diff --git "a/ASE/mcp_output/analysis.json" "b/ASE/mcp_output/analysis.json"
new file mode 100644--- /dev/null
+++ "b/ASE/mcp_output/analysis.json"
@@ -0,0 +1,12312 @@
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+            "pbc"
+          ],
+          "primitive_neighbor_list": [
+            "quantities",
+            "pbc",
+            "cell",
+            "positions",
+            "cutoff",
+            "numbers",
+            "self_interaction",
+            "use_scaled_positions",
+            "max_nbins"
+          ],
+          "neighbor_list": [
+            "quantities",
+            "a",
+            "cutoff",
+            "self_interaction",
+            "max_nbins"
+          ],
+          "first_neighbors": [
+            "natoms",
+            "first_atom"
+          ],
+          "get_connectivity_matrix": [
+            "nl",
+            "sparse"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "nomad",
+        "functions": [
+          "download",
+          "main",
+          "nmd2https",
+          "nomad_entry_to_images",
+          "read",
+          "section_system_to_atoms"
+        ],
+        "classes": [
+          "NomadEntry"
+        ],
+        "function_signatures": {
+          "nmd2https": [
+            "uri"
+          ],
+          "download": [
+            "uri"
+          ],
+          "read": [
+            "fd",
+            "_includekeys"
+          ],
+          "section_system_to_atoms": [
+            "section"
+          ],
+          "nomad_entry_to_images": [
+            "section"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "parallel",
+        "functions": [
+          "broadcast",
+          "distribute_cpus",
+          "get_txt",
+          "parallel_function",
+          "parallel_generator",
+          "paropen",
+          "parprint",
+          "register_parallel_cleanup_function"
+        ],
+        "classes": [
+          "DummyMPI",
+          "MPI4PY"
+        ],
+        "function_signatures": {
+          "get_txt": [
+            "txt",
+            "rank"
+          ],
+          "paropen": [
+            "name",
+            "mode",
+            "buffering"
+          ],
+          "parprint": [],
+          "broadcast": [
+            "obj",
+            "root",
+            "comm"
+          ],
+          "parallel_function": [
+            "func"
+          ],
+          "parallel_generator": [
+            "generator"
+          ],
+          "register_parallel_cleanup_function": [],
+          "distribute_cpus": [
+            "size",
+            "comm"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "phasediagram",
+        "functions": [
+          "bisect",
+          "float2str",
+          "parse_formula",
+          "print_results",
+          "solvated"
+        ],
+        "classes": [
+          "PhaseDiagram",
+          "Pourbaix"
+        ],
+        "function_signatures": {
+          "parse_formula": [
+            "formula"
+          ],
+          "float2str": [
+            "x"
+          ],
+          "solvated": [
+            "symbols"
+          ],
+          "bisect": [
+            "A",
+            "X",
+            "Y",
+            "f"
+          ],
+          "print_results": [
+            "results"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "phonons",
+        "functions": [],
+        "classes": [
+          "Displacement",
+          "Phonons"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "quaternions",
+        "functions": [],
+        "classes": [
+          "Quaternion",
+          "Quaternions"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "symbols",
+        "functions": [
+          "string2symbols",
+          "symbols2numbers"
+        ],
+        "classes": [
+          "Symbols"
+        ],
+        "function_signatures": {
+          "string2symbols": [
+            "s"
+          ],
+          "symbols2numbers": [
+            "symbols"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "thermochemistry",
+        "functions": [],
+        "classes": [
+          "CrystalThermo",
+          "HarmonicThermo",
+          "HinderedThermo",
+          "IdealGasThermo",
+          "ThermoChem"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "units",
+        "functions": [
+          "create_units"
+        ],
+        "classes": [
+          "Units"
+        ],
+        "function_signatures": {
+          "create_units": [
+            "codata_version"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "adsorb",
+        "functions": [
+          "build",
+          "estimate_lattice_constant"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "build": [],
+          "estimate_lattice_constant": [
+            "name",
+            "crystalstructure",
+            "covera"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "bulk",
+        "functions": [
+          "bulk"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "bulk": [
+            "name",
+            "crystalstructure",
+            "a",
+            "c",
+            "covera",
+            "u",
+            "orthorhombic",
+            "cubic"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "general_surface",
+        "functions": [
+          "build",
+          "ext_gcd",
+          "surface"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "surface": [
+            "lattice",
+            "indices",
+            "layers",
+            "vacuum",
+            "tol",
+            "termination"
+          ],
+          "build": [
+            "lattice",
+            "basis",
+            "layers",
+            "tol"
+          ],
+          "ext_gcd": [
+            "a",
+            "b"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "molecule",
+        "functions": [
+          "molecule"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "molecule": [
+            "name",
+            "vacuum"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "ribbon",
+        "functions": [
+          "graphene_nanoribbon"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "graphene_nanoribbon": [
+            "n",
+            "m",
+            "type",
+            "saturated",
+            "C_H",
+            "C_C",
+            "vacuum",
+            "magnetic",
+            "initial_mag",
+            "sheet",
+            "main_element",
+            "saturate_element"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "root",
+        "functions": [
+          "bcc111_root",
+          "fcc111_root",
+          "hcp0001_root",
+          "root_surface",
+          "root_surface_analysis"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "hcp0001_root": [
+            "symbol",
+            "root",
+            "size",
+            "a",
+            "c",
+            "vacuum",
+            "orthogonal"
+          ],
+          "fcc111_root": [
+            "symbol",
+            "root",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal"
+          ],
+          "bcc111_root": [
+            "symbol",
+            "root",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal"
+          ],
+          "root_surface": [
+            "primitive_slab",
+            "root",
+            "swap_alpha",
+            "eps"
+          ],
+          "root_surface_analysis": [
+            "primitive_slab",
+            "root",
+            "allow_above",
+            "eps"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "rotate",
+        "functions": [
+          "minimize_rotation_and_translation",
+          "quaternion_to_matrix",
+          "rotation_matrix_from_points"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "rotation_matrix_from_points": [
+            "m0",
+            "m1"
+          ],
+          "quaternion_to_matrix": [
+            "q"
+          ],
+          "minimize_rotation_and_translation": [
+            "target",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "supercells",
+        "functions": [
+          "find_optimal_cell_shape",
+          "get_deviation_from_optimal_cell_shape",
+          "make_supercell"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_deviation_from_optimal_cell_shape": [
+            "cell",
+            "target_shape",
+            "norm"
+          ],
+          "find_optimal_cell_shape": [
+            "cell",
+            "target_size",
+            "target_shape",
+            "lower_limit",
+            "upper_limit",
+            "verbose"
+          ],
+          "make_supercell": [
+            "prim",
+            "P"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "surface",
+        "functions": [
+          "add_adsorbate",
+          "add_vacuum",
+          "bcc100",
+          "bcc110",
+          "bcc111",
+          "diamond100",
+          "diamond111",
+          "fcc100",
+          "fcc110",
+          "fcc111",
+          "fcc211",
+          "hcp0001",
+          "hcp10m10",
+          "mx2"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "fcc100": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "fcc110": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "bcc100": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "bcc110": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "bcc111": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "fcc111": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "hcp0001": [
+            "symbol",
+            "size",
+            "a",
+            "c",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "hcp10m10": [
+            "symbol",
+            "size",
+            "a",
+            "c",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "diamond100": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "diamond111": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal",
+            "periodic"
+          ],
+          "add_adsorbate": [
+            "slab",
+            "adsorbate",
+            "height",
+            "position",
+            "offset",
+            "mol_index"
+          ],
+          "add_vacuum": [
+            "atoms",
+            "vacuum"
+          ],
+          "fcc211": [
+            "symbol",
+            "size",
+            "a",
+            "vacuum",
+            "orthogonal"
+          ],
+          "mx2": [
+            "formula",
+            "kind",
+            "a",
+            "thickness",
+            "size",
+            "vacuum"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "tools",
+        "functions": [
+          "cut",
+          "minimize_tilt",
+          "minimize_tilt_ij",
+          "niggli_reduce",
+          "niggli_reduce_cell",
+          "rotate",
+          "rotation_matrix",
+          "sort",
+          "stack"
+        ],
+        "classes": [
+          "IncompatibleCellError"
+        ],
+        "function_signatures": {
+          "cut": [
+            "atoms",
+            "a",
+            "b",
+            "c",
+            "clength",
+            "origo",
+            "nlayers",
+            "extend",
+            "tolerance",
+            "maxatoms"
+          ],
+          "stack": [
+            "atoms1",
+            "atoms2",
+            "axis",
+            "cell",
+            "fix",
+            "maxstrain",
+            "distance",
+            "reorder",
+            "output_strained"
+          ],
+          "rotation_matrix": [
+            "a1",
+            "a2",
+            "b1",
+            "b2"
+          ],
+          "rotate": [
+            "atoms",
+            "a1",
+            "a2",
+            "b1",
+            "b2",
+            "rotate_cell",
+            "center"
+          ],
+          "minimize_tilt_ij": [
+            "atoms",
+            "modified",
+            "fixed",
+            "fold_atoms"
+          ],
+          "minimize_tilt": [
+            "atoms",
+            "order",
+            "fold_atoms"
+          ],
+          "niggli_reduce_cell": [
+            "cell"
+          ],
+          "niggli_reduce": [
+            "atoms"
+          ],
+          "sort": [
+            "atoms",
+            "tags"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "tube",
+        "functions": [
+          "nanotube"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "nanotube": [
+            "n",
+            "m",
+            "length",
+            "bond",
+            "symbol",
+            "verbose",
+            "vacuum"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.build",
+        "module": "voids",
+        "functions": [
+          "voids"
+        ],
+        "classes": [
+          "RepulsivePotential"
+        ],
+        "function_signatures": {
+          "voids": [
+            "atoms_in"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "abinit",
+        "functions": [],
+        "classes": [
+          "Abinit"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "aims",
+        "functions": [],
+        "classes": [
+          "Aims",
+          "AimsCube"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "amber",
+        "functions": [
+          "map"
+        ],
+        "classes": [
+          "Amber",
+          "SANDER"
+        ],
+        "function_signatures": {
+          "map": [
+            "atoms",
+            "top"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "ase_qmmm_manyqm",
+        "functions": [
+          "get_neighbor_list",
+          "get_qm_atoms"
+        ],
+        "classes": [
+          "AseQmmmManyqm",
+          "LinkAtom"
+        ],
+        "function_signatures": {
+          "get_neighbor_list": [
+            "system"
+          ],
+          "get_qm_atoms": [
+            "indexfilename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "calculator",
+        "functions": [
+          "compare_atoms",
+          "equal",
+          "get_calculator",
+          "kptdensity2monkhorstpack",
+          "kpts2mp",
+          "kpts2ndarray",
+          "kpts2sizeandoffsets"
+        ],
+        "classes": [
+          "CalculationFailed",
+          "Calculator",
+          "CalculatorError",
+          "CalculatorSetupError",
+          "EigenvalOccupationMixin",
+          "EnvironmentError",
+          "FileIOCalculator",
+          "InputError",
+          "Parameters",
+          "PropertyNotImplementedError",
+          "PropertyNotPresent",
+          "ReadError",
+          "SCFError"
+        ],
+        "function_signatures": {
+          "compare_atoms": [
+            "atoms1",
+            "atoms2",
+            "tol"
+          ],
+          "get_calculator": [
+            "name"
+          ],
+          "equal": [
+            "a",
+            "b",
+            "tol"
+          ],
+          "kptdensity2monkhorstpack": [
+            "atoms",
+            "kptdensity",
+            "even"
+          ],
+          "kpts2mp": [
+            "atoms",
+            "kpts",
+            "even"
+          ],
+          "kpts2sizeandoffsets": [
+            "size",
+            "density",
+            "gamma",
+            "even",
+            "atoms"
+          ],
+          "kpts2ndarray": [
+            "kpts",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "castep",
+        "functions": [
+          "create_castep_keywords",
+          "get_castep_command",
+          "get_castep_pp_path",
+          "get_castep_version",
+          "import_castep_keywords",
+          "make_cell_dict",
+          "make_param_dict",
+          "shell_stdouterr"
+        ],
+        "classes": [
+          "Castep",
+          "CastepCell",
+          "CastepInputFile",
+          "CastepOption",
+          "CastepOptionDict",
+          "CastepParam",
+          "CastepVersionError",
+          "ConversionError"
+        ],
+        "function_signatures": {
+          "get_castep_version": [
+            "castep_command"
+          ],
+          "create_castep_keywords": [
+            "castep_command",
+            "filename",
+            "force_write",
+            "path",
+            "fetch_only"
+          ],
+          "make_cell_dict": [
+            "data"
+          ],
+          "make_param_dict": [
+            "data"
+          ],
+          "get_castep_pp_path": [
+            "castep_pp_path"
+          ],
+          "get_castep_command": [
+            "castep_command"
+          ],
+          "shell_stdouterr": [
+            "raw_command",
+            "cwd"
+          ],
+          "import_castep_keywords": [
+            "castep_command",
+            "filename",
+            "path"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "checkpoint",
+        "functions": [
+          "atoms_almost_equal"
+        ],
+        "classes": [
+          "Checkpoint",
+          "CheckpointCalculator",
+          "DevNull",
+          "NoCheckpoint"
+        ],
+        "function_signatures": {
+          "atoms_almost_equal": [
+            "a",
+            "b",
+            "tol"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "cp2k",
+        "functions": [
+          "parse_input"
+        ],
+        "classes": [
+          "CP2K",
+          "Cp2kShell",
+          "InputSection"
+        ],
+        "function_signatures": {
+          "parse_input": [
+            "inp"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "crystal",
+        "functions": [],
+        "classes": [
+          "CRYSTAL",
+          "PointChargePotential"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "dacapo",
+        "functions": [
+          "np2num",
+          "restart"
+        ],
+        "classes": [
+          "Dacapo"
+        ],
+        "function_signatures": {
+          "np2num": [
+            "a",
+            "typecode"
+          ],
+          "restart": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "dftb",
+        "functions": [
+          "read_max_angular_momentum"
+        ],
+        "classes": [
+          "Dftb",
+          "PointChargePotential"
+        ],
+        "function_signatures": {
+          "read_max_angular_momentum": [
+            "path"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "dftd3",
+        "functions": [],
+        "classes": [
+          "DFTD3"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "dmol",
+        "functions": [
+          "find_transformation",
+          "grd_to_file",
+          "read_grd"
+        ],
+        "classes": [
+          "DMol3"
+        ],
+        "function_signatures": {
+          "find_transformation": [
+            "atoms1",
+            "atoms2",
+            "verbose",
+            "only_cell"
+          ],
+          "grd_to_file": [
+            "atoms",
+            "grd_file",
+            "new_file"
+          ],
+          "read_grd": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "eam",
+        "functions": [],
+        "classes": [
+          "EAM"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "elk",
+        "functions": [],
+        "classes": [
+          "ELK"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "emt",
+        "functions": [],
+        "classes": [
+          "EMT"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "espresso",
+        "functions": [],
+        "classes": [
+          "Espresso"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "exciting",
+        "functions": [],
+        "classes": [
+          "Exciting"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "ff",
+        "functions": [
+          "get_limits"
+        ],
+        "classes": [
+          "ForceField"
+        ],
+        "function_signatures": {
+          "get_limits": [
+            "indices"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "fleur",
+        "functions": [],
+        "classes": [
+          "FLEUR"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "gaussian",
+        "functions": [],
+        "classes": [
+          "Gaussian"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "general",
+        "functions": [],
+        "classes": [
+          "Calculator"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "gromacs",
+        "functions": [
+          "do_clean"
+        ],
+        "classes": [
+          "Gromacs"
+        ],
+        "function_signatures": {
+          "do_clean": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "gulp",
+        "functions": [],
+        "classes": [
+          "Conditions",
+          "GULP",
+          "GULPOptimizer"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "interface",
+        "functions": [],
+        "classes": [
+          "Calculator",
+          "DFTCalculator"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "interfacechecker",
+        "functions": [
+          "check_interface",
+          "main_gpaw",
+          "main_octopus"
+        ],
+        "classes": [
+          "Args",
+          "Error",
+          "InterfaceChecker"
+        ],
+        "function_signatures": {
+          "check_interface": [
+            "calc"
+          ],
+          "main_gpaw": [],
+          "main_octopus": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "lammpslib",
+        "functions": [
+          "convert_cell",
+          "is_upper_triangular",
+          "unit_convert",
+          "write_lammps_data"
+        ],
+        "classes": [
+          "LAMMPSlib"
+        ],
+        "function_signatures": {
+          "is_upper_triangular": [
+            "arr",
+            "atol"
+          ],
+          "convert_cell": [
+            "ase_cell"
+          ],
+          "unit_convert": [
+            "quantity",
+            "units"
+          ],
+          "write_lammps_data": [
+            "filename",
+            "atoms",
+            "atom_types",
+            "comment",
+            "cutoff",
+            "molecule_ids",
+            "charges",
+            "units"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "lammpsrun",
+        "functions": [
+          "write_lammps_data"
+        ],
