LICENSE
README.md
setup.py
ipamd/__init__.py
ipamd.egg-info/PKG-INFO
ipamd.egg-info/SOURCES.txt
ipamd.egg-info/dependency_links.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/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/dev-calvados.xml
ipamd/data/forcefield/mpipi.xml
ipamd/plugins/analysis/data_process/distribution.py
ipamd/plugins/analysis/data_process/flatten.py
ipamd/plugins/analysis/data_process/merge.py
ipamd/plugins/analysis/data_process/normalize.py
ipamd/plugins/analysis/data_process/plot.py
ipamd/plugins/analysis/data_process/print.py
ipamd/plugins/analysis/data_process/save.py
ipamd/plugins/analysis/data_process/to_df.py
ipamd/plugins/analysis/operator/contact_map.py
ipamd/plugins/analysis/operator/density.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/builder/converter/align_center.py
ipamd/plugins/builder/converter/merge_nearest.py
ipamd/plugins/builder/converter/read_xml.py
ipamd/plugins/builder/converter/remove_image.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/genbox/enneutral.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/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/new_simulation_box.py
ipamd/plugins/builder/generator/protein_from_pdb.py
ipamd/plugins/builder/generator/spiral_protein.py
ipamd/plugins/sakuanna/pretier.py
ipamd/plugins/sakuanna/statistic.py
ipamd/plugins/simulation/force/ah.py
ipamd/plugins/simulation/force/bond_harmonic.py
ipamd/plugins/simulation/force/debye.py
ipamd/plugins/simulation/force/pppm.py
ipamd/plugins/simulation/force/wf.py
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/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/md.py
ipamd/public/models/sequence.py
ipamd/public/utils/__init__.py
ipamd/public/utils/config.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/plugin_manager.py
ipamd/public/utils/xml.py