bioemu 0.1.0__tar.gz

bioemu-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+    MIT License
+
+    Copyright (c) Microsoft Corporation.
+
+    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
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+    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

bioemu-0.1.0/MANIFEST.in

@@ -0,0 +1,2 @@
+include src/bioemu/config/**/*.yaml
+include src/bioemu/config/**/*.yml

bioemu-0.1.0/NOTICE.md

@@ -0,0 +1,214 @@
+NOTICES
+
+This project incorporates material as listed below or described in the code.
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+   Copyright 2024 AlQuraishi Laboratory 
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
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+       http://www.apache.org/licenses/LICENSE-2.0
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+Copyright 2021 AlQuraishi Laboratory
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+https://github.com/aqlaboratory/openfold
+--------------------

bioemu-0.1.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: bioemu
+Version: 0.1.0
+Summary: Biomolecular emulator
+Requires-Python: >=3.10
+License-File: LICENSE
+License-File: NOTICE.md
+Requires-Dist: mdtraj>=1.9.9
+Requires-Dist: torch_geometric==2.6.1
+Requires-Dist: torch==2.4.0
+Requires-Dist: torchvision
+Requires-Dist: modelcif==0.7
+Requires-Dist: bio>=1.5.9
+Requires-Dist: fire==0.7.0
+Requires-Dist: huggingface-hub
+Requires-Dist: hydra-core
+Requires-Dist: dm-tree
+Requires-Dist: stackprinter
+Requires-Dist: typer
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: md
+Requires-Dist: openmm==8.2.0; extra == "md"
+Requires-Dist: pdb2pqr==3.4.1; extra == "md"