+        "classes": [
+          "LAMMPS",
+          "Prism",
+          "SpecialTee"
+        ],
+        "function_signatures": {
+          "write_lammps_data": [
+            "fileobj",
+            "atoms",
+            "specorder",
+            "force_skew",
+            "prismobj",
+            "velocities"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "lj",
+        "functions": [],
+        "classes": [
+          "LennardJones"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "loggingcalc",
+        "functions": [],
+        "classes": [
+          "LoggingCalculator"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "mopac",
+        "functions": [],
+        "classes": [
+          "MOPAC"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "morse",
+        "functions": [],
+        "classes": [
+          "MorsePotential"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "nwchem",
+        "functions": [],
+        "classes": [
+          "KPoint",
+          "NWChem"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "octopus",
+        "functions": [
+          "atoms2kwargs",
+          "block2list",
+          "boxshape_is_ase_compatible",
+          "generate_input",
+          "get_input_units",
+          "get_octopus_keywords",
+          "input_line_iter",
+          "is_orthorhombic",
+          "kwargs2atoms",
+          "kwargs2cell",
+          "list2block",
+          "main",
+          "normalize_keywords",
+          "octbool2bool",
+          "parse_input_file",
+          "process_special_kwargs",
+          "read_eigenvalues_file",
+          "read_static_info",
+          "read_static_info_eigenvalues",
+          "read_static_info_energy",
+          "read_static_info_kpoints",
+          "unpad",
+          "unpad_smarter"
+        ],
+        "classes": [
+          "OctNamespace",
+          "Octopus",
+          "OctopusIOError",
+          "OctopusKeywordError",
+          "OctopusParseError"
+        ],
+        "function_signatures": {
+          "read_eigenvalues_file": [
+            "fd"
+          ],
+          "process_special_kwargs": [
+            "atoms",
+            "kwargs"
+          ],
+          "is_orthorhombic": [
+            "cell"
+          ],
+          "get_input_units": [
+            "kwargs"
+          ],
+          "unpad": [
+            "pbc",
+            "arr"
+          ],
+          "unpad_smarter": [
+            "pbc",
+            "arr"
+          ],
+          "octbool2bool": [
+            "value"
+          ],
+          "list2block": [
+            "name",
+            "rows"
+          ],
+          "normalize_keywords": [
+            "kwargs"
+          ],
+          "get_octopus_keywords": [],
+          "input_line_iter": [
+            "lines"
+          ],
+          "block2list": [
+            "namespace",
+            "lines",
+            "header"
+          ],
+          "parse_input_file": [
+            "fd"
+          ],
+          "kwargs2cell": [
+            "kwargs"
+          ],
+          "boxshape_is_ase_compatible": [
+            "kwargs"
+          ],
+          "kwargs2atoms": [
+            "kwargs",
+            "directory"
+          ],
+          "atoms2kwargs": [
+            "atoms",
+            "use_ase_cell"
+          ],
+          "generate_input": [
+            "atoms",
+            "kwargs",
+            "normalized2pretty"
+          ],
+          "read_static_info_kpoints": [
+            "fd"
+          ],
+          "read_static_info_eigenvalues": [
+            "fd",
+            "energy_unit"
+          ],
+          "read_static_info_energy": [
+            "fd",
+            "energy_unit"
+          ],
+          "read_static_info": [
+            "fd"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "onetep",
+        "functions": [],
+        "classes": [
+          "Onetep"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "qmmm",
+        "functions": [
+          "combine_lj_lorenz_berthelot",
+          "wrap"
+        ],
+        "classes": [
+          "EIQMMM",
+          "Embedding",
+          "ForceConstantCalculator",
+          "ForceQMMM",
+          "LJInteractions",
+          "LJInteractionsGeneral",
+          "RescaledCalculator",
+          "SimpleQMMM"
+        ],
+        "function_signatures": {
+          "wrap": [
+            "D",
+            "cell",
+            "pbc"
+          ],
+          "combine_lj_lorenz_berthelot": [
+            "sigmaqm",
+            "sigmamm",
+            "epsilonqm",
+            "epsilonmm"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "singlepoint",
+        "functions": [],
+        "classes": [
+          "SinglePointCalculator",
+          "SinglePointDFTCalculator",
+          "SinglePointKPoint"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "socketio",
+        "functions": [
+          "actualunixsocketname"
+        ],
+        "classes": [
+          "IPIProtocol",
+          "SocketClient",
+          "SocketClosed",
+          "SocketIOCalculator",
+          "SocketServer"
+        ],
+        "function_signatures": {
+          "actualunixsocketname": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "test",
+        "functions": [
+          "gradient_test",
+          "make_test_dft_calculation",
+          "numeric_force"
+        ],
+        "classes": [
+          "FreeElectrons",
+          "TestCalculator",
+          "TestPotential"
+        ],
+        "function_signatures": {
+          "make_test_dft_calculation": [],
+          "numeric_force": [
+            "atoms",
+            "a",
+            "i",
+            "d"
+          ],
+          "gradient_test": [
+            "atoms",
+            "indices"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "tip3p",
+        "functions": [],
+        "classes": [
+          "PointChargePotential",
+          "TIP3P"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "tip4p",
+        "functions": [],
+        "classes": [
+          "TIP4P"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "turbomole",
+        "functions": [
+          "add_data_group",
+          "delete_data_group",
+          "execute",
+          "read_data_group",
+          "read_output"
+        ],
+        "classes": [
+          "PointChargePotential",
+          "Turbomole",
+          "TurbomoleOptimizer"
+        ],
+        "function_signatures": {
+          "read_output": [
+            "regex"
+          ],
+          "execute": [
+            "args",
+            "input_str",
+            "error_test",
+            "stdout_tofile"
+          ],
+          "add_data_group": [
+            "data_group",
+            "string",
+            "raw"
+          ],
+          "read_data_group": [
+            "data_group"
+          ],
+          "delete_data_group": [
+            "data_group"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators",
+        "module": "vdwcorrection",
+        "functions": [
+          "get_logging_file_descriptor"
+        ],
+        "classes": [
+          "vdWTkatchenko09prl"
+        ],
+        "function_signatures": {
+          "get_logging_file_descriptor": [
+            "calculator"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.demon",
+        "module": "demon",
+        "functions": [],
+        "classes": [
+          "Demon",
+          "Parameters_deMon"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.demon",
+        "module": "demon_io",
+        "functions": [
+          "parse_xray"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "parse_xray": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo",
+        "module": "changed",
+        "functions": [
+          "ados_changed",
+          "calculate_stress_changed",
+          "charge_mixing_changed",
+          "convergence_changed",
+          "decoupling_changed",
+          "dipole_changed",
+          "dw_changed",
+          "electronic_minimization_changed",
+          "extpot_changed",
+          "fftgrid_changed",
+          "ft_changed",
+          "kpts_changed",
+          "mdos_changed",
+          "nbands_changed",
+          "ncoutput_changed",
+          "occupationstatistics_changed",
+          "pseudopotentials_changed",
+          "pw_changed",
+          "spinpol_changed",
+          "status_changed",
+          "symmetry_changed",
+          "xc_changed"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "kpts_changed": [
+            "calc",
+            "x"
+          ],
+          "electronic_minimization_changed": [
+            "calc",
+            "x"
+          ],
+          "spinpol_changed": [
+            "calc",
+            "x"
+          ],
+          "symmetry_changed": [
+            "calc",
+            "x"
+          ],
+          "xc_changed": [
+            "calc",
+            "x"
+          ],
+          "calculate_stress_changed": [
+            "calc",
+            "x"
+          ],
+          "ados_changed": [
+            "calc",
+            "x"
+          ],
+          "convergence_changed": [
+            "calc",
+            "x"
+          ],
+          "charge_mixing_changed": [
+            "calc",
+            "x"
+          ],
+          "decoupling_changed": [
+            "calc",
+            "x"
+          ],
+          "dipole_changed": [
+            "calc",
+            "x"
+          ],
+          "extpot_changed": [
+            "calc",
+            "x"
+          ],
+          "fftgrid_changed": [
+            "calc",
+            "x"
+          ],
+          "ncoutput_changed": [
+            "calc",
+            "x"
+          ],
+          "nbands_changed": [
+            "calc",
+            "x"
+          ],
+          "occupationstatistics_changed": [
+            "calc",
+            "x"
+          ],
+          "pw_changed": [
+            "calc",
+            "x"
+          ],
+          "dw_changed": [
+            "calc",
+            "x"
+          ],
+          "ft_changed": [
+            "calc",
+            "x"
+          ],
+          "mdos_changed": [
+            "calc",
+            "x"
+          ],
+          "pseudopotentials_changed": [
+            "calc",
+            "x"
+          ],
+          "status_changed": [
+            "calc",
+            "x"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo",
+        "module": "jacapo",
+        "functions": [
+          "read"
+        ],
+        "classes": [
+          "DacapoAbnormalTermination",
+          "DacapoAborted",
+          "DacapoDryrun",
+          "DacapoInput",
+          "DacapoRunning",
+          "Jacapo"
+        ],
+        "function_signatures": {
+          "read": [
+            "ncfile"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo",
+        "module": "mayavis",
+        "functions": [
+          "plot_atoms",
+          "plot_cylinder"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "plot_cylinder": [
+            "start",
+            "end",
+            "tube_radius",
+            "color"
+          ],
+          "plot_atoms": [
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo",
+        "module": "validate",
+        "functions": [
+          "get_dacapopath",
+          "valid_ados",
+          "valid_ascii_debug",
+          "valid_atoms",
+          "valid_boolean",
+          "valid_calculate_stress",
+          "valid_charge_mixing",
+          "valid_convergence",
+          "valid_decoupling",
+          "valid_dipole",
+          "valid_dw",
+          "valid_electronic_minimization",
+          "valid_external_dipole",
+          "valid_extracharge",
+          "valid_fftgrid",
+          "valid_fixmagmom",
+          "valid_float",
+          "valid_ft",
+          "valid_int",
+          "valid_int_or_float",
+          "valid_kpts",
+          "valid_mdos",
+          "valid_nbands",
+          "valid_nc",
+          "valid_ncoutput",
+          "valid_occupationstatistics",
+          "valid_pseudopotentials",
+          "valid_psp",
+          "valid_pw",
+          "valid_spinpol",
+          "valid_status",
+          "valid_stay_alive",
+          "valid_str",
+          "valid_symmetry",
+          "valid_xc"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_dacapopath": [],
+          "valid_int": [
+            "x"
+          ],
+          "valid_float": [
+            "x"
+          ],
+          "valid_int_or_float": [
+            "x"
+          ],
+          "valid_boolean": [
+            "x"
+          ],
+          "valid_str": [
+            "x"
+          ],
+          "valid_atoms": [
+            "x"
+          ],
+          "valid_pw": [
+            "x"
+          ],
+          "valid_dw": [
+            "x"
+          ],
+          "valid_xc": [
+            "x"
+          ],
+          "valid_nbands": [
+            "x"
+          ],
+          "valid_ft": [
+            "x"
+          ],
+          "valid_spinpol": [
+            "x"
+          ],
+          "valid_fixmagmom": [
+            "x"
+          ],
+          "valid_symmetry": [
+            "x"
+          ],
+          "valid_calculate_stress": [
+            "x"
+          ],
+          "valid_kpts": [
+            "x"
+          ],
+          "valid_dipole": [
+            "x"
+          ],
+          "valid_nc": [
+            "x"
+          ],
+          "valid_status": [
+            "x"
+          ],
+          "valid_pseudopotentials": [
+            "x"
+          ],
+          "valid_extracharge": [
+            "x"
+          ],
+          "valid_ascii_debug": [
+            "x"
+          ],
+          "valid_ncoutput": [
+            "x"
+          ],
+          "valid_ados": [
+            "x"
+          ],
+          "valid_decoupling": [
+            "x"
+          ],
+          "valid_external_dipole": [
+            "x"
+          ],
+          "valid_stay_alive": [
+            "x"
+          ],
+          "valid_fftgrid": [
+            "x"
+          ],
+          "valid_convergence": [
+            "x"
+          ],
+          "valid_charge_mixing": [
+            "x"
+          ],
+          "valid_electronic_minimization": [
+            "x"
+          ],
+          "valid_occupationstatistics": [
+            "x"
+          ],
+          "valid_mdos": [
+            "x"
+          ],
+          "valid_psp": [
+            "x"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "bader",
+        "functions": [],
+        "classes": [
+          "Bader"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "bandstructure",
+        "functions": [],
+        "classes": [
+          "BandStructure"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "bee",
+        "functions": [
+          "GetEnsembleEnergies",
+          "MakeEnsemble"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "MakeEnsemble": [
+            "N",
+            "seed"
+          ],
+          "GetEnsembleEnergies": [
+            "atoms",
+            "c"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "findsym",
+        "functions": [],
+        "classes": [
+          "FINDSYM"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "jmath",
+        "functions": [
+          "vinterp3d"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "vinterp3d": [
+            "x",
+            "y",
+            "z",
+            "u",
+            "xi",
+            "yi",
+            "zi"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "sgroup",
+        "functions": [],
+        "classes": [
+          "SGROUP"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "symmol",
+        "functions": [],
+        "classes": [
+          "SYMMOL"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.jacapo.utils",
+        "module": "wannier",
+        "functions": [
+          "cartesian2scaled",
+          "coordinate_array_from_unit_vectors",
+          "coordinates_from_function_values",
+          "dagger",
+          "project",
+          "scaled2cartesian",
+          "translate"
+        ],
+        "classes": [
+          "Translation_Operator",
+          "Wannier"
+        ],
+        "function_signatures": {
+          "dagger": [
+            "matrix",
+            "copy"
+          ],
+          "project": [
+            "a",
+            "b"
+          ],
+          "translate": [
+            "array",
+            "translation"
+          ],
+          "cartesian2scaled": [
+            "basis",
+            "cart"
+          ],
+          "scaled2cartesian": [
+            "basis",
+            "scaled"
+          ],
+          "coordinate_array_from_unit_vectors": [
+            "shape",
+            "gridunitvectors",
+            "origin",
+            "indexfunction"
+          ],
+          "coordinates_from_function_values": [
+            "dimensions",
+            "functionvalues"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.openmx",
+        "module": "dos",
+        "functions": [
+          "input_command"
+        ],
+        "classes": [
+          "DOS"
+        ],
+        "function_signatures": {
+          "input_command": [
+            "calc",
+            "executable_name",
+            "input_files",
+            "argument_format"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.openmx",
+        "module": "openmx",
+        "functions": [],
+        "classes": [
+          "OpenMX"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.openmx",
+        "module": "parameters",
+        "functions": [],
+        "classes": [
+          "OpenMXParameters"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.openmx",
+        "module": "reader",
+        "functions": [
+          "get_atomic_formula",
+          "get_file_name",
+          "get_parameters",
+          "get_results",
+          "get_standard_key",
+          "get_standard_parameters",
+          "read_band_file",
+          "read_bool",
+          "read_chemical_potential",
+          "read_dipole",
+          "read_eigenvalues",
+          "read_electron_valency",
+          "read_energy",
+          "read_file",
+          "read_float",
+          "read_forces",
+          "read_integer",
+          "read_list_bool",
+          "read_list_float",
+          "read_list_int",
+          "read_magmoms_and_total_magmom",
+          "read_matrix",
+          "read_openmx",
+          "read_scaled_positions",
+          "read_scfout_file",
+          "read_stress_tensor",
+          "read_string",
+          "read_tuple_float",
+          "read_tuple_integer",
+          "rn"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_openmx": [
+            "filename",
+            "debug"
+          ],
+          "read_file": [
+            "filename",
+            "debug"
+          ],
+          "read_scfout_file": [
+            "filename"
+          ],
+          "read_band_file": [
+            "filename"
+          ],
+          "read_electron_valency": [
+            "filename"
+          ],
+          "rn": [
+            "line",
+            "n"
+          ],
+          "read_tuple_integer": [
+            "line"
+          ],
+          "read_tuple_float": [
+            "line"
+          ],
+          "read_integer": [
+            "line"
+          ],
+          "read_float": [
+            "line"
+          ],
+          "read_string": [
+            "line"
+          ],
+          "read_bool": [
+            "line"
+          ],
+          "read_list_int": [
+            "line"
+          ],
+          "read_list_float": [
+            "line"
+          ],
+          "read_list_bool": [
+            "line"
+          ],
+          "read_matrix": [
+            "line",
+            "key",
+            "f"
+          ],
+          "read_stress_tensor": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "read_magmoms_and_total_magmom": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "read_energy": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "read_eigenvalues": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "read_forces": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "read_dipole": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "read_scaled_positions": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "read_chemical_potential": [
+            "line",
+            "f",
+            "debug"
+          ],
+          "get_parameters": [
+            "out_data",
+            "log_data",
+            "restart_data",
+            "scfout_data",
+            "dat_data",
+            "band_data"
+          ],
+          "get_standard_key": [
+            "key"
+          ],
+          "get_standard_parameters": [
+            "parameters"
+          ],
+          "get_atomic_formula": [
+            "out_data",
+            "log_data",
+            "restart_data",
+            "scfout_data",
+            "dat_data",
+            "scaled_positions"
+          ],
+          "get_results": [
+            "out_data",
+            "log_data",
+            "restart_data",
+            "scfout_data",
+            "dat_data",
+            "band_data"
+          ],
+          "get_file_name": [
+            "extension",
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.openmx",
+        "module": "writer",
+        "functions": [
+          "get_atoms_cont_orbitals",
+          "get_atoms_speciesandcoordinates",
+          "get_atoms_unitvectors",
+          "get_band_kpath",
+          "get_band_kpath_unitcell",
+          "get_cutoff_radius_and_orbital",
+          "get_definition_of_atomic_species",
+          "get_eigensolver",
+          "get_hubbard_u_values",
+          "get_kpath",
+          "get_lda_u_switches",
+          "get_md_fixed_xyz",
+          "get_md_init_velocity",
+          "get_md_tempcontrol",
+          "get_mo_kpoint",
+          "get_noncollinear_switches",
+          "get_openmx_key",
+          "get_orbital_direction",
+          "get_pseudo_potential_suffix",
+          "get_scf_kgrid",
