biotite 1.5.0__cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/interface/rdkit/mol.py

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+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.interface.rdkit"
+__author__ = "Patrick Kunzmann, Simon Mathis"
+__all__ = ["to_mol", "from_mol"]
+
+import copy
+import numbers
+import warnings
+from collections import defaultdict
+import numpy as np
+import rdkit.Chem.AllChem as Chem
+from rdkit.Chem import SanitizeFlags
+from rdkit.rdBase import BlockLogs
+from biotite.interface.version import requires_version
+from biotite.interface.warning import LossyConversionWarning
+from biotite.structure.atoms import AtomArray, AtomArrayStack
+from biotite.structure.bonds import BondList, BondType
+from biotite.structure.error import BadStructureError
+
+_KEKULIZED_TO_AROMATIC_BOND_TYPE = {
+    BondType.SINGLE: BondType.AROMATIC_SINGLE,
+    BondType.DOUBLE: BondType.AROMATIC_DOUBLE,
+    BondType.TRIPLE: BondType.AROMATIC_TRIPLE,
+}
+_BIOTITE_TO_RDKIT_BOND_TYPE = {
+    BondType.ANY: Chem.BondType.UNSPECIFIED,
+    BondType.SINGLE: Chem.BondType.SINGLE,
+    BondType.DOUBLE: Chem.BondType.DOUBLE,
+    BondType.TRIPLE: Chem.BondType.TRIPLE,
+    BondType.QUADRUPLE: Chem.BondType.QUADRUPLE,
+    BondType.AROMATIC_SINGLE: Chem.BondType.AROMATIC,
+    BondType.AROMATIC_DOUBLE: Chem.BondType.AROMATIC,
+    BondType.AROMATIC_TRIPLE: Chem.BondType.AROMATIC,
+    BondType.AROMATIC: Chem.BondType.AROMATIC,
+    # Dative bonds may lead to a KekulizeException and may potentially be deprecated
+    # in the future (https://github.com/rdkit/rdkit/discussions/6995)
+    BondType.COORDINATION: Chem.BondType.SINGLE,
+}
+_RDKIT_TO_BIOTITE_BOND_TYPE = {
+    Chem.BondType.UNSPECIFIED: BondType.ANY,
+    Chem.BondType.SINGLE: BondType.SINGLE,
+    Chem.BondType.DOUBLE: BondType.DOUBLE,
+    Chem.BondType.TRIPLE: BondType.TRIPLE,
+    Chem.BondType.QUADRUPLE: BondType.QUADRUPLE,
+    Chem.BondType.DATIVE: BondType.COORDINATION,
+}
+_STANDARD_ANNOTATIONS = frozenset(
+    {
+        "chain_id",
+        "res_id",
+        "ins_code",
+        "res_name",
+        "hetero",
+        "atom_name",
+        "element",
+        "charge",
+        "b_factor",
+        "occupancy",
+        "altloc_id",
+    }
+)
+
+
+# `Conformer.SetPositions()` was added in RDKit 2024.09.1
+@requires_version("rdkit", ">=2024.09.1")
+def to_mol(
+    atoms,
+    kekulize=False,
+    use_dative_bonds=False,
+    include_extra_annotations=(),
+    explicit_hydrogen=None,
+):
+    """
+    Convert an :class:`.AtomArray` or :class:`.AtomArrayStack` into a
+    :class:`rdkit.Chem.rdchem.Mol`.
+
+    Parameters
+    ----------
+    atoms : AtomArray or AtomArrayStack
+        The molecule to be converted.
+        Must have an associated :class:`BondList`.
+    kekulize : bool, optional
+        If set to true, aromatic bonds are represented by single, double and triple
+        bonds.
+        By default, aromatic bond types are converted to
+        :attr:`rdkit.rdchem.BondType.AROMATIC`.
+    use_dative_bonds : bool, optional
+        If set to true, :attr:`BondType.COORDINATION` bonds are translated to
+        :attr:`rdkit.rdchem.BondType.DATIVE` bonds instead of
+        :attr:`rdkit.rdchem.BondType.SINGLE` bonds.
