diff --git a/docs/source/calculators.rst b/docs/source/calculators.rst
index 874e322a..99f51631 100644
--- a/docs/source/calculators.rst
+++ b/docs/source/calculators.rst
@@ -4,8 +4,7 @@ Calculators
 .. toctree::
   :maxdepth: 1
 
-  Calculator <_autosummary/stko.calculators.Calculator>
-
+  Calculator <_autosummary/stko.Calculator>
   MMFFEnergy <_autosummary/stko.MMFFEnergy>
   UFFEnergy <_autosummary/stko.UFFEnergy>
   OpenBabelEnergy <_autosummary/stko.OpenBabelEnergy>
diff --git a/docs/source/molecular.rst b/docs/source/molecular.rst
index 9bc5f934..e17ac55d 100644
--- a/docs/source/molecular.rst
+++ b/docs/source/molecular.rst
@@ -4,15 +4,15 @@ Molecular
 .. toctree::
   :maxdepth: 1
 
-  PositionedAtom <_autosummary/stko.molecular.atoms.PositionedAtom>
-  dummy atom (Du) <_autosummary/stko.molecular.atoms.Du>
-  MDAnalysis <_autosummary/stko.molecular.conversion.MDAnalysis>
-  ZMatrix <_autosummary/stko.molecular.conversion.ZMatrix>
-  MoleculeSplitter <_autosummary/stko.molecular.molecule_modifiers.MoleculeSplitter>
-  MoleculeTransformer <_autosummary/stko.molecular.molecule_modifiers.MoleculeTransformer>
-  Network <_autosummary/stko.molecular.networkx.Network>
-  UnitCell <_autosummary/stko.molecular.periodic.UnitCell>
-  TopologyExtractor <_autosummary/stko.molecular.topology_extractor.TopologyExtractor>
-  TopologyInfo <_autosummary/stko.molecular.topology_extractor.TopologyInfo>
-  Torsion <_autosummary/stko.molecular.torsion.Torsion>
-  TorsionInfo <_autosummary/stko.molecular.TorsionInfo>
+  PositionedAtom <_autosummary/stko.PositionedAtom>
+  dummy atom (Du) <_autosummary/stko.Du>
+  MDAnalysis <_autosummary/stko.MDAnalysis>
+  ZMatrix <_autosummary/stko.ZMatrix>
+  MoleculeSplitter <_autosummary/stko.MoleculeSplitter>
+  MoleculeTransformer <_autosummary/stko.MoleculeTransformer>
+  Network <_autosummary/stko.Network>
+  UnitCell <_autosummary/stko.UnitCell>
+  TopologyExtractor <_autosummary/stko.TopologyExtractor>
+  TopologyInfo <_autosummary/stko.TopologyInfo>
+  Torsion <_autosummary/stko.Torsion>
+  TorsionInfo <_autosummary/stko.TorsionInfo>
diff --git a/docs/source/optimizers.rst b/docs/source/optimizers.rst
index 82859875..c153809c 100644
--- a/docs/source/optimizers.rst
+++ b/docs/source/optimizers.rst
@@ -4,9 +4,9 @@ Optimizers
 .. toctree::
   :maxdepth: 1
 
-  Optimizer <_autosummary/stko.optimizers.Optimizer>
-  OptimizerSequence <_autosummary/stko.optimizers.OptimizerSequence>
-  TryCatchOptimizer <_autosummary/stko.optimizers.TryCatchOptimizer>
+  Optimizer <_autosummary/stko.Optimizer>
+  OptimizerSequence <_autosummary/stko.OptimizerSequence>
+  TryCatchOptimizer <_autosummary/stko.TryCatchOptimizer>
 