+          "get_species",
+          "get_spin_direction",
+          "get_spinpol",
+          "get_up_down_spin",
+          "get_wannier_initial_projectors",
+          "get_xc",
+          "parameters_to_keywords",
+          "write_bool",
+          "write_float",
+          "write_integer",
+          "write_list_bool",
+          "write_list_float",
+          "write_list_int",
+          "write_matrix",
+          "write_openmx",
+          "write_string",
+          "write_tuple_bool",
+          "write_tuple_float",
+          "write_tuple_integer"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_openmx": [
+            "label",
+            "atoms",
+            "parameters",
+            "properties",
+            "system_changes"
+          ],
+          "parameters_to_keywords": [
+            "label",
+            "atoms",
+            "parameters",
+            "properties",
+            "system_changes"
+          ],
+          "get_species": [
+            "symbols"
+          ],
+          "get_xc": [
+            "xc"
+          ],
+          "get_eigensolver": [
+            "atoms",
+            "parameters"
+          ],
+          "get_scf_kgrid": [
+            "kpts",
+            "scf_kgrid",
+            "atoms"
+          ],
+          "get_definition_of_atomic_species": [
+            "atoms",
+            "parameters"
+          ],
+          "get_cutoff_radius_and_orbital": [
+            "element",
+            "orbital"
+          ],
+          "get_pseudo_potential_suffix": [
+            "element",
+            "xc"
+          ],
+          "get_atoms_speciesandcoordinates": [
+            "atoms",
+            "parameters"
+          ],
+          "get_up_down_spin": [
+            "magmom",
+            "element",
+            "xc"
+          ],
+          "get_spin_direction": [
+            "magmoms"
+          ],
+          "get_orbital_direction": [],
+          "get_noncollinear_switches": [],
+          "get_lda_u_switches": [],
+          "get_spinpol": [
+            "atoms",
+            "parameters"
+          ],
+          "get_atoms_unitvectors": [
+            "atoms",
+            "parameters"
+          ],
+          "get_hubbard_u_values": [
+            "atoms",
+            "parameters"
+          ],
+          "get_atoms_cont_orbitals": [
+            "atoms",
+            "parameters"
+          ],
+          "get_md_fixed_xyz": [
+            "atoms",
+            "parameters"
+          ],
+          "get_md_tempcontrol": [
+            "atoms",
+            "parameters"
+          ],
+          "get_md_init_velocity": [
+            "atoms",
+            "parameters"
+          ],
+          "get_band_kpath_unitcell": [
+            "atoms",
+            "parameters"
+          ],
+          "get_band_kpath": [
+            "atoms",
+            "parameters"
+          ],
+          "get_mo_kpoint": [
+            "atoms",
+            "parameters"
+          ],
+          "get_wannier_initial_projectors": [
+            "atoms",
+            "parameters"
+          ],
+          "get_kpath": [
+            "self",
+            "kpts",
+            "symbols",
+            "band_kpath",
+            "eps"
+          ],
+          "write_string": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_tuple_integer": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_tuple_float": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_tuple_bool": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_integer": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_float": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_bool": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_list_int": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_list_bool": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_list_float": [
+            "f",
+            "key",
+            "value"
+          ],
+          "write_matrix": [
+            "f",
+            "key",
+            "value"
+          ],
+          "get_openmx_key": [
+            "key"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "base_siesta",
+        "functions": [],
+        "classes": [
+          "BaseSiesta",
+          "SiestaParameters"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "import_functions",
+        "functions": [
+          "get_valence_charge",
+          "readDIM",
+          "readHSX",
+          "readPLD",
+          "readWFSX",
+          "read_rho",
+          "read_vca_synth_block",
+          "xv_to_atoms"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "xv_to_atoms": [
+            "filename"
+          ],
+          "read_rho": [
+            "fname"
+          ],
+          "get_valence_charge": [
+            "filename"
+          ],
+          "read_vca_synth_block": [
+            "filename",
+            "species_number"
+          ],
+          "readHSX": [
+            "fname"
+          ],
+          "readDIM": [
+            "fname"
+          ],
+          "readPLD": [
+            "fname",
+            "norbitals",
+            "natoms"
+          ],
+          "readWFSX": [
+            "fname"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "import_ion_xml",
+        "functions": [
+          "extract_orbital",
+          "extract_pao_elements",
+          "extract_projector",
+          "getNodeText",
+          "get_data_elements",
+          "get_ion"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_ion": [
+            "fname"
+          ],
+          "getNodeText": [
+            "node"
+          ],
+          "get_data_elements": [
+            "name",
+            "dtype"
+          ],
+          "extract_pao_elements": [
+            "ion",
+            "doc"
+          ],
+          "extract_orbital": [
+            "orb_xml"
+          ],
+          "extract_projector": [
+            "pro_xml"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "mbpt_lcao",
+        "functions": [],
+        "classes": [
+          "MBPT_LCAO"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "mbpt_lcao_io",
+        "functions": [],
+        "classes": [
+          "MBPT_LCAO_Parameters",
+          "MBPT_LCAO_Properties_figure",
+          "read_hdf5_data",
+          "read_mbpt_lcao_output",
+          "read_text_data"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "mbpt_lcao_utils",
+        "functions": [
+          "delete_blanc",
+          "delete_number_string",
+          "dim_y",
+          "interpolate",
+          "pol2cross_sec",
+          "readBasis_spec",
+          "readSiestaFA",
+          "read_color_file",
+          "read_file",
+          "read_number",
+          "recover_data_string",
+          "recover_species",
+          "save_line",
+          "str2float",
+          "str2int"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_file": [
+            "fname"
+          ],
+          "delete_blanc": [
+            "L"
+          ],
+          "read_number": [
+            "L"
+          ],
+          "recover_data_string": [
+            "fname",
+            "string"
+          ],
+          "save_line": [
+            "Lnb",
+            "Cnb",
+            "LINE"
+          ],
+          "dim_y": [
+            "Cnb",
+            "L"
+          ],
+          "read_color_file": [
+            "fname"
+          ],
+          "readSiestaFA": [
+            "fname"
+          ],
+          "readBasis_spec": [
+            "fname",
+            "nb_species"
+          ],
+          "str2float": [
+            "string"
+          ],
+          "str2int": [
+            "string"
+          ],
+          "recover_species": [
+            "string"
+          ],
+          "delete_number_string": [
+            "string"
+          ],
+          "pol2cross_sec": [
+            "p",
+            "omg"
+          ],
+          "interpolate": [
+            "x",
+            "y",
+            "nb_pts"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "parameters",
+        "functions": [
+          "format_fdf",
+          "format_key",
+          "format_value"
+        ],
+        "classes": [
+          "PAOBasisBlock",
+          "Species"
+        ],
+        "function_signatures": {
+          "format_fdf": [
+            "key",
+            "value"
+          ],
+          "format_value": [
+            "value"
+          ],
+          "format_key": [
+            "key"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "siesta",
+        "functions": [],
+        "classes": [
+          "Siesta3_2",
+          "SiestaTrunk462"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.siesta",
+        "module": "siesta_raman",
+        "functions": [],
+        "classes": [
+          "SiestaRaman"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.vasp",
+        "module": "create_input",
+        "functions": [],
+        "classes": [
+          "GenerateVaspInput"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.vasp",
+        "module": "interactive",
+        "functions": [],
+        "classes": [
+          "VaspInteractive"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.vasp",
+        "module": "vasp",
+        "functions": [],
+        "classes": [
+          "Vasp",
+          "VaspChargeDensity",
+          "VaspDos",
+          "xdat2traj"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.calculators.vasp",
+        "module": "vasp2",
+        "functions": [],
+        "classes": [
+          "Vasp2"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "band_structure",
+        "functions": [
+          "main"
+        ],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {
+          "main": [
+            "args",
+            "parser"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "build",
+        "functions": [
+          "build_bulk",
+          "build_molecule"
+        ],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {
+          "build_molecule": [
+            "args"
+          ],
+          "build_bulk": [
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "complete",
+        "functions": [
+          "complete",
+          "match"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "match": [
+            "word"
+          ],
+          "complete": [
+            "word",
+            "previous",
+            "line",
+            "point"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "completion",
+        "functions": [
+          "update"
+        ],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {
+          "update": [
+            "filename",
+            "commands"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "convert",
+        "functions": [],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "find",
+        "functions": [
+          "allpaths",
+          "check",
+          "main"
+        ],
+        "classes": [
+          "CLICommand",
+          "FakeDB"
+        ],
+        "function_signatures": {
+          "main": [
+            "args"
+          ],
+          "allpaths": [
+            "folder",
+            "include",
+            "exclude"
+          ],
+          "check": [
+            "path",
+            "query",
+            "verbose"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "info",
+        "functions": [
+          "print_formats",
+          "print_info"
+        ],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {
+          "print_info": [],
+          "print_formats": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "main",
+        "functions": [
+          "main",
+          "old"
+        ],
+        "classes": [
+          "CLIError",
+          "Formatter"
+        ],
+        "function_signatures": {
+          "main": [
+            "prog",
+            "description",
+            "version",
+            "commands",
+            "hook",
+            "args"
+          ],
+          "old": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "nomad",
+        "functions": [],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "nomadget",
+        "functions": [],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "reciprocal",
+        "functions": [
+          "plot_reciprocal_cell"
+        ],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {
+          "plot_reciprocal_cell": [
+            "atoms",
+            "path",
+            "k_points",
+            "ibz_k_points",
+            "plot_vectors",
+            "dimension",
+            "output",
+            "verbose"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cli",
+        "module": "run",
+        "functions": [
+          "str2dict"
+        ],
+        "classes": [
+          "CLICommand",
+          "Runner"
+        ],
+        "function_signatures": {
+          "str2dict": [
+            "s",
+            "namespace",
+            "sep"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "base",
+        "functions": [],
+        "classes": [
+          "ClusterBase"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "cluster",
+        "functions": [],
+        "classes": [
+          "Cluster"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "compounds",
+        "functions": [],
+        "classes": [
+          "AuCu3Factory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "cubic",
+        "functions": [],
+        "classes": [
+          "BodyCenteredCubicFactory",
+          "FaceCenteredCubicFactory",
+          "SimpleCubicFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "decahedron",
+        "functions": [
+          "Decahedron"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "Decahedron": [
+            "symbol",
+            "p",
+            "q",
+            "r",
+            "latticeconstant"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "factory",
+        "functions": [
+          "GCD",
+          "cross",
+          "reduce_miller"
+        ],
+        "classes": [
+          "ClusterFactory"
+        ],
+        "function_signatures": {
+          "cross": [
+            "a",
+            "b"
+          ],
+          "GCD": [
+            "a",
+            "b"
+          ],
+          "reduce_miller": [
+            "hkl"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "hexagonal",
+        "functions": [],
+        "classes": [
+          "GraphiteFactory",
+          "HexagonalClosedPackedFactory",
+          "HexagonalFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "icosahedron",
+        "functions": [
+          "Icosahedron"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "Icosahedron": [
+            "symbol",
+            "noshells",
+            "latticeconstant"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "octahedron",
+        "functions": [
+          "Octahedron"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "Octahedron": [
+            "symbol",
+            "length",
+            "cutoff",
+            "latticeconstant",
+            "alloy"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster",
+        "module": "wulff",
+        "functions": [
+          "make_atoms",
+          "wulff_construction"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "wulff_construction": [
+            "symbol",
+            "surfaces",
+            "energies",
+            "size",
+            "structure",
+            "rounding",
+            "latticeconstant",
+            "debug",
+            "maxiter"
+          ],
+          "make_atoms": [
+            "symbol",
+            "surfaces",
+            "energies",
+            "factor",
+            "structure",
+            "latticeconstant"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster.data",
+        "module": "fcc",
+        "functions": [
+          "surface_centering",
+          "surface_fitting"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "surface_fitting": [
+            "surfaces"
+          ],
+          "surface_centering": [
+            "surfaces",
+            "basis",
+            "debug"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.cluster.data",
+        "module": "symmetry",
+        "functions": [
+          "apply_neighbor_symmetry",
+          "get_all_symmetries",
+          "get_neighbor_symmetries",
+          "get_surface_symmetries"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_all_symmetries": [
+            "symmetries",
+            "max"
+          ],
+          "get_neighbor_symmetries": [
+            "symmetries",
+            "neighbor_positions",
+            "neighbor_numbers"
+          ],
+          "get_surface_symmetries": [
+            "symmetries",
+            "surface_names",
+            "surface_numbers"
+          ],
+          "apply_neighbor_symmetry": [
+            "neighbors",
+            "symmetry"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.collections",
+        "module": "collection",
+        "functions": [],
+        "classes": [
+          "Collection"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.collections",
+        "module": "create",
+        "functions": [
+          "dcdft",
+          "g2"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "dcdft": [],
+          "g2": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "dbh24",
+        "functions": [
+          "create_dbh24_system",
+          "get_dbh24_Vb",
+          "get_dbh24_Vf",
+          "get_dbh24_charge",
+          "get_dbh24_final_states",
+          "get_dbh24_initial_states",
+          "get_dbh24_magmoms",
+          "get_dbh24_tst"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "create_dbh24_system": [
+            "name"
+          ],
+          "get_dbh24_magmoms": [
+            "name"
+          ],
+          "get_dbh24_charge": [
+            "name"
+          ],
+          "get_dbh24_Vf": [
+            "name"
+          ],
+          "get_dbh24_Vb": [
+            "name"
+          ],
+          "get_dbh24_initial_states": [
+            "name"
+          ],
+          "get_dbh24_final_states": [
+            "name"
+          ],
+          "get_dbh24_tst": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "g2_1",
+        "functions": [
+          "get_atomization_energy",
+          "get_ionization_energy"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_ionization_energy": [
+            "name",
+            "vertical"
+          ],
+          "get_atomization_energy": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "g2_1_ref",
+        "functions": [
+          "convert"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "convert": [
+            "input",
+            "column"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "gmtkn30",
+        "functions": [
+          "download_file",
+          "format_data",
+          "main",
+          "read_charge",
+          "read_charge_filter",
+          "read_charges",
+          "read_geometry",
+          "read_geometry_filter",
+          "read_html",
+          "read_number_of_unpaired_electrons",
+          "read_number_of_unpaired_electrons_filter",
+          "read_numbers_of_unpaired_electrons",
+          "read_structures",
+          "table2reference",
+          "table2results",
+          "unzip_file"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "download_file": [
+            "url",
+            "filename",
+            "dir"
+          ],
+          "read_charge_filter": [
+            "s"
+          ],
+          "read_charge": [
+            "filename",
+            "dir"
+          ],
+          "read_charges": [
+            "dirname",
+            "dir"
+          ],
+          "read_number_of_unpaired_electrons_filter": [
+            "s"
+          ],
+          "read_number_of_unpaired_electrons": [
+            "filename",
+            "dir"
+          ],
+          "read_numbers_of_unpaired_electrons": [
+            "dirname",
+            "dir"
+          ],
+          "read_geometry_filter": [
+            "s"
+          ],
+          "read_geometry": [
+            "filename",
+            "dir"
+          ],
+          "read_structures": [
+            "dirname",
+            "dir"
+          ],
+          "read_html": [
+            "filename",
+            "dir"
+          ],
+          "table2reference": [
+            "ncompounds",
+            "table"
+          ],
+          "table2results": [
+            "nsets",
+            "table",
+            "mode"
+          ],
+          "unzip_file": [
+            "filename",
+            "dir"
+          ],
+          "format_data": [
+            "database",
+            "geometries",
+            "no_unpaired_electrons",
+            "charges"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "isotopes",
+        "functions": [
+          "download_isotope_data"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "download_isotope_data": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "molecules",
+        "functions": [
+          "latex",
+          "rest"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "latex": [
+            "name"
+          ],
+          "rest": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "s22",
+        "functions": [
+          "create_s22_system",
+          "get_interaction_energy_cc",
+          "get_interaction_energy_s22",
+          "get_interaction_energy_s22x5",
+          "get_name",
+          "get_number_of_dimer_atoms",
+          "get_s22_number",
+          "get_s22x5_distance",
+          "get_s22x5_id",
+          "identify_s22_sys"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "create_s22_system": [
+            "name",
+            "dist"
+          ],
+          "identify_s22_sys": [
+            "name",
+            "dist"
+          ],
+          "get_s22x5_id": [
+            "name"
+          ],
+          "get_s22_number": [
+            "name",
+            "dist"
+          ],
+          "get_interaction_energy_cc": [
+            "name",
