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Data generation working.
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‎README.md

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@@ -40,6 +40,13 @@ source .venv/bin/activate
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### Setup with `mamba` or `conda`
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Additional dependencies:
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```bash
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conda create --name jamun-extras python=3.10 -y
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conda activate jamun-extras
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conda install -c conda-forge ambertools=23 openmm pdbfixer pyemma -y
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```
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Create an environment:
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```bash
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mamba create -n jamun-env python=3.11 -y
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We provide a script that uses [AmberTools](https://ambermd.org/AmberTools.php), specifically `tleap`. If you have a `.pdb` file already, then you can skip this step.
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#### Generate `.pdb` file
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First, install AmberTools23 following [instructions here](https://ambermd.org/GetAmber.php#ambertools):
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```bash
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conda create --name AmberTools23

‎env/requirements-analysis.txt

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@@ -37,6 +37,8 @@ dill==0.3.9
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# pathos
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docker-pycreds==0.4.0
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# via wandb
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exceptiongroup==1.2.2
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# via ipython
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executing==2.1.0
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# via stack-data
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fonttools==4.55.3
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numpy==1.23.4
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# via
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# -c env/constraints-analysis.txt
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# -c (workspace)
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# ase
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# cftime
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# contourpy

‎env/requirements.txt

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@@ -17,7 +17,7 @@ cftime==1.6.2 ; python_full_version >= '3.12'
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cftime==1.6.4.post1 ; python_full_version < '3.12'
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charset-normalizer==3.4.0
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click==8.1.7
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colorama==0.4.6 ; platform_system == 'Windows' and sys_platform != 'darwin' and sys_platform != 'linux'
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colorama==0.4.6 ; platform_system == 'Windows'
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contourpy==1.3.1
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cycler==0.12.1
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docker-pycreds==0.4.0
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kiwisolver==1.4.7
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lightning==2.4.0
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lightning-utilities==0.11.9
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lovelyplots==1.0.2
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markupsafe==3.0.2
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matplotlib==3.10.0
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mdtraj==1.10.2
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networkx==3.4.2
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ninja==1.11.1.3
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numpy==1.23.4
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nvidia-cublas-cu12==12.4.5.8 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cuda-cupti-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cuda-nvrtc-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cuda-runtime-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cudnn-cu12==9.1.0.70 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cufft-cu12==11.2.1.3 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-curand-cu12==10.3.5.147 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cusolver-cu12==11.6.1.9 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cusparse-cu12==12.3.1.170 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-nccl-cu12==2.21.5 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-nvjitlink-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-nvtx-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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nvidia-cublas-cu12==12.4.5.8 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-cuda-cupti-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-cuda-nvrtc-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-cuda-runtime-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-cudnn-cu12==9.1.0.70 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-cufft-cu12==11.2.1.3 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-curand-cu12==10.3.5.147 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-cusolver-cu12==11.6.1.9 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-cusparse-cu12==12.3.1.170 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-nccl-cu12==2.21.5 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-nvjitlink-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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nvidia-nvtx-cu12==12.4.127 ; platform_machine == 'x86_64' and platform_system == 'Linux'