   Aligner <_autosummary/stko.Aligner>
   Collapser <_autosummary/stko.Collapser>
diff --git a/pyproject.toml b/pyproject.toml
index abd084a0..db9f684b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -89,5 +89,8 @@ module = [
   "vabene.*",
   "setuptools.*",
   "stk.*",
+  "networkx.*",
+  "openbabel.*",
+  "MDAnalysis.*",
 ]
 ignore_missing_imports = true
\ No newline at end of file
diff --git a/src/stko/__init__.py b/src/stko/__init__.py
index 466ee0c7..a4679330 100644
--- a/src/stko/__init__.py
+++ b/src/stko/__init__.py
@@ -1,4 +1,235 @@
-from .utilities import *  # noqa
-from .optimizers import *  # noqa
-from .calculators import *  # noqa
-from .molecular import *  # noqa
+from stko.calculators.calculators import Calculator
+from stko.calculators.extractors.extractor import Extractor
+from stko.calculators.extractors.orca_extractor import OrcaExtractor
+from stko.calculators.extractors.xtb_extractor import XTBExtractor
+from stko.calculators.open_babel_calculators import (
+    ForceFieldSetupError,
+    OpenBabelEnergy,
+    OpenBabelError,
+)
+from stko.calculators.orca_calculators import OrcaEnergy, OrcaOptimizerError
+from stko.calculators.planarity_calculators.planarity_calculators import (
+    PlanarityCalculator,
+)
+from stko.calculators.rdkit_calculators import MMFFEnergy, UFFEnergy
+from stko.calculators.results.energy_results import EnergyResults
+from stko.calculators.results.orca_results import OrcaResults
+from stko.calculators.results.planarity_results import PlanarityResults
+from stko.calculators.results.results import Results
+from stko.calculators.results.rmsd_results import RmsdResults
+from stko.calculators.results.shape_results import ShapeResults
+from stko.calculators.results.torsion_results import (
+    ConstructedMoleculeTorsionResults,
+    TorsionResults,
+)
+from stko.calculators.results.xtb_results import XTBResults
+from stko.calculators.rmsd_calculators import (
+    DifferentAtomException,
+    DifferentMoleculeException,
+    RmsdCalculator,
+    RmsdCalculatorError,
+    RmsdMappedCalculator,
+)
+from stko.calculators.shape_calculators import ShapeCalculator
+from stko.calculators.torsion_calculators import (
+    ConstructedMoleculeTorsionCalculator,
+    MatchedTorsionCalculator,
+    TorsionCalculator,
+)
+from stko.calculators.xtb_calculators import XTBEnergy
+from stko.molecular.atoms.dummy_atom import Du
+from stko.molecular.atoms.positioned_atom import PositionedAtom
+from stko.molecular.conversion.md_analysis import MDAnalysis
+from stko.molecular.conversion.z_matrix import ConversionError, ZMatrix
+from stko.molecular.molecule_modifiers.molecule_splitter import (
+    MoleculeSplitter,
+)
+from stko.molecular.molecule_modifiers.molecule_transformer import (
+    MoleculeTransformer,
+)
+from stko.molecular.networkx.network import Network
+from stko.molecular.periodic.unitcell import UnitCell
+from stko.molecular.periodic.utilities import (
+    cap_absolute_value,
+    get_approximate_cell_size,
+    get_from_parameters,
+)
+from stko.molecular.topology_extractor.topology_extractor import (
+    TopologyExtractor,
+)
+from stko.molecular.topology_extractor.topology_info import TopologyInfo
+from stko.molecular.torsion.torsion import Torsion
+from stko.molecular.torsion.torsion_info import TorsionInfo
+from stko.optimizers.aligner import (
+    Aligner,
+    AlignmentPotential,
+)
+from stko.optimizers.collapser import (
+    Collapser,
+    CollapserMC,
+)
+from stko.optimizers.gulp import (
+    ExpectedMetal,
+    GulpUFFMDOptimizer,
+    GulpUFFOptimizer,
+    UFFTyperError,
+)
+from stko.optimizers.macromodel import (
+    MacroModel,
+    MacroModelConversionError,
+    MacroModelForceField,
+    MacroModelForceFieldError,
+    MacroModelInputError,
+    MacroModelLewisStructureError,
+    MacroModelMD,
+    MacroModelOptimizationError,
+    MacroModelPathError,
+)
+from stko.optimizers.open_babel import OpenBabel
+from stko.optimizers.optimizers import (
+    Optimizer,
+    OptimizerSequence,
+    TryCatchOptimizer,
+)
+from stko.optimizers.rdkit import ETKDG, MMFF, UFF, MetalOptimizer
+from stko.optimizers.xtb import (
+    XTB,
+    XTBCREST,
+    XTBFF,
+    XTBFFCREST,
+    CRESTNotCompletedError,
+    CRESTNotStartedError,
+    CRESTOptimizerError,
+    CRESTSettingConflictError,
+    XTBConvergenceError,
