diff --git a/.githooks/commit-msg b/.githooks/commit-msg
index 4a797199..d29021e8 100755
--- a/.githooks/commit-msg
+++ b/.githooks/commit-msg
@@ -96,6 +96,24 @@ if [[ "$lowercase_message" =~ ^ci(\(.+\))?: ]]; then
   group="CI"
 fi
 
+#pylint
+if [[ "$lowercase_message" =~ ^pylint(\(.+\))?: ]]; then
+  matched=true
+  group="Pylint"
+fi
+
+if [[ "$lowercase_message" =~ ^admin(\(.+\))?: ]]; then
+  matched=true
+  group="Administrative"
+fi
+
+#random stuff that doesn't fit into any of the above categories
+#starting with a $
+if [[ "$lowercase_message" =~ ^\$ ]]; then
+  matched=true
+  group="Random"
+fi
+
 # ... (similar checks for other patterns in the list)
 
 # No match found
@@ -120,6 +138,9 @@ if ! $matched; then
   echo "  - Example:        example:, examples:"
   echo "  - Dependency:     deps:"
   echo "  - CI:             ci:"
+  echo "  - Pylint:         pylint:"
+  echo "  - Administrative: admin:"
+  echo "  - Random:         $"
   # ... (similar output for other patterns in the list)
   echo "  - --------------------------------------------\n"
 
diff --git a/.github/.pylint_cache/PQAnalysis_1.stats b/.github/.pylint_cache/PQAnalysis_1.stats
index 1e305c7e..c172a63d 100644
Binary files a/.github/.pylint_cache/PQAnalysis_1.stats and b/.github/.pylint_cache/PQAnalysis_1.stats differ
diff --git a/.gitignore b/.gitignore
index 46077241..a59a74fa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,7 +6,7 @@ build/
 _version.py
 **/*.ipynb
 
-.github/.pylint_cache
+.github/.pylint_cache/__*
 
 .coverage
 coverage.xml
diff --git a/PQAnalysis/io/base.py b/PQAnalysis/io/base.py
index 7ba0a90b..e0e6eb1c 100644
--- a/PQAnalysis/io/base.py
+++ b/PQAnalysis/io/base.py
@@ -78,6 +78,7 @@ def __init__(
         self.filename = filename
 
         self.mode = FileWritingMode(mode)
+        self.original_mode = FileWritingMode(mode)
 
     def open(self) -> None:
         """
@@ -144,13 +145,15 @@ class :py:class:`~PQAnalysis.io.formats.FileWritingMode`.
         """
         mode = FileWritingMode(mode)
 
-        if (mode == FileWritingMode.WRITE and self.filename is not None
-                and os.path.isfile(self.filename)):
+        if (
+            mode == FileWritingMode.WRITE and self.filename is not None and
+            os.path.isfile(self.filename)
+        ):
             self.logger.error(
                 (
-                f"File {self.filename} already exists. "
-                "Use mode \'a\' to append to the file or mode "
-                "\'o\' to overwrite the file."
+                    f"File {self.filename} already exists. "
+                    "Use mode \'a\' to append to the file or mode "
+                    "\'o\' to overwrite the file."
                 ),
                 exception=FileWritingModeError
             )
@@ -211,8 +214,8 @@ def __init__(self, filename: str | List[str]) -> None:
                 if not os.path.isfile(_filename):
                     self.logger.error(
                         (
-                        "At least one of the given files does not exist. "
-                        f"File {_filename} not found."
+                            "At least one of the given files does not exist. "
+                            f"File {_filename} not found."
                         ),
                         exception=PQFileNotFoundError
                     )
diff --git a/PQAnalysis/io/topology_file/__init__.py b/PQAnalysis/io/topology_file/__init__.py
index b3c51ef2..0d792854 100644
--- a/PQAnalysis/io/topology_file/__init__.py
+++ b/PQAnalysis/io/topology_file/__init__.py
@@ -2,5 +2,7 @@
 A subpackage to handle trajectory files.
 """
 
+from .exceptions import TopologyFileError
+
 from .topology_file_reader import TopologyFileReader
 from .topology_file_writer import TopologyFileWriter
diff --git a/PQAnalysis/io/topology_file/topology_file_reader.py b/PQAnalysis/io/topology_file/topology_file_reader.py
index cc27ee88..79ba6782 100644
--- a/PQAnalysis/io/topology_file/topology_file_reader.py
+++ b/PQAnalysis/io/topology_file/topology_file_reader.py
@@ -6,13 +6,14 @@
 
 import logging
 
-from beartype.typing import List
+from beartype.typing import List, Tuple
 
 from PQAnalysis.io.base import BaseReader
 from PQAnalysis.topology import Bond, BondedTopology, Angle, Dihedral
 from PQAnalysis.utils.custom_logging import setup_logger
-from PQAnalysis import __package_name__
+from PQAnalysis.utils.string import is_comment_line
 from PQAnalysis.type_checking import runtime_type_checking
+from PQAnalysis import __package_name__
 
 from .exceptions import TopologyFileError
 
@@ -83,14 +84,14 @@ def _get_definitions(self) -> dict[str, List[str]]:
         with open(self.filename, "r", encoding="utf-8") as file:
             lines = file.readlines()
 
-            # remove all #.... parts from all lines
-            lines = [line.split("#")[0] for line in lines]
-
-            # remove all empty lines
-            lines = [line for line in lines if line.strip()]
+            # remove all comment lines and empty lines
+            no_comment_lines = [
+                line for line in lines if
+                not is_comment_line(line, comment_token="#", empty_line=True)
+            ]
 
             # check if last line is END else raise error
-            if lines[-1].strip().lower() != "end":
+            if no_comment_lines[-1].strip().lower() != "end":
                 self.logger.error(
                     "Something went wrong. Each block should end with 'END'",
                     exception=TopologyFileError,
@@ -101,9 +102,12 @@ def _get_definitions(self) -> dict[str, List[str]]:
             block = []
             for line in lines:
                 if line.strip().lower() == "end":
+                    block.append(line)
                     blocks.append(block)
                     block = []
-                else:
+                elif not is_comment_line(
+                    line, comment_token="#", empty_line=True
+                ):
                     block.append(line)
 
             # make a dictionary for each block with the key
@@ -201,7 +205,10 @@ def _parse_bonds(self, block: List[str]) -> List[Bond]:
             If the number of columns in the block is not 3 or 4.
         """
         bonds = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 4:
                 index, target_index, bond_type, _ = line.split()
                 is_linker = True
@@ -220,6 +227,7 @@ def _parse_bonds(self, block: List[str]) -> List[Bond]:
                     index2=int(target_index),
                     bond_type=int(bond_type),
                     is_linker=is_linker,
+                    comment=comment
                 )
             )
 
@@ -251,7 +259,10 @@ def _parse_angles(self, block: List[str]) -> List[Angle]:
             If the number of columns in the block is not 4 or 5.
         """
         angles = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 5:
                 index1, index2, index3, angle_type, _ = line.split()
                 is_linker = True
@@ -271,6 +282,7 @@ def _parse_angles(self, block: List[str]) -> List[Angle]:
                     index3=int(index3),
                     angle_type=int(angle_type),
                     is_linker=is_linker,
+                    comment=comment
                 )
             )
 
