├── .DS_Store ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── docs ├── .DS_Store ├── docs │ ├── .DS_Store │ ├── img │ │ ├── .DS_Store │ │ ├── MC_diagram.png │ │ └── flowchart.png │ ├── index.md │ ├── input_parameters.md │ ├── installation.md │ ├── output.md │ └── run.md └── mkdocs.yml ├── examples ├── example_ini_files │ ├── adf_input.ini │ ├── gaussian_input.ini │ ├── mc_input.ini │ └── orca_input.ini └── example_runs │ ├── monte_carlo │ ├── MetalDock.log │ ├── data_set │ │ └── compound_1 │ │ │ ├── compound_1.pdbqt │ │ │ ├── compound_1_c.xyz │ │ │ └── protein_1.pdbqt │ ├── input.ini │ ├── metal_dock_optimize.dat │ ├── run.sh │ └── slurm-9807103.out │ ├── no_vacancy_coordination_sphere │ ├── ADF │ │ ├── 2bzh_B_HB1.xyz │ │ ├── input.ini │ │ └── run.sh │ ├── GAUSSIAN │ │ ├── 2bzh.pdb │ │ ├── 2bzh_B_HB1.xyz │ │ ├── input.ini │ │ └── run.sh │ └── ORCA │ │ ├── 2bzh.pdb │ │ ├── 2bzh_B_HB1.xyz │ │ ├── input.ini │ │ └── run.sh │ └── vacancy_coordination_sphere │ ├── ADF │ ├── 1jzi.pdb │ ├── 1jzi_D_REP.xyz │ ├── input.ini │ └── run.sh │ ├── GAUSSIAN │ ├── 1jzi.pdb │ ├── 1jzi_D_REP.xyz │ ├── input.ini │ └── run.sh │ └── ORCA │ ├── 1jzi.pdb │ ├── 1jzi_D_REP.xyz │ ├── input.ini │ └── run.sh ├── metaldock ├── pyproject.toml ├── setup.cfg └── src ├── .DS_Store ├── external ├── AutoDock │ ├── autodock4 │ └── autogrid4 └── AutoDockTools │ ├── AD4.1_bound.dat │ ├── AD4_parameters.dat │ ├── AutoDockBondClassifier.py │ ├── Conformation.py │ ├── GridParameters.py │ ├── LICENSE │ ├── MolKit │ ├── APBSParameters.py │ ├── GapFinder.py │ ├── LICENSE │ ├── MolecularDescriptor.py │ ├── PDBdict.py │ ├── PDBresidueNames.py │ ├── PROSS.py │ ├── RELNOTES │ ├── WaterBuilder.py │ ├── __init__.py │ ├── amberPrmTop.py │ ├── bondClassifier.py │ ├── bondSelector.py │ ├── chargeCalculator.py │ ├── chargeMass.py │ ├── data │ │ ├── CVS │ │ │ ├── Entries │ │ │ ├── Repository │ │ │ ├── Root │ │ │ └── Tag │ │ ├── __init__.py │ │ ├── __init__.py.bak │ │ ├── all.in │ │ ├── all_amino94.in │ │ ├── all_amino94_dat.py │ │ ├── all_aminoct94.in │ │ ├── all_aminoct94_dat.py │ │ ├── all_aminont94.in │ │ ├── all_aminont94_dat.py │ │ ├── all_dat.py │ │ ├── all_nuc94.in │ │ ├── all_nuc94_dat.py │ │ ├── allct.in │ │ ├── allct_dat.py │ │ ├── allnt.in │ │ ├── allnt_dat.py │ │ ├── build_all_in.py │ │ ├── build_all_in.py.bak │ │ ├── nh2e.in │ │ ├── nh2e_dat.py │ │ ├── opls_nacl.in │ │ ├── opls_nacl_dat.py │ │ ├── opls_uni.in │ │ ├── opls_uni_dat.py │ │ ├── opls_unict.in │ │ ├── opls_unict_dat.py │ │ ├── opls_unint.in │ │ ├── opls_unint_dat.py │ │ ├── parm94.dat │ │ ├── qkollua.py │ │ ├── rotamer.def │ │ ├── uni_dat.py │ │ ├── unict_dat.py │ │ └── unint_dat.py │ ├── distanceSelector.py │ ├── genPdbParser.py │ ├── getsecondarystructure.py │ ├── groParser.py │ ├── hydrogenBondBuilder.py │ ├── hydrogenBuilder.py │ ├── interactionDescriptor.py │ ├── introduction.py │ ├── listSet.py │ ├── mmcifParser.py │ ├── mmcifWriter.py │ ├── mol2Parser.py │ ├── molecule.py │ ├── moleculeParser.py │ ├── moleculeWriter.py │ ├── oxtBuilder.py │ ├── parm94_dat.py │ ├── pdbParser.py │ ├── pdbWriter.py │ ├── pqrWriter.py │ ├── protein.py │ ├── radii_patterns.py │ ├── rotamerLib.py │ ├── sdfParser.py │ ├── sequence.py │ ├── sets.py │ ├── stringSelector.py │ ├── torTree.py │ ├── trajParser.py │ ├── tree.py │ └── waterBuilder.py │ ├── MoleculePreparation.py │ ├── PyBabel │ ├── CVS │ │ ├── Entries │ │ ├── Entries.Log │ │ ├── Repository │ │ ├── Root │ │ └── Tag │ ├── LICENSE │ ├── RELNOTES │ ├── __init__.py │ ├── addh.py │ ├── aromatic.py │ ├── atomTypes.py │ ├── babelAtomTypes.py │ ├── babelElements.py │ ├── bo.py │ ├── cycle.py │ ├── gasteiger.py │ ├── source.list │ ├── tools.py │ └── util.py │ ├── ResultParser.py │ ├── __init__.py │ ├── atomTypeTools.py │ ├── cluster.py │ ├── energyConstants.py │ ├── mglutil │ ├── math │ │ ├── CVS │ │ │ ├── Entries │ │ │ ├── Entries.Log │ │ │ ├── Repository │ │ │ ├── Root │ │ │ └── Tag │ │ ├── TensorModule.py │ │ ├── VectorModule.py │ │ ├── __init__.py │ │ ├── crystal.py │ │ ├── gridDescriptor.py │ │ ├── julie12019854k.rot │ │ ├── kinematics.py │ │ ├── kinematicstest.py │ │ ├── kmeansClustering.py │ │ ├── munkres.py │ │ ├── munkresLICENSE │ │ ├── ncoords.py │ │ ├── ncoordstest.py │ │ ├── rigidFit.py │ │ ├── rmsd.py │ │ ├── rmsdtest.py │ │ ├── rotax.py │ │ ├── statetocoords.py │ │ ├── statetocoordstest.py │ │ ├── stats.py │ │ ├── torsion.py │ │ ├── transformation.py │ │ ├── transformationtest.py │ │ └── usr.py │ └── util │ │ ├── CVS │ │ ├── Entries │ │ ├── Entries.Log │ │ ├── Repository │ │ ├── Root │ │ └── Tag │ │ ├── __init__.py │ │ ├── callback.py │ │ ├── colorUtil.py │ │ ├── defaultPalettes.py │ │ ├── idleUtil.py │ │ ├── misc.py │ │ ├── packageFilePath.py │ │ ├── parser.py │ │ ├── qhullUtils.py │ │ ├── recentFiles.py │ │ ├── relpath.py │ │ ├── repeatPrinter.py │ │ ├── tree.py │ │ └── uniq.py │ ├── prepare_gpf4.py │ ├── prepare_receptor4.py │ └── sol_par.py └── metal_dock ├── .gitignore ├── __init__.py ├── adf_engine.py ├── 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