LICENSE
README.md
setup.py
ipamd/__init__.py
ipamd/cli.py
ipamd.egg-info/PKG-INFO
ipamd.egg-info/SOURCES.txt
ipamd.egg-info/dependency_links.txt
ipamd.egg-info/entry_points.txt
ipamd.egg-info/requires.txt
ipamd.egg-info/top_level.txt
ipamd/app/__init__.py
ipamd/app/analysis.py
ipamd/app/builder.py
ipamd/app/data_process.py
ipamd/app/md_analysis.py
ipamd/app/sakuanna.py
ipamd/app/simulation.py
ipamd/app/lib/galamost.so
ipamd/data/forcefield/Calvados1.xml
ipamd/data/forcefield/Calvados2.xml
ipamd/data/forcefield/Calvados3.xml
ipamd/data/forcefield/Calvados_lc.xml
ipamd/data/forcefield/HPS-Urry.xml
ipamd/data/forcefield/HPST.xml
ipamd/data/forcefield/droplet_prepare.xml
ipamd/data/forcefield/mpipi.xml
ipamd/data/forcefield/slab_prepare.xml
ipamd/plugins/analysis/data_process/distribution.py
ipamd/plugins/analysis/data_process/merge.py
ipamd/plugins/analysis/data_process/normalize.py
ipamd/plugins/analysis/data_process/save.py
ipamd/plugins/analysis/data_process/__pycache__/merge.cpython-312.pyc
ipamd/plugins/analysis/data_process/__pycache__/normalize.cpython-312.pyc
ipamd/plugins/analysis/data_process/__pycache__/save.cpython-312.pyc
ipamd/plugins/analysis/operator/contact_map.py
ipamd/plugins/analysis/operator/flory_monomer.py
ipamd/plugins/analysis/operator/flory_multimer.py
ipamd/plugins/analysis/operator/momentum.py
ipamd/plugins/analysis/operator/potential.py
ipamd/plugins/analysis/operator/rg.py
ipamd/plugins/analysis/operator/ripley.py
ipamd/plugins/analysis/operator/rmsd.py
ipamd/plugins/analysis/operator/rmsf.py
ipamd/plugins/analysis/operator/temperature.py
ipamd/plugins/analysis/operator/__pycache__/contact_map.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/flory_monomer.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/flory_multimer.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/momentum.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/potential.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/rg.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/ripley.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/rmsd.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/rmsf.cpython-312.pyc
ipamd/plugins/analysis/operator/__pycache__/temperature.cpython-312.pyc
ipamd/plugins/builder/converter/align_center.py
ipamd/plugins/builder/converter/merge_nearest.py
ipamd/plugins/builder/converter/read_xml.py
ipamd/plugins/builder/converter/to_aa.py
ipamd/plugins/builder/converter/to_cif.py
ipamd/plugins/builder/converter/to_pdb.py
ipamd/plugins/builder/converter/to_xml.py
ipamd/plugins/builder/converter/unwrap.py
ipamd/plugins/builder/converter/__pycache__/align_center.cpython-312.pyc
ipamd/plugins/builder/converter/__pycache__/merge_nearest.cpython-312.pyc
ipamd/plugins/builder/converter/__pycache__/read_xml.cpython-312.pyc
ipamd/plugins/builder/converter/__pycache__/to_aa.cpython-312.pyc
ipamd/plugins/builder/converter/__pycache__/to_cif.cpython-312.pyc
ipamd/plugins/builder/converter/__pycache__/to_pdb.cpython-312.pyc
ipamd/plugins/builder/converter/__pycache__/to_xml.cpython-312.pyc
ipamd/plugins/builder/converter/__pycache__/unwrap.cpython-312.pyc
ipamd/plugins/builder/genbox/enneutral.py
ipamd/plugins/builder/genbox/place_molecule_at.py
ipamd/plugins/builder/genbox/place_molecule_periodically.py
ipamd/plugins/builder/genbox/place_molecule_randomly.py
ipamd/plugins/builder/genbox/sub_box.py
ipamd/plugins/builder/genbox/__pycache__/enneutral.cpython-312.pyc
ipamd/plugins/builder/genbox/__pycache__/place_molecule_at.cpython-312.pyc
ipamd/plugins/builder/genbox/__pycache__/place_molecule_periodically.cpython-312.pyc
ipamd/plugins/builder/genbox/__pycache__/place_molecule_randomly.cpython-312.pyc
ipamd/plugins/builder/genbox/__pycache__/sub_box.cpython-312.pyc
ipamd/plugins/builder/generator/1a2b_protein_from_pdb.py
ipamd/plugins/builder/generator/af2.py
ipamd/plugins/builder/generator/box_from_xml.py
ipamd/plugins/builder/generator/cg_molecule_from_pdb.py
ipamd/plugins/builder/generator/download_pdb.py
ipamd/plugins/builder/generator/gen_elastic_network.py
ipamd/plugins/builder/generator/linear_protein.py
ipamd/plugins/builder/generator/molecule_from_xml.py
ipamd/plugins/builder/generator/new_simulation_box.py
ipamd/plugins/builder/generator/phosphorylate.py
ipamd/plugins/builder/generator/protein_from_pdb.py
ipamd/plugins/builder/generator/spiral_protein.py
ipamd/plugins/builder/generator/stacked_protein.py
ipamd/plugins/builder/generator/update.py
