biotite 1.5.0__cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/structure/io/pdbqt/file.py

@@ -0,0 +1,688 @@
+# 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.structure.io.pdbqt"
+__author__ = "Patrick Kunzmann, Daniel Bauer"
+__all__ = ["PDBQTFile"]
+
+import warnings
+import numpy as np
+from biotite.file import InvalidFileError, TextFile
+from biotite.structure.atoms import AtomArray, AtomArrayStack
+from biotite.structure.bonds import (
+    BondList,
+    BondType,
+    find_connected,
+    find_rotatable_bonds,
+)
+from biotite.structure.charges import partial_charges
+from biotite.structure.error import BadStructureError
+
+PARAMETRIZED_ELEMENTS = [
+    "H",
+    "C",
+    "N",
+    "O",
+    "P",
+    "S",
+    "F",
+    "Cl",
+    "Br",
+    "I",
+    "Mg",
+    "Ca",
+    "Mn",
+    "Fe",
+    "Zn",
+]
+
+
+class PDBQTFile(TextFile):
+    """
+    This class represents an *AutoDock* PDBQT file.
+
+    This class only provides rudimentary support for reading/writing
+    the pure atom information.
+
+    EXPERIMENTAL: Future API changes are probable.
+
+    Examples
+    --------
+
+    Write biotin as flexible ligand into a PDBQT file:
+
+    >>> import os.path
+    >>> ligand = residue("BTN")
+    >>> file = PDBQTFile()
+    >>> mask = file.set_structure(ligand, rotatable_bonds="all")
+    >>> # Print removed nonpolar hydrogen atoms
+    >>> print(ligand[~mask])
+    HET         0  BTN H101   H         3.745    1.171    0.974
+    HET         0  BTN H102   H         4.071    1.343   -0.767
+    HET         0  BTN H91    H         2.802   -0.740   -1.211
+    HET         0  BTN H92    H         2.476   -0.912    0.530
+    HET         0  BTN H81    H         1.289    1.265    0.523
+    HET         0  BTN H82    H         1.616    1.437   -1.218
+    HET         0  BTN H71    H         0.346   -0.646   -1.662
+    HET         0  BTN H72    H         0.020   -0.818    0.079
+    HET         0  BTN H2     H        -0.838    1.576   -1.627
+    HET         0  BTN H61    H        -3.797    1.837    1.286
+    HET         0  BTN H62    H        -3.367    2.738   -0.205
+    HET         0  BTN H5     H        -4.307    0.812   -1.205
+    HET         0  BTN H4     H        -2.451   -0.038   -2.252
+    >>> print(file)
+    ROOT
+    HETATM    1 C11  BTN     0       5.089  -0.280   0.173  1.00  0.00     0.258 C
+    HETATM    2 O11  BTN     0       4.956  -1.473   0.030  1.00  0.00    -0.264 OA
+    ENDROOT
+    BRANCH   1   3
+    HETATM    3 O12  BTN     0       6.299   0.233   0.444  1.00  0.00    -0.331 OA
+    HETATM   17 HO2  BTN     0       7.034  -0.391   0.517  1.00  0.00     0.221 HD
+    ENDBRANCH   1   3
+    BRANCH   1   4
+    HETATM    4 C10  BTN     0       3.896   0.631   0.039  1.00  0.00     0.105 C
+    BRANCH   4   5
+    HETATM    5 C9   BTN     0       2.651  -0.200  -0.276  1.00  0.00     0.010 C
+    BRANCH   5   6
+    HETATM    6 C8   BTN     0       1.440   0.725  -0.412  1.00  0.00     0.002 C
+    BRANCH   6   7
+    HETATM    7 C7   BTN     0       0.196  -0.106  -0.727  1.00  0.00     0.016 C
+    BRANCH   7   8
+    HETATM    8 C2   BTN     0      -1.015   0.819  -0.863  1.00  0.00     0.065 C
+    HETATM    9 S1   BTN     0      -1.419   1.604   0.751  1.00  0.00    -0.154 SA
+    HETATM   10 C6   BTN     0      -3.205   1.827   0.371  1.00  0.00     0.090 C
+    HETATM   11 C5   BTN     0      -3.530   0.581  -0.476  1.00  0.00     0.091 C
+    HETATM   12 N1   BTN     0      -3.970  -0.507   0.412  1.00  0.00    -0.239 NA
+    HETATM   13 C3   BTN     0      -3.141  -1.549   0.271  1.00  0.00     0.272 C
+    HETATM   14 O3   BTN     0      -3.271  -2.589   0.888  1.00  0.00    -0.259 OA
+    HETATM   15 N2   BTN     0      -2.154  -1.343  -0.612  1.00  0.00    -0.239 NA
+    HETATM   16 C4   BTN     0      -2.289   0.010  -1.175  1.00  0.00     0.093 C
+    HETATM   18 HN1  BTN     0      -4.738  -0.474   1.004  1.00  0.00     0.132 HD
+    HETATM   19 HN2  BTN     0      -1.462  -1.982  -0.843  1.00  0.00     0.132 HD
+    ENDBRANCH   7   8
+    ENDBRANCH   6   7
+    ENDBRANCH   5   6
+    ENDBRANCH   4   5
+    ENDBRANCH   1   4
+    TORSDOF 6
+    >>> file.write(os.path.join(path_to_directory, "1l2y_mod.pdb"))
+    """
+
+    def get_remarks(self, model=None):
+        """
+        Get the content of ``REMARKS`` lines.
