cosmol-viewer 0.1.3.dev3__cp37-abi3-macosx_11_0_arm64.whl → 0.1.4__cp37-abi3-macosx_11_0_arm64.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,
@@ -189,7 +189,8 @@ class Viewer:
         interval: float,
         loops: int,
         width: float = 800.0,
-        height: float = 600.0
+        height: float = 600.0,
+        smooth: bool = False
     ) -> "Viewer":
         """
         Play an animation of multiple frames.
@@ -200,6 +201,8 @@ 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
+            interpolating between frames.
 
         # Returns
           - Viewer: The created viewer instance.
@@ -303,6 +306,7 @@ class Molecules:
     """
 
     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": ...

cosmol_viewer-0.1.4.dist-info/METADATA

@@ -0,0 +1,107 @@
+Metadata-Version: 2.4
+Name: cosmol-viewer
+Version: 0.1.4
+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
+
+<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"/>
+  </a>
+  <a href="https://pypi.org/project/cosmol_viewer/">
+    <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"/>
+  </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 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`).
+
+---
+
+## Quick concepts
+
+- **Scene**: container for shapes (molecules, spheres, lines, 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.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?**
+- Single call API (hand off responsibility to the viewer).
+- Built-in timing & loop control.
+- Optional `smooth` interpolation between frames for visually pleasing playback even when input frame rate is low.
+
+**Why keep `update`?**
+- `update` is ideal for real-time simulations, MD runs, or streaming data where frames are not precomputed. It provides strict fidelity (no interpolation) and minimal latency.
+
+---
+
+## Installation
+
+```sh
+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
+from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
+
+with open("molecule.sdf", "r") as f:
+    sdf = f.read()
+    mol = Molecules(parse_sdf(sdf)).centered()
+
+scene = Scene()
+scene.scale(0.1)
+scene.add_shape(mol, "mol")
+
+viewer = Viewer.render(scene, width=600, height=400)
+
+print("Press Any Key to exit...", end='', flush=True)
+_ = input()  # Keep the viewer open until you decide to close
+```
+
+### 2. Animation playback with `Viewer.play`
+
+```python
+from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
+import time
+
+interval = 0.033   # ~30 FPS
+
+frames = []
+
+for i in range(1, 10):
+    with open(f"frames/frame_{i}.sdf", "r") as f:
+        sdf = f.read()
+        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)
+```
+
+## Documentation
+
+For API reference and advanced usage, please see the [latest documentation](https://cosmol-repl.github.io/COSMol-viewer).
+

cosmol_viewer-0.1.4.dist-info/RECORD

@@ -0,0 +1,7 @@
+cosmol_viewer-0.1.4.dist-info/METADATA,sha256=49VUM-fWJZOrqzrBNa3mdU6Np-faZk9q4wGPa_TxioU,3574
+cosmol_viewer-0.1.4.dist-info/WHEEL,sha256=gOHyQdiSQeKttFRzSnw4phRI5RWXgJRaZ2Lc4suoeWU,102
+cosmol_viewer/__init__.py,sha256=K33zoYpHqUVvpFdMVxmCtw4uKj9ZXrGuQD4D4DuUmjk,135
+cosmol_viewer/__init__.pyi,sha256=lq3cc-eCn1xDmxxf4yKG8N6uvXsc2g5mpithyJbZPQc,8427
+cosmol_viewer/cosmol_viewer.abi3.so,sha256=phNHWG1tCiYtEDxU9nRYxPxe6ArTiTaf24SwN_nme2s,15911968
+cosmol_viewer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+cosmol_viewer-0.1.4.dist-info/RECORD,,

{cosmol_viewer-0.1.3.dev3.dist-info → cosmol_viewer-0.1.4.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: maturin (1.9.4)
+Generator: maturin (1.9.6)
 Root-Is-Purelib: false
 Tag: cp37-abi3-macosx_11_0_arm64