+            "dist"
+          ],
+          "get_interaction_energy_s22": [
+            "name",
+            "dist"
+          ],
+          "get_interaction_energy_s22x5": [
+            "name",
+            "dist",
+            "correct_offset"
+          ],
+          "get_name": [
+            "name",
+            "dist"
+          ],
+          "get_number_of_dimer_atoms": [
+            "name",
+            "dist"
+          ],
+          "get_s22x5_distance": [
+            "name",
+            "dist"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.data",
+        "module": "tmxr200x",
+        "functions": [
+          "download_file",
+          "main",
+          "pdftotext",
+          "read_geometries"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "download_file": [
+            "url",
+            "filename",
+            "dir"
+          ],
+          "read_geometries": [
+            "filename",
+            "dir"
+          ],
+          "pdftotext": [
+            "filename"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "app",
+        "functions": [
+          "cif",
+          "connect_databases",
+          "download",
+          "gui",
+          "image",
+          "index",
+          "initialize_databases",
+          "json1",
+          "oldcif",
+          "pages",
+          "plot",
+          "robots",
+          "row",
+          "sqlite1",
+          "tofile",
+          "xyz"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "connect_databases": [
+            "uris"
+          ],
+          "initialize_databases": [],
+          "index": [
+            "project"
+          ],
+          "image": [
+            "project",
+            "name"
+          ],
+          "cif": [
+            "project",
+            "name"
+          ],
+          "plot": [
+            "project",
+            "uid",
+            "png"
+          ],
+          "gui": [
+            "project",
+            "id"
+          ],
+          "row": [
+            "project",
+            "uid"
+          ],
+          "tofile": [
+            "project",
+            "query",
+            "type",
+            "limit"
+          ],
+          "download": [
+            "f"
+          ],
+          "xyz": [
+            "project",
+            "id"
+          ],
+          "json1": [
+            "project",
+            "id"
+          ],
+          "sqlite1": [
+            "project",
+            "id"
+          ],
+          "robots": [],
+          "oldcif": [
+            "stuff"
+          ],
+          "pages": [
+            "page",
+            "nrows",
+            "limit"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "cli",
+        "functions": [
+          "main"
+        ],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {
+          "main": [
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "convert",
+        "functions": [
+          "convert",
+          "main"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "convert": [
+            "name",
+            "opts"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "core",
+        "functions": [
+          "check",
+          "connect",
+          "convert_str_to_int_float_or_str",
+          "float_to_time_string",
+          "lock",
+          "now",
+          "parse_selection",
+          "str_represents",
+          "time_string_to_float"
+        ],
+        "classes": [
+          "Database"
+        ],
+        "function_signatures": {
+          "now": [],
+          "check": [
+            "key_value_pairs"
+          ],
+          "str_represents": [
+            "value",
+            "t"
+          ],
+          "connect": [
+            "name",
+            "type",
+            "create_indices",
+            "use_lock_file",
+            "append",
+            "serial"
+          ],
+          "lock": [
+            "method"
+          ],
+          "convert_str_to_int_float_or_str": [
+            "value"
+          ],
+          "parse_selection": [
+            "selection"
+          ],
+          "time_string_to_float": [
+            "s"
+          ],
+          "float_to_time_string": [
+            "t",
+            "long"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "jsondb",
+        "functions": [],
+        "classes": [
+          "JSONDatabase"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "plot",
+        "functions": [
+          "atoms2png",
+          "dct2plot"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "atoms2png": [
+            "atoms",
+            "filename"
+          ],
+          "dct2plot": [
+            "dct",
+            "name",
+            "filename",
+            "show"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "postgresql",
+        "functions": [
+          "insert_nan_and_inf",
+          "remove_nan_and_inf",
+          "schema_update"
+        ],
+        "classes": [
+          "Connection",
+          "Cursor",
+          "PostgreSQLDatabase"
+        ],
+        "function_signatures": {
+          "remove_nan_and_inf": [
+            "obj"
+          ],
+          "insert_nan_and_inf": [
+            "obj"
+          ],
+          "schema_update": [
+            "sql"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "row",
+        "functions": [
+          "atoms2dict"
+        ],
+        "classes": [
+          "AtomsRow",
+          "FancyDict"
+        ],
+        "function_signatures": {
+          "atoms2dict": [
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "sqlite",
+        "functions": [
+          "float_if_not_none"
+        ],
+        "classes": [
+          "SQLite3Database"
+        ],
+        "function_signatures": {
+          "float_if_not_none": [
+            "x"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "summary",
+        "functions": [
+          "convert_old_layout",
+          "create_table",
+          "default_layout",
+          "miscellaneous_section"
+        ],
+        "classes": [
+          "Summary"
+        ],
+        "function_signatures": {
+          "create_table": [
+            "row",
+            "header",
+            "keys",
+            "key_descriptions",
+            "digits"
+          ],
+          "default_layout": [
+            "row",
+            "key_descriptions",
+            "prefix"
+          ],
+          "miscellaneous_section": [
+            "row",
+            "key_descriptions",
+            "exclude"
+          ],
+          "convert_old_layout": [
+            "page"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "table",
+        "functions": [
+          "cut",
+          "cutlist",
+          "get_sql_columns",
+          "plural"
+        ],
+        "classes": [
+          "Row",
+          "Table"
+        ],
+        "function_signatures": {
+          "get_sql_columns": [
+            "columns"
+          ],
+          "plural": [
+            "n",
+            "word"
+          ],
+          "cut": [
+            "txt",
+            "length"
+          ],
+          "cutlist": [
+            "lst",
+            "length"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.db",
+        "module": "web",
+        "functions": [
+          "process_metadata"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "process_metadata": [
+            "db",
+            "html"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "dft",
+        "functions": [
+          "get_distribution_moment"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_distribution_moment": [
+            "x",
+            "y",
+            "order"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "band_structure",
+        "functions": [
+          "get_band_structure"
+        ],
+        "classes": [
+          "BandStructure",
+          "BandStructurePlot"
+        ],
+        "function_signatures": {
+          "get_band_structure": [
+            "atoms",
+            "calc"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "bandgap",
+        "functions": [
+          "bandgap",
+          "find_gap",
+          "get_band_gap"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_band_gap": [
+            "calc",
+            "direct",
+            "spin",
+            "output"
+          ],
+          "bandgap": [
+            "calc",
+            "direct",
+            "spin",
+            "output",
+            "eigenvalues",
+            "efermi",
+            "kpts"
+          ],
+          "find_gap": [
+            "ev_k",
+            "ec_k",
+            "direct"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "bee",
+        "functions": [
+          "BEEF_Ensemble",
+          "ensemble",
+          "readbee"
+        ],
+        "classes": [
+          "BEEFEnsemble"
+        ],
+        "function_signatures": {
+          "ensemble": [
+            "energy",
+            "contributions",
+            "xc",
+            "verbose"
+          ],
+          "readbee": [
+            "fname",
+            "all"
+          ],
+          "BEEF_Ensemble": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "bz",
+        "functions": [
+          "bz1d_plot",
+          "bz2d_plot",
+          "bz3d_plot",
+          "bz_vertices"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "bz_vertices": [
+            "icell"
+          ],
+          "bz3d_plot": [
+            "cell",
+            "vectors",
+            "paths",
+            "points",
+            "elev",
+            "scale",
+            "interactive"
+          ],
+          "bz2d_plot": [
+            "cell",
+            "vectors",
+            "paths",
+            "points"
+          ],
+          "bz1d_plot": [
+            "cell",
+            "vectors",
+            "paths",
+            "points"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "dos",
+        "functions": [
+          "ltidos"
+        ],
+        "classes": [
+          "DOS"
+        ],
+        "function_signatures": {
+          "ltidos": [
+            "cell",
+            "eigs",
+            "energies",
+            "weights"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "kpoints",
+        "functions": [
+          "bandpath",
+          "get_cellinfo",
+          "get_monkhorst_pack_size_and_offset",
+          "get_monkhorst_shape",
+          "get_special_points",
+          "kpoint_convert",
+          "labels_from_kpts",
+          "monkhorst_pack",
+          "monkhorst_pack_interpolate",
+          "parse_path_string"
+        ],
+        "classes": [
+          "CellInfo"
+        ],
+        "function_signatures": {
+          "monkhorst_pack": [
+            "size"
+          ],
+          "get_monkhorst_pack_size_and_offset": [
+            "kpts"
+          ],
+          "get_monkhorst_shape": [
+            "kpts"
+          ],
+          "kpoint_convert": [
+            "cell_cv",
+            "skpts_kc",
+            "ckpts_kv"
+          ],
+          "parse_path_string": [
+            "s"
+          ],
+          "bandpath": [
+            "path",
+            "cell",
+            "npoints"
+          ],
+          "labels_from_kpts": [
+            "kpts",
+            "cell",
+            "eps"
+          ],
+          "get_cellinfo": [
+            "cell",
+            "lattice",
+            "eps"
+          ],
+          "get_special_points": [
+            "cell",
+            "lattice",
+            "eps"
+          ],
+          "monkhorst_pack_interpolate": [
+            "path",
+            "values",
+            "icell",
+            "bz2ibz",
+            "size",
+            "offset"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "pdos",
+        "functions": [],
+        "classes": [
+          "DOS",
+          "DOSPlot"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "stm",
+        "functions": [
+          "delta",
+          "dos2current",
+          "find_height",
+          "interpolate"
+        ],
+        "classes": [
+          "STM"
+        ],
+        "function_signatures": {
+          "dos2current": [
+            "bias",
+            "dos"
+          ],
+          "interpolate": [
+            "q",
+            "heights"
+          ],
+          "find_height": [
+            "ldos",
+            "current",
+            "h",
+            "z0"
+          ],
+          "delta": [
+            "biases",
+            "bias",
+            "width"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.dft",
+        "module": "wannier",
+        "functions": [
+          "calculate_weights",
+          "gram_schmidt",
+          "gram_schmidt_single",
+          "lowdin",
+          "md_min",
+          "neighbor_k_search",
+          "random_orthogonal_matrix",
+          "rotation_from_projection",
+          "rotation_from_projection2",
+          "steepest_descent"
+        ],
+        "classes": [
+          "Wannier"
+        ],
+        "function_signatures": {
+          "gram_schmidt": [
+            "U"
+          ],
+          "gram_schmidt_single": [
+            "U",
+            "n"
+          ],
+          "lowdin": [
+            "U",
+            "S"
+          ],
+          "neighbor_k_search": [
+            "k_c",
+            "G_c",
+            "kpt_kc",
+            "tol"
+          ],
+          "calculate_weights": [
+            "cell_cc"
+          ],
+          "random_orthogonal_matrix": [
+            "dim",
+            "seed",
+            "real"
+          ],
+          "steepest_descent": [
+            "func",
+            "step",
+            "tolerance"
+          ],
+          "md_min": [
+            "func",
+            "step",
+            "tolerance",
+            "verbose"
+          ],
+          "rotation_from_projection2": [
+            "proj_nw",
+            "fixed"
+          ],
+          "rotation_from_projection": [
+            "proj_nw",
+            "fixed",
+            "ortho"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "ga",
+        "functions": [
+          "get_neighbor_list",
+          "get_parametrization",
+          "get_raw_score",
+          "set_neighbor_list",
+          "set_parametrization",
+          "set_raw_score"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "set_raw_score": [
+            "atoms",
+            "raw_score"
+          ],
+          "get_raw_score": [
+            "atoms"
+          ],
+          "set_parametrization": [
+            "atoms",
+            "parametrization"
+          ],
+          "get_parametrization": [
+            "atoms"
+          ],
+          "set_neighbor_list": [
+            "atoms",
+            "neighbor_list"
+          ],
+          "get_neighbor_list": [
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "adsorbate_comparators",
+        "functions": [
+          "count_ads"
+        ],
+        "classes": [
+          "AdsorbateCountComparator",
+          "AdsorptionMetalsComparator",
+          "AdsorptionSitesComparator"
+        ],
+        "function_signatures": {
+          "count_ads": [
+            "atoms",
+            "adsorbate"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "adsorbate_operators",
+        "functions": [],
+        "classes": [
+          "AddAdsorbate",
+          "AdsorbateOperator",
+          "CutSpliceCrossoverWithAdsorbates",
+          "MoveAdsorbate",
+          "RemoveAdsorbate"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "convergence",
+        "functions": [],
+        "classes": [
+          "Convergence",
+          "GenerationRepetitionConvergence",
+          "NeverConvergence",
+          "RawScoreConvergence"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "cutandsplicepairing",
+        "functions": [
+          "get_distance"
+        ],
+        "classes": [
+          "CutAndSplicePairing",
+          "Position"
+        ],
+        "function_signatures": {
+          "get_distance": [
+            "point",
+            "cutting_plane",
+            "cutting_point"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "data",
+        "functions": [
+          "split_description",
+          "test_raw_score"
+        ],
+        "classes": [
+          "DataConnection",
+          "PrepareDB"
+        ],
+        "function_signatures": {
+          "split_description": [
+            "desc"
+          ],
+          "test_raw_score": [
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "element_crossovers",
+        "functions": [],
+        "classes": [
+          "ElementCrossover",
+          "OnePointElementCrossover",
+          "TwoPointElementCrossover"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "element_mutations",
+        "functions": [
+          "chunks",
+          "get_row_column",
+          "mendeleiev_table"
+        ],
+        "classes": [
+          "ElementMutation",
+          "FullElementMutation",
+          "MoveDownMutation",
+          "MoveLeftMutation",
+          "MoveRightMutation",
+          "MoveUpMutation",
+          "RandomElementMutation"
+        ],
+        "function_signatures": {
+          "chunks": [
+            "l",
+            "n"
+          ],
+          "mendeleiev_table": [],
+          "get_row_column": [
+            "element"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "multiprocessingrun",
+        "functions": [],
+        "classes": [
+          "MultiprocessingRun"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "offspring_creator",
+        "functions": [],
+        "classes": [
+          "OffspringCreator",
+          "OperationSelector"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "parallellocalrun",
+        "functions": [],
+        "classes": [
+          "ParallelLocalRun"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "particle_comparator",
+        "functions": [],
+        "classes": [
+          "NNMatComparator"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "particle_crossovers",
+        "functions": [],
+        "classes": [
+          "Crossover",
+          "CutSpliceCrossover"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "particle_mutations",
+        "functions": [],
+        "classes": [
+          "COM2surfPermutation",
+          "Mutation",
+          "Poor2richPermutation",
+          "RandomMutation",
+          "RandomPermutation",
+          "RandomSubstitute",
+          "Rich2poorPermutation",
+          "SymmetricSubstitute"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "pbs_queue_run",
+        "functions": [],
+        "classes": [
+          "PBSQueueRun"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "population",
+        "functions": [
+          "count_looks_like"
+        ],
+        "classes": [
+          "FitnessSharingPopulation",
+          "MultiObjectivePopulation",
+          "Population",
+          "RandomPopulation",
+          "RankFitnessPopulation"
+        ],
+        "function_signatures": {
+          "count_looks_like": [
+            "a",
+            "all_cand",
+            "comp"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "relax_attaches",
+        "functions": [],
+        "classes": [
+          "VariansBreak"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "slab_operators",
+        "functions": [
+          "dummy_func",
+          "get_add_remove_lists",
+          "get_layer_comps",
+          "get_minority_element",
+          "get_ordered_composition",
+          "minority_element_segregate",
+          "permute2",
+          "replace_element",
+          "same_layer_comp"
+        ],
+        "classes": [
+          "CutSpliceSlabCrossover",
+          "NeighborhoodElementMutation",
+          "RandomCompositionMutation",
+          "RandomElementMutation",
+          "RandomSlabPermutation",
+          "SlabOperator",
+          "SymmetrySlabPermutation"
+        ],
+        "function_signatures": {
+          "permute2": [
+            "atoms"
+          ],
+          "replace_element": [
+            "atoms",
+            "element_out",
+            "element_in"
+          ],
+          "get_add_remove_lists": [],
+          "get_minority_element": [
+            "atoms"
+          ],
+          "minority_element_segregate": [
+            "atoms",
+            "layer_tag"
+          ],
+          "same_layer_comp": [
+            "atoms"
+          ],
+          "get_layer_comps": [
+            "atoms",
+            "eps"
+          ],
+          "get_ordered_composition": [
+            "syms",
+            "pools"
+          ],
+          "dummy_func": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "standard_comparators",
+        "functions": [
+          "get_sorted_dist_list"
+        ],
+        "classes": [
+          "AtomsComparator",
+          "CompositionComparator",
+          "EnergyComparator",
+          "InteratomicDistanceComparator",
+          "NoComparator",
+          "RawScoreComparator",
+          "SequentialComparator",
+          "StringComparator"
+        ],
+        "function_signatures": {
+          "get_sorted_dist_list": [
+            "atoms",
+            "mic"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "standardmutations",
+        "functions": [],
+        "classes": [
+          "MirrorMutation",
+          "PermutationMutation",
+          "RattleMutation"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "startgenerator",
+        "functions": [
+          "random_pos"
+        ],
+        "classes": [
+          "StartGenerator"
+        ],
+        "function_signatures": {
+          "random_pos": [
+            "box"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.ga",
+        "module": "utilities",
+        "functions": [
+          "atoms_too_close",
+          "atoms_too_close_two_sets",
+          "closest_distances_generator",
+          "db_call_with_error_tol",
+          "get_all_atom_types",
+          "get_angles_distribution",
+          "get_atoms_connections",
