Molecular dynamics - #43
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…b into molecular_dynamics
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first version of tutorial and notebook for short Molecular Dynamics simulations for predicted structures ( see Feat: Molecular Dynamics after Structure Prediction #31 )
supports proteins, small molecules, ions, DNA/RNA; included in tests
supports Boltz and Alphafold 3 (server and local) .cif input
two tool modules, to look up smiles from CCD and clean termini of DNA/RNA
first version of an analysis notebook to analyze MD trajectory
does not support PTMs yet
does not support membranes (treats them as small molecules)