bioemu-0.1.0/README.md

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+
+<h1>
+<p align="center">
+    <img src="assets/emu.png" alt="BioEmu logo" width="300"/>
+</p>
+</h1>
+
+[![DOI:10.1101/2024.12.05.626885](https://zenodo.org/badge/DOI/10.1101/2024.12.05.626885.svg)](https://doi.org/10.1101/2024.12.05.626885)
+[![Requires Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
+
+
+# Biomolecular Emulator (BioEmu)
+
+Biomolecular Emulator (BioEmu for short) is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence.
+
+For more information, see our [preprint](https://www.biorxiv.org/content/10.1101/2024.12.05.626885v1.abstract).
+
+This repository contains inference code and model weights.
+
+## Table of Contents
+- [Installation](#installation)
+- [Sampling structures](#sampling-structures)
+- [Citation](#citation)
+- [Get in touch](#get-in-touch)
+
+## Installation
+
+bioemu is provided as pip-installable package:
+
+```bash
+pip install bioemu
+```
+
+> [!NOTE]
+> The first time `bioemu` is used to sample structures, it will also need to setup Colabfold on the side. This process can take ~5-10 mins.
+
+
+## Sampling structures
+You can sample structures for a given protein sequence using the `sample` module. To run a tiny test using the default model parameters and denoising settings:
+```
+python -m bioemu.sample --sequence GYDPETGTWG --num_samples 10 --output_dir ~/test-chignolin
+```
+
+Alternatively, you can use the Python API:
+
+```python
+from bioemu.sample import main as sample
+sample(sequence='GYDPETGTWG', num_samples=10, output_dir='~/test_chignolin')
+```
+
+The model parameters will be automatically downloaded from [huggingface](https://huggingface.co/microsoft/bioemu). See [sample.py](./src/bioemu/sample.py) for more options.
+
+Sampling times will depend on sequence length and available infrastructure. The following table gives times for collecting 1000 samples measured on an A100 GPU with 80 GB VRAM for sequences of different lengths (using a `batch_size_100=20` setting in `sample.py`):
+ | sequence length | time / min |
+ | --------------: | ---------: |
+ |             100 |          4 |
+ |             300 |         40 |
+ |             600 |        150 |
+
+
+## Reproducing results from the preprint
+You can use this code together with code from [bioemu-benchmarks](https://github.com/microsoft/bioemu-benchmarks) to approximately reproduce results from our [preprint](https://www.biorxiv.org/content/10.1101/2024.12.05.626885v1).
+
+The `bioemu-v1.0` checkpoint contains the model weights used to produce the results in the preprint. Due to simplifications made in the embedding computation and a more efficient sampler, the results obtained with this code are not identical but consistent with the statistics shown in the preprint, i.e., mode coverage and free energy errors averaged over the proteins in a test set. Results for individual proteins may differ. For more details, please check the [BIOEMU_RESULTS.md](https://github.com/microsoft/bioemu-benchmarks/blob/main/bioemu_benchmarks/BIOEMU_RESULTS.md) document on the bioemu-benchmarks repository.
+
+
+## Citation
+If you are using our code or model, please consider citing our work:
+```bibtex
+@article {BioEmu2024,
+    author = {Lewis, Sarah and Hempel, Tim and Jim{\'e}nez-Luna, Jos{\'e} and Gastegger, Michael and Xie, Yu and Foong, Andrew Y. K. and Satorras, Victor Garc{\'\i}a and Abdin, Osama and Veeling, Bastiaan S. and Zaporozhets, Iryna and Chen, Yaoyi and Yang, Soojung and Schneuing, Arne and Nigam, Jigyasa and Barbero, Federico and Stimper, Vincent and Campbell, Andrew and Yim, Jason and Lienen, Marten and Shi, Yu and Zheng, Shuxin and Schulz, Hannes and Munir, Usman and Clementi, Cecilia and No{\'e}, Frank},
+    title = {Scalable emulation of protein equilibrium ensembles with generative deep learning},
+    year = {2024},
+    doi = {10.1101/2024.12.05.626885},
+    journal = {bioRxiv}
+}
+```
+
+## Side-chain reconstruction and MD-relaxation
+BioEmu outputs structures in backbone frame representation.
+To reconstruct the side-chains, several tools are available. 
+As an example, we provide a script to conduct side-chain reconstruction with HPacker (https://github.com/gvisani/hpacker), and provide an interface for running a short molecular dynamics (MD) equilibration.
+HPacker is a method for protein side-chain packing based on holographic rotationally equivariant convolutional neural networks (https://arxiv.org/abs/2311.09312).
+
+This code is experimental and is provided for research purposes only. Further testing/development are needed before considering its application in real-world scenarios or production environments.
+
+### Install side-chain reconstruction tools
+Clone and install the HPacker code and other dependencies with
+```bash
+./setup_sidechain_relax.sh
+```
+
+This will install some additional dependences for running MD relaxation in the `bioemu` environment. It will also install HPacker in a separate conda environment called `hpacker`.
+
+### Use side-chain reconstruction tools
+Inside the `bioemu` enviroment, run side-chain reconstruction with:
+```bash
+python -m bioemu.sidechain_relax --pdb-path path/to/topology.pdb --xtc-path path/to/samples.xtc
+```
+By default, side-chain reconstruction and local energy minimization are performed (no full MD integration for efficiency reasons).
+Note that the runtime of this code scales with the size of the system.
+We suggest running this code on a selection of samples rather than the full set.
+
+There are two other options:
+- To only run side-chain reconstruction without MD equilibration, add `--no-md-equil`.
+- To run a short NVT equilibration (0.1 ns), add `--md-protocol nvt_equil`
+
+To see the full list of options, call `python -m bioemu.sidechain_relax --help`.
+
+The script saves reconstructed all-heavy-atom structures in `samples_sidechain_rec.{pdb,xtc}` and MD-equilibrated structures in `samples_md_equil.{pdb,xtc}` (filename to be altered with `--outname other_name`).
+
+## Third-party code
+The code in the `openfold` subdirectory is copied from [openfold](https://github.com/aqlaboratory/openfold) with minor modifications. The modifications are described in the relevant source files.
+## Get in touch
+If you have any questions not covered here, please create an issue or contact the BioEmu team by writing to the corresponding author on our [preprint](https://doi.org/10.1101/2024.12.05.626885).