+    XTBOptimizerError,
+)
+from stko.utilities.utilities import (
+    MAEExtractor,
+    WrapperNotInstalledException,
+    XTBInvalidSolventError,
+    calculate_angle,
+    calculate_dihedral,
+    get_atom_distance,
+    get_atom_maps,
+    get_long_bond_ids,
+    get_metal_atoms,
+    get_metal_bonds,
+    get_plane_normal,
+    get_torsion_info_angles,
+    has_h_atom,
+    has_metal_atom,
+    is_inequivalent_atom,
+    is_valid_xtb_solvent,
+    metal_atomic_numbers,
+    mol_from_mae_file,
+    move_generated_macromodel_files,
+    to_rdkit_mol_without_metals,
+    vector_angle,
+)
+
+__all__ = [
+    "WrapperNotInstalledException",
+    "MAEExtractor",
+    "mol_from_mae_file",
+    "move_generated_macromodel_files",
+    "XTBInvalidSolventError",
+    "is_valid_xtb_solvent",
+    "is_inequivalent_atom",
+    "get_plane_normal",
+    "has_h_atom",
+    "has_metal_atom",
+    "metal_atomic_numbers",
+    "get_metal_atoms",
+    "get_metal_bonds",
+    "to_rdkit_mol_without_metals",
+    "get_atom_distance",
+    "get_long_bond_ids",
+    "calculate_dihedral",
+    "vector_angle",
+    "calculate_angle",
+    "get_torsion_info_angles",
+    "get_atom_maps",
+    "Aligner",
+    "AlignmentPotential",
+    "Collapser",
+    "CollapserMC",
+    "ExpectedMetal",
+    "UFFTyperError",
+    "GulpUFFMDOptimizer",
+    "GulpUFFOptimizer",
+    "MacroModel",
+    "MacroModelConversionError",
+    "MacroModelForceField",
+    "MacroModelForceFieldError",
+    "MacroModelInputError",
+    "MacroModelLewisStructureError",
+    "MacroModelMD",
+    "MacroModelOptimizationError",
+    "MacroModelPathError",
+    "OpenBabel",
+    "Optimizer",
+    "OptimizerSequence",
+    "TryCatchOptimizer",
+    "MMFF",
+    "UFF",
+    "ETKDG",
+    "MetalOptimizer",
+    "XTB",
+    "XTBConvergenceError",
+    "CRESTNotCompletedError",
+    "CRESTNotStartedError",
+    "CRESTOptimizerError",
+    "CRESTSettingConflictError",
+    "XTBCREST",
+    "XTBFF",
+    "XTBFFCREST",
+    "XTBOptimizerError",
+    "PositionedAtom",
+    "Du",
+    "MDAnalysis",
+    "ZMatrix",
+    "ConversionError",
+    "MoleculeSplitter",
+    "MoleculeTransformer",
+    "Network",
+    "UnitCell",
+    "cap_absolute_value",
+    "get_approximate_cell_size",
+    "get_from_parameters",
+    "TopologyExtractor",
+    "TopologyInfo",
+    "Torsion",
+    "TorsionInfo",
+    "XTBEnergy",
+    "Calculator",
+    "TorsionCalculator",
+    "ConstructedMoleculeTorsionCalculator",
+    "MatchedTorsionCalculator",
+    "ShapeCalculator",
+    "RmsdCalculator",
+    "RmsdMappedCalculator",
+    "RmsdCalculatorError",
+    "DifferentAtomException",
+    "DifferentMoleculeException",
+    "MMFFEnergy",
+    "UFFEnergy",
+    "OrcaOptimizerError",
+    "OrcaEnergy",
+    "OpenBabelEnergy",
+    "OpenBabelError",
+    "ForceFieldSetupError",
+    "PlanarityCalculator",
+    "XTBResults",
+    "TorsionResults",
+    "ConstructedMoleculeTorsionResults",
+    "ShapeResults",
+    "RmsdResults",
+    "Results",
+    "PlanarityResults",
+    "OrcaResults",
+    "EnergyResults",
+    "XTBExtractor",
+    "OrcaExtractor",
+    "Extractor",
+]
diff --git a/src/stko/calculators/__init__.py b/src/stko/calculators/__init__.py
index 4ca82966..e69de29b 100644
--- a/src/stko/calculators/__init__.py
+++ b/src/stko/calculators/__init__.py
@@ -1,9 +0,0 @@
-from .calculators import *  # noqa
-from .xtb_calculators import *  # noqa
-from .rdkit_calculators import *  # noqa
-from .torsion_calculators import *  # noqa
-from .shape_calculators import *  # noqa
-from .orca_calculators import *  # noqa
-from .open_babel_calculators import *  # noqa
-from .rmsd_calculators import *  # noqa
-from .planarity_calculators import *  # noqa
diff --git a/src/stko/calculators/extractors/__init__.py b/src/stko/calculators/extractors/__init__.py
index 9b558cc3..e69de29b 100644
--- a/src/stko/calculators/extractors/__init__.py
+++ b/src/stko/calculators/extractors/__init__.py
@@ -1,3 +0,0 @@
-from .extractor import *  # noqa
-from .xtb_extractor import *  # noqa
-from .orca_extractor import *  # noqa
diff --git a/src/stko/calculators/extractors/orca_extractor.py b/src/stko/calculators/extractors/orca_extractor.py
index 964de856..8051f725 100644
--- a/src/stko/calculators/extractors/orca_extractor.py
+++ b/src/stko/calculators/extractors/orca_extractor.py
@@ -10,7 +10,7 @@
 