@@ -302,7 +314,10 @@ def _parse_dihedrals(self, block: List[str]) -> List[Dihedral]:
             If the number of columns in the block is not 5 or 6.
         """
         dihedrals = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 6:
                 index1, index2, index3, index4, dihedral_type, _ = line.split()
                 is_linker = True
@@ -323,6 +338,7 @@ def _parse_dihedrals(self, block: List[str]) -> List[Dihedral]:
                     index4=int(index4),
                     dihedral_type=int(dihedral_type),
                     is_linker=is_linker,
+                    comment=comment
                 )
             )
 
@@ -354,7 +370,10 @@ def _parse_impropers(self, block: List[str]) -> List[Dihedral]:
             If the number of columns in the block is not 5 or 6.
         """
         dihedrals = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 6:
                 index1, index2, index3, index4, dihedral_type, _ = line.split()
                 is_linker = True
@@ -376,6 +395,7 @@ def _parse_impropers(self, block: List[str]) -> List[Dihedral]:
                     dihedral_type=int(dihedral_type),
                     is_linker=is_linker,
                     is_improper=True,
+                    comment=comment
                 )
             )
 
@@ -407,7 +427,10 @@ def _parse_shake(self, block: List[str]) -> List[Bond]:
             If the number of columns in the block is not 3 or 4.
         """
         shake_bonds = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 4:
                 index, target_index, distance, _ = line.split()
                 is_linker = True
@@ -422,7 +445,33 @@ def _parse_shake(self, block: List[str]) -> List[Bond]:
                     equilibrium_distance=float(distance),
                     is_linker=is_linker,
                     is_shake=True,
+                    comment=comment
                 )
             )
 
         return shake_bonds
+
+    @staticmethod
+    def _get_data_line_comment(line: str) -> Tuple[str, str | None]:
+        """
+        Get the data and the comment from a line.
+
+        Parameters
+        ----------
+        line : str
+            A line from the topology file.
+
+        Returns
+        -------
+        tuple[str, str]
+            A tuple with the data and the comment.
+        """
+        splitted_line = line.split("#")
+        data = splitted_line[0].strip()
+
+        if len(splitted_line) > 1:
+            comment = "#".join(splitted_line[1:]).strip()
+        else:
+            comment = None
+
+        return data, comment
diff --git a/PQAnalysis/io/topology_file/topology_file_writer.py b/PQAnalysis/io/topology_file/topology_file_writer.py
index 1c55bea1..690d9798 100644
--- a/PQAnalysis/io/topology_file/topology_file_writer.py
+++ b/PQAnalysis/io/topology_file/topology_file_writer.py
@@ -10,12 +10,17 @@
 
 from beartype.typing import List
 
+from PQAnalysis import __package_name__
 from PQAnalysis.io.base import BaseWriter
 from PQAnalysis.io.formats import FileWritingMode
-from PQAnalysis.topology import BondedTopology, Topology
 from PQAnalysis.utils.custom_logging import setup_logger
-from PQAnalysis import __package_name__
 from PQAnalysis.type_checking import runtime_type_checking
+from PQAnalysis.topology import BondedTopology, Topology
+from PQAnalysis.topology.bonded_topology import (
+    Bond,
+    Angle,
+    Dihedral,
+)
 
 from .exceptions import TopologyFileError
 
@@ -35,15 +40,16 @@ class TopologyFileWriter(BaseWriter):
     @runtime_type_checking
     def __init__(
         self,
-        filename: str,
-        mode: str | FileWritingMode = "w"
+        filename: str | None = None,
+        mode: str | FileWritingMode = "w",
     ) -> None:
         """
         Parameters
         ----------
-        filename : str
-            The name of the topology file
-        mode: str | FileWritingMode
+        filename : str, optional
+            The name of the topology file, Default is None, which means that the
+            output is printed to stdout.
+        mode: str | FileWritingMode, optional
             The writing mode. Default is "w".
             The writing mode can be either a string or a FileWritingMode enum value.
             Possible values are:
@@ -79,13 +85,13 @@ def write(self, bonded_topology: Topology | BondedTopology) -> None:
             If the bonded topology is not a Topology or BondedTopology object.
         """
 
-        if isinstance(bonded_topology,
-            Topology) and bonded_topology.bonded_topology is not None:
+        if isinstance(
+            bonded_topology, Topology
+        ) and bonded_topology.bonded_topology is not None:
             bonded_topology = bonded_topology.bonded_topology
         elif not isinstance(bonded_topology, BondedTopology):
             self.logger.error(
-                "Invalid bonded topology.",
-                exception=TopologyFileError
+                "Invalid bonded topology.", exception=TopologyFileError
             )
 
         self.open()
@@ -102,9 +108,7 @@ def write(self, bonded_topology: Topology | BondedTopology) -> None:
 
     @classmethod
     def _write_bond_info(
-        cls,
-        bonded_topology: BondedTopology,
-        file: File
+        cls, bonded_topology: BondedTopology, file: File
     ) -> None:
         """
         Determines if the bonded topology contains bonds and 
@@ -116,7 +120,15 @@ def _write_bond_info(
             The bonded topology object containing the bond information.
         file : File
             The file object to write the bond information to.
+            
+        Raises
+        ------
+        TopologyFileError
+            If any bond in the bonded topology does not have a bond type defined.
         """
+
+        cls._check_type_given(bonded_topology.bonds, "bond")
+
         if len(bonded_topology.bonds) != 0:
             lines = cls._get_bond_lines(bonded_topology)
             for line in lines:
@@ -124,9 +136,7 @@ def _write_bond_info(
 
     @classmethod
     def _write_angle_info(
-        cls,
-        bonded_topology: BondedTopology,
-        file: File
+        cls, bonded_topology: BondedTopology, file: File
     ) -> None:
         """
         Determines if the bonded topology contains angles and
@@ -138,7 +148,15 @@ def _write_angle_info(
             The bonded topology object containing the angle information.
         file : File 
             The file object to write the angle information to.
+        
+        Raises
+        ------
+        TopologyFileError
+            If any angle in the bonded topology does not have an angle type defined.
         """
+
+        cls._check_type_given(bonded_topology.angles, "angle")
+
         if len(bonded_topology.angles) != 0:
             lines = cls._get_angle_lines(bonded_topology)
             for line in lines:
@@ -146,9 +164,7 @@ def _write_angle_info(
 
     @classmethod
     def _write_dihedral_info(
-        cls,
-        bonded_topology: BondedTopology,
-        file: File
+        cls, bonded_topology: BondedTopology, file: File
     ) -> None:
         """
         Determines if the bonded topology contains dihedrals and
@@ -160,7 +176,15 @@ def _write_dihedral_info(
             The bonded topology object containing the dihedral information.
         file : File
             The file object to write the dihedral information to.
+            
+        Raises
+        ------
+        TopologyFileError
+            If any dihedral in the bonded topology does not have a dihedral type defined.
         """
+
+        cls._check_type_given(bonded_topology.dihedrals, "dihedral")
+
         if len(bonded_topology.dihedrals) != 0:
             lines = cls._get_dihedral_lines(bonded_topology)
             for line in lines:
@@ -168,9 +192,7 @@ def _write_dihedral_info(
 
