LICENSE
MANIFEST.in
README.md
pyproject.toml
equilibration/__init__.py
equilibration/amber/eq/step0_minimization.mdin
equilibration/amber/eq/step1_equilibration.mdin
equilibration/amber/eq/step2_equilibration.mdin
equilibration/amber/eq/step3_equilibration.mdin
equilibration/amber/eq/step4_equilibration.mdin
equilibration/amber/eq/step5_equilibration.mdin
equilibration/amber/eq/step6_equilibration.mdin
equilibration/amber/production/NPAT/step7_production.mdin
equilibration/amber/production/NPT/step7_production.mdin
equilibration/amber/production/NPgT/step7_production.mdin
equilibration/amber/production/NVT/step7_production.mdin
equilibration/gromacs/eq/step6.0_minimization.mdp
equilibration/gromacs/eq/step6.1_equilibration.mdp
equilibration/gromacs/eq/step6.2_equilibration.mdp
equilibration/gromacs/eq/step6.3_equilibration.mdp
equilibration/gromacs/eq/step6.4_equilibration.mdp
equilibration/gromacs/eq/step6.5_equilibration.mdp
equilibration/gromacs/eq/step6.6_equilibration.mdp
equilibration/gromacs/production/NPAT/step7_production.mdp
equilibration/gromacs/production/NPT/step7_production.mdp
equilibration/gromacs/production/NPgT/step7_production.mdp
equilibration/gromacs/production/NVT/step7_production.mdp
equilibration/namd/eq/step6.1_equilibration.inp
equilibration/namd/eq/step6.2_equilibration.inp
equilibration/namd/eq/step6.3_equilibration.inp
equilibration/namd/eq/step6.4_equilibration.inp
equilibration/namd/eq/step6.5_equilibration.inp
equilibration/namd/eq/step6.6_equilibration.inp
equilibration/namd/production/NPAT/step7_production.inp
equilibration/namd/production/NPT/step7_production.inp
equilibration/namd/production/NPgT/step7_production.inp
equilibration/namd/production/NVT/step7_production.inp
equilibration/openmm/eq/step6.1_equilibration.inp
equilibration/openmm/eq/step6.2_equilibration.inp
equilibration/openmm/eq/step6.3_equilibration.inp
equilibration/openmm/eq/step6.4_equilibration.inp
equilibration/openmm/eq/step6.5_equilibration.inp
equilibration/openmm/eq/step6.6_equilibration.inp
equilibration/openmm/production/NPAT/step7_production.inp
equilibration/openmm/production/NPT/step7_production.inp
equilibration/openmm/production/NPgT/step7_production.inp
equilibration/openmm/production/NVT/step7_production.inp
equilibration/openmm/scripts/omm_barostat.py
equilibration/openmm/scripts/omm_readinputs.py
equilibration/openmm/scripts/omm_readparams.py
equilibration/openmm/scripts/omm_restraints.py
equilibration/openmm/scripts/omm_rewrap.py
equilibration/openmm/scripts/omm_vfswitch.py
equilibration/openmm/scripts/openmm_run.py
gatewizard/__init__.py
gatewizard.egg-info/PKG-INFO
gatewizard.egg-info/SOURCES.txt
gatewizard.egg-info/dependency_links.txt
gatewizard.egg-info/requires.txt
gatewizard.egg-info/top_level.txt
gatewizard/core/__init__.py
gatewizard/core/assembly.py
gatewizard/core/builder.py
gatewizard/core/file_manager.py
gatewizard/core/job_monitor.py
gatewizard/core/mempro.py
gatewizard/core/minimize_selection.py
gatewizard/core/preparation.py
gatewizard/core/short_gaps.py
gatewizard/core/structure_checker.py
gatewizard/core/structure_manager.py
gatewizard/core/titration.py
gatewizard/data/__init__.py
gatewizard/data/packmol_memgen_lipids.json
gatewizard/tools/__init__.py
gatewizard/tools/equilibration.py
gatewizard/tools/force_fields.py
gatewizard/tools/ligand_parametrization.py
gatewizard/tools/namd_water.py
gatewizard/tools/packmol_hydration.py
gatewizard/tools/peptide_cap_parametrization.py
gatewizard/tools/validators.py
gatewizard/utils/__init__.py
gatewizard/utils/amber_analysis.py