 import re
 
-from .extractor import Extractor
+from stko.calculators.extractors.extractor import Extractor
 
 
 class OrcaExtractor(Extractor):
diff --git a/src/stko/calculators/extractors/xtb_extractor.py b/src/stko/calculators/extractors/xtb_extractor.py
index 0fb96470..c69e90a8 100644
--- a/src/stko/calculators/extractors/xtb_extractor.py
+++ b/src/stko/calculators/extractors/xtb_extractor.py
@@ -10,7 +10,7 @@
 
 import re
 
-from .extractor import Extractor
+from stko.calculators.extractors.extractor import Extractor
 
 
 class XTBExtractor(Extractor):
diff --git a/src/stko/calculators/open_babel_calculators.py b/src/stko/calculators/open_babel_calculators.py
index 17587a5d..e7aabe42 100644
--- a/src/stko/calculators/open_babel_calculators.py
+++ b/src/stko/calculators/open_babel_calculators.py
@@ -16,9 +16,9 @@
 except ImportError:
     openbabel = None
 
-from ..utilities import WrapperNotInstalledException
-from .calculators import Calculator
-from .results import EnergyResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.energy_results import EnergyResults
+from stko.utilities.utilities import WrapperNotInstalledException
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/calculators/orca_calculators.py b/src/stko/calculators/orca_calculators.py
index cd5cbfed..850ecee9 100644
--- a/src/stko/calculators/orca_calculators.py
+++ b/src/stko/calculators/orca_calculators.py
@@ -15,8 +15,8 @@
 import subprocess as sp
 import uuid
 
-from .calculators import Calculator
-from .results import OrcaResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.orca_results import OrcaResults
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/calculators/planarity_calculators/__init__.py b/src/stko/calculators/planarity_calculators/__init__.py
index caa4108c..e69de29b 100644
--- a/src/stko/calculators/planarity_calculators/__init__.py
+++ b/src/stko/calculators/planarity_calculators/__init__.py
@@ -1 +0,0 @@
-from .planarity_calculators import *  # noqa
diff --git a/src/stko/calculators/planarity_calculators/planarity_calculators.py b/src/stko/calculators/planarity_calculators/planarity_calculators.py
index 2cd8eb04..9abb3ec2 100644
--- a/src/stko/calculators/planarity_calculators/planarity_calculators.py
+++ b/src/stko/calculators/planarity_calculators/planarity_calculators.py
@@ -12,8 +12,8 @@
 
 import numpy as np
 
-from ..calculators import Calculator
-from ..results import PlanarityResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.planarity_results import PlanarityResults
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/calculators/rdkit_calculators.py b/src/stko/calculators/rdkit_calculators.py
index fe8b2568..fe748970 100644
--- a/src/stko/calculators/rdkit_calculators.py
+++ b/src/stko/calculators/rdkit_calculators.py
@@ -13,8 +13,8 @@
 
 from rdkit.Chem import AllChem as rdkit
 
-from .calculators import Calculator
-from .results import EnergyResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.energy_results import EnergyResults
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/calculators/results/__init__.py b/src/stko/calculators/results/__init__.py
index 515794e6..e69de29b 100644
--- a/src/stko/calculators/results/__init__.py
+++ b/src/stko/calculators/results/__init__.py
@@ -1,8 +0,0 @@
-from .energy_results import *  # noqa
-from .orca_results import *  # noqa
-from .rmsd_results import *  # noqa
-from .planarity_results import *  # noqa
-from .results import *  # noqa
-from .shape_results import *  # noqa
-from .torsion_results import *  # noqa
-from .xtb_results import *  # noqa
diff --git a/src/stko/calculators/results/energy_results.py b/src/stko/calculators/results/energy_results.py
index 9a5cc715..d551b3ce 100644
--- a/src/stko/calculators/results/energy_results.py
+++ b/src/stko/calculators/results/energy_results.py
@@ -8,7 +8,7 @@
 