     @classmethod
     def _write_improper_info(
-        cls,
-        bonded_topology: BondedTopology,
-        file: File
+        cls, bonded_topology: BondedTopology, file: File
     ) -> None:
         """
         Writes the improper information to the file.
@@ -182,6 +204,9 @@ def _write_improper_info(
         file : File
             The file object to write the improper information to.
         """
+
+        cls._check_type_given(bonded_topology.impropers, "improper")
+
         if len(bonded_topology.impropers) != 0:
             lines = cls._get_improper_lines(bonded_topology)
             for line in lines:
@@ -189,9 +214,7 @@ def _write_improper_info(
 
     @classmethod
     def _write_shake_info(
-        cls,
-        bonded_topology: BondedTopology,
-        file: File
+        cls, bonded_topology: BondedTopology, file: File
     ) -> None:
         """
         Writes the shake information to the file.
@@ -208,6 +231,40 @@ def _write_shake_info(
             for line in lines:
                 print(line, file=file)
 
+    @classmethod
+    def _check_type_given(
+        cls, types: List[Bond | Angle | Dihedral], type_name: str
+    ) -> None:
+        """
+        Check if the type is given for each bond, angle, or dihedral.
+
+        Parameters
+        ----------
+        types : List[Bond | Angle | Dihedral]
+            The list of bonds, angles, or dihedrals to check.
+        type_name : str
+            The name of the type to check.
+        """
+
+        def get_type(type_: Bond | Angle | Dihedral) -> int | None:
+
+            if isinstance(type_, Bond):
+                return type_.bond_type
+
+            if isinstance(type_, Angle):
+                return type_.angle_type
+
+            return type_.dihedral_type
+
+        if any(get_type(type_) is None for type_ in types):
+            cls.logger.error(
+                (
+                    f"In order to write the {type_name} information in 'PQ' topology format, "
+                    f"all {type_name}s must have a {type_name} type defined."
+                ),
+                exception=TopologyFileError
+            )
+
     @staticmethod
     def _get_bond_lines(bonded_topology: BondedTopology) -> List[str]:
         """
@@ -233,7 +290,7 @@ def _get_bond_lines(bonded_topology: BondedTopology) -> List[str]:
         """
         n_unique_indices = len(bonded_topology.unique_bond1_indices)
         n_unique_target_indices = len(bonded_topology.unique_bond2_indices)
-        n_linkers = len(bonded_topology.linkers)
+        n_linkers = len(bonded_topology.bond_linkers)
 
         lines = []
 
@@ -242,7 +299,15 @@ def _get_bond_lines(bonded_topology: BondedTopology) -> List[str]:
         )
 
         for bond in bonded_topology.bonds:
-            lines.append(f"{bond.index1} {bond.index2} {bond.bond_type}")
+            line = f"{bond.index1:>5d} {bond.index2:>5d} {bond.bond_type:>5d}"
+
+            if bond.is_linker:
+                line += " *"
+
+            if bond.comment is not None:
+                line += f" # {bond.comment}"
+
+            lines.append(line)
 
         lines.append("END")
 
@@ -273,7 +338,7 @@ def _get_angle_lines(bonded_topology: BondedTopology) -> List[str]:
         """
         n_unique_indices1 = len(bonded_topology.unique_angle1_indices)
         n_unique_indices2 = len(bonded_topology.unique_angle2_indices)
-        n_unique_indices3 = len(bonded_topology.unique_angle_target_indices)
+        n_unique_indices3 = len(bonded_topology.unique_angle3_indices)
         n_linkers = len(bonded_topology.angle_linkers)
 
         lines = []
@@ -284,11 +349,19 @@ def _get_angle_lines(bonded_topology: BondedTopology) -> List[str]:
         )
 
         for angle in bonded_topology.angles:
-            lines.append(
-                f"{angle.index1} {angle.index2} "
-                f"{angle.index3} {angle.angle_type}"
+            line = (
+                f"{angle.index1:>5d} {angle.index2:>5d} "
+                f"{angle.index3:>5d} {angle.angle_type:>5d}"
             )
 
+            if angle.is_linker:
+                line += " *"
+
+            if angle.comment is not None:
+                line += f" # {angle.comment}"
+
+            lines.append(line)
+
         lines.append("END")
 
         return lines
@@ -329,11 +402,20 @@ def _get_dihedral_lines(bonded_topology: BondedTopology) -> List[str]:
         )
 
         for dihedral in bonded_topology.dihedrals:
-            lines.append(
-                f"{dihedral.index1} {dihedral.index2} {dihedral.index3} "
-                f"{dihedral.index4} {dihedral.dihedral_type}"
+            line = (
+                f"{dihedral.index1:>5d} {dihedral.index2:>5d} "
+                f"{dihedral.index3:>5d} {dihedral.index4:>5d} "
+                f"{dihedral.dihedral_type:>5d}"
             )
 
+            if dihedral.is_linker:
+                line += " *"
+
+            if dihedral.comment is not None:
+                line += f" # {dihedral.comment}"
+
+            lines.append(line)
+
         lines.append("END")
 
         return lines
@@ -374,11 +456,21 @@ def _get_improper_lines(bonded_topology: BondedTopology) -> List[str]:
         )
 
         for improper in bonded_topology.impropers:
-            lines.append(
-                f"{improper.index1} {improper.index2} {improper.index3} "
-                f"{improper.index4} {improper.improper_type}"
+
+            line = (
+                f"{improper.index1:>5d} {improper.index2:>5d} "
+                f"{improper.index3:>5d} {improper.index4:>5d} "
+                f"{improper.dihedral_type:>5d}"
             )
 
+            if improper.is_linker:
+                line += " *"
+
+            if improper.comment is not None:
+                line += f" # {improper.comment}"
+
+            lines.append(line)
+
         lines.append("END")
 
         return lines
@@ -420,11 +512,17 @@ def _get_shake_lines(bonded_topology: BondedTopology) -> List[str]:
 
         for bond in bonded_topology.shake_bonds:
             linker = "*" if bond.is_linker else ""
-            lines.append(
-                f"{bond.index1} {bond.index2} "
-                f"{bond.equilibrium_distance} {linker}"
+
+            line = (
+                f"{bond.index1:>5d} {bond.index2:>5d} "
+                f"{bond.equilibrium_distance:16.12f}\t{linker}"
             )
 
+            if bond.comment is not None:
+                line += f" # {bond.comment}"
+
+            lines.append(line)
+
         lines.append("END")
 
         return lines
diff --git a/PQAnalysis/io/traj_file/frame_reader.py b/PQAnalysis/io/traj_file/frame_reader.py
index 1a615ce7..ebdb00d3 100644
--- a/PQAnalysis/io/traj_file/frame_reader.py
+++ b/PQAnalysis/io/traj_file/frame_reader.py
@@ -251,7 +251,9 @@ def _check_qmcfc(
         return value, atoms
 
     def _get_topology(
-        self, atoms: List[str], topology: Topology | None
+        self,
+        atoms: List[str],
+        topology: Topology | None,
     ) -> Topology:
         """
         Returns the topology of the frame.
diff --git a/PQAnalysis/io/traj_file/trajectory_reader.py b/PQAnalysis/io/traj_file/trajectory_reader.py
index bc3ddb83..e1fa84b9 100644
--- a/PQAnalysis/io/traj_file/trajectory_reader.py
+++ b/PQAnalysis/io/traj_file/trajectory_reader.py
@@ -222,6 +222,10 @@ def frame_generator(
                 # Read the lines of the file using tqdm for progress bar
                 for line in self.file:
 
