sawnergy 1.0.0__tar.gz

sawnergy-1.0.0/LICENSE

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sawnergy-1.0.0/NOTICE

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+SAWNERGY
+Copyright (c) 2025 Yehor Mishchyriak
+
+This product includes software developed by Yehor Mishchyriak.

sawnergy-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sawnergy
+Version: 1.0.0
+Summary: Toolkit for transforming molecular dynamics (MD) trajectories into rich graph representations
+Home-page: https://github.com/Yehor-Mishchyriak/SAWNERGY
+Author: Yehor Mishchyriak
+License: Apache-2.0
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy>=2.0
+Requires-Dist: zarr>=3.0
+Requires-Dist: threadpoolctl>=3.0
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: psutil>=5.9
+Requires-Dist: ym-pure-ml>=1.2.0
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# SAWNERGY
+
+A toolkit for transforming molecular dynamics (MD) trajectories into rich graph representations, sampling
+random and self-avoiding walks, learning node embeddings, and visualising residue interaction networks (RINs). SAWNERGY
+keeps the full workflow — from `cpptraj` output to skip-gram embeddings (node2vec approach) — inside Python, backed by efficient Zarr-based archives and optional GPU acceleration.
+
+---
+
+## Why SAWNERGY?
+
+- **Bridge simulations and graph ML**: Convert raw MD trajectories into residue interaction networks ready for graph
+  algorithms and downstream machine learning tasks.
+- **Deterministic, shareable artefacts**: Every stage produces compressed Zarr archives that contain both data and metadata so runs can be reproduced, shared, or inspected later.
+- **High-performance data handling**: Heavy arrays live in shared memory during walk sampling to allow parallel processing without serealization overhead; archives are written in chunked, compressed form for fast read/write.
+- **Flexible embedding backends**: Train skip-gram with negative sampling (SGNS) models using either PureML or PyTorch.
+- **Visualization out of the box**: Plot and animate residue networks without leaving Python, using the data produced by RINBuilder
+
+---
+
+## Pipeline at a Glance
+
+```
+MD Trajectory + Topology
+          │
+          ▼
+      RINBuilder 
+          │   →  RIN archive (.zip/.zarr) → Visualizer (display/animate RINs)
+          ▼
+        Walker
+          │   →  Walks archive (RW/SAW per frame)
+          ▼
+       Embedder
+          │   →  Embedding archive (frame × vocab × dim)
+          ▼
+     Downstream ML
+```
+
+Each stage consumes the archive produced by the previous one. Metadata embedded in the archives ensures frame order,
+node indexing, and RNG seeds stay consistent across the toolchain.
+
+---
+
+## Core Components
+
+### `sawnergy.rin.RINBuilder`
+
+* Wraps the AmberTools `cpptraj` executable to:
+  - compute per-frame electrostatic (EMAP) and van der Waals (VMAP) energy matrices at the atomic level,
+  - project atom–atom interactions to residue–residue interactions using compositional masks,
+  - prune, symmetrise, remove self-interactions, and L1-normalise the matrices,
+  - compute per-residue centres of mass (COM) over the same frames.
+* Outputs a compressed Zarr archive with transition matrices, optional prenormalised energies, COM snapshots, and rich
+  metadata (frame range, pruning quantile, molecule ID, etc.).
+* Supports parallel `cpptraj` execution, batch processing, and keeps temporary stores tidy via
+  `ArrayStorage.compress_and_cleanup`.
+
+### `sawnergy.visual.Visualizer`
+
+* Opens RIN archives, resolves dataset names from attributes, and renders nodes plus attractive/repulsive edge bundles
+  in 3D using Matplotlib.
+* Allows both static frame visualization and trajectory animation.
+* Handles backend selection (`Agg` fallback in headless environments) and offers convenient colour palettes via
+  `visualizer_util`.
+
+### `sawnergy.walks.Walker`
+
+* Attaches to the RIN archive and loads attractive/repulsive transition matrices into shared memory using
+  `walker_util.SharedNDArray` so multiple processes can sample without copying.
+* Samples random walks (RW) and self-avoiding walks (SAW), optionally time-aware, that is, walks move through transition matrices with transition probabilities proportional to cosine similarity between the current and next frame. Randomness is controlled by the seed passed to the class constructor.
+* Persists walks as `(time, walk_id, length+1)` tensors (1-based node indices) alongside metadata such as
+  `walk_length`, `walks_per_node`, and RNG scheme.
+
+### `sawnergy.embedding.Embedder`
+
+* Consumes walk archives, generates skip-gram pairs, and normalises them to 0-based indices.
+* Provides a unified interface to SGNS implementations:
+  - **PureML backend** (`SGNS_PureML`): works with the `pureml` ecosystem, optimistic for CPU training.
+  - **PyTorch backend** (`SGNS_Torch`): uses `torch.nn.Embedding` plays nicely with GPUs.
