LICENSE
README.md
pyproject.toml
CondenSimAdapter/__init__.py
CondenSimAdapter.egg-info/PKG-INFO
CondenSimAdapter.egg-info/SOURCES.txt
CondenSimAdapter.egg-info/dependency_links.txt
CondenSimAdapter.egg-info/entry_points.txt
CondenSimAdapter.egg-info/requires.txt
CondenSimAdapter.egg-info/top_level.txt
CondenSimAdapter/backmap/__init__.py
CondenSimAdapter/backmap/backmapper.py
CondenSimAdapter/backmap/cg2all/__init__.py
CondenSimAdapter/backmap/cg2all/data/calpha_geometry_params.dat
CondenSimAdapter/backmap/cg2all/data/martini.top
CondenSimAdapter/backmap/cg2all/data/martini2.top
CondenSimAdapter/backmap/cg2all/data/martini3.top
CondenSimAdapter/backmap/cg2all/data/primo.top
CondenSimAdapter/backmap/cg2all/data/residue_constants.pkl
CondenSimAdapter/backmap/cg2all/data/residue_geometry_params.bound.dat
CondenSimAdapter/backmap/cg2all/data/residue_geometry_params.harmonic.dat
CondenSimAdapter/backmap/cg2all/lib/__init__.py
CondenSimAdapter/backmap/cg2all/lib/libcg.py
CondenSimAdapter/backmap/cg2all/lib/libconfig.py
CondenSimAdapter/backmap/cg2all/lib/libdata.py
CondenSimAdapter/backmap/cg2all/lib/libloss.py
CondenSimAdapter/backmap/cg2all/lib/libmetric.py
CondenSimAdapter/backmap/cg2all/lib/libmodel.py
CondenSimAdapter/backmap/cg2all/lib/libpdb.py
CondenSimAdapter/backmap/cg2all/lib/libter.py
CondenSimAdapter/backmap/cg2all/lib/model_downloader.py
CondenSimAdapter/backmap/cg2all/lib/numpy_basics.py
CondenSimAdapter/backmap/cg2all/lib/residue_constants.py
CondenSimAdapter/backmap/cg2all/lib/residue_constants_base.py
CondenSimAdapter/backmap/cg2all/lib/snippets.py
CondenSimAdapter/backmap/cg2all/lib/torch_basics.py
CondenSimAdapter/backmap/cg2all/model/.gitkeep
CondenSimAdapter/backmap/cg2all/model/__init__.py
CondenSimAdapter/backmap/se3transformer/__init__.py
CondenSimAdapter/backmap/se3transformer/basis.py
CondenSimAdapter/backmap/se3transformer/fiber.py
CondenSimAdapter/backmap/se3transformer/snippets.py
CondenSimAdapter/backmap/se3transformer/transformer.py
CondenSimAdapter/backmap/se3transformer/utils.py
CondenSimAdapter/backmap/se3transformer/layers/__init__.py
CondenSimAdapter/backmap/se3transformer/layers/attention.py
CondenSimAdapter/backmap/se3transformer/layers/convolution.py
CondenSimAdapter/backmap/se3transformer/layers/linear.py
CondenSimAdapter/backmap/se3transformer/layers/norm.py
CondenSimAdapter/backmap/se3transformer/layers/pooling.py
CondenSimAdapter/cli/__init__.py
CondenSimAdapter/cli/__main__.py
CondenSimAdapter/cli/commands.py
CondenSimAdapter/cli/shared.py
CondenSimAdapter/cli/commands_refactored/__init__.py
CondenSimAdapter/cli/commands_refactored/backmap_command.py
CondenSimAdapter/cli/commands_refactored/cg_command.py
CondenSimAdapter/cli/commands_refactored/droplet_density_command.py
CondenSimAdapter/cli/commands_refactored/forcefield_command.py
CondenSimAdapter/cli/commands_refactored/info_command.py
CondenSimAdapter/cli/commands_refactored/init_command.py
CondenSimAdapter/cli/commands_refactored/minimize_command.py
CondenSimAdapter/cli/commands_refactored/models_command.py
CondenSimAdapter/cli/commands_refactored/pace_opt_command.py
CondenSimAdapter/cli/commands_refactored/to_run_command.py
CondenSimAdapter/core/__init__.py
CondenSimAdapter/core/config.py
CondenSimAdapter/core/molecule.py
CondenSimAdapter/core/sasa.py
CondenSimAdapter/core/simulation.py
CondenSimAdapter/core/topology.py
CondenSimAdapter/core/forcefield/__init__.py
CondenSimAdapter/core/forcefield/base.py
CondenSimAdapter/core/forcefield/calvados.py
CondenSimAdapter/core/forcefield/cocomo.py
CondenSimAdapter/core/forcefield/hps.py
CondenSimAdapter/core/forcefield/mpipi.py
CondenSimAdapter/core/forcefield/data/HPS_Urry_parameters.csv
CondenSimAdapter/core/forcefield/data/recharged_params.txt