+                    # Break the generator if the trajectory_stop is reached
+                    if trajectory_stop <= frame_index:
+                        return
+
                     stripped_line = line.strip()
                     if stripped_line == "" or not stripped_line[0].isdigit():
                         frame_lines.append(line)
@@ -239,10 +243,7 @@ def frame_generator(
 
                             # Check if the number of frames yielded is equal to the
                             # total number of frames
-                            if not (
-                                frame_index < trajectory_start or
-                                frame_index >= trajectory_stop
-                            ):
+                            if frame_index >= trajectory_start:
                                 yield frame  # only yield the frame if it is within the range
                                 progress_bar.update(
                                     1
@@ -251,7 +252,7 @@ def frame_generator(
                             # then increment the frame index
                             frame_index += 1
 
-                            if self.constant_topology and self.topology is not None:
+                            if self.constant_topology and self.topology is None:
                                 self.topology = frame.topology
 
                         frame_lines = [line]
@@ -267,18 +268,16 @@ def frame_generator(
 
                     last_cell = frame.cell
 
-                    # Check if the number of frames yielded is equal to the total number of frames
-                    if not (
-                        frame_index < trajectory_start or
-                        frame_index >= trajectory_stop
-                    ):
+                    # Check if the number of frames yielded is equal to the
+                    # total number of frames
+                    if frame_index >= trajectory_start:
                         yield frame  # only yield the frame if it is within the range
                         progress_bar.update(1)  # update the progress bar
 
                     # then increment the frame index
                     frame_index += 1
 
-                if self.constant_topology and self.topology is not None:
+                if self.constant_topology and self.topology is None:
                     self.topology = frame.topology
 
     @runtime_type_checking
diff --git a/PQAnalysis/topology/bonded_topology/__init__.py b/PQAnalysis/topology/bonded_topology/__init__.py
index 816e255f..3387e867 100644
--- a/PQAnalysis/topology/bonded_topology/__init__.py
+++ b/PQAnalysis/topology/bonded_topology/__init__.py
@@ -1,3 +1,8 @@
 """
 A subpackage for the bonded topology of an atomic system.
 """
+
+from .bond import Bond
+from .angle import Angle
+from .dihedral import Dihedral
+from .bonded_topology import BondedTopology
diff --git a/PQAnalysis/topology/bonded_topology/angle.py b/PQAnalysis/topology/bonded_topology/angle.py
index c3c38c12..e1f34377 100644
--- a/PQAnalysis/topology/bonded_topology/angle.py
+++ b/PQAnalysis/topology/bonded_topology/angle.py
@@ -22,6 +22,7 @@ def __init__(
         equilibrium_angle: PositiveReal | None = None,
         angle_type: PositiveInt | None = None,
         is_linker: bool = False,
+        comment: str | None = None
     ) -> None:
         """
         Parameters
@@ -38,6 +39,8 @@ def __init__(
             The type of the angle, by default None.
         is_linker : bool, optional
             A flag to indicate if the angle is a linker, by default False.
+        comment : str, optional
+            A comment for the angle, by default None.
         """
 
         self.index1 = index1
@@ -46,6 +49,7 @@ def __init__(
         self.equilibrium_angle = equilibrium_angle
         self.angle_type = angle_type
         self.is_linker = is_linker
+        self.comment = comment
 
     def copy(self) -> "Angle":
         """
@@ -63,6 +67,7 @@ def copy(self) -> "Angle":
             equilibrium_angle=self.equilibrium_angle,
             angle_type=self.angle_type,
             is_linker=self.is_linker,
+            comment=self.comment
         )
 
     def __eq__(self, value: object) -> bool:
diff --git a/PQAnalysis/topology/bonded_topology/bond.py b/PQAnalysis/topology/bonded_topology/bond.py
index dff5bf94..280f5f3b 100644
--- a/PQAnalysis/topology/bonded_topology/bond.py
+++ b/PQAnalysis/topology/bonded_topology/bond.py
@@ -22,6 +22,7 @@ def __init__(
         bond_type: PositiveInt | None = None,
         is_linker: bool = False,
         is_shake: bool = False,
+        comment: str | None = None
     ) -> None:
         """
         Parameters
@@ -38,6 +39,8 @@ def __init__(
             A flag to indicate if the bond is a linker, by default False.
         is_shake : bool, optional
             A flag to indicate if the bond is a shake bond, by default False.
+        comment : str, optional
+            A comment for the bond, by default None.
         """
 
         self.index1 = index1
@@ -46,6 +49,7 @@ def __init__(
         self.bond_type = bond_type
         self.is_linker = is_linker
         self.is_shake = is_shake
+        self.comment = comment
 
     def copy(self) -> "Bond":
         """
@@ -63,6 +67,7 @@ def copy(self) -> "Bond":
             bond_type=self.bond_type,
             is_linker=self.is_linker,
             is_shake=self.is_shake,
+            comment=self.comment
         )
 
     def __eq__(self, value: object) -> bool:
diff --git a/PQAnalysis/topology/bonded_topology/bonded_topology.py b/PQAnalysis/topology/bonded_topology/bonded_topology.py
index 698f95dd..6c2beba8 100644
--- a/PQAnalysis/topology/bonded_topology/bonded_topology.py
+++ b/PQAnalysis/topology/bonded_topology/bonded_topology.py
@@ -112,7 +112,7 @@ def extend_shake_bonds(
 
         max_index_shake_bonds = max(
             [bond.index1
-            for bond in shake_bonds] + [bond.index2 for bond in shake_bonds]
+             for bond in shake_bonds] + [bond.index2 for bond in shake_bonds]
         )
 
         if n_atoms_per_extension is None:
@@ -120,8 +120,8 @@ def extend_shake_bonds(
         elif n_atoms_per_extension < max_index_shake_bonds:
             self.logger.error(
                 (
-                "n_atoms_per_extension must be greater or equal "
-                "than the highest index in the provided shake bonds."
+                    "n_atoms_per_extension must be greater or equal "
+                    "than the highest index in the provided shake bonds."
                 ),
                 exception=PQValueError
             )
diff --git a/PQAnalysis/topology/bonded_topology/dihedral.py b/PQAnalysis/topology/bonded_topology/dihedral.py
index 83bd4858..2a4a93d3 100644
--- a/PQAnalysis/topology/bonded_topology/dihedral.py
+++ b/PQAnalysis/topology/bonded_topology/dihedral.py
@@ -24,6 +24,7 @@ def __init__(
         dihedral_type: int | None = None,
         is_linker: bool = False,
         is_improper: bool = False,
+        comment: str | None = None
     ) -> None:
         """
         Parameters
@@ -44,6 +45,8 @@ def __init__(
             A flag to indicate if the dihedral is a linker, by default False.
         is_improper : bool, optional
             A flag to indicate if the dihedral is an improper dihedral, by default False.
+        comment : str, optional
+            A comment for the dihedral, by default None.
         """
 
         self.index1 = index1
@@ -54,6 +57,7 @@ def __init__(
         self.dihedral_type = dihedral_type
         self.is_linker = is_linker
         self.is_improper = is_improper
+        self.comment = comment
 
