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environment.yaml
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environment.yaml
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name: prtm
channels:
- conda-forge
- bioconda
- pytorch
- dglteam/label/cu118
- pyg
- nvidia
dependencies:
- conda-forge::python=3.10
- conda-forge::setuptools=59.5.0
- conda-forge::pip
- conda-forge::openmm==8.0.0
- conda-forge::pdbfixer==1.9
- conda-forge::cudatoolkit=11.8.*
- bioconda::tmalign
- bioconda::hmmer==3.3.2
- bioconda::hhsuite==3.3.0
- bioconda::kalign2==2.04
- pytorch::pytorch==2.0.1
- pytorch::torchdata==0.7.1
- pytorch-cuda=11.8
- dglteam/label/cu118::dgl
- pytorch-lightning==2.0.2
- astropy==5.3
- wandb==0.15.3
- biopandas==0.4.1
- biopython==1.81
- biotite==0.37.0
- chex==0.1.7
- deepspeed==0.9.2
- dgllife==0.3.2
- dm-haiku==0.0.8
- dm-tree==0.1.7
- e3nn==0.5.1
- einops==0.6.1
- hydra-core==1.3.2
- jax==0.4.11
- louvain==0.8.0
- modelcif==0.7
- conda-forge::networkx==3.1
- numba==0.57.0
- numpy
- pandas
- scikit-learn
- scipy
- seaborn
- sympy
- tqdm
- nglview
- jupyterlab
- matplotlib
- omegaconf==2.3.0
- prody==2.4.0
- conda-forge::openbabel==3.1.1
- optax==0.1.5
- conda-forge::rdkit==2023.03.1
- conda-forge::scanpy==1.9.3
- pyg::pyg==2.3.0
- pyg::pytorch-sparse==0.6.17
- pyg::pytorch-scatter==2.1.1
- pyg::pytorch-cluster==1.6.1
- ray-core==2.4.0
- transformers==4.29.2
- tensorboard==2.11.2
- spyrmsd==0.5.2
- python-igraph==0.10.3
- pynvml==11.0.0
- decorator==5.1.0
- pip:
- boto3
- botocore
- opt-einsum-fx>=0.1.4
- opt-einsum>=3.3.0
- charset-normalizer
- colossalai
- gdown
- gitpython
- huggingface_hub
- immutabledict
- libmsym
- lie_learn
- lifelines
- mpl-scatter-density
- packaging
- prettytable
- protobuf
- py3Dmol
- pyaml
- pyfaidx
- pytest
- requests
- subword-nmt
- threadpoolctl
- typing-extensions
- urllib3
- wget
- git+https://github.com/NVIDIA/dllogger.git