CondenSimAdapter/core/forcefield/data/residues_CALVADOS2.csv
CondenSimAdapter/core/forcefield/data/residues_CALVADOS3.csv
CondenSimAdapter/extern/__init__.py
CondenSimAdapter/forcefield/__init__.py
CondenSimAdapter/forcefield/registry.py
CondenSimAdapter/forcefield/a99SBdisp.ff/a99SBdisp_water.gro
CondenSimAdapter/forcefield/a99SBdisp.ff/a99SBdisp_water.itp
CondenSimAdapter/forcefield/a99SBdisp.ff/aminoacids.arn
CondenSimAdapter/forcefield/a99SBdisp.ff/aminoacids.c.tdb
CondenSimAdapter/forcefield/a99SBdisp.ff/aminoacids.hdb
CondenSimAdapter/forcefield/a99SBdisp.ff/aminoacids.n.tdb
CondenSimAdapter/forcefield/a99SBdisp.ff/aminoacids.r2b
CondenSimAdapter/forcefield/a99SBdisp.ff/aminoacids.rtp
CondenSimAdapter/forcefield/a99SBdisp.ff/aminoacids.vsd
CondenSimAdapter/forcefield/a99SBdisp.ff/atomtypes.atp
CondenSimAdapter/forcefield/a99SBdisp.ff/ffbonded.itp
CondenSimAdapter/forcefield/a99SBdisp.ff/ffnonbonded.itp
CondenSimAdapter/forcefield/a99SBdisp.ff/forcefield.doc
CondenSimAdapter/forcefield/a99SBdisp.ff/forcefield.itp
CondenSimAdapter/forcefield/a99SBdisp.ff/ions.itp
CondenSimAdapter/forcefield/a99SBdisp.ff/watermodels.dat
CondenSimAdapter/forcefield/amber03wsc.ff/aminoacids.arn
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CondenSimAdapter/forcefield/amber03wsc.ff/aminoacids.hdb
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CondenSimAdapter/forcefield/amber03wsc.ff/aminoacids.r2b
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CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/Makefile.am
CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/Makefile.in
CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/aminoacids.arn
CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/aminoacids.c.tdb
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CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/aminoacids.vsd
CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/atomtypes.atp
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CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/dna.r2b
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CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/rna.r2b
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CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/spc.itp
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CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/tip3p.itp
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CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/tip5p.itp
CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/urea.itp
CondenSimAdapter/forcefield/amber14sb_parmbsc1.ff/watermodels.dat
CondenSimAdapter/forcefield/amber99sb-ildn.ff/aminoacids.arn
CondenSimAdapter/forcefield/amber99sb-ildn.ff/aminoacids.c.tdb
CondenSimAdapter/forcefield/amber99sb-ildn.ff/aminoacids.hdb
CondenSimAdapter/forcefield/amber99sb-ildn.ff/aminoacids.n.tdb
CondenSimAdapter/forcefield/amber99sb-ildn.ff/aminoacids.r2b
CondenSimAdapter/forcefield/amber99sb-ildn.ff/aminoacids.rtp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/aminoacids.vsd
CondenSimAdapter/forcefield/amber99sb-ildn.ff/atomtypes.atp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/dna.arn
CondenSimAdapter/forcefield/amber99sb-ildn.ff/dna.hdb
CondenSimAdapter/forcefield/amber99sb-ildn.ff/dna.r2b
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CondenSimAdapter/forcefield/amber99sb-ildn.ff/ffbonded.itp
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CondenSimAdapter/forcefield/amber99sb-ildn.ff/forcefield.doc
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CondenSimAdapter/forcefield/amber99sb-ildn.ff/rna.arn
CondenSimAdapter/forcefield/amber99sb-ildn.ff/rna.hdb
CondenSimAdapter/forcefield/amber99sb-ildn.ff/rna.r2b