gatewizard/utils/bilayer_utils.py
gatewizard/utils/config.py
gatewizard/utils/energy_stride.py
gatewizard/utils/equilibration_cluster_script.py
gatewizard/utils/equilibration_failure.py
gatewizard/utils/equilibration_job_metadata.py
gatewizard/utils/equilibration_resources.py
gatewizard/utils/equilibration_resume.py
gatewizard/utils/equilibration_templates.py
gatewizard/utils/fatslim_apl.py
gatewizard/utils/fix_pbc_worker.py
gatewizard/utils/gridmat_md_apl.py
gatewizard/utils/gromacs_analysis.py
gatewizard/utils/helpers.py
gatewizard/utils/ions.py
gatewizard/utils/large_pdb.py
gatewizard/utils/lipid_bilayer_analysis.py
gatewizard/utils/log_io.py
gatewizard/utils/logger.py
gatewizard/utils/matplotlib_renderer.py
gatewizard/utils/namd_analysis.py
gatewizard/utils/openmm_analysis.py
gatewizard/utils/optional_deps.py
gatewizard/utils/packmol_memgen_data.py
gatewizard/utils/pdb_frame.py
gatewizard/utils/peptide_residues.py
gatewizard/utils/plot_spec.py
gatewizard/utils/protein_capping.py
gatewizard/utils/residue_mapping.py
gatewizard/utils/residue_restore.py
gatewizard/utils/trajectory_analysis.py
gatewizard/utils/trajectory_tools.py
gatewizard/utils/cluster/__init__.py
gatewizard/utils/cluster/midrun.py
gatewizard/utils/cluster/modules.py
gatewizard/utils/cluster/paths.py
gatewizard/utils/cluster/probe.py
gatewizard/utils/cluster/resources.py
gatewizard/utils/cluster/ssh.py
gatewizard/utils/cluster/templates.py
gatewizard/utils/cluster/types.py
gatewizard/utils/cluster/scheduler/__init__.py
gatewizard/utils/cluster/scheduler/base.py
gatewizard/utils/cluster/scheduler/pbs.py
gatewizard/utils/cluster/scheduler/slurm.py
scripts/build_docs_pdf.py
scripts/export_packmol_lipids.py
scripts/gen_api_dictionary.py
tests/__init__.py
tests/example_runner.py
tests/test_analysis.py
tests/test_assembly.py
tests/test_builder.py
tests/test_cluster.py
tests/test_complete_missing_atoms.py
tests/test_cpptraj_mask.py
tests/test_energy_stride.py
tests/test_equilibration.py
tests/test_equilibration_amber.py
tests/test_equilibration_gromacs.py
tests/test_equilibration_job_metadata.py
tests/test_equilibration_openmm.py
tests/test_equilibration_resources.py
tests/test_equilibration_resume.py
tests/test_equilibration_templates.py
tests/test_fatslim_apl.py
tests/test_fix_pbc_amber_center.py
tests/test_fix_pbc_job_status.py
tests/test_fix_pbc_ndx.py
tests/test_gridmat_md_apl.py
tests/test_gromacs_analysis.py
tests/test_ions.py
tests/test_large_pdb.py
tests/test_ligand_forcefield.py
tests/test_lipid_bilayer_analysis.py
tests/test_mempro.py
tests/test_minimize_selection.py
tests/test_namd_gpu_resident.py
tests/test_namd_log_progress.py
tests/test_namd_water.py
tests/test_openmm_log_progress.py
tests/test_optional_deps.py
tests/test_packmol_hydration.py
tests/test_pdb_frame.py
tests/test_peptide_residues.py
tests/test_plot_spec.py
tests/test_preparation.py
tests/test_preserve_pdb4amber.py
tests/test_residue_mapping.py
tests/test_residue_restore.py
tests/test_short_gaps.py
tests/test_structure_checker.py
tests/test_structure_manager.py
tests/test_titration.py
tests/analysis_examples/analysis_example_01.py
tests/analysis_examples/analysis_example_02.py
tests/analysis_examples/analysis_example_03.py
tests/analysis_examples/analysis_example_04.py
tests/analysis_examples/analysis_example_05.py
tests/analysis_examples/analysis_example_06.py
tests/analysis_examples/analysis_example_07.py
tests/analysis_examples/analysis_example_08.py
tests/analysis_examples/analysis_example_09.py
tests/analysis_examples/analysis_example_10.py