 """
 
-from .results import Results
+from stko.calculators.results.results import Results
 
 
 class EnergyResults(Results):
diff --git a/src/stko/calculators/results/orca_results.py b/src/stko/calculators/results/orca_results.py
index b479cdc8..a74f3796 100644
--- a/src/stko/calculators/results/orca_results.py
+++ b/src/stko/calculators/results/orca_results.py
@@ -8,8 +8,8 @@
 
 """
 
-from ..extractors import OrcaExtractor
-from .results import Results
+from stko.calculators.extractors.orca_extractor import OrcaExtractor
+from stko.calculators.results.results import Results
 
 
 class OrcaResults(Results):
diff --git a/src/stko/calculators/results/planarity_results.py b/src/stko/calculators/results/planarity_results.py
index 3c4a30f7..c6f358a8 100644
--- a/src/stko/calculators/results/planarity_results.py
+++ b/src/stko/calculators/results/planarity_results.py
@@ -8,7 +8,7 @@
 
 """
 
-from .results import Results
+from stko.calculators.results.results import Results
 
 
 class PlanarityResults(Results):
diff --git a/src/stko/calculators/results/rmsd_results.py b/src/stko/calculators/results/rmsd_results.py
index f1048fae..377e84a8 100644
--- a/src/stko/calculators/results/rmsd_results.py
+++ b/src/stko/calculators/results/rmsd_results.py
@@ -8,7 +8,7 @@
 
 """
 
-from .results import Results
+from stko.calculators.results.results import Results
 
 
 class RmsdResults(Results):
diff --git a/src/stko/calculators/results/shape_results.py b/src/stko/calculators/results/shape_results.py
index 13f0e417..28a6400d 100644
--- a/src/stko/calculators/results/shape_results.py
+++ b/src/stko/calculators/results/shape_results.py
@@ -8,7 +8,7 @@
 
 """
 
-from .results import Results
+from stko.calculators.results.results import Results
 
 
 class ShapeResults(Results):
diff --git a/src/stko/calculators/results/torsion_results.py b/src/stko/calculators/results/torsion_results.py
index 53cd027f..51a20923 100644
--- a/src/stko/calculators/results/torsion_results.py
+++ b/src/stko/calculators/results/torsion_results.py
@@ -11,9 +11,10 @@
 
 from collections import defaultdict
 
-from ...molecular.torsion import Torsion, TorsionInfo
-from ...utilities import calculate_dihedral
-from .results import Results
+from stko.calculators.results.results import Results
+from stko.molecular.torsion.torsion import Torsion
+from stko.molecular.torsion.torsion_info import TorsionInfo
+from stko.utilities.utilities import calculate_dihedral
 
 
 class TorsionResults(Results):
diff --git a/src/stko/calculators/results/xtb_results.py b/src/stko/calculators/results/xtb_results.py
index 15853793..dc12ce22 100644
--- a/src/stko/calculators/results/xtb_results.py
+++ b/src/stko/calculators/results/xtb_results.py
@@ -8,8 +8,8 @@
 
 """
 
-from ..extractors import XTBExtractor
-from .results import Results
+from stko.calculators.extractors.xtb_extractor import XTBExtractor
+from stko.calculators.results.results import Results
 
 
 class XTBResults(Results):
diff --git a/src/stko/calculators/rmsd_calculators.py b/src/stko/calculators/rmsd_calculators.py
index d9960d0a..111bde06 100644
--- a/src/stko/calculators/rmsd_calculators.py
+++ b/src/stko/calculators/rmsd_calculators.py
@@ -15,9 +15,9 @@
 import stk
 from scipy.spatial.distance import cdist
 
-from ..utilities import is_inequivalent_atom
-from .calculators import Calculator
-from .results import RmsdResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.rmsd_results import RmsdResults
+from stko.utilities.utilities import is_inequivalent_atom
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/calculators/shape_calculators.py b/src/stko/calculators/shape_calculators.py
index af5de2a6..84090c44 100644
--- a/src/stko/calculators/shape_calculators.py
+++ b/src/stko/calculators/shape_calculators.py
@@ -12,8 +12,8 @@
 
 from rdkit.Chem import Descriptors3D as D3D
 
-from .calculators import Calculator
-from .results import ShapeResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.shape_results import ShapeResults
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/calculators/torsion_calculators.py b/src/stko/calculators/torsion_calculators.py
index f369a2ce..bc1d70e1 100644
--- a/src/stko/calculators/torsion_calculators.py
+++ b/src/stko/calculators/torsion_calculators.py
@@ -13,10 +13,13 @@
 
