manimol 0.2.0__tar.gz

manimol-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 MANIMOL developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

manimol-0.2.0/PKG-INFO

@@ -0,0 +1,185 @@
+Metadata-Version: 2.4
+Name: manimol
+Version: 0.2.0
+Summary: MANIMOL ensemble-relational conformer generation and compact-library construction
+Author: MANIMOL developers
+License: MIT License
+        
+        Copyright (c) 2026 MANIMOL developers
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Keywords: molecular conformers,conformer generation,chemical informatics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == "test"
+Provides-Extra: build
+Requires-Dist: build>=1.0; extra == "build"
+Requires-Dist: twine>=4.0; extra == "build"
+Provides-Extra: full
+Requires-Dist: torch>=2.3; extra == "full"
+Requires-Dist: torch-geometric>=2.5; extra == "full"
+Requires-Dist: rdkit; extra == "full"
+Requires-Dist: scipy>=1.10; extra == "full"
+Requires-Dist: tqdm>=4.66; extra == "full"
+Requires-Dist: pyyaml>=6; extra == "full"
+Dynamic: license-file
+
+# MANIMOL
+
+MANIMOL predicts ensemble-derived pairwise mean/dispersion relational priors
+from molecular graphs, uses them in torsional proposal generation, and builds
+compact conformer libraries by reference-free selection.
+
+The installable software is separated from large research artifacts:
+
+- **PyPI:** lightweight numerical utilities and the complete checkpoint-backed
+  inference source;
+- **external files:** checkpoints and processed/raw datasets supplied by the
+  user or a release;
+- **source repository:** training and paper-specific experiment scripts.
+
+No GEOM, Platinum, or PDBbind data and no model checkpoint are redistributed
+by this package.
+
+## Install
+
+```bash
+python -m pip install manimol
+python -m pip install 'manimol[full]'
+```
+
+The base install only needs NumPy. The `full` extra adds PyTorch, PyTorch
+Geometric, RDKit, SciPy, tqdm, and PyYAML. GPU-enabled PyTorch should be
+installed for the user's CUDA environment when needed.
+
+## What is included
+
+The wheel contains the existing MANIMOL implementation, including graph
+preprocessing; Stage-I graph and mean/dispersion heads; cross-fragment
+torsional context; dispersion-to-width control; probability-guided and
+noise-conditioned proposal branches; candidate-pool generation and
+oversampling; reference-free selection; ETKDG initialization; MMFF-based
+geometric preparation; filtering and RMSD deduplication; COV/AMR utilities;
+and checkpoint loading.
+
+The package is assembled from the repository's real inference modules. It
+does not reimplement a simplified model under a new namespace.
+
+## Full inference
+
+`manimol-infer` delegates to the same Stage-I/Stage-II entry point used by the
+project. It requires a compatible checkpoint and the processed/raw dataset
+records expected by that entry point:
+
+```bash
+manimol-infer \
+  --base_checkpoint /path/to/stage2_best.pth \
+  --denoiser_checkpoint /path/to/denoiser.pth \
+  --checkpoint /path/to/stage2_best.pth \
+  --dataset Drugs \
+  --data_root /path/to/data \
+  --raw_prefix geom_drugs \
+  --split test \
+  --device cuda \
+  --use_dispersion_proposal \
+  --select_candidates precision2r \
+  --output_dir results/manimol
+```
+
+The package default is a 15-fold candidate oversampling factor. Override it
+with `--oversample_factor` for another protocol. The underlying options remain
+available, including P-basin checkpoints, MMFF settings, energy-aware
+selectors, deduplication, RMSD backends, and metric thresholds:
+
+```bash
+manimol-infer --help
+```
+
+The checkpoint family, raw-prefix naming, and preprocessing must match. A
+wheel alone cannot reproduce a paper table without those external artifacts.
+
+## Python API
+
+The lightweight numerical utilities remain directly importable:
+
+```python
+import numpy as np
+from manimol import density_centrality_select, ensemble_pairwise_prior
+
+conformers = np.load("conformers.npy")  # (n_conformers, n_atoms, 3)
+mean, dispersion = ensemble_pairwise_prior(conformers)
+indices = density_centrality_select(conformers, k=20)
+library = conformers[indices]
+```
+
+For the complete model-backed path, `ManiMol` is a thin wrapper around the
+real inference entry point. It uses the benchmark dataset contract rather than
+inventing a separate SMILES-to-PyG adapter:
+
+```python
+from manimol import ManiMol
+
+model = ManiMol.from_pretrained(
+    "/path/to/stage2_best.pth",
+    device="cuda",
+    denoiser_checkpoint="/path/to/denoiser.pth",
+)
+model.generate(
+    data_root="/path/to/data",
+    output_dir="results/manimol",
+    dataset="Drugs",
+    raw_prefix="geom_drugs",
+    split="test",
+    select_candidates="precision2r",
+)
+```
+
+Generated SDF/metrics/log artifacts are written to `output_dir`. A direct
+`generate(smiles=...)` adapter is intentionally not claimed in this release:
+the production implementation expects graph, torsion-index, and conformer
+record fields. A future adapter should reuse the exact repository graph
+builder and be validated against this full path first.
+
+## Source layout
+
+The runtime modules needed by the real entry point are kept under `src/`,
+including `models/`, `dataset/`, `utils/`, and the inference modules. Training
+and benchmark launchers remain in the source repository and are not needed to
+run a released checkpoint.
+
+## Development checks
+
+```bash
+python -m pip install -e '.[test,build]'
+pytest
+python -m build
+```
+
+The lightweight tests do not require PyTorch, PyTorch Geometric, or RDKit. The
+full path should be smoke-tested in an environment containing the `full`
+dependencies and a compatible checkpoint before release.