CondenSimAdapter/forcefield/amber99sb-ildn.ff/rna.rtp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/spc.itp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/spce.itp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/tip3p.itp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/tip4p.itp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/tip4pew.itp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/tip5p.itp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/urea.itp
CondenSimAdapter/forcefield/amber99sb-ildn.ff/watermodels.dat
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/aminoacids.arn
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/aminoacids.c.tdb
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/aminoacids.hdb
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/aminoacids.n.tdb
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/aminoacids.r2b
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CondenSimAdapter/forcefield/amber99sbws-STQp.ff/aminoacids.vsd
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/atomtypes.atp
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/dna.arn
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/dna.hdb
CondenSimAdapter/forcefield/amber99sbws-STQp.ff/dna.r2b
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CondenSimAdapter/forcefield/amber99sbws-STQp.ff/rna.r2b
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CondenSimAdapter/forcefield/amber99sbws-STQp.ff/tip4p2005.itp
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CondenSimAdapter/forcefield/amber99sbws-stq.ff/aminoacids.arn
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CondenSimAdapter/forcefield/des-amber.ff/ions.itp
CondenSimAdapter/forcefield/des-amber.ff/tip3p.itp
CondenSimAdapter/forcefield/des-amber.ff/tip4pd.itp
CondenSimAdapter/forcefield/des-amber.ff/tip4pd_rerun.itp
CondenSimAdapter/forcefield/des-amber.ff/watermodels.dat
CondenSimAdapter/legacy/pace_asm_top_builder/prepare_pace_asm.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/C-N-ter-debug.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/C-N-ter.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/add-cap.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/change_resid.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/comb_top.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/insert_param.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/pace_genCONH2.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/rpl_posre.py
CondenSimAdapter/legacy/pace_asm_top_builder/scripts/genpair/insert_param.py
CondenSimAdapter/legacy/pace_top_builder/C-N-ter.py
CondenSimAdapter/legacy/pace_top_builder/change_molecule_name.py
CondenSimAdapter/legacy/pace_top_builder/change_resid.py
CondenSimAdapter/legacy/pace_top_builder/genPair.py
CondenSimAdapter/legacy/pace_top_builder/insert_param.py
CondenSimAdapter/legacy/pace_top_builder/insert_posre.py
CondenSimAdapter/legacy/pace_top_builder/prepare_peptide.py
CondenSimAdapter/legacy/pace_top_builder/ring_refine.py
CondenSimAdapter/minimize/__init__.py
CondenSimAdapter/minimize/config_loader.py
CondenSimAdapter/minimize/minimizer.py
CondenSimAdapter/minimize/openmm_runner.py
CondenSimAdapter/minimize/softcore.py
CondenSimAdapter/minimize/topology_builder.py
CondenSimAdapter/minimize/worker.py
CondenSimAdapter/src/__init__.py
CondenSimAdapter/src/device_utils.py
CondenSimAdapter/src/pdb_tool.py
CondenSimAdapter/src/plumed_generator.py
tests/test_adapter_backmap_smoke.py
tests/test_adapter_cg_config.py
tests/test_adapter_cg_simulator_smoke.py
tests/test_adapter_minimize_smoke.py
tests/test_forcefield_registry_cli.py
tests/test_integration_calvados_sim.py
tests/test_integration_cg2all.py
tests/test_integration_minimize_gromacs.py
tests/test_sasa.py