 from rdkit.Chem import TorsionFingerprints
 
-from ..molecular.torsion import Torsion
-from ..utilities.utilities import get_atom_maps
-from .calculators import Calculator
-from .results import ConstructedMoleculeTorsionResults, TorsionResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.torsion_results import (
+    ConstructedMoleculeTorsionResults,
+    TorsionResults,
+)
+from stko.molecular.torsion.torsion import Torsion
+from stko.utilities.utilities import get_atom_maps
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/calculators/xtb_calculators.py b/src/stko/calculators/xtb_calculators.py
index fe70fba4..b34bcbfe 100644
--- a/src/stko/calculators/xtb_calculators.py
+++ b/src/stko/calculators/xtb_calculators.py
@@ -14,9 +14,12 @@
 import subprocess as sp
 import uuid
 
-from ..utilities import XTBInvalidSolventError, is_valid_xtb_solvent
-from .calculators import Calculator
-from .results import XTBResults
+from stko.calculators.calculators import Calculator
+from stko.calculators.results.xtb_results import XTBResults
+from stko.utilities.utilities import (
+    XTBInvalidSolventError,
+    is_valid_xtb_solvent,
+)
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/molecular/__init__.py b/src/stko/molecular/__init__.py
index b198efbd..e69de29b 100644
--- a/src/stko/molecular/__init__.py
+++ b/src/stko/molecular/__init__.py
@@ -1,7 +0,0 @@
-from .atoms import *  # noqa
-from .conversion import *  # noqa
-from .molecule_modifiers import *  # noqa
-from .networkx import *  # noqa
-from .periodic import *  # noqa
-from .topology_extractor import *  # noqa
-from .torsion import *  # noqa
diff --git a/src/stko/molecular/atoms/__init__.py b/src/stko/molecular/atoms/__init__.py
index 96a9d5f0..e69de29b 100644
--- a/src/stko/molecular/atoms/__init__.py
+++ b/src/stko/molecular/atoms/__init__.py
@@ -1,2 +0,0 @@
-from .dummy_atom import *  # noqa
-from .positioned_atom import *  # noqa
diff --git a/src/stko/molecular/conversion/__init__.py b/src/stko/molecular/conversion/__init__.py
index 46653346..e69de29b 100644
--- a/src/stko/molecular/conversion/__init__.py
+++ b/src/stko/molecular/conversion/__init__.py
@@ -1,2 +0,0 @@
-from .z_matrix import *  # noqa
-from .md_analysis import *  # noqa
diff --git a/src/stko/molecular/conversion/md_analysis.py b/src/stko/molecular/conversion/md_analysis.py
index 9c4eee15..a6718576 100644
--- a/src/stko/molecular/conversion/md_analysis.py
+++ b/src/stko/molecular/conversion/md_analysis.py
@@ -10,7 +10,7 @@
 
 import logging
 
-from ...utilities import WrapperNotInstalledException
+from stko.utilities.utilities import WrapperNotInstalledException
 
 try:
     import MDAnalysis as mda
diff --git a/src/stko/molecular/conversion/z_matrix.py b/src/stko/molecular/conversion/z_matrix.py
index e9d74a9d..cae28649 100644
--- a/src/stko/molecular/conversion/z_matrix.py
+++ b/src/stko/molecular/conversion/z_matrix.py
@@ -10,7 +10,7 @@
 
 import logging
 
-from ...utilities.utilities import (
+from stko.utilities.utilities import (
     calculate_angle,
     calculate_dihedral,
     get_atom_distance,
diff --git a/src/stko/molecular/molecule_modifiers/__init__.py b/src/stko/molecular/molecule_modifiers/__init__.py
index 07efdfbf..e69de29b 100644
--- a/src/stko/molecular/molecule_modifiers/__init__.py
+++ b/src/stko/molecular/molecule_modifiers/__init__.py
@@ -1,2 +0,0 @@
-from .molecule_splitter import *  # noqa
-from .molecule_transformer import *  # noqa
diff --git a/src/stko/molecular/molecule_modifiers/molecule_splitter.py b/src/stko/molecular/molecule_modifiers/molecule_splitter.py
index a1915925..eee20b56 100644
--- a/src/stko/molecular/molecule_modifiers/molecule_splitter.py
+++ b/src/stko/molecular/molecule_modifiers/molecule_splitter.py
@@ -14,7 +14,7 @@
 import stk
 from rdkit.Chem import AllChem as rdkit
 