+          "get_atoms_distribution",
+          "get_connections_index",
+          "get_distance_matrix",
+          "get_mic_distance",
+          "get_neighborlist",
+          "get_nndist",
+          "get_nnmat",
+          "get_nnmat_string",
+          "get_rdf",
+          "get_rings",
+          "get_trajectory",
+          "save_trajectory"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "closest_distances_generator": [
+            "atom_numbers",
+            "ratio_of_covalent_radii"
+          ],
+          "get_mic_distance": [
+            "p1",
+            "p2",
+            "cell",
+            "pbc"
+          ],
+          "db_call_with_error_tol": [
+            "db_cursor",
+            "expression",
+            "args"
+          ],
+          "save_trajectory": [
+            "confid",
+            "trajectory",
+            "folder"
+          ],
+          "get_trajectory": [
+            "fname"
+          ],
+          "atoms_too_close": [
+            "a",
+            "bl"
+          ],
+          "atoms_too_close_two_sets": [
+            "a",
+            "b",
+            "bl"
+          ],
+          "get_all_atom_types": [
+            "slab",
+            "atom_numbers_to_optimize"
+          ],
+          "get_distance_matrix": [
+            "atoms",
+            "self_distance"
+          ],
+          "get_rdf": [
+            "atoms",
+            "rmax",
+            "nbins",
+            "distance_matrix",
+            "elements",
+            "no_dists"
+          ],
+          "get_nndist": [
+            "atoms",
+            "distance_matrix"
+          ],
+          "get_nnmat": [
+            "atoms",
+            "mic"
+          ],
+          "get_nnmat_string": [
+            "atoms",
+            "decimals",
+            "mic"
+          ],
+          "get_connections_index": [
+            "atoms",
+            "max_conn",
+            "no_count_types"
+          ],
+          "get_atoms_connections": [
+            "atoms",
+            "max_conn",
+            "no_count_types"
+          ],
+          "get_angles_distribution": [
+            "atoms",
+            "ang_grid"
+          ],
+          "get_neighborlist": [
+            "atoms",
+            "dx",
+            "no_count_types"
+          ],
+          "get_atoms_distribution": [
+            "atoms",
+            "number_of_bins",
+            "max_distance",
+            "center",
+            "no_count_types"
+          ],
+          "get_rings": [
+            "atoms",
+            "rings"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.geometry",
+        "module": "cell",
+        "functions": [
+          "angle",
+          "cell_to_cellpar",
+          "cellpar_to_cell",
+          "complete_cell",
+          "crystal_structure_from_cell",
+          "is_orthorhombic",
+          "metric_from_cell",
+          "orthorhombic",
+          "unit_vector"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "unit_vector": [
+            "x"
+          ],
+          "angle": [
+            "x",
+            "y"
+          ],
+          "cell_to_cellpar": [
+            "cell",
+            "radians"
+          ],
+          "cellpar_to_cell": [
+            "cellpar",
+            "ab_normal",
+            "a_direction"
+          ],
+          "metric_from_cell": [
+            "cell"
+          ],
+          "crystal_structure_from_cell": [
+            "cell",
+            "eps",
+            "niggli_reduce"
+          ],
+          "complete_cell": [
+            "cell"
+          ],
+          "is_orthorhombic": [
+            "cell"
+          ],
+          "orthorhombic": [
+            "cell"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.geometry",
+        "module": "distance",
+        "functions": [
+          "distance"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "distance": [
+            "s1",
+            "s2",
+            "permute"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.geometry",
+        "module": "geometry",
+        "functions": [
+          "find_mic",
+          "get_angles",
+          "get_distances",
+          "get_duplicate_atoms",
+          "get_layers",
+          "wrap_positions"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "wrap_positions": [
+            "positions",
+            "cell",
+            "pbc",
+            "center",
+            "eps"
+          ],
+          "get_layers": [
+            "atoms",
+            "miller",
+            "tolerance"
+          ],
+          "find_mic": [
+            "D",
+            "cell",
+            "pbc"
+          ],
+          "get_angles": [
+            "v1",
+            "v2",
+            "cell",
+            "pbc"
+          ],
+          "get_distances": [
+            "p1",
+            "p2",
+            "cell",
+            "pbc"
+          ],
+          "get_duplicate_atoms": [
+            "atoms",
+            "cutoff",
+            "delete"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "add",
+        "functions": [],
+        "classes": [
+          "AddAtoms"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "ag",
+        "functions": [],
+        "classes": [
+          "CLICommand"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "calculator",
+        "functions": [],
+        "classes": [
+          "AIMS_Window",
+          "EAM_Window",
+          "ExpertDeleteButton",
+          "GPAW_Window",
+          "InfoButton",
+          "LJ_Window",
+          "SetCalculator",
+          "VASP_Window"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "celleditor",
+        "functions": [],
+        "classes": [
+          "CellEditor"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "colors",
+        "functions": [],
+        "classes": [
+          "ColorWindow"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "constraints",
+        "functions": [],
+        "classes": [
+          "Constraints"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "crystal",
+        "functions": [],
+        "classes": [
+          "SetupBulkCrystal"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "defaults",
+        "functions": [
+          "read_defaults"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_defaults": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "energyforces",
+        "functions": [],
+        "classes": [
+          "EnergyForces",
+          "OutputFieldMixin"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "execute",
+        "functions": [],
+        "classes": [
+          "Execute"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "graphene",
+        "functions": [],
+        "classes": [
+          "SetupGraphene"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "graphs",
+        "functions": [
+          "make_plot"
+        ],
+        "classes": [
+          "Graphs"
+        ],
+        "function_signatures": {
+          "make_plot": [
+            "data",
+            "i",
+            "expr",
+            "type",
+            "show"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "gui",
+        "functions": [
+          "webpage"
+        ],
+        "classes": [
+          "GUI"
+        ],
+        "function_signatures": {
+          "webpage": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "images",
+        "functions": [],
+        "classes": [
+          "Images"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "minimize",
+        "functions": [],
+        "classes": [
+          "Minimize",
+          "MinimizeMixin"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "modify",
+        "functions": [],
+        "classes": [
+          "ModifyAtoms"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "movie",
+        "functions": [],
+        "classes": [
+          "Movie"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "nanoparticle",
+        "functions": [],
+        "classes": [
+          "SetupNanoparticle"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "nanotube",
+        "functions": [],
+        "classes": [
+          "SetupNanotube"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "pipe",
+        "functions": [
+          "main"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "progress",
+        "functions": [
+          "fraction"
+        ],
+        "classes": [
+          "DefaultProgressIndicator",
+          "DummyProgressIndicator",
+          "GpawProgressIndicator",
+          "GpawStream",
+          "LoggerStream"
+        ],
+        "function_signatures": {
+          "fraction": [
+            "value",
+            "maximum"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "quickinfo",
+        "functions": [
+          "info"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "info": [
+            "gui"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "render",
+        "functions": [],
+        "classes": [
+          "Render"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "repeat",
+        "functions": [],
+        "classes": [
+          "Repeat"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "rot_tools",
+        "functions": [
+          "rotate_about_vec",
+          "rotate_vec",
+          "rotate_vec_into_newvec"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "rotate_about_vec": [
+            "vecU",
+            "theta"
+          ],
+          "rotate_vec_into_newvec": [
+            "aVec",
+            "intoVec"
+          ],
+          "rotate_vec": [
+            "rot_mat",
+            "vec"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "rotate",
+        "functions": [],
+        "classes": [
+          "Rotate"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "save",
+        "functions": [
+          "save_dialog"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "save_dialog": [
+            "gui",
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "settings",
+        "functions": [],
+        "classes": [
+          "Settings"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "simulation",
+        "functions": [],
+        "classes": [
+          "Simulation"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "status",
+        "functions": [
+          "formula"
+        ],
+        "classes": [
+          "Status"
+        ],
+        "function_signatures": {
+          "formula": [
+            "Z"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "surfaceslab",
+        "functions": [],
+        "classes": [
+          "SetupSurfaceSlab"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "ui",
+        "functions": [
+          "about",
+          "bind",
+          "error",
+          "helpbutton",
+          "helpwindow",
+          "show_io_error"
+        ],
+        "classes": [
+          "ASEFileChooser",
+          "ASEGUIWindow",
+          "BaseWindow",
+          "Button",
+          "CheckButton",
+          "Entry",
+          "Label",
+          "MainWindow",
+          "MenuItem",
+          "RadioButton",
+          "RadioButtons",
+          "Row",
+          "Rows",
+          "Scale",
+          "SpinBox",
+          "Text",
+          "Widget",
+          "Window"
+        ],
+        "function_signatures": {
+          "error": [
+            "title",
+            "message"
+          ],
+          "about": [
+            "name",
+            "version",
+            "webpage"
+          ],
+          "helpbutton": [
+            "text"
+          ],
+          "helpwindow": [
+            "text"
+          ],
+          "bind": [
+            "callback",
+            "modifier"
+          ],
+          "show_io_error": [
+            "filename",
+            "err"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "utils",
+        "functions": [
+          "get_magmoms"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_magmoms": [
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "view",
+        "functions": [
+          "get_bonds",
+          "get_cell_coordinates"
+        ],
+        "classes": [
+          "View"
+        ],
+        "function_signatures": {
+          "get_cell_coordinates": [
+            "cell",
+            "shifted"
+          ],
+          "get_bonds": [
+            "atoms",
+            "covalent_radii"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.gui",
+        "module": "widgets",
+        "functions": [
+          "pybutton",
+          "pywindow"
+        ],
+        "classes": [
+          "Element"
+        ],
+        "function_signatures": {
+          "pybutton": [
+            "title",
+            "callback"
+          ],
+          "pywindow": [
+            "title",
+            "callback"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "abinit",
+        "functions": [
+          "read_abinit",
+          "write_abinit"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_abinit": [
+            "filename"
+          ],
+          "write_abinit": [
+            "filename",
+            "atoms",
+            "cartesian",
+            "long_format"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "aims",
+        "functions": [
+          "read_aims",
+          "read_aims_output",
+          "read_energy",
+          "write_aims"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_aims": [
+            "filename"
+          ],
+          "write_aims": [
+            "filename",
+            "atoms",
+            "scaled",
+            "velocities",
+            "ghosts",
+            "info_str"
+          ],
+          "read_energy": [
+            "filename"
+          ],
+          "read_aims_output": [
+            "filename",
+            "index"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "animation",
+        "functions": [
+          "write_animation"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_animation": [
+            "filename",
+            "images",
+            "writer",
+            "interval",
+            "save_count",
+            "show_unit_cell",
+            "save_parameters"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "bader",
+        "functions": [
+          "attach_charges"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "attach_charges": [
+            "atoms",
+            "fileobj",
+            "displacement"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "bundlemanipulate",
+        "functions": [
+          "copy_frames",
+          "read_bundle_info"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "copy_frames": [
+            "inbundle",
+            "outbundle",
+            "start",
+            "end",
+            "step",
+            "verbose"
+          ],
+          "read_bundle_info": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "bundletrajectory",
+        "functions": [
+          "main",
+          "print_bundletrajectory_info",
+          "read_bundletrajectory",
+          "write_bundletrajectory"
+        ],
+        "classes": [
+          "BundleTrajectory",
+          "PickleBundleBackend",
+          "UlmBundleBackend"
+        ],
+        "function_signatures": {
+          "read_bundletrajectory": [
+            "filename",
+            "index"
+          ],
+          "write_bundletrajectory": [
+            "filename",
+            "images"
+          ],
+          "print_bundletrajectory_info": [
+            "filename"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "castep",
+        "functions": [
+          "read_castep",
+          "read_castep_castep",
+          "read_castep_castep_old",
+          "read_castep_cell",
+          "read_castep_geom",
+          "read_castep_md",
+          "read_castep_phonon",
+          "read_cell",
+          "read_freeform",
+          "read_geom",
+          "read_md",
+          "read_param",
+          "read_phonon",
+          "read_seed",
+          "write_castep_cell",
+          "write_cell",
+          "write_freeform",
+          "write_param"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_freeform": [
+            "fd",
+            "outputobj"
+          ],
+          "write_cell": [
+            "filename",
+            "atoms",
+            "positions_frac",
+            "castep_cell",
+            "force_write"
+          ],
+          "write_castep_cell": [
+            "fd",
+            "atoms",
+            "positions_frac",
+            "force_write",
+            "precision",
+            "magnetic_moments",
+            "castep_cell"
+          ],
+          "read_freeform": [
+            "fd"
+          ],
+          "read_cell": [
+            "filename",
+            "index"
+          ],
+          "read_castep_cell": [
+            "fd",
+            "index",
+            "calculator_args",
+            "find_spg",
+            "units"
+          ],
+          "read_castep": [
+            "filename",
+            "index"
+          ],
+          "read_castep_castep": [
+            "fd",
+            "index"
+          ],
+          "read_castep_castep_old": [
+            "fd",
+            "index"
+          ],
+          "read_geom": [
+            "filename",
+            "index",
+            "units"
+          ],
+          "read_castep_geom": [
+            "fd",
+            "index",
+            "units"
+          ],
+          "read_phonon": [
+            "filename",
+            "index",
+            "read_vib_data",
+            "gamma_only",
+            "frequency_factor",
+            "units"
+          ],
+          "read_castep_phonon": [
+            "fd",
+            "index",
+            "read_vib_data",
+            "gamma_only",
+            "frequency_factor",
+            "units"
+          ],
+          "read_md": [
+            "filename",
+            "index",
+            "return_scalars",
+            "units"
+          ],
+          "read_castep_md": [
+            "fd",
+            "index",
+            "return_scalars",
+            "units"
+          ],
+          "read_param": [
+            "filename",
+            "calc",
+            "fd",
+            "get_interface_options"
+          ],
+          "write_param": [
+            "filename",
+            "param",
+            "check_checkfile",
+            "force_write",
+            "interface_options"
+          ],
+          "read_seed": [
+            "seed",
+            "new_seed",
+            "ignore_internal_keys"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "cfg",
+        "functions": [
+          "read_cfg",
+          "write_cfg",
+          "write_clr"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_cfg": [
+            "f",
+            "a"
+          ],
+          "write_clr": [
+            "f",
+            "atoms"
+          ],
+          "read_cfg": [
+            "f"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "cif",
+        "functions": [
+          "convert_value",
+          "parse_block",
+          "parse_cif",
+          "parse_items",
+          "parse_loop",
+          "parse_multiline_string",
+          "parse_singletag",
+          "read_cif",
+          "split_chem_form",
+          "tags2atoms",
+          "write_cif"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "convert_value": [
+            "value"
+          ],
+          "parse_multiline_string": [
+            "lines",
+            "line"
+          ],
+          "parse_singletag": [
+            "lines",
+            "line"
+          ],
+          "parse_loop": [
+            "lines"
+          ],
+          "parse_items": [
+            "lines",
+            "line"
+          ],
+          "parse_block": [
+            "lines",
+            "line"
+          ],
+          "parse_cif": [
+            "fileobj"
+          ],
+          "tags2atoms": [
+            "tags",
+            "store_tags",
+            "primitive_cell",
+            "subtrans_included",
+            "fractional_occupancies"
+          ],
+          "read_cif": [
+            "fileobj",
+            "index",
+            "store_tags",
+            "primitive_cell",
+            "subtrans_included",
+            "fractional_occupancies"
+          ],
+          "split_chem_form": [
+            "comp_name"
+          ],
+          "write_cif": [
+            "fileobj",
+            "images",
+            "format"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "cmdft",
+        "functions": [
+          "read_cmdft"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_cmdft": [
+            "fileobj"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "crystal",
+        "functions": [
+          "read_crystal",
+          "write_crystal"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_crystal": [
+            "filename",
+            "atoms"
+          ],
+          "read_crystal": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "cube",
+        "functions": [
+          "read_cube",
+          "read_cube_data",
+          "write_cube"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_cube": [
+            "fileobj",
+            "atoms",
+            "data",
+            "origin",
+            "comment"
+          ],
+          "read_cube": [
+            "fileobj",
+            "read_data",
+            "program",
+            "verbose"
+          ],
+          "read_cube_data": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "dacapo",
+        "functions": [
+          "read_dacapo",
+          "read_dacapo_text"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_dacapo_text": [
+            "fileobj"
+          ],
+          "read_dacapo": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "db",
+        "functions": [
+          "read_db",
+          "write_db"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_db": [
+            "filename",
+            "index"
+          ],
+          "write_db": [
+            "filename",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "dftb",