manimol-0.2.0/README.md

@@ -0,0 +1,134 @@
+# MANIMOL
+
+MANIMOL predicts ensemble-derived pairwise mean/dispersion relational priors
+from molecular graphs, uses them in torsional proposal generation, and builds
+compact conformer libraries by reference-free selection.
+
+The installable software is separated from large research artifacts:
+
+- **PyPI:** lightweight numerical utilities and the complete checkpoint-backed
+  inference source;
+- **external files:** checkpoints and processed/raw datasets supplied by the
+  user or a release;
+- **source repository:** training and paper-specific experiment scripts.
+
+No GEOM, Platinum, or PDBbind data and no model checkpoint are redistributed
+by this package.
+
+## Install
+
+```bash
+python -m pip install manimol
+python -m pip install 'manimol[full]'
+```
+
+The base install only needs NumPy. The `full` extra adds PyTorch, PyTorch
+Geometric, RDKit, SciPy, tqdm, and PyYAML. GPU-enabled PyTorch should be
+installed for the user's CUDA environment when needed.
+
+## What is included
+
+The wheel contains the existing MANIMOL implementation, including graph
+preprocessing; Stage-I graph and mean/dispersion heads; cross-fragment
+torsional context; dispersion-to-width control; probability-guided and
+noise-conditioned proposal branches; candidate-pool generation and
+oversampling; reference-free selection; ETKDG initialization; MMFF-based
+geometric preparation; filtering and RMSD deduplication; COV/AMR utilities;
+and checkpoint loading.
+
+The package is assembled from the repository's real inference modules. It
+does not reimplement a simplified model under a new namespace.
+
+## Full inference
+
+`manimol-infer` delegates to the same Stage-I/Stage-II entry point used by the
+project. It requires a compatible checkpoint and the processed/raw dataset
+records expected by that entry point:
+
+```bash
+manimol-infer \
+  --base_checkpoint /path/to/stage2_best.pth \
+  --denoiser_checkpoint /path/to/denoiser.pth \
+  --checkpoint /path/to/stage2_best.pth \
+  --dataset Drugs \
+  --data_root /path/to/data \
+  --raw_prefix geom_drugs \
+  --split test \
+  --device cuda \
+  --use_dispersion_proposal \
+  --select_candidates precision2r \
+  --output_dir results/manimol
+```
+
+The package default is a 15-fold candidate oversampling factor. Override it
+with `--oversample_factor` for another protocol. The underlying options remain
+available, including P-basin checkpoints, MMFF settings, energy-aware
+selectors, deduplication, RMSD backends, and metric thresholds:
+
+```bash
+manimol-infer --help
+```
+
+The checkpoint family, raw-prefix naming, and preprocessing must match. A
+wheel alone cannot reproduce a paper table without those external artifacts.
+
+## Python API
+
+The lightweight numerical utilities remain directly importable:
+
+```python
+import numpy as np
+from manimol import density_centrality_select, ensemble_pairwise_prior
+
+conformers = np.load("conformers.npy")  # (n_conformers, n_atoms, 3)
+mean, dispersion = ensemble_pairwise_prior(conformers)
