├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── changelog.md ├── env.yml ├── env_gpu.yml ├── setup.cfg ├── setup.py ├── streamd ├── __init__.py ├── analysis │ ├── __init__.py │ ├── md_system_analysis.py │ ├── plot_build.py │ ├── run_analysis.py │ └── xvg2png.py ├── example │ ├── instructions.txt │ ├── ligand.mol │ └── protein_HIS.pdb ├── mcpbpy_md │ ├── __init__.py │ └── mcbpy_md.py ├── preparation │ ├── __init__.py │ ├── complex_preparation.py │ ├── ligand_preparation.py │ ├── mcpbpy_preparation.py │ ├── md_files_preparation.py │ └── nonstandard_solvent_preparation.py ├── prolif │ ├── __init__.py │ ├── prolif2png.py │ ├── prolif_frame_map.py │ └── run_prolif.py ├── run_gbsa.py ├── run_md.py ├── scripts │ ├── __init__.py │ ├── com │ │ ├── 1.com │ │ ├── 2.com │ │ └── 3.com │ ├── gbsa │ │ └── mmpbsa.in │ ├── getcharge.py │ ├── mcpbpy_scripts │ │ └── protein.in │ ├── mdp │ │ ├── ions.mdp │ │ ├── md.mdp │ │ ├── minim.mdp │ │ ├── npt.mdp │ │ └── nvt.mdp │ ├── mol2_fix_coordsbonds.py │ ├── pdb2mol.py │ ├── pmed_amb2gmx.py │ ├── prepare_Gaussian_input.py │ ├── script_sh │ │ ├── continue_md.sh │ │ ├── equlibration.sh │ │ ├── ligand_mol2prep.sh │ │ ├── ligand_mol2prep_by_gaussian.sh │ │ ├── ligand_prep.sh │ │ ├── md.sh │ │ ├── md_analysis.sh │ │ ├── md_ligand_analysis.sh │ │ └── solv_ions.sh │ └── tleap.in ├── tests │ ├── README.md │ ├── __init__.py │ ├── analysis_test.py │ ├── config_cli_test.py │ ├── conftest.py │ ├── data │ │ ├── ligand.mol │ │ ├── mdrun_test │ │ │ ├── md_preparation │ │ │ │ ├── ligands │ │ │ │ │ └── 1ke7_LS3 │ │ │ │ │ │ ├── 1ke7_LS3.gro │ │ │ │ │ │ ├── 1ke7_LS3.mol2 │ │ │ │ │ │ ├── 1ke7_LS3.top │ │ │ │ │ │ ├── posre_1ke7_LS3.itp │ │ │ │ │ │ └── resid.txt │ │ │ │ └── protein │ │ │ │ │ └── protein_HIS │ │ │ │ │ ├── posre.itp │ │ │ │ │ ├── protein_HIS.gro │ │ │ │ │ └── topol.top │ │ │ └── md_run │ │ │ │ └── protein_HIS_1ke7_LS3 │ │ │ │ ├── 1ke7_LS3.itp │ │ │ │ ├── all.itp │ │ │ │ ├── all_ligand_resid.txt │ │ │ │ ├── index.ndx │ │ │ │ ├── md_fit.xtc │ │ │ │ ├── md_out.tpr │ │ │ │ ├── md_out.xtc │ │ │ │ ├── posre.itp │ │ │ │ ├── solv_ions.gro │ │ │ │ └── topol.top │ │ ├── mmpbsa.in │ │ ├── paint_by_file_exp.csv │ │ ├── protein_HIS.pdb │ │ └── rmsd_files │ │ │ ├── rmsd_protein_HIS_1BJU_ligand.csv │ │ │ ├── rmsd_protein_HIS_1BJV_ligand.csv │ │ │ ├── rmsd_protein_HIS_1C5Q_ligand.csv │ │ │ ├── rmsd_protein_HIS_1C5S_ligand.csv │ │ │ └── rmsd_protein_HIS_1C5T_ligand.csv │ ├── decomp_dat_parser_test.py │ ├── gbsa_test.py │ ├── import_test.py │ ├── md_test.py │ ├── plot_build_test.py │ ├── preparation_test.py │ ├── prolif_test.py │ └── system_name_test.py └── utils │ ├── __init__.py │ ├── dask_init.py │ └── utils.py └── streamd_logo.png /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ci-lab-cz/streamd/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /MANIFEST.in: 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