     def copy(self) -> "Dihedral":
         """
@@ -72,7 +76,8 @@ def copy(self) -> "Dihedral":
             equilibrium_angle=self.equilibrium_angle,
             dihedral_type=self.dihedral_type,
             is_linker=self.is_linker,
-            is_improper=self.is_improper
+            is_improper=self.is_improper,
+            comment=self.comment
         )
 
     def __eq__(self, value: object) -> bool:
diff --git a/PQAnalysis/topology/shake_topology.py b/PQAnalysis/topology/shake_topology.py
index bb3df741..da3d6bf4 100644
--- a/PQAnalysis/topology/shake_topology.py
+++ b/PQAnalysis/topology/shake_topology.py
@@ -7,15 +7,19 @@
 
 from beartype.typing import List
 
+from PQAnalysis import __package_name__
 from PQAnalysis.traj import Trajectory
 from PQAnalysis.types import Np1DIntArray, Np2DIntArray
-from PQAnalysis.io import BaseWriter, FileWritingMode
 from PQAnalysis.type_checking import runtime_type_checking
 from PQAnalysis.utils.custom_logging import setup_logger
 from PQAnalysis.exceptions import PQValueError
-from PQAnalysis import __package_name__
+from PQAnalysis.io import (
+    FileWritingMode,
+    TopologyFileWriter,
+)
 
 from .selection import SelectionCompatible, Selection
+from .bonded_topology import BondedTopology, Bond
 
 
 
@@ -192,33 +196,32 @@ def write_topology(
             - "o": overwrite
         """
 
-        writer = BaseWriter(filename, mode=mode)
-        writer.open()
-
-        print(
-            (
-                f"SHAKE {len(self.indices)}  "
-                f"{len(np.unique(self.target_indices))}  0"
-            ),
-            file=writer.file
-        )
+        shake_bonds = []
+        if self.line_comments is None:
+            comments = [None] * len(self.indices)
+        else:
+            comments = self.line_comments
 
         for i, index in enumerate(self.indices):
-            target_index = self.target_indices[i]
+            index = index + 1
+            target_index = self.target_indices[i] + 1
             distance = self.distances[i]
-
-            print(
-                f"{index+1} {target_index+1} {distance}",
-                end="",
-                file=writer.file
+            comment = comments[i]
+
+            bond = Bond(
+                index1=index,
+                index2=target_index,
+                equilibrium_distance=distance,
+                is_shake=True,
+                comment=comment
             )
 
-            if self.line_comments is not None:
-                print(f"  # {self.line_comments[i]}", file=writer.file)
-            else:
-                print("", file=writer.file)
+            shake_bonds.append(bond)
+
+        topology = BondedTopology(shake_bonds=shake_bonds)
 
-        print("END", file=writer.file)
+        writer = TopologyFileWriter(filename, mode)
+        writer.write(topology)
 
     @property
     def selection_object(self) -> SelectionCompatible:
diff --git a/PQAnalysis/types.py b/PQAnalysis/types.py
index db172695..e99facf5 100644
--- a/PQAnalysis/types.py
+++ b/PQAnalysis/types.py
@@ -12,7 +12,7 @@
 #: A type hint for positive integers
 PositiveInt = NewType(
     "PositiveInt",
-    Annotated[int, Is[lambda int: int > 0]],
+    Annotated[int | np.int_, Is[lambda int: int > 0]],
 )
 
 # :A type hint for positive real numbers
diff --git a/PQAnalysis/utils/string.py b/PQAnalysis/utils/string.py
new file mode 100644
index 00000000..a7daea6c
--- /dev/null
+++ b/PQAnalysis/utils/string.py
@@ -0,0 +1,29 @@
+"""
+This module contains utility functions for string manipulation.
+"""
+
+
+
+def is_comment_line(line: str, comment_token="#", empty_line=False) -> bool:
+    """
+    Returns whether the line is a comment line.
+
+    Parameters
+    ----------
+    line : str
+        The line to be checked.
+    comment_token : str, optional
+        The token that indicates a comment line, by default "#".
+    empty_line : bool, optional
+        Whether an empty line should be considered a comment line, by default False.
+
+    Returns
+    -------
+    bool
+        Whether the line is a comment line.
+    """
+
+    if empty_line and not line.strip():
+        return True
+
+    return line.strip().startswith(comment_token)
diff --git a/examples/add_molecules/shake_perylene.top b/examples/add_molecules/shake_perylene.top
index 1e86d4cb..84089b9e 100644
--- a/examples/add_molecules/shake_perylene.top
+++ b/examples/add_molecules/shake_perylene.top
@@ -1,5 +1,5 @@
 SHAKE 12  12  0
-7 1 1.1007868486266905
+7 1 1.1007868486266905  # put here some comment
 10 5 1.102015725191353
 11 6 1.102015725191353
 14 9 1.102015725191353
diff --git a/pytest.ini b/pytest.ini
index 88269560..48192988 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -7,6 +7,7 @@ markers =
     io
     analysis
     utils
+    integration
 
 testpaths = 
     tests
diff --git a/tests/__init__.py b/tests/__init__.py
index aece9ef9..41442810 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -4,5 +4,7 @@
 
 import os
 
-__beartype_level__ = os.environ.get("PQANALYSIS_BEARTYPE_LEVEL", "DEBUG")
+__beartype_level__ = os.environ.get("PQANALYSIS_BEARTYPE_LEVEL", "RELEASE")
 __beartype_level__ = __beartype_level__.upper()
+
+os.environ['CONSTANT_SEED'] = '42'
diff --git a/tests/conftest.py b/tests/conftest.py
index db4df2e4..03038e32 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -6,9 +6,10 @@
 import shutil
 import logging
 
+from contextlib import contextmanager
+
 import pytest
 
-from contextlib import contextmanager
 from _pytest.logging import LogCaptureHandler, _remove_ansi_escape_sequences
 from beartype.roar import BeartypeCallHintParamViolation
 
@@ -37,6 +38,25 @@ def tmpdir():
 
 
 
+@pytest.fixture(scope="function")
+def test_integration_folder(example_dir):
+
+    tmpdir = "tmpdir"
+
+    if os.path.exists(tmpdir) and os.path.isdir(tmpdir):
+        shutil.rmtree(tmpdir)
+
+    shutil.copytree(os.path.join("examples", example_dir), tmpdir)
+
+    os.chdir(tmpdir)
+
+    yield tmpdir
+
+    os.chdir("..")
+    shutil.rmtree(tmpdir)
+
+
+
 @pytest.fixture(scope="function")
 def test_with_data_dir(example_dir):
 
@@ -69,9 +89,7 @@ def text(self) -> str:
 
     @contextmanager
     def catch_logs(
-        self,
-        level: int,
-        logger: logging.Logger
+        self, level: int, logger: logging.Logger
     ) -> LogCaptureHandler:
         """Set the level for capturing of logs. After the end of the 'with' statement,
         the level is restored to its original value.
@@ -119,15 +137,16 @@ def assert_logging_with_exception(
     **kwargs
 ):
 