+        This may have the undesired side effect that a
+        :class:`rdkit.Chem.rdchem.KekulizeException` is raised for some molecules, when
+        the returned :class:`rdkit.Chem.rdchem.Mol` is kekulized.
+    include_extra_annotations : list of str, optional
+        Names of annotation arrays in `atoms` that are added as atom-level property with
+        the same name to the returned :class:`rdkit.Chem.rdchem.Mol`.
+        These properties can be accessed with :meth:`rdkit.Chem.rdchem.Mol.GetProp()`.
+        Note that standard annotations (e.g. ``'chain_id', 'atom_name', 'res_name'``)
+        are always included per default. These standard annotations can be accessed
+        with :meth:`rdkit.Chem.rdchem.Atom.GetPDBResidueInfo()` for each atom in the
+        returned :class:`rdkit.Chem.rdchem.Mol`.
+    explicit_hydrogen : bool, optional
+        If set to true, the conversion process expects that all hydrogen atoms are
+        explicit, i.e. each each hydrogen atom must be part of the :class:`AtomArray`.
+        If set to false, the conversion process treats all hydrogen atoms as implicit.
+        By default, explicit hydrogen atoms are only assumed if any hydrogen atoms are
+        present in `atoms`.
+
+    Returns
+    -------
+    mol : rdkit.Chem.rdchem.Mol
+        The *RDKit* molecule.
+        If the input `atoms` is an :class:`AtomArrayStack`, all models are included
+        as conformers with conformer IDs starting from ``0``.
+
+    Raises
+    ------
+    BadStructureError
+        If the input `atoms` does not have an associated :class:`BondList`.
+        Also raises a :class:`BadStructureError`, if `explicit_hydrogen` is set to
+        ``False`` despite hydrogen atoms being present in `atoms`.
+
+    Notes
+    -----
+    The atoms in the return value are in the same order as the input `atoms`,
+    i.e. indices pointing to the :class:`rdkit.Chem.rdchem.Mol` can be used to point to
+    the same atoms in the :class:`.AtomArray`.
+
+    Examples
+    --------
+
+    >>> from rdkit.Chem import MolToSmiles
+    >>> alanine_atom_array = residue("ALA")
+    >>> mol = to_mol(alanine_atom_array)
+    >>> print(MolToSmiles(mol))
+    [H]OC(=O)C([H])(N([H])[H])C([H])([H])[H]
+
+    By default, ``'atom_name'`` is stored in RDKit's PDBResidueInfo grouping
+    for each atom. We can access it manually as below
+
+    >>> for atom in mol.GetAtoms():
+    ...     print(atom.GetPDBResidueInfo().GetName())
+    N
+    CA
+    C
+    O
+    CB
+    OXT
+    H
+    H2
+    HA
+    HB1
+    HB2
+    HB3
+    HXT
+    """
+    hydrogen_mask = atoms.element == "H"
+    _has_hydrogen = hydrogen_mask.any()
+    if explicit_hydrogen is None:
+        explicit_hydrogen = _has_hydrogen
+    elif explicit_hydrogen:
+        if not _has_hydrogen:
+            warnings.warn(
+                "No hydrogen found, although 'explicit_hydrogen' is 'True'. "
+                "This may lead to radicals after sanitization in RDKit.",
+                UserWarning,
+            )
+    else:
+        if _has_hydrogen:
+            raise BadStructureError(
+                "Hydrogen atoms are present in the input, although 'explicit_hydrogen' "
+                "is set to 'False'"
+            )
+        atoms = atoms[..., ~hydrogen_mask]
+
+    mol = Chem.EditableMol(Chem.Mol())
+
+    has_annot = frozenset(atoms.get_annotation_categories())
+    extra_annot = set(include_extra_annotations) - _STANDARD_ANNOTATIONS
+
+    for i in range(atoms.array_length()):
+        rdkit_atom = Chem.Atom(atoms.element[i].capitalize())
+        if explicit_hydrogen:
+            # ... tell RDKit to not assume any implicit hydrogens
+            rdkit_atom.SetNoImplicit(True)
+        if "charge" in has_annot:
+            rdkit_atom.SetFormalCharge(atoms.charge[i].item())
+
