Change to init organisation.

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>

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>

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>

pyproject.toml

@@ -89,5 +89,8 @@ module = [
   "vabene.*",
   "setuptools.*",
   "stk.*",
+  "networkx.*",
+  "openbabel.*",
+  "MDAnalysis.*",
 ]
 ignore_missing_imports = true

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",
+]

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

src/stko/calculators/extractors/__init__.py

@@ -1,3 +0,0 @@
-from .extractor import *  # noqa
-from .xtb_extractor import *  # noqa
-from .orca_extractor import *  # noqa

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):

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):

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__)
 

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__)
 

src/stko/calculators/planarity_calculators/__init__.py

@@ -1 +0,0 @@
-from .planarity_calculators import *  # noqa

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__)
 

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__)
 

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

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):