+
+        Parameters
+        ----------
+        model : int, optional
+            If this parameter is given, the function will return a
+            string from the remarks corresponding to the given
+            model number (starting at 1).
+            Negative values are used to index models starting from the
+            last model insted of the first model.
+            If this parameter is omitted, a list of strings
+            containing all models will be returned, even if the
+            structure contains only one model.
+
+        Returns
+        -------
+        lines : str or list of str
+            The content of ``REMARKS`` lines, without the leading
+            ``'REMARKS'``.
+        """
+        # Line indices where a new model starts
+        model_start_i = np.array(
+            [i for i in range(len(self.lines)) if self.lines[i].startswith(("MODEL"))],
+            dtype=int,
+        )
+        # Line indices with ATOM or HETATM records
+        remark_line_i = np.array(
+            [i for i in range(len(self.lines)) if self.lines[i].startswith("REMARK")],
+            dtype=int,
+        )
+        # Structures containing only one model may omit MODEL record
+        # In these cases model starting index is set to 0
+        if len(model_start_i) == 0:
+            model_start_i = np.array([0])
+
+        if model is None:
+            # Add exclusive end of file
+            model_start_i = np.concatenate((model_start_i, [len(self.lines)]))
+            remarks = []
+            for i in range(len(model_start_i) - 1):
+                start = model_start_i[i]
+                stop = model_start_i[i + 1]
+                model_remark_line_i = remark_line_i[
+                    (remark_line_i >= start) & (remark_line_i < stop)
+                ]
+                remarks.append(
+                    "\n".join([self.lines[i][7:] for i in model_remark_line_i])
+                )
+            return remarks
+
+        else:
+            last_model = len(model_start_i)
+            if model == 0:
+                raise ValueError("The model index must not be 0")
+            # Negative models mean index starting from last model
+            model = last_model + model + 1 if model < 0 else model
+
+            if model < last_model:
+                line_filter = (remark_line_i >= model_start_i[model - 1]) & (
+                    remark_line_i < model_start_i[model]
+                )
+            elif model == last_model:
+                line_filter = remark_line_i >= model_start_i[model - 1]
+            else:
+                raise ValueError(
+                    f"The file has {last_model} models, "
+                    f"the given model {model} does not exist"
+                )
+            remark_line_i = remark_line_i[line_filter]
+
+            # Do not include 'REMARK ' itself -> begin from pos 8
+            return "\n".join([self.lines[i][7:] for i in remark_line_i])
+
+    def get_structure(self, model=None):
+        """
+        Get an :class:`AtomArray` or :class:`AtomArrayStack` from the
+        PDBQT file.
+
+        Parameters
+        ----------
+        model : int, optional
+            If this parameter is given, the function will return an
+            :class:`AtomArray` from the atoms corresponding to the given
+            model number (starting at 1).
+            Negative values are used to index models starting from the
+            last model insted of the first model.
+            If this parameter is omitted, an :class:`AtomArrayStack`
+            containing all models will be returned, even if the
+            structure contains only one model.
+
+        Returns
+        -------
+        array : AtomArray or AtomArrayStack
+            The return type depends on the `model` parameter.