+* Both `SGNS_PureML` and `SGNS_Torch` accept training hyperparameters such as batch_size, LR, optimizer and LR_scheduler, etc.
+* Exposes `embed_frame` (single frame) and `embed_all` (all frames, deterministic seeding per frame) which return the
+  learned input embedding matrices and write them to disk when requested.
+
+### Supporting Utilities
+
+* `sawnergy.sawnergy_util`
+  - `ArrayStorage`: thin wrapper over Zarr v3 with helpers for chunk management, attribute coercion to JSON, and transparent compression to `.zip` archives.
+  - Parallel helpers (`elementwise_processor`, `compose_steps`, etc.), temporary file management, logging, and runtime
+    inspection utilities.
+* `sawnergy.logging_util.configure_logging`: configure rotating file/console logging consistently across scripts.
+
+---
+
+## Archive Layouts
+
+| Archive | Key datasets (name → shape, dtype) | Important attributes (root `attrs`) |
+|---|---|---|
+| **RIN** | `ATTRACTIVE_transitions` → **(T, N, N)**, float32  •  `REPULSIVE_transitions` → **(T, N, N)**, float32 (optional)  •  `ATTRACTIVE_energies` → **(T, N, N)**, float32 (optional)  •  `REPULSIVE_energies` → **(T, N, N)**, float32 (optional)  •  `COM` → **(T, N, 3)**, float32 | `time_created` (ISO) • `com_name` = `"COM"` • `molecule_of_interest` (int) • `frame_range` = `(start, end)` inclusive • `frame_batch_size` (int) • `prune_low_energies_frac` (float in [0,1]) • `attractive_transitions_name` / `repulsive_transitions_name` (dataset names or `None`) • `attractive_energies_name` / `repulsive_energies_name` (dataset names or `None`) |
+| **Walks** | `ATTRACTIVE_RWs` → **(T, N·num_RWs, L+1)**, int32 (optional)  •  `REPULSIVE_RWs` → **(T, N·num_RWs, L+1)**, int32 (optional)  •  `ATTRACTIVE_SAWs` → **(T, N·num_SAWs, L+1)**, int32 (optional)  •  `REPULSIVE_SAWs` → **(T, N·num_SAWs, L+1)**, int32 (optional)  <br/>_Note:_ node IDs are **1-based**.| `time_created` (ISO) • `seed` (int) • `rng_scheme` = `"SeedSequence.spawn_per_batch_v1"` • `num_workers` (int) • `in_parallel` (bool) • `batch_size_nodes` (int) • `num_RWs` / `num_SAWs` (ints) • `node_count` (N) • `time_stamp_count` (T) • `walk_length` (L) • `walks_per_node` (int) • `attractive_RWs_name` / `repulsive_RWs_name` / `attractive_SAWs_name` / `repulsive_SAWs_name` (dataset names or `None`) • `walks_layout` = `"time_leading_3d"` |
+| **Embeddings** | `FRAME_EMBEDDINGS` → **(frames_written, vocab_size, D)**, typically float32 | `time_created` (ISO) • `seed` (int) • `rng_scheme` = `"SeedSequence.spawn_per_frame_v1"` • `source_walks_path` (str) • `model_base` = `"torch"` or `"pureml"` • `rin_type` = `"attr"` or `"repuls"` • `using_mode` = `"RW"|"SAW"|"merged"` • `window_size` (int) • `alpha` (float; noise exponent) • `dimensionality` = D • `num_negative_samples` (int) • `num_epochs` (int) • `batch_size` (int) • `shuffle_data` (bool) • `frames_written` (int) • `vocab_size` (int) • `frame_count` (int) • `embedding_dtype` (str) • `frame_embeddings_name` = `"FRAME_EMBEDDINGS"` • `arrays_per_chunk` (int) • `compression_level` (int) |
+
+**Notes**
+
+- In **RIN**, `T` equals the number of frame **batches** written (i.e., `frame_range` swept in steps of `frame_batch_size`). `ATTRACTIVE/REPULSIVE_energies` are **pre-normalised** absolute energies (written only when `keep_prenormalized_energies=True`), whereas `ATTRACTIVE/REPULSIVE_transitions` are the **row-wise L1-normalised** versions used for sampling.
+- All archives are Zarr v3 groups. ArrayStorage also maintains per-block metadata in root attrs: `array_chunk_size_in_block`, `array_shape_in_block`, and `array_dtype_in_block` (dicts keyed by dataset name). You’ll see these in every archive.
+
+---
+
+## Installation
+
+   ```bash
+   pip install sawnergy
+   ```
+
+> **Note:** RIN building requires `cpptraj` (AmberTools). Ensure it is discoverable via `$PATH` or the `CPPTRAJ`
+> environment variable.