+        "functions": [
+          "read_dftb",
+          "read_dftb_lattice",
+          "read_dftb_velocities",
+          "write_dftb",
+          "write_dftb_velocities"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_dftb": [
+            "filename"
+          ],
+          "read_dftb_velocities": [
+            "atoms",
+            "filename"
+          ],
+          "read_dftb_lattice": [
+            "fileobj",
+            "images"
+          ],
+          "write_dftb_velocities": [
+            "atoms",
+            "filename"
+          ],
+          "write_dftb": [
+            "filename",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "dlp4",
+        "functions": [
+          "read_dlp4",
+          "write_dlp4"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_dlp4": [
+            "f"
+          ],
+          "write_dlp4": [
+            "f",
+            "atoms",
+            "levcfg",
+            "title"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "dmol",
+        "functions": [
+          "read_dmol_arc",
+          "read_dmol_car",
+          "read_dmol_incoor",
+          "write_dmol_arc",
+          "write_dmol_car",
+          "write_dmol_incoor"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_dmol_car": [
+            "filename",
+            "atoms"
+          ],
+          "read_dmol_car": [
+            "filename"
+          ],
+          "write_dmol_incoor": [
+            "filename",
+            "atoms",
+            "bohr"
+          ],
+          "read_dmol_incoor": [
+            "filename",
+            "bohr"
+          ],
+          "write_dmol_arc": [
+            "filename",
+            "images"
+          ],
+          "read_dmol_arc": [
+            "filename",
+            "index"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "elk",
+        "functions": [
+          "read_elk"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_elk": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "eon",
+        "functions": [
+          "read_eon",
+          "read_states",
+          "write_eon"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_eon": [
+            "fileobj"
+          ],
+          "read_states": [
+            "states_dir"
+          ],
+          "write_eon": [
+            "fileobj",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "eps",
+        "functions": [
+          "write_eps"
+        ],
+        "classes": [
+          "EPS"
+        ],
+        "function_signatures": {
+          "write_eps": [
+            "filename",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "espresso",
+        "functions": [
+          "cell_to_ibrav",
+          "construct_namelist",
+          "ffloat",
+          "get_atomic_positions",
+          "get_cell_parameters",
+          "grep_valence",
+          "ibrav_to_cell",
+          "infix_float",
+          "kspacing_to_grid",
+          "label_to_symbol",
+          "parse_pwo_start",
+          "read_espresso_in",
+          "read_espresso_out",
+          "read_fortran_namelist",
+          "str_to_value",
+          "write_espresso_in"
+        ],
+        "classes": [
+          "Namelist"
+        ],
+        "function_signatures": {
+          "read_espresso_out": [
+            "fileobj",
+            "index",
+            "results_required"
+          ],
+          "parse_pwo_start": [
+            "lines",
+            "index"
+          ],
+          "read_espresso_in": [
+            "fileobj"
+          ],
+          "ibrav_to_cell": [
+            "system"
+          ],
+          "get_atomic_positions": [
+            "lines",
+            "n_atoms",
+            "cell",
+            "alat"
+          ],
+          "get_cell_parameters": [
+            "lines",
+            "alat"
+          ],
+          "str_to_value": [
+            "string"
+          ],
+          "read_fortran_namelist": [
+            "fileobj"
+          ],
+          "ffloat": [
+            "string"
+          ],
+          "label_to_symbol": [
+            "label"
+          ],
+          "infix_float": [
+            "text"
+          ],
+          "construct_namelist": [
+            "parameters",
+            "warn"
+          ],
+          "grep_valence": [
+            "pseudopotential"
+          ],
+          "cell_to_ibrav": [
+            "cell",
+            "ibrav"
+          ],
+          "kspacing_to_grid": [
+            "atoms",
+            "spacing",
+            "calculated_spacing"
+          ],
+          "write_espresso_in": [
+            "fd",
+            "atoms",
+            "input_data",
+            "pseudopotentials",
+            "kspacing",
+            "kpts",
+            "koffset"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "etsf",
+        "functions": [
+          "read_etsf",
+          "write_etsf"
+        ],
+        "classes": [
+          "ETSFReader",
+          "ETSFWriter"
+        ],
+        "function_signatures": {
+          "read_etsf": [
+            "filename"
+          ],
+          "write_etsf": [
+            "filename",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "exciting",
+        "functions": [
+          "atoms2etree",
+          "read_exciting",
+          "write_exciting"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_exciting": [
+            "fileobj",
+            "index"
+          ],
+          "write_exciting": [
+            "filename",
+            "images"
+          ],
+          "atoms2etree": [
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "extxyz",
+        "functions": [
+          "ixyzchunks",
+          "key_val_dict_to_str",
+          "key_val_str_to_dict",
+          "key_val_str_to_dict_regex",
+          "output_column_format",
+          "parse_properties",
+          "read_xyz",
+          "write_xyz"
+        ],
+        "classes": [
+          "ImageIterator",
+          "XYZChunk",
+          "XYZError"
+        ],
+        "function_signatures": {
+          "key_val_str_to_dict": [
+            "string",
+            "sep"
+          ],
+          "key_val_str_to_dict_regex": [
+            "s"
+          ],
+          "key_val_dict_to_str": [
+            "d",
+            "sep"
+          ],
+          "parse_properties": [
+            "prop_str"
+          ],
+          "ixyzchunks": [
+            "fd"
+          ],
+          "read_xyz": [
+            "fileobj",
+            "index",
+            "properties_parser"
+          ],
+          "output_column_format": [
+            "atoms",
+            "columns",
+            "arrays",
+            "write_info",
+            "results"
+          ],
+          "write_xyz": [
+            "fileobj",
+            "images",
+            "comment",
+            "columns",
+            "write_info",
+            "write_results",
+            "plain",
+            "vec_cell",
+            "append"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "findsym",
+        "functions": [
+          "write_findsym"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_findsym": [
+            "fileobj",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "formats",
+        "functions": [
+          "filetype",
+          "get_compression",
+          "get_ioformat",
+          "initialize",
+          "iread",
+          "open_with_compression",
+          "parse_filename",
+          "read",
+          "string2index",
+          "wrap_read_function",
+          "write"
+        ],
+        "classes": [
+          "UnknownFileTypeError"
+        ],
+        "function_signatures": {
+          "initialize": [
+            "format"
+          ],
+          "get_ioformat": [
+            "format"
+          ],
+          "get_compression": [
+            "filename"
+          ],
+          "open_with_compression": [
+            "filename",
+            "mode"
+          ],
+          "wrap_read_function": [
+            "read",
+            "filename",
+            "index"
+          ],
+          "write": [
+            "filename",
+            "images",
+            "format",
+            "parallel",
+            "append"
+          ],
+          "read": [
+            "filename",
+            "index",
+            "format",
+            "parallel"
+          ],
+          "iread": [
+            "filename",
+            "index",
+            "format",
+            "parallel"
+          ],
+          "parse_filename": [
+            "filename",
+            "index"
+          ],
+          "string2index": [
+            "string"
+          ],
+          "filetype": [
+            "filename",
+            "read",
+            "guess"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "fortranfile",
+        "functions": [],
+        "classes": [
+          "FortranFile"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "gaussian",
+        "functions": [
+          "read_gaussian",
+          "read_gaussian_out",
+          "write_gaussian"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_gaussian_out": [
+            "filename",
+            "index",
+            "quantity"
+          ],
+          "read_gaussian": [
+            "filename"
+          ],
+          "write_gaussian": [
+            "filename",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "gaussian_reader",
+        "functions": [],
+        "classes": [
+          "GaussianReader"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "gen",
+        "functions": [
+          "read_gen",
+          "write_gen"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_gen": [
+            "fileobj"
+          ],
+          "write_gen": [
+            "fileobj",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "gpaw_out",
+        "functions": [
+          "read_gpaw_out"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_gpaw_out": [
+            "fileobj",
+            "index"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "gpw",
+        "functions": [
+          "read_gpw",
+          "read_old_gpw"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_gpw": [
+            "filename"
+          ],
+          "read_old_gpw": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "gromacs",
+        "functions": [
+          "read_gromacs",
+          "write_gromacs"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_gromacs": [
+            "filename"
+          ],
+          "write_gromacs": [
+            "fileobj",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "gromos",
+        "functions": [
+          "read_gromos",
+          "write_gromos"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_gromos": [
+            "fileobj",
+            "index"
+          ],
+          "write_gromos": [
+            "fileobj",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "iwm",
+        "functions": [
+          "read_iwm"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_iwm": [
+            "fileobj",
+            "index"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "jsonio",
+        "functions": [
+          "decode",
+          "intkey",
+          "numpyfy",
+          "object_hook",
+          "read_json"
+        ],
+        "classes": [
+          "MyEncoder"
+        ],
+        "function_signatures": {
+          "object_hook": [
+            "dct"
+          ],
+          "intkey": [
+            "key"
+          ],
+          "numpyfy": [
+            "obj"
+          ],
+          "decode": [
+            "txt"
+          ],
+          "read_json": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "jsv",
+        "functions": [
+          "read_jsv",
+          "write_jsv"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_jsv": [
+            "f"
+          ],
+          "write_jsv": [
+            "f",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "lammpsdata",
+        "functions": [
+          "read_lammps_data"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_lammps_data": [
+            "fileobj",
+            "Z_of_type",
+            "style",
+            "sort_by_id",
+            "units"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "lammpsrun",
+        "functions": [
+          "read_lammps_dump"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_lammps_dump": [
+            "fileobj",
+            "index",
+            "order",
+            "atomsobj"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "magres",
+        "functions": [
+          "read_magres",
+          "tensor_string",
+          "write_magres"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_magres": [
+            "fd",
+            "include_unrecognised"
+          ],
+          "tensor_string": [
+            "tensor"
+          ],
+          "write_magres": [
+            "fd",
+            "image"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "mol",
+        "functions": [
+          "read_mol"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_mol": [
+            "fileobj"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "mustem",
+        "functions": [
+          "read_mustem",
+          "write_mustem"
+        ],
+        "classes": [
+          "XtlmuSTEMWriter"
+        ],
+        "function_signatures": {
+          "read_mustem": [
+            "filename"
+          ],
+          "write_mustem": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "netcdftrajectory",
+        "functions": [
+          "read_netcdftrajectory",
+          "write_netcdftrajectory"
+        ],
+        "classes": [
+          "NetCDFTrajectory"
+        ],
+        "function_signatures": {
+          "read_netcdftrajectory": [
+            "filename",
+            "index"
+          ],
+          "write_netcdftrajectory": [
+            "filename",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "nomad_json",
+        "functions": [
+          "read_nomad_json"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_nomad_json": [
+            "fd",
+            "index"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "nwchem",
+        "functions": [
+          "read_nwchem",
+          "read_nwchem_output",
+          "write_nwchem"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_nwchem_output": [
+            "filename"
+          ],
+          "read_nwchem": [
+            "filename"
+          ],
+          "write_nwchem": [
+            "filename",
+            "atoms",
+            "geometry"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "octopus",
+        "functions": [
+          "read_octopus"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_octopus": [
+            "fileobj",
+            "get_kwargs"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "opls",
+        "functions": [
+          "twochar"
+        ],
+        "classes": [
+          "AnglesData",
+          "BondData",
+          "CutoffList",
+          "DihedralsData",
+          "OPLSStructure",
+          "OPLSff"
+        ],
+        "function_signatures": {
+          "twochar": [
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "pickletrajectory",
+        "functions": [
+          "dict2constraints",
+          "print_trajectory_info",
+          "read_trajectory",
+          "stringnify_info",
+          "unstringnify_info",
+          "write_trajectory"
+        ],
+        "classes": [
+          "PickleTrajectory"
+        ],
+        "function_signatures": {
+          "stringnify_info": [
+            "info"
+          ],
+          "unstringnify_info": [
+            "stringnified"
+          ],
+          "read_trajectory": [
+            "filename",
+            "index"
+          ],
+          "write_trajectory": [
+            "filename",
+            "images"
+          ],
+          "dict2constraints": [
+            "d"
+          ],
+          "print_trajectory_info": [
+            "filename"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "plt",
+        "functions": [
+          "read_plt",
+          "write_plt"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_plt": [
+            "filename",
+            "atoms",
+            "data"
+          ],
+          "read_plt": [
+            "fileobj"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "png",
+        "functions": [
+          "write_png"
+        ],
+        "classes": [
+          "PNG"
+        ],
+        "function_signatures": {
+          "write_png": [
+            "filename",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "pov",
+        "functions": [
+          "get_bondpairs",
+          "pa",
+          "pc",
+          "write_pov"
+        ],
+        "classes": [
+          "POVRAY"
+        ],
+        "function_signatures": {
+          "pa": [
+            "array"
+          ],
+          "pc": [
+            "array"
+          ],
+          "get_bondpairs": [
+            "atoms",
+            "radius"
+          ],
+          "write_pov": [
+            "filename",
+            "atoms",
+            "run_povray",
+            "stderr"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "proteindatabank",
+        "functions": [
+          "read_atom_line",
+          "read_proteindatabank",
+          "write_proteindatabank"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_atom_line": [
+            "line_full"
+          ],
+          "read_proteindatabank": [
+            "fileobj",
+            "index",
+            "read_arrays"
+          ],
+          "write_proteindatabank": [
+            "fileobj",
+            "images",
+            "write_arrays"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "io",
+        "functions": [
+          "write_py"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_py": [
+            "fileobj",
+            "images"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "qbox",
+        "functions": [
+          "read_qbox"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_qbox": [
+            "f",
+            "index"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "res",
+        "functions": [
+          "read_res",
+          "write_res"
+        ],
+        "classes": [
+          "Res"
+        ],
+        "function_signatures": {
+          "read_res": [
+            "filename",
+            "index"
+          ],
+          "write_res": [
+            "filename",
+            "images",
+            "write_info",
+            "write_results",
+            "significant_figures"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "sdf",
+        "functions": [
+          "read_sdf"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_sdf": [
+            "fileobj"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "siesta",
+        "functions": [
+          "read_fdf",
+          "read_struct_out"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_fdf": [
+            "fname"
+          ],
+          "read_struct_out": [
+            "fname"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "trajectory",
+        "functions": [
+          "Trajectory",
+          "convert",
+          "get_header_data",
+          "headers_equal",
+          "main",
+          "read_atoms",
+          "read_traj",
+          "write_atoms",
+          "write_traj"
+        ],
+        "classes": [
+          "OldCalculatorWrapper",
+          "TrajectoryReader",
+          "TrajectoryWriter"
+        ],
+        "function_signatures": {
+          "Trajectory": [
+            "filename",
+            "mode",
+            "atoms",
+            "properties",
+            "master"
+          ],
+          "get_header_data": [
+            "atoms"
+          ],
+          "headers_equal": [
+            "headers1",
+            "headers2"
+          ],
+          "read_atoms": [
+            "backend",
+            "header"
+          ],
+          "write_atoms": [
+            "backend",
+            "atoms",
+            "write_header"
+          ],
+          "read_traj": [
+            "fd",
+            "index"
+          ],
+          "write_traj": [
+            "fd",
+            "images"
+          ],
+          "convert": [
+            "name"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "turbomole",
+        "functions": [
+          "read_turbomole",
+          "read_turbomole_gradient",
+          "write_turbomole"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_turbomole": [
+            "fd"
+          ],
+          "read_turbomole_gradient": [
+            "fd",
+            "index"
+          ],
+          "write_turbomole": [
+            "fd",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "ulm",
+        "functions": [
+          "align",
+          "copy",
+          "file_has_fileno",
+          "open",
+          "print_ulm_info",
+          "read_header",
+          "readints",
+          "writeint"
+        ],
+        "classes": [
+          "CLICommand",
+          "DummyWriter",
+          "InvalidULMFileError",
+          "NDArrayReader",
+          "Reader",
+          "Writer"
+        ],
+        "function_signatures": {
+          "open": [
+            "filename",
+            "mode",
+            "index",
+            "tag"
+          ],
+          "align": [
+            "fd"
+          ],
+          "writeint": [
+            "fd",
+            "n",
+            "pos"
+          ],
+          "readints": [
+            "fd",
+            "n"
+          ],
+          "file_has_fileno": [
+            "fd"
+          ],
+          "read_header": [
+            "fd"
+          ],
+          "print_ulm_info": [
+            "filename",
+            "index",
+            "verbose"
+          ],
+          "copy": [
+            "reader",
+            "writer",
+            "exclude",
+            "name"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "utils",
+        "functions": [
+          "cell_to_lines",
+          "generate_writer_variables",