+        """
+        # Line indices where a new model starts
+        model_start_i = np.array(
+            [i for i in range(len(self.lines)) if self.lines[i].startswith(("MODEL"))],
+            dtype=int,
+        )
+        # Line indices with ATOM or HETATM records
+        atom_line_i = np.array(
+            [
+                i
+                for i in range(len(self.lines))
+                if self.lines[i].startswith(("ATOM", "HETATM"))
+            ],
+            dtype=int,
+        )
+        # Structures containing only one model may omit MODEL record
+        # In these cases model starting index is set to 0
+        if len(model_start_i) == 0:
+            model_start_i = np.array([0])
+
+        if model is None:
+            depth = len(model_start_i)
+            length = self._get_model_length(model_start_i, atom_line_i)
+            array = AtomArrayStack(depth, length)
+            # Line indices for annotation determination
+            # Annotation is determined from model 1,
+            # therefore from ATOM records before second MODEL record
+            if len(model_start_i) == 1:
+                annot_i = atom_line_i
+            else:
+                annot_i = atom_line_i[atom_line_i < model_start_i[1]]
+            # Line indices for coordinate determination
+            coord_i = atom_line_i
+
+        else:
+            last_model = len(model_start_i)
+            if model == 0:
+                raise ValueError("The model index must not be 0")
+            # Negative models mean index starting from last model
+            model = last_model + model + 1 if model < 0 else model
+
+            if model < last_model:
+                line_filter = (atom_line_i >= model_start_i[model - 1]) & (
+                    atom_line_i < model_start_i[model]
+                )
+            elif model == last_model:
+                line_filter = atom_line_i >= model_start_i[model - 1]
+            else:
+                raise ValueError(
+                    f"The file has {last_model} models, "
+                    f"the given model {model} does not exist"
+                )
+            annot_i = coord_i = atom_line_i[line_filter]
+            array = AtomArray(len(coord_i))
+
+        # Save atom IDs for later sorting into the original atom order
+        atom_id = np.zeros(array.array_length(), int)
+
+        # Create annotation arrays
+        chain_id = np.zeros(array.array_length(), array.chain_id.dtype)
+        res_id = np.zeros(array.array_length(), array.res_id.dtype)
+        ins_code = np.zeros(array.array_length(), array.ins_code.dtype)
+        res_name = np.zeros(array.array_length(), array.res_name.dtype)
+        hetero = np.zeros(array.array_length(), array.hetero.dtype)
+        atom_name = np.zeros(array.array_length(), array.atom_name.dtype)
+        element = np.zeros(array.array_length(), array.element.dtype)
+
+        # Fill annotation array
+        # i is index in array, line_i is line index
+        for i, line_i in enumerate(annot_i):
+            line = self.lines[line_i]
+
+            atom_id[i] = int(line[6:11])
+            chain_id[i] = line[21].strip()
+            res_id[i] = int(line[22:26])
+            ins_code[i] = line[26].strip()
+            res_name[i] = line[17:20].strip()
+            hetero[i] = False if line[0:4] == "ATOM" else True
+            atom_name[i] = line[12:16].strip()
+            element[i] = line[76:78].strip()
+
+        # Add annotation arrays to atom array (stack)
+        array.chain_id = chain_id
+        array.res_id = res_id
+        array.ins_code = ins_code
+        array.res_name = res_name
+        array.hetero = hetero
+        array.atom_name = atom_name
+        array.element = element
+
+        # Fill in coordinates
+        if isinstance(array, AtomArray):
+            for i, line_i in enumerate(coord_i):
+                line = self.lines[line_i]
+                array.coord[i, 0] = float(line[30:38])
+                array.coord[i, 1] = float(line[38:46])
+                array.coord[i, 2] = float(line[46:54])
+
+        elif isinstance(array, AtomArrayStack):
+            m = 0
+            i = 0
+            for line_i in atom_line_i:
+                if m < len(model_start_i) - 1 and line_i > model_start_i[m + 1]:
+                    m += 1
+                    i = 0
+                line = self.lines[line_i]
+                array.coord[m, i, 0] = float(line[30:38])
+                array.coord[m, i, 1] = float(line[38:46])
+                array.coord[m, i, 2] = float(line[46:54])
+                i += 1
+
+        # Sort into the original atom order
+        array = array[..., np.argsort(atom_id)]
+
+        return array
+
+    def set_structure(
+        self,
+        atoms,
+        charges=None,
+        atom_types=None,
+        rotatable_bonds=None,
+        root=None,
+        include_torsdof=True,
+    ):
+        """
+        Write an :class:`AtomArray` into the PDBQT file.
+
+        Parameters
+        ----------
+        atoms : AtomArray, shape=(n,)
+            The atoms to be written into this file.