+        # add standard pdb annotations
+        rdkit_atom_res_info = Chem.AtomPDBResidueInfo(
+            atomName=atoms.atom_name[i].item(),
+            residueName=atoms.res_name[i].item(),
+            chainId=atoms.chain_id[i].item(),
+            residueNumber=atoms.res_id[i].item(),
+            isHeteroAtom=atoms.hetero[i].item(),
+            insertionCode=atoms.ins_code[i].item(),
+        )
+        if "occupancy" in has_annot:
+            rdkit_atom_res_info.SetOccupancy(atoms.occupancy[i].item())
+        if "b_factor" in has_annot:
+            rdkit_atom_res_info.SetTempFactor(atoms.b_factor[i].item())
+        if "altloc_id" in has_annot:
+            rdkit_atom_res_info.SetAltLoc(atoms.altloc_id[i].item())
+        rdkit_atom.SetPDBResidueInfo(rdkit_atom_res_info)
+
+        # add extra annotations
+        for annot_name in extra_annot:
+            _set_property(
+                rdkit_atom, annot_name, atoms.get_annotation(annot_name)[i].item()
+            )
+
+        # add atom to molecule
+        mol.AddAtom(rdkit_atom)
+
+    if atoms.bonds is None:
+        raise BadStructureError("An AtomArray with associated BondList is required")
+    if kekulize:
+        bonds = atoms.bonds.copy()
+        bonds.remove_aromaticity()
+    else:
+        bonds = atoms.bonds
+    for atom_i, atom_j, bond_type in bonds.as_array():
+        if not use_dative_bonds and bond_type == BondType.COORDINATION:
+            bond_type = BondType.SINGLE
+        mol.AddBond(
+            atom_i.item(), atom_j.item(), _BIOTITE_TO_RDKIT_BOND_TYPE[bond_type]
+        )
+
+    # Create a proper 'frozen' Mol object
+    mol = mol.GetMol()
+    coord = atoms.coord
+    if coord.ndim == 2:
+        # Handle AtomArray and AtomArrayStack consistently
+        coord = coord[None, :, :]
+    for model_coord in coord:
+        conformer = Chem.Conformer(mol.GetNumAtoms())
+        # RDKit silently expects the data to be in C-contiguous order
+        # Otherwise the coordinates would be completely misassigned
+        # (https://github.com/rdkit/rdkit/issues/8221)
+        conformer.SetPositions(np.ascontiguousarray(model_coord, dtype=np.float64))
+        conformer.Set3D(True)
+        mol.AddConformer(conformer)
+
+    return mol
+
+
+@requires_version("rdkit", ">=2020")
+def from_mol(mol, conformer_id=None, add_hydrogen=None):
+    """
+    Convert a :class:`rdkit.Chem.rdchem.Mol` into an :class:`.AtomArray` or
+    :class:`.AtomArrayStack`.
+
+    Parameters
+    ----------
+    mol : rdkit.Chem.rdchem.Mol
+        The molecule to be converted.
+    conformer_id : int or {"2D", "3D"}, optional
+        The ID of the conformer to be converted.
+        If set to "2D" or "3D", an :class:`AtomArrayStack` with only the 2D or 3D
+        conformer is returned, respectively.
+        By default, an :class:`AtomArrayStack` with all conformers (2D and 3D) is
+        returned.
+    add_hydrogen : bool, optional
+        If set to true, explicit hydrogen atoms are always added.
+        If set to false, explicit hydrogen atoms are never added.
+        By default, explicit hydrogen atoms are only added, if hydrogen atoms are not
+        already present.
+
+    Returns
+    -------
+    atoms : AtomArray or AtomArrayStack
+        The converted atoms.
+        An :class:`AtomArray` is returned if an integer `conformer_id` is given.
+        Otherwise, an :class:`AtomArrayStack` is returned.
+        If the input `mol` does not have a conformer, an `AtomArrayStack` with a
+        single model, where all coordinates are *NaN*, is returned.
+
+    Notes
+    -----
+    The atoms in the return value are in the same order as the input `mol`,
+    i.e. indices pointing to the :class:`rdkit.Chem.rdchem.Mol` can be used to point to
+    the same atoms in the :class:`.AtomArray`.
