patinae 0.4.0__tar.gz

patinae-0.4.0/Cargo.toml

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+[workspace]
+resolver = "2"
+members = [
+    "crates/patinae-settings",
+    "crates/patinae-color",
+    "crates/patinae-mol",
+    "crates/patinae-select",
+    "crates/patinae-io",
+    "crates/patinae-render",
+    "crates/patinae-scene",
+    "crates/patinae-cmd",
+    "crates/patinae-framework",
+    "crates/patinae-plugin",
+    "crates/patinae-plugin-host",
+    "crates/patinae-algos",
+    "crates/patinae-session",
+    "plugins/hello",
+    "plugins/ipc",
+    "plugins/python",
+    "plugins/raytracer",
+    "bench",
+    "patinae",
+]
+default-members = [
+    "crates/patinae-settings",
+    "crates/patinae-color",
+    "crates/patinae-mol",
+    "crates/patinae-select",
+    "crates/patinae-io",
+    "crates/patinae-render",
+    "crates/patinae-scene",
+    "crates/patinae-cmd",
+    "crates/patinae-framework",
+    "crates/patinae-plugin",
+    "crates/patinae-plugin-host",
+    "crates/patinae-algos",
+    "crates/patinae-session",
+    "patinae",
+]
+# python API requires maturin to build (use: cd python && maturin build)
+# web viewer is built separately with wasm-pack (use: cd web && npm run build)
+exclude = ["python", "web"]
+
+[workspace.package]
+version = "0.4.0"
+edition = "2021"
+authors = ["Pavel Yakovlev"]
+license = "BSD-3-Clause"
+repository = "https://github.com/zmactep/patinae"
+homepage = "https://github.com/zmactep/patinae"
+documentation = "https://github.com/zmactep/patinae"
+
+[workspace.lints.rust]
+unsafe_op_in_unsafe_fn = "warn"
+
+[workspace.lints.clippy]
+correctness = { level = "warn", priority = -1 }
+suspicious = { level = "warn", priority = -1 }
+style = { level = "warn", priority = -1 }
+complexity = { level = "warn", priority = -1 }
+perf = { level = "warn", priority = -1 }
+undocumented_unsafe_blocks = "warn"
+
+[workspace.dependencies]
+# Internal crates
+patinae-settings = { version = "0.4.0", path = "crates/patinae-settings" }
+patinae-color = { version = "0.4.0", path = "crates/patinae-color" }
+patinae-mol = { version = "0.4.0", path = "crates/patinae-mol" }
+patinae-select = { version = "0.4.0", path = "crates/patinae-select" }
+patinae-io = { version = "0.4.0", path = "crates/patinae-io" }
+patinae-render = { version = "0.4.0", path = "crates/patinae-render", default-features = false }
+patinae-scene = { version = "0.4.0", path = "crates/patinae-scene", default-features = false }
+patinae-cmd = { version = "0.4.0", path = "crates/patinae-cmd", default-features = false }
+patinae-algos = { version = "0.4.0", path = "crates/patinae-algos" }
+patinae-session = { version = "0.4.0", path = "crates/patinae-session" }
+patinae-framework = { version = "0.4.0", path = "crates/patinae-framework" }
+patinae-plugin = { version = "0.4.0", path = "crates/patinae-plugin" }
+patinae-plugin-host = { version = "0.4.0", path = "crates/patinae-plugin-host" }
+
+# External dependencies
+bitflags = { version = "2", features = ["serde"] }
+lin_alg = { version = "1.1", features = ["computer_graphics"] }
+wgpu = "28"
+nom = "7"
+thiserror = "2"
+log = "0.4"
+libloading = "0.8"
+env_logger = "0.11"
+bytemuck = { version = "1", features = ["derive"] }
+ahash = { version = "0.8", features = ["serde"] }
+smallvec = { version = "1", features = ["serde"] }
+memmap2 = "0.9"
+flate2 = "1"
+rayon = "1"
+bitvec = "1"
+phf = { version = "0.11", features = ["macros"] }
+image = { version = "0.25", default-features = false, features = ["png"] }
+ab_glyph = "0.2"
+shellexpand = "3"
+dirs = "5"
+serde = { version = "1", features = ["derive", "rc"] }
+serde_json = "1"
+rmp-serde = "1"
+rustls = { version = "0.23", default-features = false, features = ["ring", "logging", "std", "tls12"] }
+tokio = { version = "1", features = ["rt-multi-thread", "sync", "time"] }
+webbrowser = "1.2"
+
+# Slint integration (Patinae GUI)
+slint = { version = "1.16", default-features = false, features = ["compat-1-2", "backend-winit", "renderer-femtovg-wgpu", "unstable-wgpu-28", "unstable-winit-030"] }
+
+[profile.release]
+lto = "fat"
+codegen-units = 1
+strip = true
+opt-level = "s"
+
+[profile.bench]
+debug = 1
+
+[profile.dev-fast]
+inherits = "release"
+opt-level = 1
+lto = false
+codegen-units = 256
+incremental = true
+strip = false