+            Must have an associated :class:`BondList`.
+        charges : ndarray, shape=(n,), dtype=float, optional
+            Partial charges for each atom in `atoms`.
+            By default, the charges are calculated using the PEOE method
+            (:func:`partial_charges()`).
+        atom_types : ndarray, shape=(n,), dtype="U1", optional
+            Custom *AutoDock* atom types for each atom in `atoms`.
+        rotatable_bonds : None or 'rigid' or 'all' or BondList, optional
+            This parameter describes, how rotatable bonds are handled,
+            with respect to ``ROOT``, ``BRANCH`` and ``ENDBRANCH``
+            lines.
+
+                - ``None`` - The molecule is handled as rigid receptor:
+                  No ``ROOT``, ``BRANCH`` and ``ENDBRANCH`` lines will
+                  be written.
+                - ``'rigid'`` - The molecule is handled as rigid ligand:
+                  Only a ``ROOT`` line will be written.
+                - ``'all'`` - The molecule is handled as flexible
+                  ligand:
+                  A ``ROOT`` line will be written and all rotatable
+                  bonds are included using ``BRANCH`` and ``ENDBRANCH``
+                  lines.
+                - :class:`BondList` - The molecule is handled as
+                  flexible ligand:
+                  A ``ROOT`` line will be written and all bonds in the
+                  given :class:`BondList` are considered flexible via
+                  ``BRANCH`` and ``ENDBRANCH`` lines.
+
+        root : int, optional
+            Specifies the index of the atom following the ``ROOT`` line.
+            Setting the root atom is useful for specifying the *anchor*
+            in flexible side chains.
+            This parameter has no effect, if `rotatable_bonds` is
+            ``None``.
+            By default, the first atom is also the root atom.
+        include_torsdof : bool, optional
+            By default, a ``TORSDOF`` (torsional degrees of freedom)
+            record is written at the end of the file.
+            By setting this parameter to false, the record is omitted.
+
+        Returns
+        -------
+        mask : ndarray, shape=(n,), dtype=bool
+            A boolean mask, that is ``False`` for each atom of the input
+            ``atoms``, that was removed due to being a nonpolar
+            hydrogen.
+        """
+        # Check if AtomArray is suitable for PDBQT
+        max_atoms, max_residues = 99999, 9999
+        if atoms.array_length() > max_atoms:
+            warnings.warn(f"More then {max_atoms:,} atoms per model")
+        if (atoms.res_id > max_residues).any():
+            warnings.warn(f"Residue IDs exceed {max_residues:,}")
+        if np.isnan(atoms.coord).any():
+            raise BadStructureError("Coordinates contain 'NaN' values")
+        if any([len(name) > 1 for name in atoms.chain_id]):
+            raise BadStructureError("Some chain IDs exceed 1 character")
+        if any([len(name) > 3 for name in atoms.res_name]):
+            raise BadStructureError("Some residue names exceed 3 characters")
+        if any([len(name) > 4 for name in atoms.atom_name]):
+            raise BadStructureError("Some atom names exceed 4 characters")
+
+        if charges is None:
+            charges = partial_charges(atoms)
+            charges[np.isnan(charges)] = 0
+        else:
+            if np.isnan(charges).any():
+                raise ValueError("Input charges contain NaN values")
+
+        # Get AutoDock atom types and remove nonpolar hydrogen atoms
+        atoms, charges, types, mask = convert_atoms(atoms, charges)
+        # Overwrite calculated atom types with input atom types
+        if atom_types is not None:
+            types = atom_types[mask]
+
+        if rotatable_bonds is None:
+            # No rotatable bonds -> the BondList contains no bonds
+            rotatable_bonds = BondList(atoms.bonds.get_atom_count())
+            use_root = False
+        elif rotatable_bonds == "rigid":
+            rotatable_bonds = BondList(atoms.bonds.get_atom_count())
+            use_root = True
+        elif rotatable_bonds == "all":
+            rotatable_bonds = find_rotatable_bonds(atoms.bonds)
+            use_root = True
+        else:
+            if rotatable_bonds.ndim != 2 or rotatable_bonds.shape[1] != 2:
+                raise ValueError("An (nx2) array is expected for rotatable bonds")
+            rotatable_bonds = BondList(len(mask), np.asarray(rotatable_bonds))[mask]
+            use_root = True
+
+        if root is None:
+            root_index = 0
+        else:
+            # Find new index of root atom, since the index might have
+            # been shifted due to removed atoms
+            original_indices = np.arange(len(mask))
+            new_indices = original_indices[mask]
+            try:
+                root_index = np.where(new_indices == root)[0][0]
+            except IndexError:
+                raise ValueError(
+                    "The given root atom index points to an nonpolar hydrogen "
+                    "atom, that has been removed"
+                )
+            # Add bonds of the rigid root to rotatable bonds,