bioemu-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "bioemu"
+version = "0.1.0"
+description = "Biomolecular emulator"
+authors = [
+]
+requires-python = ">=3.10"
+dependencies = [
+    "mdtraj>=1.9.9",
+    "torch_geometric==2.6.1",
+    "torch==2.4.0",
+    "torchvision",
+    "modelcif==0.7",
+    "bio>=1.5.9",
+    "fire==0.7.0",
+    "huggingface-hub",
+    "hydra-core",
+    "dm-tree",
+    "stackprinter",
+    "typer"
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest", # For developers
+    "pytest-cov",
+    "pre-commit",
+]
+md = [
+    "openmm==8.2.0",
+    "pdb2pqr==3.4.1"
+]
+
+[tool.black]
+line-length = 100
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+  | bioemu/openfold
+)/
+'''
+
+[tool.isort]
+profile = "black"
+line_length = 100
+known_first_party = [
+    "bioemu",
+]
+
+[tool.mypy]
+verbosity = 0
+
+[[tool.mypy.overrides]]
+module = [
+    "Bio.*",
+    "git.*",
+    "hydra.*",
+    "IPython.*",
+    "matplotlib.*",
+    "mdtraj.*",
+    "numpy.*",
+    "openmm.*",
+    "tqdm.*",
+    "torch.*",
+    "torch_geometric.*",
+    "torch_scatter.*",
+    "pandas.*",
+    "pdbfixer.*",
+    "pytest.*",
+    "omegaconf.*",
+    "scipy.*",
+    "sklearn.*",
+]
+ignore_missing_imports = true
+
+
+
+
+[tool.ruff]
+line-length = 100
+
+[tool.ruff.lint]
+# Check https://beta.ruff.rs/docs/rules/ for full list of rules
+select = [
+  "E", "W",  # pycodestyle
+  "F",  # Pyflakes
+  # "C90",  # mccabe
+  # "I",  # isort
+  # "N",  # pep8-naming
+  # "D",  # pydocstyle
+  "UP",  # pyupgrade
+  # "YTT",  # flake8-2020
+  # "ANN",  # flake8-annotations
+  # "S",  # flake8-bandit
+  # "BLE",  # flake8-blind-except
+  # "FBT",  # flake8-boolean-trap
+  # "B",  # flake8-bugbear
+  # "A",  # flake8-builtins
+  # "COM",  # flake8-commas
+  # "C4",  # flake8-comprehensions
+  # "DTZ",  # flake8-datetimez
+  # "T10",  # flake8-debugger
+  # "DJ",  # flake8-django
+  # "EM",  # flake8-errmsg
+  # "EXE",  # flake8-executable
+  # "ISC",  # flake8-implicit-str-concat
+  # "ICN",  # flake8-import-conventions
+  # "G",  # flake8-logging-format
+  # "INP",  # flake8-no-pep420
+  # "PIE",  # flake8-pie
+  # "T20",  # flake8-print
+  # "PYI",  # flake8-pyi
+  # "PT",  # flake8-pytest-style
+  # "Q",  # flake8-quotes
+  # "RSE",  # flake8-raise
+  # "RET",  # flake8-return
+  # "SLF",  # flake8-self
+  # "SIM",  # flake8-simplify
+  # "TID",  # flake8-tidy-imports
+  # "TCH",  # flake8-type-checking
+  # "ARG",  # flake8-unused-arguments
+  # "PTH",  # flake8-use-pathlib
+  # "ERA",  # eradicate
+  # "PD",  # pandas-vet
+  # "PGH",  # pygrep-hooks
+  # "PLC",  # pylint-convention
+  "PLE",  # pylint-error
+  # "PLR",  # pylint-refactor
+  # "PLW",  # pylint-warning
+  # "TRY",  # tryceratops
+  # "NPY",  # numpy
+  # "RUF",  # ruff
+]
+ignore = [
+  # W605: invalid escape sequence -- triggered by pseudo-LaTeX in comments
+  "W605",
+  # E501: Line too long -- triggered by comments and such. black deals with shortening.
+  "E501",
+  # E402: Module level import not at top of file -- triggered by python path manipulations
+  "E402",
+  # E741:  Do not use variables named 'l', 'o', or 'i' -- disagree with PEP8
+  "E741",
+]
+extend-safe-fixes = [
+  "UP"
+]
+exclude=["openfold"]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.patch", "*.sh", "*.md"]