+          "make_patch_list"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "generate_writer_variables": [
+            "writer",
+            "atoms",
+            "rotation",
+            "show_unit_cell",
+            "radii",
+            "bbox",
+            "colors",
+            "scale",
+            "maxwidth",
+            "extra_offset"
+          ],
+          "cell_to_lines": [
+            "writer",
+            "cell"
+          ],
+          "make_patch_list": [
+            "writer"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "v_sim",
+        "functions": [
+          "read_v_sim",
+          "write_v_sim"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_v_sim": [
+            "filename"
+          ],
+          "write_v_sim": [
+            "filename",
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "vasp",
+        "functions": [
+          "atomtypes_outpot",
+          "get_atomtypes",
+          "get_atomtypes_from_formula",
+          "read_vasp",
+          "read_vasp_out",
+          "read_vasp_xdatcar",
+          "read_vasp_xml",
+          "write_vasp"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_atomtypes": [
+            "fname"
+          ],
+          "atomtypes_outpot": [
+            "posfname",
+            "numsyms"
+          ],
+          "get_atomtypes_from_formula": [
+            "formula"
+          ],
+          "read_vasp": [
+            "filename"
+          ],
+          "read_vasp_out": [
+            "filename",
+            "index",
+            "force_consistent"
+          ],
+          "read_vasp_xdatcar": [
+            "filename",
+            "index"
+          ],
+          "read_vasp_xml": [
+            "filename",
+            "index"
+          ],
+          "write_vasp": [
+            "filename",
+            "atoms",
+            "label",
+            "direct",
+            "sort",
+            "symbol_count",
+            "long_format",
+            "vasp5",
+            "ignore_constraints"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "vtkxml",
+        "functions": [
+          "write_vti",
+          "write_vtu"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_vti": [
+            "filename",
+            "atoms",
+            "data"
+          ],
+          "write_vtu": [
+            "filename",
+            "atoms",
+            "data"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "wien2k",
+        "functions": [
+          "c2p",
+          "cellconst",
+          "coorsys",
+          "read_scf",
+          "read_struct",
+          "write_struct"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_scf": [
+            "filename"
+          ],
+          "read_struct": [
+            "filename",
+            "ase"
+          ],
+          "write_struct": [
+            "filename",
+            "atoms2",
+            "rmt",
+            "lattice",
+            "zza"
+          ],
+          "cellconst": [
+            "metT"
+          ],
+          "coorsys": [
+            "latconst"
+          ],
+          "c2p": [
+            "lattice"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "x3d",
+        "functions": [
+          "atom_lines",
+          "write_html",
+          "write_x3d"
+        ],
+        "classes": [
+          "WriteToFile",
+          "X3D"
+        ],
+        "function_signatures": {
+          "write_x3d": [
+            "filename",
+            "atoms",
+            "format"
+          ],
+          "write_html": [
+            "filename",
+            "atoms"
+          ],
+          "atom_lines": [
+            "atom"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "xsd",
+        "functions": [
+          "CPK_or_BnS",
+          "read_xsd",
+          "write_xsd"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "read_xsd": [
+            "fd"
+          ],
+          "CPK_or_BnS": [
+            "element"
+          ],
+          "write_xsd": [
+            "fd",
+            "atoms",
+            "connectivity"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "xsf",
+        "functions": [
+          "iread_xsf",
+          "read_xsf",
+          "write_xsf"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write_xsf": [
+            "fileobj",
+            "images",
+            "data"
+          ],
+          "iread_xsf": [
+            "fileobj",
+            "read_data"
+          ],
+          "read_xsf": [
+            "fileobj",
+            "index",
+            "read_data"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.io",
+        "module": "xyz",
+        "functions": [
+          "simple_read_xyz",
+          "simple_write_xyz"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "simple_read_xyz": [
+            "fileobj",
+            "index"
+          ],
+          "simple_write_xyz": [
+            "fileobj",
+            "images",
+            "comment"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "lattice",
+        "functions": [
+          "bulk"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "bulk": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "bravais",
+        "functions": [
+          "cross",
+          "reduceindex"
+        ],
+        "classes": [
+          "Bravais",
+          "Lattice",
+          "MillerInfo"
+        ],
+        "function_signatures": {
+          "cross": [
+            "a",
+            "b"
+          ],
+          "reduceindex": [
+            "M"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "compounds",
+        "functions": [],
+        "classes": [
+          "AuCu3Factory",
+          "AuCuFactory",
+          "CsClFactory",
+          "HexagonalFe2O3Factory",
+          "NaClFactory",
+          "TriclinicFe2O3Factory",
+          "ZnSFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "cubic",
+        "functions": [],
+        "classes": [
+          "BodyCenteredCubicFactory",
+          "DiamondFactory",
+          "FaceCenteredCubicFactory",
+          "SimpleCubicFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "hexagonal",
+        "functions": [],
+        "classes": [
+          "GrapheneFactory",
+          "GraphiteFactory",
+          "HexagonalClosedPackedFactory",
+          "HexagonalFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "monoclinic",
+        "functions": [],
+        "classes": [
+          "BaseCenteredMonoclinicFactory",
+          "SimpleMonoclinicFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "orthorhombic",
+        "functions": [],
+        "classes": [
+          "BaseCenteredOrthorhombicFactory",
+          "BodyCenteredOrthorhombicFactory",
+          "FaceCenteredOrthorhombicFactory",
+          "SimpleOrthorhombicFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "tetragonal",
+        "functions": [],
+        "classes": [
+          "CenteredTetragonalFactory",
+          "SimpleTetragonalFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.lattice",
+        "module": "triclinic",
+        "functions": [],
+        "classes": [
+          "TriclinicFactory"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "fix",
+        "functions": [],
+        "classes": [
+          "FixRotation"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "langevin",
+        "functions": [],
+        "classes": [
+          "Langevin"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "logger",
+        "functions": [],
+        "classes": [
+          "MDLogger"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "md",
+        "functions": [],
+        "classes": [
+          "MolecularDynamics"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "npt",
+        "functions": [],
+        "classes": [
+          "NPT",
+          "WeakMethodWrapper"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "nptberendsen",
+        "functions": [],
+        "classes": [
+          "Inhomogeneous_NPTBerendsen",
+          "NPTBerendsen"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "nvtberendsen",
+        "functions": [],
+        "classes": [
+          "NVTBerendsen"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "velocitydistribution",
+        "functions": [
+          "MaxwellBoltzmannDistribution",
+          "PhononHarmonics",
+          "Stationary",
+          "ZeroRotation",
+          "n_BE",
+          "phonon_harmonics"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "MaxwellBoltzmannDistribution": [
+            "atoms",
+            "temp",
+            "communicator",
+            "force_temp",
+            "rng"
+          ],
+          "Stationary": [
+            "atoms"
+          ],
+          "ZeroRotation": [
+            "atoms"
+          ],
+          "n_BE": [
+            "temp",
+            "omega"
+          ],
+          "phonon_harmonics": [
+            "force_constants",
+            "masses",
+            "temp",
+            "rng",
+            "quantum",
+            "failfast"
+          ],
+          "PhononHarmonics": [
+            "atoms",
+            "force_constants",
+            "temp",
+            "rng",
+            "quantum",
+            "failfast"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.md",
+        "module": "verlet",
+        "functions": [],
+        "classes": [
+          "VelocityVerlet"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "basin",
+        "functions": [],
+        "classes": [
+          "BasinHopping"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "bfgs",
+        "functions": [],
+        "classes": [
+          "BFGS",
+          "oldBFGS"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "bfgslinesearch",
+        "functions": [
+          "wrap_function"
+        ],
+        "classes": [
+          "BFGSLineSearch"
+        ],
+        "function_signatures": {
+          "wrap_function": [
+            "function",
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "fire",
+        "functions": [],
+        "classes": [
+          "FIRE"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "fmin_bfgs",
+        "functions": [
+          "approx_fprime",
+          "fmin_bfgs",
+          "line_search",
+          "vecnorm",
+          "wrap_function",
+          "zoom"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "fmin_bfgs": [
+            "f",
+            "x0",
+            "fprime",
+            "args",
+            "gtol",
+            "norm",
+            "epsilon",
+            "maxiter",
+            "full_output",
+            "disp",
+            "retall",
+            "callback",
+            "maxstep"
+          ],
+          "vecnorm": [
+            "x",
+            "ord"
+          ],
+          "wrap_function": [
+            "function",
+            "args"
+          ],
+          "zoom": [
+            "a_lo",
+            "a_hi",
+            "phi_lo",
+            "phi_hi",
+            "derphi_lo",
+            "phi",
+            "derphi",
+            "phi0",
+            "derphi0",
+            "c1",
+            "c2"
+          ],
+          "line_search": [
+            "f",
+            "myfprime",
+            "xk",
+            "pk",
+            "gfk",
+            "old_fval",
+            "old_old_fval",
+            "args",
+            "c1",
+            "c2",
+            "amax"
+          ],
+          "approx_fprime": [
+            "xk",
+            "f",
+            "epsilon"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "lbfgs",
+        "functions": [],
+        "classes": [
+          "LBFGS",
+          "LBFGSLineSearch"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "mdmin",
+        "functions": [],
+        "classes": [
+          "MDMin"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "minimahopping",
+        "functions": [
+          "floatornan"
+        ],
+        "classes": [
+          "CombinedAxis",
+          "ComparePositions",
+          "MHPlot",
+          "MinimaHopping",
+          "PassedMinimum"
+        ],
+        "function_signatures": {
+          "floatornan": [
+            "value"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "oldqn",
+        "functions": [
+          "f",
+          "find_lamda",
+          "get_hessian_inertia",
+          "scale_radius_energy",
+          "scale_radius_force"
+        ],
+        "classes": [
+          "GoodOldQuasiNewton"
+        ],
+        "function_signatures": {
+          "f": [
+            "lamda",
+            "Gbar",
+            "b",
+            "radius"
+          ],
+          "scale_radius_energy": [
+            "f",
+            "r"
+          ],
+          "scale_radius_force": [
+            "f",
+            "r"
+          ],
+          "find_lamda": [
+            "upperlimit",
+            "Gbar",
+            "b",
+            "radius"
+          ],
+          "get_hessian_inertia": [
+            "eigenvalues"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "optimize",
+        "functions": [],
+        "classes": [
+          "Dynamics",
+          "Optimizer"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize",
+        "module": "sciopt",
+        "functions": [],
+        "classes": [
+          "Converged",
+          "OptimizerConvergenceError",
+          "SciPyFmin",
+          "SciPyFminBFGS",
+          "SciPyFminCG",
+          "SciPyFminPowell",
+          "SciPyGradientlessOptimizer",
+          "SciPyOptimizer"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.gpmin",
+        "module": "gp",
+        "functions": [],
+        "classes": [
+          "GaussianProcess"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.gpmin",
+        "module": "gpmin",
+        "functions": [],
+        "classes": [
+          "GPMin"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.gpmin",
+        "module": "kernel",
+        "functions": [],
+        "classes": [
+          "Kernel",
+          "SE_kernel",
+          "SquaredExponential"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.gpmin",
+        "module": "prior",
+        "functions": [],
+        "classes": [
+          "CalculatorPrior",
+          "ConstantPrior",
+          "Prior",
+          "ZeroPrior"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.precon",
+        "module": "fire",
+        "functions": [],
+        "classes": [
+          "PreconFIRE"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.precon",
+        "module": "lbfgs",
+        "functions": [],
+        "classes": [
+          "PreconLBFGS"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.precon",
+        "module": "neighbors",
+        "functions": [
+          "estimate_nearest_neighbour_distance",
+          "get_neighbours"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_neighbours": [
+            "atoms",
+            "r_cut",
+            "self_interaction"
+          ],
+          "estimate_nearest_neighbour_distance": [
+            "atoms"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.optimize.precon",
+        "module": "precon",
+        "functions": [],
+        "classes": [
+          "C1",
+          "Exp",
+          "Exp_FF",
+          "FF",
+          "Pfrommer",
+          "Precon"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.spacegroup",
+        "module": "findsym",
+        "functions": [
+          "findsym",
+          "make_input",
+          "parse",
+          "run",
+          "unique"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "make_input": [
+            "atoms",
+            "tol",
+            "centering",
+            "types"
+          ],
+          "run": [
+            "atoms",
+            "tol",
+            "centering",
+            "types",
+            "isodata_dir"
+          ],
+          "parse": [
+            "output"
+          ],
+          "findsym": [
+            "atoms",
+            "tol",
+            "centering",
+            "types",
+            "isodata_dir"
+          ],
+          "unique": [
+            "atoms",
+            "tol",
+            "centering",
+            "types",
+            "isodata_dir"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.spacegroup",
+        "module": "spacegroup",
+        "functions": [
+          "format_symbol",
+          "get_datafile",
+          "get_spacegroup",
+          "parse_sitesym",
+          "spacegroup_from_data"
+        ],
+        "classes": [
+          "Spacegroup",
+          "SpacegroupError",
+          "SpacegroupNotFoundError",
+          "SpacegroupValueError"
+        ],
+        "function_signatures": {
+          "get_datafile": [],
+          "format_symbol": [
+            "symbol"
+          ],
+          "parse_sitesym": [
+            "symlist",
+            "sep"
+          ],
+          "spacegroup_from_data": [
+            "no",
+            "symbol",
+            "setting",
+            "centrosymmetric",
+            "scaled_primitive_cell",
+            "reciprocal_cell",
+            "subtrans",
+            "sitesym",
+            "rotations",
+            "translations",
+            "datafile"
+          ],
+          "get_spacegroup": [
+            "atoms",
+            "symprec"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.spacegroup",
+        "module": "xtal",
+        "functions": [
+          "crystal",
+          "parse_symbols"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "crystal": [
+            "symbols",
+            "basis",
+            "occupancies",
+            "spacegroup",
+            "setting",
+            "cell",
+            "cellpar",
+            "ab_normal",
+            "a_direction",
+            "size",
+            "onduplicates",
+            "symprec",
+            "pbc",
+            "primitive_cell"
+          ],
+          "parse_symbols": [
+            "symbols"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.transport",
+        "module": "calculators",
+        "functions": [],
+        "classes": [
+          "TransportCalculator"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.transport",
+        "module": "greenfunction",
+        "functions": [],
+        "classes": [
+          "GreenFunction"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.transport",
+        "module": "selfenergy",
+        "functions": [],
+        "classes": [
+          "BoxProbe",
+          "LeadSelfEnergy"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.transport",
+        "module": "stm",
+        "functions": [],
+        "classes": [
+          "STM"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.transport",
+        "module": "test_transport_calulator",
+        "functions": [
+          "write"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "write": [
+            "fname",
+            "xs",
+            "ys"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.transport",
+        "module": "tools",
+        "functions": [
+          "cutcoupling",
+          "dagger",
+          "fermidistribution",
+          "fliplr",
+          "function_integral",
+          "get_subspace",
+          "mytextread0",
+          "mytextread1",
+          "mytextwrite1",
+          "normalize",
+          "plot_path",
+          "quadlstep",
+          "rotate_matrix",
+          "subdiagonalize",
+          "tri2full"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "tri2full": [
+            "H_nn",
+            "UL"
+          ],
+          "dagger": [
+            "matrix"
+          ],
+          "rotate_matrix": [
+            "h",
+            "u"
+          ],
+          "get_subspace": [
+            "matrix",
+            "index"
+          ],
+          "normalize": [
+            "matrix",
+            "S"
+          ],
+          "subdiagonalize": [
+            "h_ii",
+            "s_ii",
+            "index_j"
+          ],
+          "cutcoupling": [
+            "h",
+            "s",
+            "index_n"
+          ],
+          "fermidistribution": [
+            "energy",
+            "kt"
+          ],
+          "fliplr": [
+            "a"
+          ],
+          "plot_path": [
+            "energy"
+          ],
+          "function_integral": [
+            "function",
+            "calcutype"
+          ],
+          "quadlstep": [
+            "f",
+            "Za",
+            "Zb",
+            "fa",
+            "fb",
+            "tol",
+            "trace",
+            "fcnt",
+            "hmin",
+            "calcutype",
+            "path_type",
+            "origin",
+            "radius"
+          ],
+          "mytextread0": [
+            "filename"
+          ],
+          "mytextread1": [
+            "filename"
+          ],
+          "mytextwrite1": [
+            "filename",
+            "mat"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase",
+        "module": "utils",
+        "functions": [
+          "convert_string_to_fd",
+          "givens",
+          "hsv",
+          "hsv2rgb",
+          "irotate",
+          "longsum",
+          "natural_cutoffs",
+          "opencew",
+          "plural",
+          "rotate",
+          "search_current_git_hash",
+          "seterr"
+        ],
+        "classes": [
+          "DevNull",
+          "Lock",
+          "OpenLock"
+        ],
+        "function_signatures": {
+          "seterr": [],
+          "plural": [
+            "n",
+            "word"
+          ],
+          "convert_string_to_fd": [
+            "name",
+            "world"
+          ],
+          "opencew": [
+            "filename",
+            "world"
+          ],
+          "search_current_git_hash": [
+            "arg",
+            "world"
+          ],
+          "rotate": [
+            "rotations",
+            "rotation"
+          ],
+          "givens": [
+            "a",
+            "b"
+          ],
+          "irotate": [
+            "rotation",
+            "initial"
+          ],
+          "hsv2rgb": [
+            "h",