+            # as they probably have been filtered out,
+            # as the root is probably a terminal atom
+            for atom, bond_type in zip(*atoms.bonds.get_bonds(root_index)):
+                rotatable_bonds.add_bond(root_index, atom, bond_type)
+
+        # Break rotatable bonds
+        # for simple branch determination in '_write_atoms()'
+        atoms.bonds.remove_bonds(rotatable_bonds)
+
+        hetero = ["HETATM" if e else "ATOM" for e in atoms.hetero]
+        if "atom_id" in atoms.get_annotation_categories():
+            atom_id = atoms.atom_id
+        else:
+            atom_id = np.arange(1, atoms.array_length() + 1)
+        occupancy = np.ones(atoms.array_length())
+        b_factor = np.zeros(atoms.array_length())
+
+        # Convert rotatable bonds into array for easier handling
+        # The bond type is irrelevant from this point on
+        rotatable_bonds = rotatable_bonds.as_array()[:, :2]
+
+        self.lines = []
+        self._write_atoms(
+            atoms,
+            charges,
+            types,
+            atom_id,
+            hetero,
+            occupancy,
+            b_factor,
+            root_index,
+            rotatable_bonds,
+            np.zeros(len(rotatable_bonds), dtype=bool),
+            use_root,
+        )
+        if include_torsdof:
+            self.lines.append(f"TORSDOF {len(rotatable_bonds)}")
+
+        return mask
+
+    def _write_atoms(
+        self,
+        atoms,
+        charges,
+        types,
+        atom_id,
+        hetero,
+        occupancy,
+        b_factor,
+        root_atom,
+        rotatable_bonds,
+        visited_rotatable_bonds,
+        is_root,
+    ):
+        if len(rotatable_bonds) != 0:
+            # Get the indices to atoms of this branch, i.e. a group of
+            # atoms that are connected by non-rotatable bonds
+            # Use 'find_connected()', since rotatable bonds were removed
+            # from the BondList before
+            this_branch_indices = find_connected(atoms.bonds, root_atom)
+            # The root atom of the branch, i.e. the atom connected by
+            # the rotatable bond should always be listed first
+            # -> Remove root atom and insert it at the beginning
+            this_branch_indices = np.insert(
+                this_branch_indices[this_branch_indices != root_atom], 0, root_atom
+            )
+        else:
+            # No rotatable bonds
+            # -> all atom are in root i.e. this branch
+            this_branch_indices = np.arange(atoms.array_length())
+
+        if is_root:
+            self.lines.append("ROOT")
+        for i in this_branch_indices:
+            self.lines.append(
+                f"{hetero[i]:6}"
+                f"{atom_id[i]:>5d} "
+                f"{atoms.atom_name[i]:4} "
+                f"{atoms.res_name[i]:3} "
+                f"{atoms.chain_id[i]:1}"
+                f"{atoms.res_id[i]:>4d}"
+                f"{atoms.ins_code[i]:1}   "
+                f"{atoms.coord[i, 0]:>8.3f}"
+                f"{atoms.coord[i, 1]:>8.3f}"
+                f"{atoms.coord[i, 2]:>8.3f}"
+                f"{occupancy[i]:>6.2f}"
+                f"{b_factor[i]:>6.2f}    "
+                f"{charges[i]:>6.3f} "
+                f"{types[i]:2}"
+            )
+        if is_root:
+            self.lines.append("ENDROOT")
+
+        if len(rotatable_bonds) == 0:
+            # No rotatable bonds -> no branching
+            return
+
+        for k, (i, j) in enumerate(rotatable_bonds):
+            if visited_rotatable_bonds[k]:
+                continue
+
+            # Create a new branch for each rotatable bond,
+            # that connects to an atom of this branch
+            if i in this_branch_indices:
+                this_br_i = i
+                new_br_i = j
+            elif j in this_branch_indices:
+                this_br_i = j
+                new_br_i = i
+            else:
+                # Rotatable bond does not start from this branch
+                continue
+
+            # Mark rotatable bond as visited as otherwise branches would
+            # be created back and forth over the same rotatable bond and
+            # this method would never terminate
+            visited_rotatable_bonds[k] = True
+
+            self.lines.append(
+                f"BRANCH {atom_id[this_br_i]:>3d} {atom_id[new_br_i]:>3d}"
+            )
+            self._write_atoms(
+                atoms,
+                charges,
+                types,
+                atom_id,
+                hetero,
+                occupancy,
+                b_factor,
+                # The root atom of the branch
+                # is the other atom of the rotatable bond
+                new_br_i,
+                rotatable_bonds,
+                visited_rotatable_bonds,
+                False,
+            )
+            self.lines.append(
+                f"ENDBRANCH {atom_id[this_br_i]:>3d} {atom_id[new_br_i]:>3d}"
+            )
+
+    def _get_model_length(self, model_start_i, atom_line_i):
+        """
+        Determine length of models and check that all models
+        have equal length.