-    with caplog_for_logger(caplog,
-        __package_name__ + "." + logging_name,
-        logging_level):
+    with caplog_for_logger(
+        caplog, __package_name__ + "." + logging_name, logging_level
+    ):
         result = None
         try:
             result = function(*args, **kwargs)
         except (PQException, BeartypeCallHintParamViolation) as e:
-            if isinstance(e,
-                BeartypeCallHintParamViolation) and exception is PQTypeError:
+            if isinstance(
+                e, BeartypeCallHintParamViolation
+            ) and exception is PQTypeError:
                 return result
             if not isinstance(e, PQException):
                 raise e
diff --git a/tests/integration_tests/__init__.py b/tests/integration_tests/__init__.py
new file mode 100644
index 00000000..cc022fb5
--- /dev/null
+++ b/tests/integration_tests/__init__.py
@@ -0,0 +1,3 @@
+"""
+This module contains the integration tests for the application.
+"""
diff --git a/tests/integration_tests/add_molecules/__init__.py b/tests/integration_tests/add_molecules/__init__.py
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/tests/integration_tests/add_molecules/__init__.py
@@ -0,0 +1 @@
+
diff --git a/tests/integration_tests/add_molecules/ref_data/combined.rst b/tests/integration_tests/add_molecules/ref_data/combined.rst
new file mode 100644
index 00000000..d8ecafc2
--- /dev/null
+++ b/tests/integration_tests/add_molecules/ref_data/combined.rst
@@ -0,0 +1,717 @@
+Box  21.8331 37.4863 20.122  90.0 90.0 90.0
+Ga    0    0    10.80180897 0.00975971 -3.2581555 1855100390000.0 1192624970000.0 3479765000000.0 2.10811445 0.91532024 -8.8107464
+Ga    0    0    -10.00852663 0.0171062 -6.63482266 -914432764000.0 960647365000.0 783691959000.0 -6.3484452 4.24061483 23.77383879
+Ga    0    0    -0.25119966 18.49209298 -3.37035417 -4140365530000.0 2317662510000.0 3338414420000.0 1.53860776 20.85514935 -10.23482177
+Ga    0    0    0.19389451 -18.6884281 -6.87031187 1061890680000.0 924732476000.0 -3492013120000.0 4.60335062 3.30309762 35.02192063
+Ga    0    0    -5.67236851 9.63479532 -3.81921114 -1773479950000.0 3792433400000.0 560673898000.0 -0.72561935 9.15585803 -18.46583344
+Ga    0    0    5.8264204 -9.33516104 -2.97949364 152052222000.0 83663154100.0 -2521120950000.0 -3.42815343 -4.78510848 -25.35489163
+Ga    0    0    5.29545723 -9.28658872 -6.45167027 -517253154000.0 2010810960000.0 693764835000.0 23.56759928 -13.16129087 18.45378663
+Ga    0    0    -5.34498931 9.36692639 -7.10859633 -59200910600.0 -1344951060000.0 -2896319550000.0 -25.69345199 2.11504613 -35.68257443
+Ga    0    0    5.2404986 8.94645198 -6.97120605 1399209180000.0 1248331080000.0 490018339000.0 2.32351986 5.83401867 -7.47667174
+Ga    0    0    -5.58704881 -9.70620955 -6.2543066 -864400598000.0 -2269529430000.0 813476500000.0 -16.43830653 -19.94019105 53.06638642
+Ga    0    0    -5.55246037 -9.37500959 -2.86440637 -1077486800000.0 484770404000.0 2450078570000.0 2.39312376 6.4253436 4.55025905
+Ga    0    0    5.5248715 9.826137 -3.6157943 5022731290000.0 -160573762000.0 -2058457980000.0 7.45440514 1.56214276 1.59212331
+Ga    0    0    -10.73909253 0.09385009 3.39987992 2485740470000.0 -382762848000.0 -632000351000.0 1.78832072 -11.33363456 8.33202039
+Ga    0    0    -10.01126369 -0.04013755 0.00732452 49080864100.0 12402901000.0 2050274250000.0 -15.03437942 -9.31300032 14.65296003
+Ga    0    0    -0.1751843 -18.64887938 3.26645348 2103027930000.0 1313237240000.0 -41287434600.0 12.03955627 -4.0905736 16.30725307
+Ga    0    0    0.65986627 -18.67446035 -0.04307119 229411003000.0 58604233400.0 111372221000.0 13.77796601 -1.23263423 -13.52262883
+Ga    0    0    -5.55451364 9.65298115 2.81936898 -215919606000.0 -623091258000.0 -636743373000.0 12.83855751 1.88938607 -6.816387
+Ga    0    0    5.67092109 -9.26323113 3.72333637 -9155927110.0 -1182562090000.0 1223590400000.0 12.88414263 -28.70932096 -13.72512832
+Ga    0    0    5.2053977 -9.0044597 0.37088505 -1114545730000.0 -1806647610000.0 -1619044800000.0 8.39233032 2.65767113 -10.03018692
+Ga    0    0    -5.3197898 9.38297287 -0.5964403 -2355395040.0 -467356579000.0 -700338412000.0 -6.5416521 0.88050758 31.42710457
+Ga    0    0    5.38919719 9.1243628 -0.21776152 3475497760000.0 -872567792000.0 -232101066000.0 -7.02636338 11.99330723 -7.38144393
+Ga    0    0    -5.2163702 -9.93538657 0.53397083 -1461077960000.0 561314783000.0 2049464080000.0 -15.84142469 15.79958786 42.3084276
+Ga    0    0    -5.76975177 -9.2812608 3.84003504 -209226771000.0 -401588908000.0 1174897840000.0 18.77879613 -4.52709797 8.21128961
+Ga    0    0    5.36484363 9.11813848 3.26759985 -3004539240000.0 2309071760000.0 -1731060070000.0 -7.75572173 -4.8474037 -42.55698861
+Ga    0    0    -10.81212816 0.00335306 -9.94061966 -1013857700000.0 955352056000.0 43319684500.0 24.82694406 -18.58165342 -31.4619932
+Ga    0    0    -10.18383431 0.03981347 6.71603848 -286697260000.0 -3230816880000.0 -223602238000.0 7.88220616 -13.79380151 3.84167321
+Ga    0    0    -0.5979212 -18.71395573 9.94830166 -1999941350000.0 1938140310000.0 330575336000.0 -12.98026154 -10.82986025 15.31499491
+Ga    0    0    0.11530883 18.62583605 6.59901297 -479416351000.0 -1859700330000.0 -1428398230000.0 -10.57647307 18.15511632 12.95197496
+Ga    0    0    -5.65346768 9.43753966 9.5639714 -66385889800.0 1177191990000.0 -51101201900.0 -0.33752754 4.68760838 -0.28453876
+Ga    0    0    5.34979375 -9.10077759 -9.79612284 1173116980000.0 -479084101000.0 -943188958000.0 19.496744 -5.47233902 -21.19680301
+Ga    0    0    5.04705583 -9.22698358 7.06814836 -1084572540000.0 -656747729000.0 4416000030000.0 -5.84441314 7.31347362 -26.40350844
+Ga    0    0    -5.81788039 9.44694591 6.16971256 152995982000.0 1673846360000.0 700904154000.0 -8.48166247 15.17714673 -22.53948703
+Ga    0    0    4.99913477 9.17591168 6.50663889 -2604424670000.0 1530191640000.0 -1756144250000.0 1.39496161 0.56859535 -15.30427589
+Ga    0    0    -5.61202125 -9.93795136 7.10113387 1375133870000.0 -543318319000.0 -876263674000.0 -23.84144224 -7.70682659 35.33058407
+Ga    0    0    -5.73257068 -9.48578969 -9.53612904 -40961915900.0 -10943042400.0 1364852330000.0 2.18376603 -10.73500281 -30.15649768
+Ga    0    0    5.68401873 9.58095378 9.72484742 -1588604360000.0 -212255081000.0 132751586000.0 11.97646761 7.90403636 38.73567059