+            "s",
+            "v"
+          ],
+          "hsv": [
+            "array",
+            "s",
+            "v"
+          ],
+          "natural_cutoffs": [
+            "atoms",
+            "mult"
+          ],
+          "longsum": [
+            "x"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "_linprog",
+        "functions": [
+          "linprog"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "linprog": [
+            "c",
+            "A_ub",
+            "b_ub",
+            "A_eq",
+            "b_eq",
+            "bounds",
+            "maxiter",
+            "disp",
+            "callback",
+            "tol",
+            "bland"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "bee",
+        "functions": [
+          "get_ensemble_energies",
+          "make_ensemble"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "make_ensemble": [
+            "N",
+            "seed"
+          ],
+          "get_ensemble_energies": [
+            "atoms",
+            "c"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "build_web_page",
+        "functions": [
+          "build"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "build": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "extrapolate",
+        "functions": [
+          "extrapolate"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "extrapolate": [
+            "x",
+            "y",
+            "n",
+            "plot",
+            "reg",
+            "txt"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "ff",
+        "functions": [
+          "get_angle_potential_gradient",
+          "get_angle_potential_hessian",
+          "get_angle_potential_reduced_hessian",
+          "get_angle_potential_reduced_hessian_test",
+          "get_angle_potential_value",
+          "get_bond_potential_gradient",
+          "get_bond_potential_hessian",
+          "get_bond_potential_reduced_hessian",
+          "get_bond_potential_reduced_hessian_test",
+          "get_bond_potential_value",
+          "get_coulomb_potential_gradient",
+          "get_coulomb_potential_hessian",
+          "get_coulomb_potential_value",
+          "get_dihedral_potential_gradient",
+          "get_dihedral_potential_hessian",
+          "get_dihedral_potential_reduced_hessian",
+          "get_dihedral_potential_reduced_hessian_test",
+          "get_dihedral_potential_value",
+          "get_morse_potential_eta",
+          "get_morse_potential_gradient",
+          "get_morse_potential_hessian",
+          "get_morse_potential_reduced_hessian",
+          "get_morse_potential_value",
+          "get_vdw_potential_gradient",
+          "get_vdw_potential_hessian",
+          "get_vdw_potential_value",
+          "model_bond_angle_dihedral",
+          "rel_pos_pbc",
+          "remove_tr_rot_vector",
+          "rotational_vectors",
+          "row",
+          "translational_vectors"
+        ],
+        "classes": [
+          "Angle",
+          "Bond",
+          "Coulomb",
+          "Dihedral",
+          "Morse",
+          "VdW"
+        ],
+        "function_signatures": {
+          "get_morse_potential_eta": [
+            "atoms",
+            "morse"
+          ],
+          "get_morse_potential_value": [
+            "atoms",
+            "morse"
+          ],
+          "get_morse_potential_gradient": [
+            "atoms",
+            "morse"
+          ],
+          "get_morse_potential_hessian": [
+            "atoms",
+            "morse",
+            "spectral"
+          ],
+          "get_morse_potential_reduced_hessian": [
+            "atoms",
+            "morse"
+          ],
+          "get_bond_potential_value": [
+            "atoms",
+            "bond"
+          ],
+          "get_bond_potential_gradient": [
+            "atoms",
+            "bond"
+          ],
+          "get_bond_potential_hessian": [
+            "atoms",
+            "bond",
+            "morses",
+            "spectral"
+          ],
+          "get_bond_potential_reduced_hessian": [
+            "atoms",
+            "bond",
+            "morses"
+          ],
+          "get_bond_potential_reduced_hessian_test": [
+            "atoms",
+            "bond"
+          ],
+          "get_angle_potential_value": [
+            "atoms",
+            "angle"
+          ],
+          "get_angle_potential_gradient": [
+            "atoms",
+            "angle"
+          ],
+          "get_angle_potential_hessian": [
+            "atoms",
+            "angle",
+            "morses",
+            "spectral"
+          ],
+          "get_angle_potential_reduced_hessian": [
+            "atoms",
+            "angle",
+            "morses"
+          ],
+          "get_angle_potential_reduced_hessian_test": [
+            "atoms",
+            "angle"
+          ],
+          "get_dihedral_potential_value": [
+            "atoms",
+            "dihedral"
+          ],
+          "get_dihedral_potential_gradient": [
+            "atoms",
+            "dihedral"
+          ],
+          "get_dihedral_potential_hessian": [
+            "atoms",
+            "dihedral",
+            "morses",
+            "spectral"
+          ],
+          "get_dihedral_potential_reduced_hessian": [
+            "atoms",
+            "dihedral",
+            "morses"
+          ],
+          "get_dihedral_potential_reduced_hessian_test": [
+            "atoms",
+            "dihedral"
+          ],
+          "get_vdw_potential_value": [
+            "atoms",
+            "vdw"
+          ],
+          "get_vdw_potential_gradient": [
+            "atoms",
+            "vdw"
+          ],
+          "get_vdw_potential_hessian": [
+            "atoms",
+            "vdw",
+            "spectral"
+          ],
+          "get_coulomb_potential_value": [
+            "atoms",
+            "coulomb"
+          ],
+          "get_coulomb_potential_gradient": [
+            "atoms",
+            "coulomb"
+          ],
+          "get_coulomb_potential_hessian": [
+            "atoms",
+            "coulomb",
+            "spectral"
+          ],
+          "rel_pos_pbc": [
+            "atoms",
+            "i",
+            "j"
+          ],
+          "translational_vectors": [
+            "atoms",
+            "mass_weighted"
+          ],
+          "rotational_vectors": [
+            "atoms",
+            "mass_weighted"
+          ],
+          "remove_tr_rot_vector": [
+            "atoms",
+            "vecin",
+            "mass_weighted"
+          ],
+          "model_bond_angle_dihedral": [
+            "atoms",
+            "cutoff"
+          ],
+          "row": [
+            "Z"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "formula",
+        "functions": [
+          "formula_hill",
+          "formula_metal"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "formula_hill": [
+            "numbers",
+            "empirical"
+          ],
+          "formula_metal": [
+            "numbers",
+            "empirical"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "linesearch",
+        "functions": [],
+        "classes": [
+          "LineSearch"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "linesearcharmijo",
+        "functions": [
+          "nullspace"
+        ],
+        "classes": [
+          "LineSearchArmijo",
+          "LinearPath",
+          "RumPath"
+        ],
+        "function_signatures": {
+          "nullspace": [
+            "A",
+            "myeps"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "memory",
+        "functions": [
+          "shapegen",
+          "shapeopt"
+        ],
+        "classes": [
+          "MemoryBase",
+          "MemorySingleton",
+          "MemoryStatistics",
+          "Singleton"
+        ],
+        "function_signatures": {
+          "shapegen": [
+            "size",
+            "ndims",
+            "ecc"
+          ],
+          "shapeopt": [
+            "maxseed",
+            "size",
+            "ndims",
+            "ecc"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "newrelease",
+        "functions": [
+          "get_version",
+          "git",
+          "main",
+          "py",
+          "py2",
+          "runcmd"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "runcmd": [
+            "cmd",
+            "output",
+            "error_ok"
+          ],
+          "py": [
+            "cmd",
+            "output"
+          ],
+          "py2": [
+            "cmd",
+            "output"
+          ],
+          "git": [
+            "cmd",
+            "error_ok"
+          ],
+          "get_version": [],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "sphinx",
+        "functions": [
+          "clean",
+          "create_png_files",
+          "creates",
+          "git_role_tmpl",
+          "mol_role",
+          "visual_inspection"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "mol_role": [
+            "role",
+            "rawtext",
+            "text",
+            "lineno",
+            "inliner",
+            "options",
+            "content"
+          ],
+          "git_role_tmpl": [
+            "urlroot",
+            "role",
+            "rawtext",
+            "text",
+            "lineno",
+            "inliner",
+            "options",
+            "content"
+          ],
+          "creates": [],
+          "create_png_files": [],
+          "clean": [],
+          "visual_inspection": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "structure_comparator",
+        "functions": [
+          "normalize"
+        ],
+        "classes": [
+          "SpgLibNotFoundError",
+          "SymmetryEquivalenceCheck"
+        ],
+        "function_signatures": {
+          "normalize": [
+            "cell"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "stylecheck",
+        "functions": [
+          "check_file",
+          "check_repository",
+          "mail",
+          "pep8",
+          "pyflakes"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "mail": [
+            "to",
+            "subject",
+            "txt"
+          ],
+          "pep8": [
+            "name"
+          ],
+          "pyflakes": [
+            "name"
+          ],
+          "check_file": [
+            "name"
+          ],
+          "check_repository": [
+            "to"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "timing",
+        "functions": [
+          "function_timer"
+        ],
+        "classes": [
+          "Timer",
+          "timer"
+        ],
+        "function_signatures": {
+          "function_timer": [
+            "func"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.utils",
+        "module": "xrdebye",
+        "functions": [],
+        "classes": [
+          "XrDebye"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.vibrations",
+        "module": "albrecht",
+        "functions": [],
+        "classes": [
+          "Albrecht"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "ase.vibrations",
+        "module": "franck_condon",
+        "functions": [],
+        "classes": [
+          "Factorial",
+          "FranckCondon",
+          "FranckCondonOverlap",
+          "FranckCondonRecursive"
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+            "viewer",
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+          ]
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+        "description": "Discovered via AST scan"
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+      {
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+        "module": "fieldplotter",
+        "functions": [],
+        "classes": [
+          "FieldPlotter",
+          "InterpolatingFunction"
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+        "function_signatures": {},
+        "description": "Discovered via AST scan"
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+        "module": "mlab",
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+        "description": "Discovered via AST scan"
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+        "functions": [
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+        "classes": [
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+        "description": "Discovered via AST scan"
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+        "package": "ase.visualize",
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+        },
+        "description": "Discovered via AST scan"
+      },
+      {
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+        },
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+          ]
+        },
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+        "module": "source.ase.cli.run",
+        "description": "Command line interface for running ASE simulations."
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+    "repo_url": "https://github.com/DeepChoudhuri/Atomic-Simulation-Environment",
+    "repo_name": "Atomic-Simulation-Environment",
+    "content": "DeepChoudhuri/Atomic-Simulation-Environment\nCore Components\nAtoms Class\nCalculators\nVASP Calculator\nCASTEP Calculator\nQuantum ESPRESSO Calculator\nOther Calculators\nFile I/O System\nConstraints\nAnalysis Tools\nNudged Elastic Band\nVibrational Analysis\nDatabase System\nDatabase Core\nDatabase Web Interface\nUser Interfaces\nGraphical User Interface\nCommand Line Interface\nUtilities and Infrastructure\nTesting Framework\nUtility Functions\nDevelopment and Contribution\nSetup and Installation\nDocumentation System\nRelease Process\nase/__init__.py\nase/atoms.py\nase/calculators/__init__.py\nase/constraints.py\nase/io/bundletrajectory.py\nase/io/pickletrajectory.py\nase/io/trajectory.py\nase/spacegroup/__init__.py\ndoc/ase/ase.rst\ndoc/ase/atom.rst\ndoc/ase/atoms.rst\ndoc/ase/build/build.rst\ndoc/ase/calculators/calculators.rst\ndoc/ase/calculators/cp2k.rst\ndoc/ase/constraints.rst\ndoc/ase/lattice.rst\ndoc/ase/spacegroup/spacegroup.rst\ndoc/conf.py\ndoc/index.rst\ndoc/install.rst\ndoc/releasenotes.rst\ndoc/static/ase.css\ndoc/templates/breadcrumbs.html\ndoc/tutorials/manipulating_atoms.rst\ndoc/tutorials/surface.rst\nThe Atomic Simulation Environment (ASE) is a Python library designed for setting up, manipulating, running, visualizing, and analyzing atomistic simulations. ASE provides a consistent programming interface for working with atoms across different computational chemistry and materials science calculators, making it easier to perform complex simulations regardless of the underlying simulation engine.\nCore Architecture\nASE is built around theAtomsclass, which serves as the primary data structure representing collections of atoms. This central object connects to various components that provide different capabilities.\nCore ASE ComponentsAtoms Class(Primary Data Structure)Calculator InterfacesAnalysis ToolsFile I/O SystemVisualization ToolsDatabase System\nCore ASE Components\nAtoms Class(Primary Data Structure)\nCalculator Interfaces\nAnalysis Tools\nFile I/O System\nVisualization Tools\nDatabase System\nSources:ase/atoms.py28-1006This diagram shows how theAtomsclass serves as the central hub around which other components are organized.\nThe Atoms Class\nTheAtomsclass represents a collection of atoms with associated properties such as positions, atomic numbers, unit cell, and boundary conditions. It can also have a calculator attached for computing energies and forces.\ncontainshasapplies111*0..1*Atoms+positions: array+numbers: array+cell: 3×3 matrix+pbc: array[bool]+calculator: Calculator+constraints: list+get_positions()+set_positions()+get_potential_energy()+get_forces()+get_stress()+get_chemical_symbols()+get_masses()Atom+position: array+number: int+tag: int+mass: float+magmom: float+charge: floatCalculatorConstraint\n+positions: array\n+numbers: array\n+cell: 3×3 matrix\n+pbc: array[bool]\n+calculator: Calculator\n+constraints: list\n+get_positions()\n+set_positions()\n+get_potential_energy()\n+get_forces()\n+get_stress()\n+get_chemical_symbols()\n+get_masses()\n+position: array\n+number: int\n+mass: float\n+magmom: float\n+charge: float\nSources:ase/atoms.py28-106TheAtomsclass provides methods for manipulating atomic structures and querying their properties.\nCalculator Interface\nCalculators perform the actual energy and force calculations on atomic systems. ASE provides a unified interface to many different computational codes, allowing users to switch between calculators with minimal code changes.\n«Interface»Calculator+calculate()+get_potential_energy()+get_forces()+get_stress()FileIOCalculator+command: string+write_input()+read_results()«Various Implementations»ElectronicStructureCalculatorsVASPCASTEPQuantum ESPRESSOGPAW...«Various Implementations»ClassicalCalculatorsEMTLennardJonesLAMMPS...\n«Interface»\n+calculate()\n+get_potential_energy()\n+get_forces()\n+get_stress()\nFileIOCalculator\n+command: string\n+write_input()\n+read_results()\n«Various Implementations»\nElectronicStructureCalculators\nQuantum ESPRESSO\n«Various Implementations»\nClassicalCalculators\nLennardJones\nSources:ase/calculators/__init__.py1-2ase/calculators/calculators.rst5-107ASE connects to over 30 different computational codes, both electronic structure and classical force field methods.\nConstraints System\nConstraints allow you to restrict certain degrees of freedom in your simulation, such as fixing atomic positions, bond lengths, or angles.\nFixConstraint+adjust_positions()+adjust_forces()+index_shuffle()FixAtoms+indices: array+adjust_positions()+adjust_forces()FixBondLengths+pairs: array+bondlengths: array+adjust_positions()+adjust_forces()FixCom+adjust_positions()+adjust_forces()FixInternals+bonds: list+angles: list+dihedrals: list+adjust_positions()+adjust_forces()\nFixConstraint\n+adjust_positions()\n+adjust_forces()\n+index_shuffle()\n+indices: array\n+adjust_positions()\n+adjust_forces()\nFixBondLengths\n+pairs: array\n+bondlengths: array\n+adjust_positions()\n+adjust_forces()\n+adjust_positions()\n+adjust_forces()\nFixInternals\n+bonds: list\n+angles: list\n+dihedrals: list\n+adjust_positions()\n+adjust_forces()\nSources:ase/constraints.py44-67ase/constraints.py100-147ase/constraints.py246-344ase/constraints.py208-236ase/constraints.py507-527\nFile I/O System\nASE provides a comprehensive I/O system for reading and writing atomic structures in various formats, including a native trajectory format for storing sequences of atomic configurations.\nTrajectory SystemFile I/O Systemread() functionwrite() functionIOFormat RegistryFormat-specific modules(xyz, pdb, vasp, etc.)Trajectory classTrajectoryReaderTrajectoryWriterBundleTrajectoryAtoms Object\nTrajectory System\nFile I/O System\nread() function\nwrite() function\nIOFormat Registry\nFormat-specific modules(xyz, pdb, vasp, etc.)\nTrajectory class\nTrajectoryReader\nTrajectoryWriter\nBundleTrajectory\nAtoms Object\nSources:ase/io/trajectory.py18-49ase/io/trajectory.py52-207ase/io/trajectory.py209-285ase/io/bundletrajectory.py46-83\nTypical Workflow\nA typical ASE workflow involves creating atomic structures, attaching calculators, performing simulations, and analyzing the results.\nSingle PointOptimizationMolecular DynamicsTransition PathVibrational AnalysisCreate AtomsSet CalculatorSimulation TypeCalculate Energy/ForcesOptimizerBFGS, LBFGS, etc.MDVerlet, Langevin, etc.NEBNudged Elastic BandVibrationsTrajectoryAnalysis & Visualization\nSingle Point\nOptimization\nMolecular Dynamics\nTransition Path\nVibrational Analysis\nCreate Atoms\nSet Calculator\nSimulation Type\nCalculate Energy/Forces\nOptimizerBFGS, LBFGS, etc.\nMDVerlet, Langevin, etc.\nNEBNudged Elastic Band\nAnalysis & Visualization\nSources:doc/tutorials/surface.rst9-31doc/tutorials/manipulating_atoms.rst32-67\nCreating Atomic Structures\nASE provides various ways to create atomic structures, including building them from scratch, using predefined functions, or reading them from files.\nSpacegroup ModuleLattice ModuleBuild Modulebulk()surface()molecule()nanotube()FaceCenteredCubicBodyCenteredCubicHexagonalClosedPackedDiamondcrystal()get_spacegroup()Atoms constructor\nSpacegroup Module\nLattice Module\nBuild Module\nFaceCenteredCubic\nBodyCenteredCubic\nHexagonalClosedPacked\nget_spacegroup()\nAtoms constructor\nSources:ase/build/build.rst9-43ase/lattice.rst13-91ase/spacegroup/__init__.py1-4\nDatabase System\nASE includes a database system for storing and retrieving atomic configurations and calculation results.\nDatabase Systemconnect() functionDatabase classDB Backends(SQLite, JSON, PostgreSQL)Flask Web InterfaceAtoms Object\nDatabase System\nconnect() function\nDatabase class\nDB Backends(SQLite, JSON, PostgreSQL)\nFlask Web Interface\nAtoms Object\nSources:doc/releasenotes.rst323-349\nInstallation and Requirements\nASE has the following dependencies:\nASEPython >= 2.7NumPy >= 1.9SciPy >= 0.14Matplotlib >= 2.0.0(Optional)tkinter(For GUI, Optional)Flask(For DB web interface, Optional)\nPython >= 2.7\nNumPy >= 1.9\nSciPy >= 0.14\nMatplotlib >= 2.0.0(Optional)\ntkinter(For GUI, Optional)\nFlask(For DB web interface, Optional)\nSources:doc/install.rst10-24\nVersion and Release History\nThe current stable version of ASE is 3.17.0 (with 3.18.0 in development), following a history of regular releases that have added features and improved performance.\n2018November3.17.0June3.16.2March3.16.02017September3.15.0June3.14.1June3.14.0February3.13.02016October3.12.0May3.11.0March3.10.0\"ASE Release Timeline (Recent)\"\nSources:ase/__init__.py14doc/releasenotes.rst16-137doc/conf.py43-44\nASE provides a comprehensive Python framework for atomistic simulations with the following key features:\nA flexibleAtomsclass for representing atomic structures\nInterfaces to many different calculators for computing energies and forces\nTools for setting up, manipulating, and analyzing atomic structures",
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+}
\ No newline at end of file