tests/analysis_examples/analysis_example_11.py
tests/analysis_examples/analysis_example_12.py
tests/analysis_examples/analysis_example_13.py
tests/analysis_examples/analysis_example_14.py
tests/analysis_examples/analysis_example_15.py
tests/builder_examples/builder_example_01.py
tests/builder_examples/builder_example_02.py
tests/builder_examples/builder_example_03.py
tests/builder_examples/builder_example_04.py
tests/builder_examples/builder_example_05.py
tests/builder_examples/builder_example_06.py
tests/builder_examples/builder_example_07.py
tests/builder_examples/builder_example_08.py
tests/builder_examples/builder_example_09.py
tests/builder_examples/builder_example_10.py
tests/builder_examples/builder_example_11.py
tests/builder_examples/builder_example_12.py
tests/builder_examples/builder_example_13.py
tests/builder_examples/builder_example_14.py
tests/builder_examples/builder_example_15.py
tests/builder_examples/builder_example_16.py
tests/builder_examples/builder_example_17.py
tests/builder_examples/builder_example_18.py
tests/builder_examples/builder_example_19.py
tests/builder_examples/builder_example_20.py
tests/builder_examples/builder_example_21.py
tests/builder_examples/builder_example_22.py
tests/builder_examples/builder_example_23.py
tests/builder_examples/builder_example_24.py
tests/builder_examples/builder_example_25.py
tests/builder_examples/builder_example_26.py
tests/builder_examples/status_utils.py
tests/equilibration_examples/equilibration_example_01.py
tests/equilibration_examples/equilibration_example_02.py
tests/equilibration_examples/equilibration_example_03.py
tests/equilibration_examples/equilibration_example_04.py
tests/equilibration_examples/equilibration_example_05.py
tests/equilibration_examples/equilibration_example_06.py
tests/equilibration_examples/equilibration_example_07.py
tests/equilibration_examples/equilibration_example_08.py
tests/equilibration_examples/equilibration_example_09.py
tests/equilibration_examples/openmm_example_01.py
tests/equilibration_examples/openmm_example_02.py
tests/equilibration_examples/openmm_example_03.py
tests/equilibration_examples/openmm_ligand_restraints/ligand_ABC_restraints/omm_barostat.py
tests/equilibration_examples/openmm_ligand_restraints/ligand_ABC_restraints/omm_readinputs.py
tests/equilibration_examples/openmm_ligand_restraints/ligand_ABC_restraints/omm_readparams.py
tests/equilibration_examples/openmm_ligand_restraints/ligand_ABC_restraints/omm_restraints.py
tests/equilibration_examples/openmm_ligand_restraints/ligand_ABC_restraints/omm_rewrap.py
tests/equilibration_examples/openmm_ligand_restraints/ligand_ABC_restraints/omm_vfswitch.py
tests/equilibration_examples/openmm_ligand_restraints/ligand_ABC_restraints/openmm_run.py
tests/equilibration_examples/openmm_ligand_restraints/standard_restraints/omm_barostat.py
tests/equilibration_examples/openmm_ligand_restraints/standard_restraints/omm_readinputs.py
tests/equilibration_examples/openmm_ligand_restraints/standard_restraints/omm_readparams.py
tests/equilibration_examples/openmm_ligand_restraints/standard_restraints/omm_restraints.py
tests/equilibration_examples/openmm_ligand_restraints/standard_restraints/omm_rewrap.py
tests/equilibration_examples/openmm_ligand_restraints/standard_restraints/omm_vfswitch.py
tests/equilibration_examples/openmm_ligand_restraints/standard_restraints/openmm_run.py
tests/equilibration_examples/openmm_ligand_restraints/taper_plus_ligand/omm_barostat.py
tests/equilibration_examples/openmm_ligand_restraints/taper_plus_ligand/omm_readinputs.py