ipamd/plugins/builder/generator/__pycache__/1a2b_protein_from_pdb.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/af2.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/box_from_xml.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/cg_molecule_from_pdb.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/download_pdb.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/gen_elastic_network.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/linear_protein.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/molecule_from_xml.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/new_simulation_box.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/phosphorylate.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/protein_from_pdb.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/spiral_protein.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/stacked_protein.cpython-312.pyc
ipamd/plugins/builder/generator/__pycache__/update.cpython-312.pyc
ipamd/plugins/data_process/average.py
ipamd/plugins/data_process/flatten.py
ipamd/plugins/data_process/normalize.py
ipamd/plugins/data_process/plot.py
ipamd/plugins/data_process/print.py
ipamd/plugins/data_process/sum.py
ipamd/plugins/data_process/to_csv.py
ipamd/plugins/data_process/to_df.py
ipamd/plugins/data_process/__pycache__/average.cpython-312.pyc
ipamd/plugins/data_process/__pycache__/flatten.cpython-312.pyc
ipamd/plugins/data_process/__pycache__/normalize.cpython-312.pyc
ipamd/plugins/data_process/__pycache__/plot.cpython-312.pyc
ipamd/plugins/data_process/__pycache__/print.cpython-312.pyc
ipamd/plugins/data_process/__pycache__/sum.cpython-312.pyc
ipamd/plugins/data_process/__pycache__/to_csv.cpython-312.pyc
ipamd/plugins/data_process/__pycache__/to_df.cpython-312.pyc
ipamd/plugins/md_analysis/batch_compute.py
ipamd/plugins/md_analysis/contact_map_v1.py
ipamd/plugins/md_analysis/contact_number.py
ipamd/plugins/md_analysis/density_align.py
ipamd/plugins/md_analysis/density_box.py
ipamd/plugins/md_analysis/density_radius.py
ipamd/plugins/md_analysis/net_charge.py
ipamd/plugins/md_analysis/__pycache__/batch_compute.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/contact_map_v1.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/contact_number.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/density.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/density_align.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/density_box.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/density_radius.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/net_charge.cpython-312.pyc
ipamd/plugins/md_analysis/__pycache__/slab_free_energy.cpython-312.pyc
ipamd/plugins/sakuanna/pretier.py
ipamd/plugins/sakuanna/sequence_from_fasta.py
ipamd/plugins/sakuanna/statistic.py
ipamd/plugins/sakuanna/tag.py
ipamd/plugins/sakuanna/to_fasta.py
ipamd/plugins/sakuanna/__pycache__/pretier.cpython-312.pyc
ipamd/plugins/sakuanna/__pycache__/sequence_from_fasta.cpython-312.pyc
ipamd/plugins/sakuanna/__pycache__/statistic.cpython-312.pyc
ipamd/plugins/sakuanna/__pycache__/tag.cpython-312.pyc
ipamd/plugins/sakuanna/__pycache__/to_fasta.cpython-312.pyc
ipamd/plugins/simulation/force/ah.py
ipamd/plugins/simulation/force/bond_harmonic.py
ipamd/plugins/simulation/force/centripetal.py
ipamd/plugins/simulation/force/debye.py
ipamd/plugins/simulation/force/pppm.py
ipamd/plugins/simulation/force/wf.py
ipamd/plugins/simulation/force/__pycache__/ah.cpython-312.pyc
ipamd/plugins/simulation/force/__pycache__/bond_harmonic.cpython-312.pyc
ipamd/plugins/simulation/force/__pycache__/centripetal.cpython-312.pyc
ipamd/plugins/simulation/force/__pycache__/debye.cpython-312.pyc
ipamd/plugins/simulation/force/__pycache__/pppm.cpython-312.pyc
ipamd/plugins/simulation/force/__pycache__/wf.cpython-312.pyc
ipamd/plugins/simulation/integrator/andersen_npt.py
ipamd/plugins/simulation/integrator/em.py
ipamd/plugins/simulation/integrator/langevin_nvt.py
ipamd/plugins/simulation/integrator/noose_hover_nvt.py
ipamd/plugins/simulation/integrator/npt_z.py
ipamd/plugins/simulation/integrator/__pycache__/andersen_npt.cpython-312.pyc
ipamd/plugins/simulation/integrator/__pycache__/em.cpython-312.pyc
ipamd/plugins/simulation/integrator/__pycache__/langevin_nvt.cpython-312.pyc
ipamd/plugins/simulation/integrator/__pycache__/noose_hover_nvt.cpython-312.pyc
ipamd/plugins/simulation/integrator/__pycache__/npt_z.cpython-312.pyc
ipamd/public/__init__.py
ipamd/public/constant.py
ipamd/public/shared_data.py
ipamd/public/models/__init__.py
ipamd/public/models/common.py
ipamd/public/models/data.py
ipamd/public/models/md.py
ipamd/public/models/sequence.py
ipamd/public/utils/__init__.py
ipamd/public/utils/config.py
ipamd/public/utils/fasta.py
ipamd/public/utils/hardware.py
ipamd/public/utils/math.py
ipamd/public/utils/monitor.py
ipamd/public/utils/output.py
ipamd/public/utils/parser.py
ipamd/public/utils/pdb.py
ipamd/public/utils/plugin_manager.py
ipamd/public/utils/plugin_manager_v1.py
ipamd/public/utils/xml.py