version: 0.1.4.dev2
+Version: 0.1.7
 Summary: Molecular visualization tools
 Author-email: 95028 <wjt@cosmol.org>
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 Project-URL: Repository, https://github.com/COSMol-repl/COSMol-viewer
 
 # COSMol-viewer
+A high-performance molecular viewer for Python and Rust, powered by a unified Rust core.
+It supports both in-notebook visualization and native desktop rendering, with smooth playback for scientific animations.
 
 <div align="center">
   <a href="https://crates.io/crates/cosmol_viewer">
-    <img src="https://img.shields.io/crates/v/cosmol_viewer.svg" alt="crates.io Latest Release"/>
+    <img src="https://img.shields.io/crates/v/cosmol_viewer.svg" alt="crates.io Latest Release" />
   </a>
   <a href="https://pypi.org/project/cosmol_viewer/">
-    <img src="https://img.shields.io/pypi/v/cosmol_viewer.svg" alt="PyPi Latest Release"/>
+    <img src="https://img.shields.io/pypi/v/cosmol_viewer.svg" alt="PyPi Latest Release" />
   </a>
   <a href="https://cosmol-repl.github.io/COSMol-viewer">
-    <img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Documentation Status"/>
+    <img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Documentation Status" />
   </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. 
+COSMol-viewer is a compact, cross-platform renderer for molecular and geometric scenes.
+Unlike purely notebook-bound solutions such as py3Dmol, COSMol-viewer runs everywhere:
 
+- Native desktop window (Python or Rust) via `egui`
+- Jupyter / IPython notebook via WASM backend
+- Rust applications
 
-A compact, high-performance renderer for molecular and scientific shapes with two usage patterns:
-
-- **Static rendering + update** — push individual scene updates from your application or simulation.
-- **Play (recommended for demonstrations & smooth playback)** — precompute frames and hand the sequence to the viewer to play back with optional interpolation (`smooth`).
+All implementations share the same Rust rendering engine, ensuring consistent performance and visual output.
 
 ---
 
 ## Quick concepts
 
-- **Scene**: container for shapes (molecules, spheres, lines, etc.).
+- **Scene**: container for shapes (molecules, proteins, spheres, etc.).
 - **Viewer.render(scene, ...)**: create a static viewer bound to a canvas (native or notebook). Good for static visualization.
-- **viewer.update(scene)**: push incremental changes (real-time / streaming use-cases).
+- **viewer.update(scene)**: push incremental changes after `Viewer.render()` (real-time / streaming use-cases).
 - **Viewer.play(frames, interval, loops, width, height, smooth)**: *recommended* for precomputed animations and demonstrations. The viewer takes care of playback timing and looping.
 
 **Why prefer `play` for demos?**
@@ -48,27 +50,23 @@ A compact, high-performance renderer for molecular and scientific shapes with tw
 
 ---
 
-## Installation
-
-```sh
-pip install cosmol-viewer
-```
+# Usage
 
----
+## python
+See examples in [Google Colab](https://colab.research.google.com/drive/1Sw72QWjQh_sbbY43jGyBOfF1AQCycmIx?usp=sharing).
 
-## Quick Start
+Install with `pip install cosmol-viewer`
 
 ### 1. Static molecular rendering
 
 ```python
 from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
+    
+mol_data  = parse_sdf(open("molecule.sdf", "r", encoding="utf-8").read())
 
-with open("molecule.sdf", "r") as f:
-    sdf = f.read()
-    mol = Molecules(parse_sdf(sdf)).centered()
+mol = Molecules(mol_data).centered()
 
 scene = Scene()
-scene.scale(0.1)
 scene.add_shape(mol, "mol")
 
 viewer = Viewer.render(scene, width=600, height=400)
@@ -81,9 +79,6 @@ _ = input()  # Keep the viewer open until you decide to close
 
 ```python
 from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
-import time
-
-interval = 0.033   # ~30 FPS
 
 frames = []
 
@@ -93,15 +88,24 @@ for i in range(1, 10):
         mol = Molecules(parse_sdf(sdf)).centered()
 
     scene = Scene()
-    scene.scale(0.1)
     scene.add_shape(mol, "mol")
-
     frames.append(scene)
 
-Viewer.play(frames, interval=interval, loops=1, width=600, height=400, smooth=True)
+Viewer.play(frames, interval=0.033, loops=-1, width=800, height=500, smooth=True) # loops=-1 for infinite repeat
 ```
 
-## Documentation
+more examples can be found in the [examples](https://github.com/COSMol-repl/COSMol-viewer/tree/main/cosmol_viewer/examples) folder:
+```bash
+cd cosmol_viewer
+python .\examples\render_protein.py
+```
+
+# Documentation
+
+Please check out our documentation at [here](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).  
+# Contact
 
+For any questions, issues, or suggestions, please contact [wjt@cosmol.org](mailto:wjt@cosmol.org) or open an issue in the repository. We will review and address them as promptly as possible.

cosmol_viewer-0.1.7.dist-info/RECORD

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+cosmol_viewer/cosmol_viewer.abi3.so,sha256=mqNEkOROmnWhd4kx8xQ040MG8XjawSgRvuY2z_6ifII,14092820
+cosmol_viewer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cosmol_viewer-0.1.7.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 @@
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-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