tests/equilibration_examples/openmm_ligand_restraints/taper_plus_ligand/omm_readparams.py
tests/equilibration_examples/openmm_ligand_restraints/taper_plus_ligand/omm_restraints.py
tests/equilibration_examples/openmm_ligand_restraints/taper_plus_ligand/omm_rewrap.py
tests/equilibration_examples/openmm_ligand_restraints/taper_plus_ligand/omm_vfswitch.py
tests/equilibration_examples/openmm_ligand_restraints/taper_plus_ligand/openmm_run.py
tests/equilibration_examples/popc_membrane/status_utils.py
tests/hydration_examples/_shared.py
tests/hydration_examples/hydration_example_01.py
tests/hydration_examples/hydration_example_02.py
tests/hydration_examples/hydration_example_03.py
tests/hydration_examples/hydration_example_04.py
tests/hydration_examples/hydration_example_05.py
tests/hydration_examples/hydration_example_06.py
tests/mempro_examples/mempro_example_01.py
tests/mempro_examples/mempro_example_02.py
tests/mempro_examples/mempro_example_03.py
tests/mempro_examples/mempro_example_04.py
tests/mempro_examples/mempro_example_05.py
tests/mempro_examples/mempro_example_06.py
tests/mempro_examples/mempro_example_07.py
tests/mempro_examples/mempro_example_08.py
tests/mempro_examples/mempro_example_09.py
tests/mempro_examples/mempro_example_10.py
tests/mempro_examples/mempro_example_11.py
tests/mempro_examples/mempro_example_12.py
tests/preparation_examples/preparation_example_01.py
tests/preparation_examples/preparation_example_02.py
tests/preparation_examples/preparation_example_03.py
tests/preparation_examples/preparation_example_04.py
tests/preparation_examples/preparation_example_05.py
tests/preparation_examples/preparation_example_06.py
tests/preparation_examples/preparation_example_07.py
tests/preparation_examples/preparation_example_08.py
tests/preparation_examples/preparation_example_09.py
tests/preparation_examples/preparation_example_10.py
tests/preparation_examples/preparation_example_11.py
tests/preparation_examples/preparation_example_12.py
tests/preparation_examples/preparation_example_13.py
tests/preparation_examples/preparation_example_14.py
tests/preparation_examples/preparation_example_15.py
tests/preparation_examples/preparation_example_16.py
tests/preparation_examples/preparation_example_17.py
tests/preparation_examples/preparation_example_18.py
tests/preparation_examples/preparation_example_19.py
tests/preparation_examples/preparation_example_20.py
tests/preparation_examples/preparation_example_21.py
tests/preparation_examples/preparation_example_22.py
tests/preparation_examples/preparation_example_23.py
tests/structure_manager_examples/structure_manager_example_01.py
tests/structure_manager_examples/structure_manager_example_02.py
tests/structure_manager_examples/structure_manager_example_03.py
tests/structure_manager_examples/structure_manager_example_04.py
tests/structure_manager_examples/structure_manager_example_05.py
tests/structure_manager_examples/structure_manager_example_06.py
tests/structure_manager_examples/structure_manager_example_07.py
tests/structure_manager_examples/structure_manager_example_08.py
tests/structure_manager_examples/structure_manager_example_09.py
tests/structure_manager_examples/structure_manager_example_10.py
tests/structure_manager_examples/structure_manager_example_11.py
tests/structure_manager_examples/structure_manager_example_12.py
tests/structure_manager_examples/structure_manager_example_13.py
tests/structure_manager_examples/structure_manager_example_14.py
tests/structure_manager_examples/structure_manager_example_15.py
tests/study_cases/prepare_systems.py