cosmol_viewer-0.1.3.dev3.dist-info/METADATA

@@ -1,179 +0,0 @@
-Metadata-Version: 2.4
-Name: cosmol-viewer
-Version: 0.1.3.dev3
-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
-
-<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"/>
-  </a>
-  <a href="https://pypi.org/project/cosmol_viewer/">
-    <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"/>
-  </a>
-</div>
-
-**COSMol-viewer** is a high-performance molecular visualization library, written in **Rust** and powered by **WebGPU**, designed for seamless integration into **Python** workflows.  
-
-- ⚡ **High-speed rendering** — GPU-accelerated performance at native speed  
-- 🧬 **Flexible input** — Load structures from `.sdf`, `.pdb`, or dynamically generated coordinates  
-- 📓 **Notebook-ready** — Fully compatible with Jupyter and Google Colab, ideal for teaching, research, and interactive demos  
-- 🔁 **Dynamic visualization** — Update molecular structures on-the-fly or play smooth preloaded animations  
-- 🎨 **Customizable** — Fine-grained control of rendering styles, camera, and scene parameters  
-
----
-
-## Installation
-
-```sh
-pip install cosmol-viewer
-```
-
----
-
-## Quick Start
-
-```python
-from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
-
-# === Step 1: Load and render a molecule ===
-with open("molecule.sdf", "r") as f:
-    sdf = f.read()
-    mol = Molecules(parse_sdf(sdf)).centered()
-
-scene = Scene()
-scene.scale(0.1)
-scene.add_shape(mol, "mol")
-
-viewer = Viewer.render(scene, width=600, height=400)  # Launch viewer
-
-print("Press Any Key to exit...", end='', flush=True)
-_ = input()  # Keep the viewer open until you decide to close
-```
-
----
-
-## Animation Modes
-
-COSMol-viewer supports **two complementary animation workflows**, depending on whether you prefer **real-time updates** or **preloaded playback**.
-
-### 1. Real-Time Updates (Frame-by-Frame Streaming)
-
-Update the molecule directly inside an existing scene:
-
-```python
-import time
-from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
-
-scene = Scene()
-scene.scale(0.1)
-
-# Initial load
-with open("frames/frame_1.sdf", "r") as f:
-    sdf = f.read()
-    mol = Molecules(parse_sdf(sdf)).centered()
-scene.add_shape(mol, "mol")
-
-viewer = Viewer.render(scene, width=600, height=400)
-
-# Update in real time
-for i in range(2, 10):
-    with open(f"frames/frame_{i}.sdf", "r") as f:
-        sdf = f.read()
-        updated_mol = Molecules(parse_sdf(sdf)).centered()
-
-    scene.update_shape("mol", updated_mol)
-    viewer.update(scene)
-
-    time.sleep(0.033)  # ~30 FPS
-
-print("Press Any Key to exit...", end='', flush=True)
-_ = input()
-```
-
-**Use cases:**  
-- Visualizing the *progress* of a simulation step-by-step  
-- Interactive experiments or streaming scenarios where frames are not known in advance  
-
-**Trade-offs:**  
-- ✅ Low memory usage — no need to preload frames  
-- ⚠️ Playback smoothness depends on computation / I/O speed → may stutter if frame generation is slow  
-
----
-
-### 2. Preloaded Playback (One-Shot Animation) (Start from 0.1.3)
-
-Load all frames into memory first, then play them back smoothly:
-
-```python
-from cosmol_viewer import Scene, Viewer, parse_sdf, Molecules
-
-frames = []
-interval = 0.033  # ~30 FPS
-
-# Preload all frames
-for i in range(1, 10):
-    with open(f"frames/frame_{i}.sdf", "r") as f:
-        sdf = f.read()
-        mol = Molecules(parse_sdf(sdf)).centered()
-
-    scene = Scene()
-    scene.scale(0.1)
-    scene.add_shape(mol, "mol")
-    frames.append(scene)
-
-# Playback once
-Viewer.play(frames, interval=interval, loops=1, width=600, height=400)
-
-print("Press Any Key to exit...", end='', flush=True)
-_ = input()
-```
-
-**Use cases:**  
-- Smooth, stable playback for presentations or teaching  
-- Demonstrating precomputed trajectories (e.g., molecular dynamics snapshots)  
-
-**Trade-offs:**  
-- ✅ Very smooth playback, independent of computation speed  
-- ⚠️ Requires preloading all frames → higher memory usage  
-- ⚠️ Longer initial load time for large trajectories  
-
----
-
-## Choosing the Right Mode
-
-- ✅ Use **real-time updates** if your frames are generated on-the-fly or memory is limited  
-- ✅ Use **preloaded playback** if you want guaranteed smooth animations and can preload your trajectory  
-
----
-
-## Exiting the Viewer
-
-> **Important:** The viewer is bound to the Python process.  
-> When your script finishes, the rendering window will close automatically.
-
-To keep the visualization alive until you are ready to exit, always add:
-
-```python
-print("Press Any Key to exit...", end='', flush=True)
-_ = input()
-```
-
-This ensures:  
-- The window stays open for inspection  
-- The user decides when to end visualization  
-- Prevents premature termination at the end of the script  
-
----
-
-## Documentation
-
-For API reference and advanced usage, please see the [latest documentation](https://cosmol-repl.github.io/COSMol-viewer).  
-

cosmol_viewer-0.1.3.dev3.dist-info/RECORD

@@ -1,7 +0,0 @@
-cosmol_viewer-0.1.3.dev3.dist-info/METADATA,sha256=ltiAY7EEIiiPUOraXmihr8Wn7dl9aU_LSoBr9NSm0rk,5289
-cosmol_viewer-0.1.3.dev3.dist-info/WHEEL,sha256=aCJZ1_TowweRDOS2CdoZm6TuOJJGZtCD10G-Asa9J1M,102
-cosmol_viewer/__init__.py,sha256=K33zoYpHqUVvpFdMVxmCtw4uKj9ZXrGuQD4D4DuUmjk,135
-cosmol_viewer/__init__.pyi,sha256=JzeDsMSjCE2ErFohX6fzrWVPUYVsEPksIVqc0b6J6DU,8256
-cosmol_viewer/cosmol_viewer.abi3.so,sha256=4h8Tn9w-EYS8qwLSsvqysQr3P1cQVQ2qUSzfA1hmezI,13790096
-cosmol_viewer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cosmol_viewer-0.1.3.dev3.dist-info/RECORD,,