+
+    All atom-level properties of `mol`
+    (obtainable with :meth:`rdkit.Chem.rdchem.Mol.GetProp()`) are added as annotation
+    array with the same name.
+    ``element`` and ``charge`` are not inferred from properties but from the
+    dedicated attributes in the :class:`rdkit.Chem.rdchem.Mol` object.
+
+    Examples
+    --------
+
+    >>> from rdkit.Chem import MolFromSmiles
+    >>> from rdkit.Chem.rdDistGeom import EmbedMolecule
+    >>> from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule
+    >>> from rdkit.Chem.rdmolops import AddHs
+    >>> mol = MolFromSmiles("C[C@@H](C(=O)O)N")
+    >>> mol = AddHs(mol)
+    >>> # Create a 3D conformer
+    >>> conformer_id = EmbedMolecule(mol)
+    >>> UFFOptimizeMolecule(mol)
+    0
+    >>> alanine_atom_array = from_mol(mol, conformer_id)
+    >>> # RDKit does not assign atom names -> for convenience, do this in Biotite
+    >>> alanine_atom_array.atom_name = create_atom_names(alanine_atom_array)
+    >>> print(alanine_atom_array)
+                0      C1     C        -1.076    1.102   -0.094
+                0      C2     C        -0.363   -0.246   -0.218
+                0      C3     C         1.129   -0.073   -0.109
+                0      O1     O         1.644    0.373    0.952
+                0      O2     O         1.943   -0.405   -1.187
+                0      N1     N        -0.861   -1.175    0.798
+                0      H1     H        -0.724    1.795   -0.888
+                0      H2     H        -2.171    0.960   -0.212
+                0      H3     H        -0.881    1.561    0.899
+                0      H4     H        -0.600   -0.664   -1.221
+                0      H5     H         2.949   -0.295   -1.132
+                0      H6     H        -0.595   -0.830    1.750
+                0      H7     H        -0.395   -2.102    0.660
+    """
+    if add_hydrogen is None:
+        add_hydrogen = not _has_explicit_hydrogen(mol)
+    if add_hydrogen:
+        mol = copy.deepcopy(mol)
+        with BlockLogs():
+            # Avoid modifying the input molecule
+            Chem.SanitizeMol(mol, SanitizeFlags.SANITIZE_ADJUSTHS)
+        mol = Chem.AddHs(mol, addCoords=False, addResidueInfo=False)
+
+    rdkit_atoms = mol.GetAtoms()
+    if rdkit_atoms is None:
+        raise BadStructureError("Could not obtains atoms from Mol")
+
+    if conformer_id in (None, "2D", "3D"):
+        conformers = [conf for conf in mol.GetConformers()]
+        if conformer_id == "2D":
+            conformers = [conf for conf in conformers if not conf.Is3D()]
+        elif conformer_id == "3D":
+            conformers = [conf for conf in conformers if conf.Is3D()]
+        if len(conformers) == 0:
+            # No conformer in 'Mol' that fulfills the criteria
+            # -> create a single model with all coordinates set to NaN
+            atoms = AtomArrayStack(1, len(rdkit_atoms))
+            atoms.coord = np.full((1, len(rdkit_atoms), 3), np.nan)
+        else:
+            atoms = AtomArrayStack(len(conformers), len(rdkit_atoms))
+            for i, conformer in enumerate(conformers):
+                atoms.coord[i] = np.array(conformer.GetPositions(), dtype=np.float32)
+    else:
+        conformer = mol.GetConformer(conformer_id)
+        atoms = AtomArray(len(rdkit_atoms))
+        atoms.coord = np.array(conformer.GetPositions(), dtype=np.float32)
+
+    extra_annotations = defaultdict(
+        # The dtype of each annotation array is inferred later
+        lambda: [None] * atoms.array_length()
+    )
+    atoms.add_annotation("charge", int)
+    atoms.add_annotation("b_factor", float)
+    atoms.add_annotation("occupancy", float)
+    atoms.add_annotation("altloc_id", str)
+
+    for rdkit_atom in rdkit_atoms:
+        _atom_idx = rdkit_atom.GetIdx()
+
+        # ... add standard annotations
+        element = rdkit_atom.GetSymbol().upper().strip()
+        atoms.element[_atom_idx] = element
+        atoms.charge[_atom_idx] = rdkit_atom.GetFormalCharge()
+
+        # ... add PDB related annotations
+        residue_info = rdkit_atom.GetPDBResidueInfo()
+        if residue_info is None:
+            # ... default values for atoms with missing residue information
+            residue_info = Chem.AtomPDBResidueInfo(
+                atomName="",
+                occupancy=0.0,
+                tempFactor=float("nan"),
+                altLoc=".",
+            )
+            if element == "H":
+                # ... attempt inferring residue information from nearest heavy atom
+                #     in case of a hydrogen atom without explicit residue information
+                nearest_heavy_atom = rdkit_atom.GetNeighbors()[0]
+                nearest_heavy_atom_res_info = nearest_heavy_atom.GetPDBResidueInfo()
+                if nearest_heavy_atom_res_info is not None:
+                    residue_info.SetChainId(nearest_heavy_atom_res_info.GetChainId())
+                    residue_info.SetResidueName(
+                        nearest_heavy_atom_res_info.GetResidueName()
+                    )
+                    residue_info.SetResidueNumber(
+                        nearest_heavy_atom_res_info.GetResidueNumber()
+                    )
+                    residue_info.SetInsertionCode(
+                        nearest_heavy_atom_res_info.GetInsertionCode()
+                    )
+                    residue_info.SetIsHeteroAtom(
+                        nearest_heavy_atom_res_info.GetIsHeteroAtom()
+                    )
+                    residue_info.SetAltLoc(nearest_heavy_atom_res_info.GetAltLoc())
+
+        atoms.chain_id[_atom_idx] = residue_info.GetChainId()
+        atoms.res_id[_atom_idx] = residue_info.GetResidueNumber()
+        atoms.ins_code[_atom_idx] = residue_info.GetInsertionCode()
+        atoms.res_name[_atom_idx] = residue_info.GetResidueName()
+        atoms.altloc_id[_atom_idx] = residue_info.GetAltLoc()
+        atoms.hetero[_atom_idx] = residue_info.GetIsHeteroAtom()
+        atoms.b_factor[_atom_idx] = residue_info.GetTempFactor()
+        atoms.occupancy[_atom_idx] = residue_info.GetOccupancy()
+        atoms.atom_name[_atom_idx] = residue_info.GetName().strip()
+
+        # ... add extra annotations
+        for annot, value in rdkit_atom.GetPropsAsDict(includePrivate=False).items():
+            extra_annotations[annot][_atom_idx] = value
+
+    for annot, array in extra_annotations.items():
+        # Handle special case of implicit hydrogen atom flags,
+        # that is set by 'AddHs()' to hydrogen atoms
+        if annot == "isImplicit":
+            annotation_array = np.array(array, dtype=bool)
+        else:
+            annotation_array = np.array(array)
+        atoms.set_annotation(annot, annotation_array)
+
+    rdkit_bonds = list(mol.GetBonds())
+    is_aromatic = np.array(
+        [bond.GetBondType() == Chem.BondType.AROMATIC for bond in rdkit_bonds]
+    )
+    if np.any(is_aromatic):
+        # Determine the kekulized order of aromatic bonds
+        # Copy as 'Kekulize()' modifies the molecule in-place
+        mol = Chem.Mol(mol)
+        try:
+            with BlockLogs():
+                Chem.Kekulize(mol)
+        except Chem.KekulizeException:
+            warnings.warn(
+                "Kekulization failed, "
+                "using 'BondType.AROMATIC' instead for aromatic bonds instead",
+                LossyConversionWarning,
+            )
+        rdkit_bonds = list(mol.GetBonds())
+    bond_array = np.full((len(rdkit_bonds), 3), BondType.ANY, dtype=np.uint32)
+    for i, bond in enumerate(rdkit_bonds):
+        bond_type = _RDKIT_TO_BIOTITE_BOND_TYPE.get(bond.GetBondType())
+        if bond_type is None:
+            warnings.warn(
+                f"Bond type '{bond.GetBondType().name}' cannot be mapped to Biotite, "
+                "using 'BondType.ANY' instead",
+                LossyConversionWarning,
+            )
+            bond_type = BondType.ANY
+        if is_aromatic[i]:
+            try:
+                bond_type = _KEKULIZED_TO_AROMATIC_BOND_TYPE[bond_type]
+            except KeyError:
+                bond_type = BondType.AROMATIC
+                warnings.warn(
+                    "Kekulization returned invalid bond type, "
+                    "using generic 'BondType.AROMATIC' instead",
