├── .github └── workflows │ └── codeql.yml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── README.md ├── SECURITY.md ├── docs ├── ai2bmd.md └── fragmentation.md ├── examples ├── abd.pdb ├── chig.pdb ├── chig_preprocessed │ ├── chig-preeq-nowat.pdb │ └── chig-preeq.pdb ├── trpcage.pdb └── ww.pdb ├── scripts └── ai2bmd └── src ├── AIMD ├── __init__.py ├── arguments.py ├── fragment.py ├── preprocess.py ├── protein.py └── simulator.py ├── Calculators ├── __init__.py ├── async_utils.py ├── bonded.py ├── calculator.py ├── combiner.py ├── device_strategy.py ├── fragment.py ├── nonbonded.py ├── pme.py ├── qmmm.py ├── tinker_async.py └── visnet_calculator.py ├── Fragmentation ├── __init__.py ├── basefrag.py ├── bondlen │ ├── AA.npz │ ├── AN.npz │ ├── ANAN.npz │ ├── CC.npz │ ├── DD.npz │ ├── EE.npz │ ├── FF.npz │ ├── GG.npz │ ├── HH.npz │ ├── HID.npz │ ├── II.npz │ ├── KK.npz │ ├── LL.npz │ ├── MM.npz │ ├── NN.npz │ ├── PP.npz │ ├── QQ.npz │ ├── RR.npz │ ├── SS.npz │ ├── TT.npz │ ├── VV.npz │ ├── WW.npz │ └── YY.npz ├── distancefrag.py ├── hydrogen │ ├── __init__.py │ ├── ctable.py │ ├── energies.py │ └── topology.py ├── mm.in └── prmtop │ ├── AA.prmtop │ ├── AN.prmtop │ ├── ANAN.prmtop │ ├── CC.prmtop │ ├── CYX.prmtop │ ├── DD.prmtop │ ├── EE.prmtop │ ├── FF.prmtop │ ├── GG.prmtop │ ├── HH.prmtop │ ├── HID.prmtop │ ├── II.prmtop │ ├── KK.prmtop │ ├── LL.prmtop │ ├── MM.prmtop │ ├── NN.prmtop │ ├── PP.prmtop │ ├── QQ.prmtop │ ├── RR.prmtop │ ├── SS.prmtop │ ├── TT.prmtop │ ├── VV.prmtop │ ├── WW.prmtop │ └── YY.prmtop ├── ViSNet ├── __init__.py ├── checkpoints │ ├── visnet-uni-2ef43f29ec78fa5fef0b3de832bfada9.ckpt │ └── visnet-uni-de11d1421ccda37ffab07d7403c8f5bb.ckpt └── model │ ├── __init__.py │ ├── output_modules.py │ ├── priors.py │ ├── utils.py │ ├── visnet.py │ └── visnet_block.py ├── main.py └── utils ├── amoebabio18.prm ├── pdb.py ├── reference.py ├── seq_dict.pkl ├── signals.py ├── system.py ├── traj2dcd.py └── utils.py /.github/workflows/codeql.yml: 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