+indices = density_centrality_select(conformers, k=20)
+library = conformers[indices]
+```
+
+For the complete model-backed path, `ManiMol` is a thin wrapper around the
+real inference entry point. It uses the benchmark dataset contract rather than
+inventing a separate SMILES-to-PyG adapter:
+
+```python
+from manimol import ManiMol
+
+model = ManiMol.from_pretrained(
+    "/path/to/stage2_best.pth",
+    device="cuda",
+    denoiser_checkpoint="/path/to/denoiser.pth",
+)
+model.generate(
+    data_root="/path/to/data",
+    output_dir="results/manimol",
+    dataset="Drugs",
+    raw_prefix="geom_drugs",
+    split="test",
+    select_candidates="precision2r",
+)
+```
+
+Generated SDF/metrics/log artifacts are written to `output_dir`. A direct
+`generate(smiles=...)` adapter is intentionally not claimed in this release:
+the production implementation expects graph, torsion-index, and conformer
+record fields. A future adapter should reuse the exact repository graph
+builder and be validated against this full path first.
+
+## Source layout
+
+The runtime modules needed by the real entry point are kept under `src/`,
+including `models/`, `dataset/`, `utils/`, and the inference modules. Training
+and benchmark launchers remain in the source repository and are not needed to
+run a released checkpoint.
+
+## Development checks
+
+```bash
+python -m pip install -e '.[test,build]'
+pytest
+python -m build
+```
+
+The lightweight tests do not require PyTorch, PyTorch Geometric, or RDKit. The
+full path should be smoke-tested in an environment containing the `full`
+dependencies and a compatible checkpoint before release.

manimol-0.2.0/pyproject.toml

@@ -0,0 +1,65 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "manimol"
+version = "0.2.0"
+description = "MANIMOL ensemble-relational conformer generation and compact-library construction"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { file = "LICENSE" }
+authors = [{ name = "MANIMOL developers" }]
+keywords = ["molecular conformers", "conformer generation", "chemical informatics"]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Chemistry",
+]
+dependencies = ["numpy>=1.23"]
+
+[project.optional-dependencies]
+test = ["pytest>=7"]
+build = ["build>=1.0", "twine>=4.0"]
+full = [
+  "torch>=2.3",
+  "torch-geometric>=2.5",
+  "rdkit",
+  "scipy>=1.10",
+  "tqdm>=4.66",
+  "pyyaml>=6",
+]
+
+[project.scripts]
+manimol-select = "manimol.cli:main"
+manimol-infer = "manimol.full_cli:main"
+
+[tool.setuptools]
+py-modules = [
+  "args_parse",
+  "candidate_corrector",
+  "candidate_scorer",
+  "exputils",
+  "infer1",
+  "infer_mean_dispersion_torsion",
+  "infer_torsion",
+  "infer_torsion5",
+  "manimol_stage1",
+  "mixture_torsion_flow",
+  "pgraph_controls",
+  "torsion_manifold",
+  "train2",
+  "train5",
+  "trainer",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["manimol*", "models*", "dataset*", "utils*", "scripts*", "mixture_flow*"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-ra"
+pythonpath = ["src"]

manimol-0.2.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+