+                    LossyConversionWarning,
+                )
+        bond_array[i, 0] = bond.GetBeginAtomIdx()
+        bond_array[i, 1] = bond.GetEndAtomIdx()
+        bond_array[i, 2] = bond_type
+    atoms.bonds = BondList(atoms.array_length(), bond_array)
+
+    return atoms
+
+
+def _has_explicit_hydrogen(mol):
+    return mol.GetNumAtoms() > mol.GetNumHeavyAtoms()
+
+
+def _set_property(atom, annot_name, value):
+    if isinstance(value, bool):
+        atom.SetBoolProp(annot_name, value)
+    elif isinstance(value, numbers.Integral):
+        atom.SetIntProp(annot_name, value)
+    elif isinstance(value, numbers.Real):
+        atom.SetDoubleProp(annot_name, value)
+    elif isinstance(value, str):
+        atom.SetProp(annot_name, value)
+    else:
+        raise TypeError(
+            f"Unsupported dtype '{type(value).__name__}' for annotation '{annot_name}'"
+        )

biotite/interface/version.py

@@ -0,0 +1,94 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.interface"
+__author__ = "Patrick Kunzmann"
+__all__ = ["VersionError", "requires_version"]
+
+
+import functools
+import importlib.metadata
+from packaging.specifiers import SpecifierSet
+from packaging.version import Version
+
+# Stores the variant of interface functions
+# compatible with the respective installed package version
+_functions_for_version = {}
+
+
+class VersionError(Exception):
+    """
+    This exception is raised when the installed version of an interfaced package is
+    incompatible with all implemented variants of a function.
+    """
+
+    pass
+
+
+def require_package(package):
+    """
+    Check if the given package is installed and raise an exception if not.
+
+    Parameters
+    ----------
+    package : str
+        The name of the package to be checked.
+
+    Raises
+    ------
+    ImportError
+        If the package is not installed.
+
+    Notes
+    -----
+    It is useful to call this function in the ``__init__.py`` of each ``interface``
+    subpackage, to obtain clear error messages about missing dependencies.
+    """
+    if importlib.util.find_spec(package) is None:
+        raise ImportError(f"'{package}' is not installed")
+
+
+def requires_version(package, version_specifier):
+    """
+    Declare a function variant that is compatible with a specific version range of the
+    interfaced package.
+
+    Parameters
+    ----------
+    package : str
+        The name of the interfaced package.
+    version_specifier : str or list of str
+        The :pep:`440` version specifier(s) for the interfaced package that are
+        compatible with the function.
+        Multiple constraints can be either given as a list of strings or as a single
+        comma-separated string.
+    """
+
+    def decorator(function):
+        @functools.wraps(function)
+        def wrapper(*args, **kwargs):
+            function_for_version = _functions_for_version.get(function.__name__)
+            if function_for_version is None:
+                raise VersionError(
+                    f"No variant of '{function.__name__}()' "
+                    f"found for installed '{package}'=={package_version}'"
+                )
+            return function_for_version(*args, **kwargs)
+
+        if isinstance(version_specifier, str):
+            specifier = SpecifierSet(version_specifier)
+        else:
+            specifier = SpecifierSet.intersection(*version_specifier)
+        try:
+            package_version = Version(importlib.metadata.version(package))
+        except importlib.metadata.PackageNotFoundError:
+            raise ImportError(
+                f"'{function.__name__}()' requires the '{package}' package"
+            )
+        if package_version in specifier:
+            _functions_for_version[function.__name__] = function
+
+        return wrapper
+
+    return decorator

biotite/interface/warning.py

@@ -0,0 +1,19 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.interface"
+__author__ = "Patrick Kunzmann"
+__all__ = ["LossyConversionWarning"]
+
+
+class LossyConversionWarning(UserWarning):
+    """
+    Warning raised, when some information is lost during conversion.