-from ..atoms import Du
+from stko.molecular.atoms.dummy_atom import Du
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/molecular/molecule_modifiers/molecule_transformer.py b/src/stko/molecular/molecule_modifiers/molecule_transformer.py
index 806c1c27..28f4f7ec 100644
--- a/src/stko/molecular/molecule_modifiers/molecule_transformer.py
+++ b/src/stko/molecular/molecule_modifiers/molecule_transformer.py
@@ -13,7 +13,7 @@
 import stk
 from rdkit.Chem import AllChem as rdkit
 
-from ..atoms import Du
+from stko.molecular.atoms.dummy_atom import Du
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/molecular/networkx/__init__.py b/src/stko/molecular/networkx/__init__.py
index 27780268..e69de29b 100644
--- a/src/stko/molecular/networkx/__init__.py
+++ b/src/stko/molecular/networkx/__init__.py
@@ -1 +0,0 @@
-from .network import *  # noqa
diff --git a/src/stko/molecular/networkx/network.py b/src/stko/molecular/networkx/network.py
index 485959ff..f192f75b 100644
--- a/src/stko/molecular/networkx/network.py
+++ b/src/stko/molecular/networkx/network.py
@@ -12,7 +12,7 @@
 
 import networkx as nx
 
-from ..atoms import PositionedAtom
+from stko.molecular.atoms.positioned_atom import PositionedAtom
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/molecular/periodic/__init__.py b/src/stko/molecular/periodic/__init__.py
index b5accac5..e69de29b 100644
--- a/src/stko/molecular/periodic/__init__.py
+++ b/src/stko/molecular/periodic/__init__.py
@@ -1,2 +0,0 @@
-from .unitcell import *  # noqa
-from .utilities import *  # noqa
diff --git a/src/stko/molecular/periodic/unitcell.py b/src/stko/molecular/periodic/unitcell.py
index 527b7b78..493fcae2 100644
--- a/src/stko/molecular/periodic/unitcell.py
+++ b/src/stko/molecular/periodic/unitcell.py
@@ -11,7 +11,7 @@
 import numpy as np
 from stk import PeriodicInfo
 
-from .utilities import get_from_parameters
+from stko.molecular.periodic.utilities import get_from_parameters
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/molecular/topology_extractor/__init__.py b/src/stko/molecular/topology_extractor/__init__.py
index ebc12431..e69de29b 100644
--- a/src/stko/molecular/topology_extractor/__init__.py
+++ b/src/stko/molecular/topology_extractor/__init__.py
@@ -1,2 +0,0 @@
-from .topology_extractor import *  # noqa
-from .topology_info import *  # noqa
diff --git a/src/stko/molecular/topology_extractor/topology_extractor.py b/src/stko/molecular/topology_extractor/topology_extractor.py
index ff471a58..f69dbd9a 100644
--- a/src/stko/molecular/topology_extractor/topology_extractor.py
+++ b/src/stko/molecular/topology_extractor/topology_extractor.py
@@ -10,8 +10,8 @@
 
 import logging
 
-from ..networkx import Network
-from .topology_info import TopologyInfo
+from stko.molecular.networkx.network import Network
+from stko.molecular.topology_extractor.topology_info import TopologyInfo
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/molecular/torsion/__init__.py b/src/stko/molecular/torsion/__init__.py
index f329e570..e69de29b 100644
--- a/src/stko/molecular/torsion/__init__.py
+++ b/src/stko/molecular/torsion/__init__.py
@@ -1,2 +0,0 @@
-from .torsion import *  # noqa
-from .torsion_info import *  # noqa
diff --git a/src/stko/optimizers/__init__.py b/src/stko/optimizers/__init__.py
index c704cdef..e69de29b 100644
--- a/src/stko/optimizers/__init__.py
+++ b/src/stko/optimizers/__init__.py
@@ -1,8 +0,0 @@
-from .aligner import *  # noqa
-from .optimizers import *  # noqa
-from .rdkit import *  # noqa
-from .gulp import *  # noqa
-from .collapser import *  # noqa
-from .xtb import *  # noqa
-from .macromodel import *  # noqa
-from .open_babel import *  # noqa
diff --git a/src/stko/optimizers/aligner.py b/src/stko/optimizers/aligner.py
index 9891cb77..2958a7ac 100644
--- a/src/stko/optimizers/aligner.py
+++ b/src/stko/optimizers/aligner.py
@@ -15,8 +15,8 @@
 import spindry as spd
 from scipy.spatial.distance import cdist
 