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omegaconf==2.3.0
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opt-einsum==3.4.0
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opt-einsum-fx==0.1.4
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sympy==1.13.1
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tenacity==9.0.0
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torch==2.5.1
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torch-cluster==1.6.3 ; (python_full_version >= '3.13' and sys_platform == 'darwin') or (python_full_version >= '3.13' and sys_platform == 'linux') or (sys_platform != 'darwin' and sys_platform != 'linux')
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torch-cluster==1.6.3 ; (sys_platform != 'darwin' and sys_platform != 'linux') or python_full_version >= '3.13'
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torch-cluster @ https://data.pyg.org/whl/torch-2.5.0%2Bcpu/torch_cluster-1.6.3-cp310-cp310-macosx_10_9_universal2.whl ; python_full_version < '3.11' and sys_platform == 'darwin'
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torch-cluster @ https://data.pyg.org/whl/torch-2.5.0%2Bcpu/torch_cluster-1.6.3-cp311-cp311-macosx_10_9_universal2.whl ; python_full_version == '3.11.*' and sys_platform == 'darwin'
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torch-cluster @ https://data.pyg.org/whl/torch-2.5.0%2Bcpu/torch_cluster-1.6.3-cp312-cp312-macosx_10_13_universal2.whl ; python_full_version == '3.12.*' and sys_platform == 'darwin'
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torch-cluster @ https://data.pyg.org/whl/torch-2.5.0%2Bcu121/torch_cluster-1.6.3%2Bpt25cu121-cp310-cp310-linux_x86_64.whl ; python_full_version < '3.11' and sys_platform == 'linux'
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torch-cluster @ https://data.pyg.org/whl/torch-2.5.0%2Bcu121/torch_cluster-1.6.3%2Bpt25cu121-cp311-cp311-linux_x86_64.whl ; python_full_version == '3.11.*' and sys_platform == 'linux'
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torch-cluster @ https://data.pyg.org/whl/torch-2.5.0%2Bcu121/torch_cluster-1.6.3%2Bpt25cu121-cp312-cp312-linux_x86_64.whl ; python_full_version == '3.12.*' and sys_platform == 'linux'
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torch-geometric==2.6.1
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torch-scatter==2.1.2 ; (python_full_version >= '3.13' and sys_platform == 'darwin') or (python_full_version >= '3.13' and sys_platform == 'linux') or (sys_platform != 'darwin' and sys_platform != 'linux')
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torch-scatter==2.1.2 ; (sys_platform != 'darwin' and sys_platform != 'linux') or python_full_version >= '3.13'
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torch-scatter @ https://data.pyg.org/whl/torch-2.5.0%2Bcpu/torch_scatter-2.1.2-cp310-cp310-macosx_10_9_universal2.whl ; python_full_version < '3.11' and sys_platform == 'darwin'
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torch-scatter @ https://data.pyg.org/whl/torch-2.5.0%2Bcpu/torch_scatter-2.1.2-cp311-cp311-macosx_10_9_universal2.whl ; python_full_version == '3.11.*' and sys_platform == 'darwin'
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torch-scatter @ https://data.pyg.org/whl/torch-2.5.0%2Bcpu/torch_scatter-2.1.2-cp312-cp312-macosx_10_13_universal2.whl ; python_full_version == '3.12.*' and sys_platform == 'darwin'
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torchmetrics==1.6.0
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torchvision==0.20.1
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tqdm==4.67.1
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triton==3.1.0 ; python_full_version < '3.13' and platform_machine == 'x86_64' and platform_system == 'Linux' and sys_platform != 'darwin' and sys_platform != 'win32'
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triton==3.1.0 ; python_full_version < '3.13' and platform_machine == 'x86_64' and platform_system == 'Linux'
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typing-extensions==4.12.2
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tzdata==2024.2
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universal-pathlib==0.2.6

‎pyproject.toml

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dependencies = {file = ["requirements.in"]}
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readme = {file = "README.md"}
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[tool.setuptools.dynamic.optional-dependencies]
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dev = {file = ["requirements-dev.in"]}
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analysis = {file = ["requirements-analysis.in"]}
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[project.scripts]
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jamun_train = "jamun.cmdline.train:main"
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[tool.uv]
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no-build-package = ["mdtraj"]
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cache-keys = [{file = "requirements.in"}, {file = "requirements-dev.in"}, {file = "requirements-analysis.in"}]
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cache-keys = [{file = "requirements.in"}]
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constraint-dependencies = ["torch==2.5.1"]
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# see https://github.com/astral-sh/uv/issues/9079

‎requirements.in

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pot
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ase
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posebusters
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lovelyplots

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