+        """
+        n_models = len(model_start_i)
+        length = None
+        for model_i in range(len(model_start_i)):
+            model_start = model_start_i[model_i]
+            model_stop = (
+                model_start_i[model_i + 1]
+                if model_i + 1 < n_models
+                else len(self.lines)
+            )
+            model_length = np.count_nonzero(
+                (atom_line_i >= model_start) & (atom_line_i < model_stop)
+            )
+            if length is None:
+                length = model_length
+            if model_length != length:
+                raise InvalidFileError(
+                    f"Model {model_i + 1} has {model_length} atoms, "
+                    f"but model 1 has {length} atoms, must be equal"
+                )
+        return length
+
+
+def convert_atoms(atoms, charges):
+    """
+    Convert atoms into *AutoDock* compatible atoms.
+
+    Parameters
+    ----------
+    atoms : AtomArray
+        The atoms to be converted.
+    charges : ndarray, dtype=float
+        Partial charges for the atoms.
+
+    Returns
+    -------
+    converted_atoms : AtomArray
+        The input `atoms`, but with deleted nonpolar hydrogen atoms.
+    charges : ndarray, dtype=float
+        The input `charges`, but with deleted entries for nonpolar
+        hydrogen atoms.
+    atom_types : ndarray, dtype="U1"
+        The *AutoDock* atom types.
+    mask : ndarray, shape=(n,), dtype=bool
+        A boolean mask, that is ``False`` for each atom of the input
+        ``atoms``, that was removed due to being a nonpolar hydrogen.
+    """
+    charges = charges.copy()
+    all_bonds, all_bond_types = atoms.bonds.get_all_bonds()
+
+    atom_types = np.zeros(atoms.array_length(), dtype="U2")
+    hydrogen_removal_mask = np.zeros(atoms.array_length(), dtype=bool)
+    for i in range(atoms.array_length()):
+        element = atoms.element[i]
+        bonded_atoms = all_bonds[i][all_bonds[i] != -1]
+        if element == "H":
+            if len(bonded_atoms) == 0:
+                # Free proton
+                atom_types[i] = "H"
+            elif len(bonded_atoms) == 1:
+                j = bonded_atoms[0]
+                bonded_element = atoms.element[j]
+                if bonded_element == "C":
+                    # Remove hydrogen and add its charge
+                    # to charge of bonded carbon
+                    charges[j] += charges[i]
+                    hydrogen_removal_mask[i] = True
+                else:
+                    atom_types[i] = "HD"
+            else:
+                raise BadStructureError(
+                    "Structure contains hydrogen with multiple bonds"
+                )
+        elif element == "C":
+            if np.isin(
+                all_bond_types[i], [BondType.AROMATIC_SINGLE, BondType.AROMATIC_DOUBLE]
+            ).any():
+                # Aromatic carbon
+                atom_types[i] = "A"
+            else:
+                # Alphatic carbon
+                atom_types[i] = "C"
+        elif element == "N":
+            atom_types[i] = "NA"
+        elif element == "O":
+            atom_types[i] = "OA"
+        elif element == "S":
+            atom_types[i] = "SA"
+        elif element.capitalize() in PARAMETRIZED_ELEMENTS:
+            atom_types[i] = element.capitalize()
+        else:
+            warnings.warn(
+                f"Element {element} is not paramtrized, "
+                f"using parameters for hydrogen instead"
+            )
+            atom_types[i] = "H"
+
+    mask = ~hydrogen_removal_mask
+    return atoms[mask], charges[mask], atom_types[mask], mask