-from ..calculators import RmsdMappedCalculator
-from .optimizers import Optimizer
+from stko.calculators.rmsd_calculators import RmsdMappedCalculator
+from stko.optimizers.optimizers import Optimizer
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/optimizers/collapser.py b/src/stko/optimizers/collapser.py
index ba2cb11b..2cc94ca5 100644
--- a/src/stko/optimizers/collapser.py
+++ b/src/stko/optimizers/collapser.py
@@ -22,8 +22,8 @@
 from scipy.spatial.distance import pdist
 from stk import PdbWriter
 
-from ..utilities import get_atom_distance
-from .optimizers import Optimizer
+from stko.optimizers.optimizers import Optimizer
+from stko.utilities.utilities import get_atom_distance
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/optimizers/gulp.py b/src/stko/optimizers/gulp.py
index 31ce40d5..0b1ec5dc 100644
--- a/src/stko/optimizers/gulp.py
+++ b/src/stko/optimizers/gulp.py
@@ -113,14 +113,14 @@
 
 from rdkit.Chem import AllChem as rdkit
 
-from ..utilities import (
+from stko.optimizers.optimizers import Optimizer
+from stko.utilities.utilities import (
     get_metal_atoms,
     get_metal_bonds,
     has_h_atom,
     has_metal_atom,
     to_rdkit_mol_without_metals,
 )
-from .optimizers import Optimizer
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/optimizers/macromodel.py b/src/stko/optimizers/macromodel.py
index 32b23ef4..2fccd49d 100644
--- a/src/stko/optimizers/macromodel.py
+++ b/src/stko/optimizers/macromodel.py
@@ -16,12 +16,12 @@
 
 import rdkit.Chem.AllChem as rdkit
 
-from ..utilities import (
+from stko.optimizers.optimizers import Optimizer
+from stko.utilities.utilities import (
     MAEExtractor,
     mol_from_mae_file,
     move_generated_macromodel_files,
 )
-from .optimizers import Optimizer
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/optimizers/open_babel.py b/src/stko/optimizers/open_babel.py
index 37102990..4aa1ed28 100644
--- a/src/stko/optimizers/open_babel.py
+++ b/src/stko/optimizers/open_babel.py
@@ -18,8 +18,8 @@
 except ImportError:
     openbabel = None
 
-from ..utilities import WrapperNotInstalledException
-from .optimizers import Optimizer
+from stko.optimizers.optimizers import Optimizer
+from stko.utilities.utilities import WrapperNotInstalledException
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/optimizers/rdkit.py b/src/stko/optimizers/rdkit.py
index 5f7de244..93ca0247 100644
--- a/src/stko/optimizers/rdkit.py
+++ b/src/stko/optimizers/rdkit.py
@@ -35,13 +35,13 @@
 import numpy as np
 import rdkit.Chem.AllChem as rdkit
 
-from ..utilities import (
+from stko.optimizers.optimizers import Optimizer
+from stko.utilities.utilities import (
     get_metal_atoms,
     get_metal_bonds,
     to_rdkit_mol_without_metals,
     vector_angle,
 )
-from .optimizers import Optimizer
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/optimizers/xtb.py b/src/stko/optimizers/xtb.py
index f7cd19b1..5d7075bc 100644
--- a/src/stko/optimizers/xtb.py
+++ b/src/stko/optimizers/xtb.py
@@ -17,9 +17,12 @@
 import subprocess as sp
 import uuid
 
-from ..calculators.extractors import XTBExtractor
-from ..utilities import XTBInvalidSolventError, is_valid_xtb_solvent
-from .optimizers import Optimizer
+from stko.calculators.extractors.xtb_extractor import XTBExtractor
+from stko.optimizers.optimizers import Optimizer
+from stko.utilities.utilities import (
+    XTBInvalidSolventError,
+    is_valid_xtb_solvent,
+)
 
 logger = logging.getLogger(__name__)
 
diff --git a/src/stko/py.typed b/src/stko/py.typed
new file mode 100644
index 00000000..e69de29b
diff --git a/src/stko/utilities/__init__.py b/src/stko/utilities/__init__.py
index b7820125..e69de29b 100644
--- a/src/stko/utilities/__init__.py
+++ b/src/stko/utilities/__init__.py
@@ -1 +0,0 @@
-from .utilities import *  # noqa