+
+---
+
+## Quick Start
+
+```python
+from pathlib import Path
+from sawnergy.logging_util import configure_logging
+from sawnergy.rin import RINBuilder
+from sawnergy.walks import Walker
+from sawnergy.embedding import Embedder
+
+import logging
+configure_logging("./logs", file_level=logging.WARNING, console_level=logging.INFO)
+
+# 1. Build a Residue Interaction Network archive
+rin_path = Path("./RIN_demo.zip")
+rin_builder = RINBuilder()
+rin_builder.build_rin(
+    topology_file="system.prmtop",
+    trajectory_file="trajectory.nc",
+    molecule_of_interest=1,
+    frame_range=(1, 100),
+    frame_batch_size=10,
+    prune_low_energies_frac=0.3,
+    output_path=rin_path,
+    include_attractive=True,
+    include_repulsive=False,
+)
+
+# 2. Sample walks from the RIN
+walker = Walker(rin_path, seed=123)
+walks_path = Path("./WALKS_demo.zip")
+walker.sample_walks(
+    walk_length=16,
+    walks_per_node=32,
+    saw_frac=0.25,
+    include_attractive=True,
+    include_repulsive=False,
+    time_aware=False,
+    output_path=walks_path,
+    in_parallel=False,
+)
+walker.close()
+
+# 3. Train embeddings per frame (PyTorch backend)
+import torch
+
+embedder = Embedder(walks_path, base="torch", seed=999)
+embeddings_path = embedder.embed_all(
+    RIN_type="attr",
+    using="merged",
+    window_size=4,
+    num_negative_samples=5,
+    num_epochs=5,
+    batch_size=1024,
+    dimensionality=128,
+    shuffle_data=True,
+    output_path="./EMBEDDINGS_demo.zip",
+    sgns_kwargs={
+        "optim": torch.optim.Adam,
+        "optim_kwargs": {"lr": 1e-3},
+        "lr_sched": torch.optim.lr_scheduler.LambdaLR,
+        "lr_sched_kwargs": {"lr_lambda": lambda _: 1.0},
+        "device": "cuda" if torch.cuda.is_available() else "cpu",
+    },
+)
+print("Embeddings written to", embeddings_path)
+```
+
+> For the PureML backend, supply the relevant optimiser and scheduler via `sgns_kwargs`
+> (for example `optim=pureml.optimizers.Adam`, `lr_sched=pureml.optimizers.CosineAnnealingLR`).
+
+---
+
+## Visualisation
+
+```python
+from sawnergy.visual import Visualizer
+
+v = sawnergy.visual.Visualizer("./RIN_demo.zip")
+v.build_frame(1,
+    node_colors="rainbow",
+    displayed_nodes="ALL",
+    displayed_pairwise_attraction_for_nodes="DISPLAYED_NODES",
+    displayed_pairwise_repulsion_for_nodes="DISPLAYED_NODES",
+    show_node_labels=True,
+    show=True
+)
+```
+
+`Visualizer` lazily loads datasets and works even in headless environments (falls back to the `Agg` backend).
+
+---
+
+## Advanced Notes
+
+- **Time-aware walks**: Set `time_aware=True`, provide `stickiness` and `on_no_options` when calling `Walker.sample_walks`.
+- **Shared memory lifecycle**: Call `Walker.close()` (or use a context manager) to release shared-memory segments.
+- **PureML vs PyTorch**: Choose the backend via `Embedder(..., base="pureml"|"torch")` and provide backend-specific
+  constructor kwargs through `sgns_kwargs` (optimizer, scheduler, device).
+- **ArrayStorage utilities**: Use `ArrayStorage` directly to peek into archives, append arrays, or manage metadata.
+
+---
+
+## Testing & Quality Assurance
+
+The automated test suite (`pytest`) synthesises deterministic cpptraj outputs and exercises the entire workflow:
+
+- RIN parsing, residue aggregation, and metadata verification.
+- Random/self-avoiding walk sampling and probability consistency with the RIN.
+- Embedding orchestration, frame ordering, SGNS pair generation property tests.
+- PureML and PyTorch SGNS smoke tests verifying finite weights and decreasing loss.
+- Visualiser smoke tests that cover data loading and artist updates.
+
+Run the suite (inside the project virtualenv):
+
+```bash
+python -m pytest
+```
+
+---
+
+## Project Structure
+
+```
+├── sawnergy/
+│   ├── rin/           # RINBuilder and cpptraj integration helpers
+│   ├── walks/         # Walker class and shared-memory utilities
+│   ├── embedding/     # Embedder + SGNS backends (PureML / PyTorch)
+│   ├── visual/        # Visualizer and palette utilities
+│   ├── logging_util.py
+│   └── sawnergy_util.py
+├── tests/             # Synthetic end-to-end tests (pytest)
+│
+└── README.md
+```
+
+---
+
+## Acknowledgements
+
+SAWNERGY builds on the AmberTools `cpptraj` ecosystem, NumPy, Matplotlib, Zarr, and PyTorch (for GPU acceleration if necessary; PureML is available by default).
+Big thanks to the upstream communities whose work makes this toolkit possible.