patinae-0.4.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024-2026, Pavel Yakovlev
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

patinae-0.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: patinae
+Version: 0.4.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Dist: pytest>=7.0 ; extra == 'dev'
+Requires-Dist: numpy>=1.20 ; extra == 'dev'
+Requires-Dist: numpy>=1.20 ; extra == 'numpy'
+Requires-Dist: anywidget>=0.9 ; extra == 'widget'
+Requires-Dist: traitlets>=5.0 ; extra == 'widget'
+Provides-Extra: dev
+Provides-Extra: numpy
+Provides-Extra: widget
+License-File: LICENSE
+Summary: Patinae: Modern molecular visualization in Rust with WebGPU rendering
+Keywords: patinae,molecular,visualization,chemistry,biology
+Author: Pavel Yakovlev
+License: BSD-3-Clause
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Homepage, https://github.com/zmactep/patinae
+Project-URL: Repository, https://github.com/zmactep/patinae
+
+# Patinae Python Bindings
+
+Python bindings for the Rust/WebGPU molecular visualization workspace.
+
+## Installation
+
+```bash
+pip install patinae
+```
+
+## Jupyter Widget
+
+The package includes an [anywidget](https://anywidget.dev/)-based widget for interactive visualization in notebooks. Works in JupyterLab, Jupyter Notebook, VS Code, and Google Colab.
+
+```bash
+pip install patinae[widget]
+```
+
+```python
+from patinae.widget import Viewer
+
+view = Viewer()
+view.show()
+cmd = view.get_cmd()
+cmd.fetch("1CRN")
+cmd.show("cartoon")
+cmd.color("green", "chain A")
+```
+
+Features:
+- **Fire-and-forget commands** — `cmd.fetch()`, `cmd.show()`, `cmd.color()`, etc.
+- **Synchronous queries** — request/response channel for commands that return data
+- **Local file loading** — load structures from the local filesystem into the browser viewer
+- **Picking support** — optional click-to-select atoms (`Viewer(picking=True)`)
+- **Configurable layout** — `width` and `height` parameters with sensible defaults
+
+## License
+
+BSD-3-Clause
+

patinae-0.4.0/README.md

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+# Patinae Python Bindings
+
+Python bindings for the Rust/WebGPU molecular visualization workspace.
+
+## Installation
+
+```bash
+pip install patinae
+```
+
+## Jupyter Widget
+
+The package includes an [anywidget](https://anywidget.dev/)-based widget for interactive visualization in notebooks. Works in JupyterLab, Jupyter Notebook, VS Code, and Google Colab.
+
+```bash
+pip install patinae[widget]
+```
+
+```python
+from patinae.widget import Viewer
+
+view = Viewer()
+view.show()
+cmd = view.get_cmd()
+cmd.fetch("1CRN")
+cmd.show("cartoon")
+cmd.color("green", "chain A")
+```
+
+Features:
+- **Fire-and-forget commands** — `cmd.fetch()`, `cmd.show()`, `cmd.color()`, etc.
+- **Synchronous queries** — request/response channel for commands that return data
+- **Local file loading** — load structures from the local filesystem into the browser viewer
+- **Picking support** — optional click-to-select atoms (`Viewer(picking=True)`)
+- **Configurable layout** — `width` and `height` parameters with sensible defaults
+
+## License
+
+BSD-3-Clause

patinae-0.4.0/crates/patinae-algos/Cargo.toml

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+[package]
+name = "patinae-algos"
+version.workspace = true
+edition.workspace = true
+authors.workspace = true
+license.workspace = true
+repository.workspace = true
+homepage.workspace = true
+documentation.workspace = true
+description = "Computational algorithms for Patinae (alignment, SVD, sequence alignment)"
+
+[features]
+default = []
+parallel = ["dep:rayon"]
+
+[dependencies]
+lin_alg = { workspace = true }
+thiserror = { workspace = true }
+phf = { workspace = true }
+bitflags = { workspace = true }
+serde = { workspace = true }
+rayon = { workspace = true, optional = true }
+
+[lints]
+workspace = true