bioemu-0.1.0/setup.cfg

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

bioemu-0.1.0/src/bioemu/chemgraph.py

@@ -0,0 +1,28 @@
+# Copyright (c) Microsoft Corporation.
+# Licensed under the MIT License.
+from __future__ import annotations
+
+import copy
+from typing import Any
+
+import torch
+from torch_geometric.data import Data
+
+
+class ChemGraph(Data):
+    node_orientations: torch.Tensor  # [num_nodes, 3, 3] or [num_nodes, 3] when it's a score (since the scores are given as rotation vectors)
+    pos: torch.Tensor  # [num_nodes, 3] score model expects this to be in nanometers.
+    edge_index: torch.Tensor  # [2, num_edges]
+    single_embeds: torch.Tensor  # [num_nodes, EVOFORMER_NODE_DIM]
+    pair_embeds: torch.Tensor  # [num_nodes**2, EVOFORMER_EDGE_DIM]
+
+    def replace(self, **kwargs: Any) -> ChemGraph:
+        """Returns a shallow copy of the ChemGraph with updated fields."""
+        out = self.__class__.__new__(self.__class__)
+        for key, value in self.__dict__.items():
+            out.__dict__[key] = value
+        out.__dict__["_store"] = copy.copy(self._store)
+        for key, value in kwargs.items():
+            out._store[key] = value
+        out._store._parent = out
+        return out

bioemu-0.1.0/src/bioemu/colabfold_setup/batch.patch

@@ -0,0 +1,6 @@
+430d429
+< 
+478a478
+>                 np.save(files.get("single_repr_evo", "npy"), result["representations_evo"]["single"])
+480a481
+>                 np.save(files.get("pair_repr_evo", "npy"), result["representations_evo"]["pair"])

bioemu-0.1.0/src/bioemu/colabfold_setup/modules.patch

@@ -0,0 +1,14 @@
+146c146
+<     ret = {'representations':representations}
+---
+>     ret = {'representations':representations, 'representations_evo': representations}
+173d172
+< 
+181d179
+< 
+216d213
+< 
+317d313
+< 
+2092d2087
+< 

bioemu-0.1.0/src/bioemu/colabfold_setup/setup.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+set -ex
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+# Set COLABFOLD_DIR to ~/.localcolabfold if dir not passed as first arg
+COLABFOLD_DIR="${1:-"~/.localcolabfold"}"
+
+echo "Setting up colabfold..."
+mkdir -p ${COLABFOLD_DIR}
+wget "https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/5fc8775114b637b5672234179c50e694ab057db4/install_colabbatch_linux.sh" -O ${COLABFOLD_DIR}/install_colabbatch_linux.sh
+# Replace 'git+https://github.com/sokrypton/ColabFold' with 'git+https://github.com/sokrypton/ColabFold@e2ca9e8f992cd65c986de5b64885d5572d8b8ad9' in install_colabbatch_linux.sh
+sed -i 's/git+https:\/\/github.com\/sokrypton\/ColabFold/git+https:\/\/github.com\/sokrypton\/ColabFold@e2ca9e8f992cd65c986de5b64885d5572d8b8ad9/g' ${COLABFOLD_DIR}/install_colabbatch_linux.sh
+chmod +x ${COLABFOLD_DIR}/install_colabbatch_linux.sh
+cd ${COLABFOLD_DIR} && bash install_colabbatch_linux.sh
+
+# Patch colabfold install
+echo "Patching colabfold installation..."
+patch ${COLABFOLD_DIR}/localcolabfold/colabfold-conda/lib/python3.10/site-packages/alphafold/model/modules.py ${SCRIPT_DIR}/modules.patch
+patch ${COLABFOLD_DIR}/localcolabfold/colabfold-conda/lib/python3.10/site-packages/colabfold/batch.py ${SCRIPT_DIR}/batch.patch
+
+echo "Colabfold installation complete!"

bioemu-0.1.0/src/bioemu/config/denoiser/dpm.yaml

@@ -0,0 +1,5 @@
+_target_: bioemu.shortcuts.dpm_solver
+_partial_: true
+eps_t: 0.001
+max_t: 0.99
+N: 30

bioemu-0.1.0/src/bioemu/config/denoiser/heun.yaml

@@ -0,0 +1,6 @@
+_target_: bioemu.shortcuts.heun_denoiser
+_partial_: true
+eps_t: 0.001
+N: 100
+max_t: 0.99
+noise: 0.5