+O    0    0    -10.83235933 0.77452627 -5.07484435 6158856250000.0 4061831090000.0 -4410316900000.0 10.01352109 -29.70655815 -11.74353744
+H    0    0    10.19689987 1.18014997 -5.419189 19604500100000.0 29019619400000.0 -6398721940000.0 -3.71470616 7.10377184 5.93227831
+O    0    0    -10.73748342 -0.81021653 -1.52821917 4548661780000.0 2644294440000.0 726174495000.0 -9.01322197 4.3759084 -4.04488865
+H    0    0    10.43960876 -1.47219892 -1.28185128 -2957897830000.0 8632100440000.0 -3172650240000.0 0.06101422 -2.11021876 -3.12325809
+O    0    0    0.06084055 -18.09980354 -5.02164775 3065523610000.0 -718575908000.0 61567766200.0 0.38380999 -5.0026525 5.32688653
+H    0    0    0.36063394 -17.19066219 -4.90828558 9892470350000.0 -4140843360000.0 9453160770000.0 1.70659275 -1.05717616 1.49827544
+O    0    0    0.49948721 17.93663023 -1.7310239 3014114650000.0 897214236000.0 2342565200000.0 -12.76430391 -1.56903104 -17.77378384
+H    0    0    1.05357389 17.15223595 -1.81456205 16174928400000.0 10673423300000.0 -2160418320000.0 1.07760248 3.1225731 0.37236285
+O    0    0    -5.10493117 8.69055526 -5.36980967 -5010642330000.0 2315055810000.0 5093705560000.0 5.1242951 9.15377224 5.13216414
+H    0    0    -4.99506327 7.73693257 -5.28150417 13652909900000.0 5728697850000.0 18737264700000.0 -2.34348794 3.4358325 0.15965548
+O    0    0    4.969171 -8.57033671 -1.49155422 313664176000.0 3833722270000.0 -2482354930000.0 -1.24022654 4.08918941 13.81123206
+H    0    0    4.31414607 -7.93648074 -1.80529616 999330609000.0 5277544480000.0 -996908958000.0 -1.65995627 -1.4408503 8.7001672
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diff --git a/tests/integration_tests/add_molecules/ref_data/mil68ga-md-01.rst b/tests/integration_tests/add_molecules/ref_data/mil68ga-md-01.rst
new file mode 120000
index 00000000..d0285d5e
--- /dev/null
+++ b/tests/integration_tests/add_molecules/ref_data/mil68ga-md-01.rst
@@ -0,0 +1 @@
+../../../../examples/add_molecules/mil68ga-md-01.rst
\ No newline at end of file
diff --git a/tests/integration_tests/add_molecules/ref_data/perylene-md-05.rst b/tests/integration_tests/add_molecules/ref_data/perylene-md-05.rst
new file mode 120000
index 00000000..c28f05ff
--- /dev/null
+++ b/tests/integration_tests/add_molecules/ref_data/perylene-md-05.rst
@@ -0,0 +1 @@
+../../../../examples/add_molecules/perylene-md-05.rst
\ No newline at end of file
diff --git a/tests/integration_tests/add_molecules/ref_data/perylene-md-05.xyz b/tests/integration_tests/add_molecules/ref_data/perylene-md-05.xyz
new file mode 120000
index 00000000..b8e32fc2
--- /dev/null
+++ b/tests/integration_tests/add_molecules/ref_data/perylene-md-05.xyz
@@ -0,0 +1 @@
+../../../../examples/add_molecules/perylene-md-05.xyz
\ No newline at end of file
diff --git a/tests/integration_tests/add_molecules/ref_data/shake_mil.top b/tests/integration_tests/add_molecules/ref_data/shake_mil.top
new file mode 120000
index 00000000..3ca6b08a
--- /dev/null
+++ b/tests/integration_tests/add_molecules/ref_data/shake_mil.top
@@ -0,0 +1 @@
+../../../../examples/add_molecules/shake_mil.top
\ No newline at end of file
diff --git a/tests/integration_tests/add_molecules/ref_data/shake_perylene.top b/tests/integration_tests/add_molecules/ref_data/shake_perylene.top
new file mode 120000
index 00000000..e6cb421a
--- /dev/null
+++ b/tests/integration_tests/add_molecules/ref_data/shake_perylene.top
@@ -0,0 +1 @@
+../../../../examples/add_molecules/shake_perylene.top
\ No newline at end of file
diff --git a/tests/integration_tests/add_molecules/ref_data/top.top b/tests/integration_tests/add_molecules/ref_data/top.top
new file mode 100644
index 00000000..4ce2bb02
--- /dev/null
+++ b/tests/integration_tests/add_molecules/ref_data/top.top
@@ -0,0 +1,194 @@
+SHAKE 192 192 0
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+  691   685   1.100786848627	 # put here some comment
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+  695   690   1.102015725191	
+  698   693   1.102015725191	
+  699   696   1.102015725191	
+  700   697   1.100786848627	
+  707   710   1.102015725191	
+  708   701   1.102015725191	
+  709   702   1.102015725191	
+  712   706   1.100786848627	
+  715   713   1.100786848627	
+  716   714   1.102015725191	
+END
diff --git a/tests/integration_tests/add_molecules/test_add_molecules.py b/tests/integration_tests/add_molecules/test_add_molecules.py
new file mode 100644
index 00000000..78511080
--- /dev/null
+++ b/tests/integration_tests/add_molecules/test_add_molecules.py
@@ -0,0 +1,68 @@
+import pathlib
+import pytest
+
+from unittest.mock import patch
+from filecmp import cmp as filecmp
+
+pytestmark = pytest.mark.integration
+
+from PQAnalysis.cli.add_molecules import main
+
+__path__ = pathlib.Path(__file__).parent.absolute()
+
+
+
+class TestAddMolecules:
+
+    """
+    Test the add_molecules function.
+    """
+
+    @pytest.mark.parametrize("example_dir", ["add_molecules"], indirect=False)
+    def test_add_molecules_no_topology(self, test_integration_folder):
+        """
+        Test the add_molecules function when no topology is given.
+        """
+        # test command line tool with certain arguments
+
+        with patch(
+            'argparse._sys.argv',
+            [
+                'add_molecules',
+                'mil68ga-md-01.rst',
+                'perylene-md-05.xyz',
+                '-o',
+                'combined.rst'
+            ]
+        ):
+            main()
+
+        filecmp("combined.rst", str(__path__ / "ref_data" / "combined.rst"))
+
+    @pytest.mark.parametrize("example_dir", ["add_molecules"], indirect=False)
+    def test_add_molecules(self, test_integration_folder):
+        """
+        Test the add_molecules function when no topology is given.
+        """
+        # test command line tool with certain arguments
+
+        with patch(
+            'argparse._sys.argv',
+            [
+                'add_molecules',
+                'mil68ga-md-01.rst',
+                'perylene-md-05.xyz',
+                '--top-file',
+                'shake_mil.top',
+                '--added-topology-file',
+                'shake_perylene.top',
+                '-o',
+                'combined.rst',
+                '--output-topology-file',
+                'top.top'
+            ]
+        ):
+            main()
+
+        filecmp("combined.rst", str(__path__ / "ref_data" / "combined.rst"))