+
+    Note that most conversion functions will be inherently lossy to some extent.
+    This warning is only raised, when the loss of information happens only for
+    some edge case.
+    """
+
+    pass

biotite/sequence/__init__.py

@@ -0,0 +1,84 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+A subpackage for handling sequences.
+
+A :class:`Sequence` can be seen as a succession of symbols.
+The set of symbols, that can occur in a sequence, is defined by an
+:class:`Alphabet`.
+For example, an unambiguous DNA sequence has an :class:`Alphabet`, that
+includes the 4 letters (strings) ``'A'``, ``'C'``, ``'G'`` and ``'T'``.
+But furthermore, an :class:`Alphabet` can also contain any immutable and
+hashable Python object like :class:`int`, :class:`tuple`, etc.
+If a :class:`Sequence` is created with at least a symbol,
+that is not in the given :class:`Alphabet`, an :class:`AlphabetError` is
+raised.
+
+Internally, a :class:`Sequence` is saved as a *NumPy* :class:`ndarray`
+of integer values, where each integer represents a symbol in the
+:class:`Alphabet`.
+For example, ``'A'``, ``'C'``, ``'G'`` and ``'T'`` would be encoded into
+0, 1, 2 and 3, respectively.
+These integer values are called *symbol code*, the encoding of an entire
+sequence of symbols is called *sequence code*.
+
+.. figure:: /static/assets/figures/symbol_encoding.png
+    :alt: Symbol encoding in Biotite
+    :scale: 50%
+
+    Taken from
+    `Kunzmann & Hamacher 2018 <https://doi.org/10.1186/s12859-018-2367-z>`_
+    licensed under `CC BY 4.0 <https://creativecommons.org/licenses/by/4.0/>`_.
+
+The size of the symbol code type in the array is determined by the
+size of the :class:`Alphabet`:
+If the :class:`Alphabet` contains 256 symbols or less, one byte is used
+per array element, between 257 and 65536 symbols, two bytes are used,
+and so on.
+
+This approach has multiple advantages:
+
+    - Wider spectrum of what kind of objects can be represented by
+      :class:`Sequence` objects
+    - Efficient memory usage and faster calculations due to
+      alphabet-tailored *symbol code* type size
+    - C-acceleration due to usage of :class:`ndarray` objects
+    - Most functions applied on :class:`Sequence` objects are
+      indifferent to the actual type of sequence.
+    - Symbol codes are directly indices for substitution matrices in
+      alignments
+    - *k-mers* can be computed fast
+
+The abstract :class:`Sequence` superclass cannot be instantiated
+directly, as it does not define an :class:`Alphabet` by itself.
+Instead usually the concrete subclasses :class:`NucleotideSequence`
+(for DNA and RNA sequences) and :class:`ProteinSequence`
+(for amino acid sequences) are used.
+These classes have defined alphabets and provide additional sequence
+type specific methods.
+The class :class:`GeneralSequence` allows the usage of a custom
+:class:`Alphabet` without the need to subclass :class:`Sequence`.
+
+Additionally, this subpackage provides support for sequence features,
+as used in e.g. GenBank or GFF files.
+A :class:`Feature` stores its key name, its qualifiers and locations.
+An :class:`Annotation` is a group of multiple :class:`Feature` objects
+and offers convenient location based indexing.
+An :class:`AnnotatedSequence` combines an :class:`Annotation` and a
+:class:`Sequence`.
+
+Sequence profiles can be created with the :class:`SequenceProfile` class.
+"""
+
+__name__ = "biotite.sequence"
+__author__ = "Patrick Kunzmann"
+
+from .alphabet import *
+from .annotation import *
+from .codon import *
+from .profile import *
+from .search import *
+from .seqtypes import *
+from .sequence import *