+        filecmp("top.top", str(__path__ / "ref_data" / "top.top"))
diff --git a/tests/io/test_topology_writer.py b/tests/io/test_topology_writer.py
new file mode 100644
index 00000000..ecacab79
--- /dev/null
+++ b/tests/io/test_topology_writer.py
@@ -0,0 +1,330 @@
+"""
+Unit tests for the topologyWriter module.
+"""
+
+import pytest
+
+from PQAnalysis.io.topology_file import TopologyFileWriter, TopologyFileError
+from PQAnalysis.topology import BondedTopology
+from PQAnalysis.topology.bonded_topology import (
+    Bond,
+    Angle,
+    Dihedral,
+)
+
+from . import pytestmark  # pylint: disable=unused-import
+
+# pylint: disable=protected-access
+
+
+
+class TestTopologyFileWriter:
+
+    """
+    Test cases for the TopologyFileWriter class.
+    """
+
+    def test__check_type_given(self):
+        """
+        Test the _check_type_given method.
+        """
+        bonds = [Bond(index1=1, index2=2, bond_type=1)]
+
+        TopologyFileWriter._check_type_given(bonds, "bond")
+
+        bonds.append(Bond(index1=2, index2=3))
+
+        with pytest.raises(TopologyFileError) as exception:
+            TopologyFileWriter._check_type_given(bonds, "bond")
+        assert str(exception.value) == (
+            "In order to write the bond information in 'PQ' topology format, "
+            "all bonds must have a bond type defined."
+        )
+
+        angles = [Angle(index1=1, index2=2, index3=3, angle_type=1)]
+
+        TopologyFileWriter._check_type_given(angles, "angle")
+
+        angles.append(Angle(index1=2, index2=3, index3=4))
+
+        with pytest.raises(TopologyFileError) as exception:
+            TopologyFileWriter._check_type_given(angles, "angle")
+        assert str(exception.value) == (
+            "In order to write the angle information in 'PQ' topology format, "
+            "all angles must have a angle type defined."
+        )
+
+        dihedrals = [
+            Dihedral(index1=1, index2=2, index3=3, index4=4, dihedral_type=1)
+        ]
+
+        TopologyFileWriter._check_type_given(dihedrals, "dihedral")
+
+        dihedrals.append(Dihedral(index1=2, index2=3, index3=4, index4=5))
+
+        with pytest.raises(TopologyFileError) as exception:
+            TopologyFileWriter._check_type_given(dihedrals, "dihedral")
+        assert str(exception.value) == (
+            "In order to write the dihedral information in 'PQ' topology format, "
+            "all dihedrals must have a dihedral type defined."
+        )
+
+    def test__get_bond_lines(self):
+        """
+        Test the _get_bond_lines method.
+        """
+        topology = BondedTopology()
+
+        lines = TopologyFileWriter._get_bond_lines(topology)
+        assert lines[0] == "BONDS 0 0 0"
+        assert lines[1] == "END"
+
+        bond1 = Bond(index1=1, index2=2, bond_type=1)
+        bond2 = Bond(index1=2, index2=3, bond_type=1, is_linker=True)
+        bond3 = Bond(
+            index1=5,
+            index2=2,
+            bond_type=1,
+            comment="This is a comment.",
+        )
+        bond4 = Bond(
+            index1=5,
+            index2=2,
+            bond_type=1,
+            is_linker=True,
+            comment="This is a comment."
+        )
+
+        topology.bonds = [bond1, bond2, bond3, bond4]
+
+        lines = TopologyFileWriter._get_bond_lines(topology)
+        assert lines[0] == "BONDS 3 2 2"
+        assert lines[1] == f"{1:>5d} {2:>5d} {1:>5d}"
+        assert lines[2] == f"{2:>5d} {3:>5d} {1:>5d} *"
+        assert lines[3] == f"{5:>5d} {2:>5d} {1:>5d} # This is a comment."
+        assert lines[4] == f"{5:>5d} {2:>5d} {1:>5d} * # This is a comment."
+        assert lines[5] == "END"
+
+    def test__get_angle_lines(self):
+        """
+        Test the _get_angle_lines method.
+        """
+        topology = BondedTopology()
+
+        lines = TopologyFileWriter._get_angle_lines(topology)
+        assert lines[0] == "ANGLES 0 0 0 0"
+        assert lines[1] == "END"
+
+        angle1 = Angle(index1=1, index2=2, index3=3, angle_type=1)
+        angle2 = Angle(
+            index1=2,
+            index2=3,
+            index3=4,
+            angle_type=1,
+            is_linker=True,
+        )
+        angle3 = Angle(
+            index1=5,
+            index2=2,
+            index3=3,
+            angle_type=1,
+            comment="This is a comment.",
+        )
+        angle4 = Angle(
+            index1=5,
+            index2=2,
+            index3=3,
+            angle_type=1,
+            is_linker=True,
+            comment="This is a comment."
+        )
+
+        topology.angles = [angle1, angle2, angle3, angle4]
+
+        lines = TopologyFileWriter._get_angle_lines(topology)
+        assert lines[0] == "ANGLES 3 2 2 2"
+        assert lines[1] == f"{1:>5d} {2:>5d} {3:>5d} {1:>5d}"
+        assert lines[2] == f"{2:>5d} {3:>5d} {4:>5d} {1:>5d} *"
+        assert lines[3] == (
+            f"{5:>5d} {2:>5d} {3:>5d} {1:>5d} "
+            "# This is a comment."
+        )
+        assert lines[4] == (
+            f"{5:>5d} {2:>5d} {3:>5d} {1:>5d} * # "
+            "This is a comment."
+        )
+        assert lines[5] == "END"
+
+    def test__get_dihedral_lines(self):
+        """
+        Test the _get_dihedral_lines method.
+        """
+        topology = BondedTopology()
+
+        lines = TopologyFileWriter._get_dihedral_lines(topology)
+        assert lines[0] == "DIHEDRALS 0 0 0 0"
+        assert lines[1] == "END"
+
+        dihedral1 = Dihedral(
+            index1=1, index2=2, index3=3, index4=4, dihedral_type=1
+        )
+        dihedral2 = Dihedral(
+            index1=2,
+            index2=3,
+            index3=4,
+            index4=5,
+            dihedral_type=1,
+            is_linker=True,
+        )
+        dihedral3 = Dihedral(
+            index1=5,
+            index2=2,
+            index3=3,
+            index4=4,
+            dihedral_type=1,
+            comment="This is a comment.",
+        )
+        dihedral4 = Dihedral(
+            index1=5,
+            index2=2,
+            index3=3,
+            index4=4,
+            dihedral_type=1,
+            is_linker=True,
+            comment="This is a comment."
+        )
+
+        topology.dihedrals = [dihedral1, dihedral2, dihedral3, dihedral4]
+
+        lines = TopologyFileWriter._get_dihedral_lines(topology)
+        assert lines[0] == "DIHEDRALS 3 2 2 2"
+        assert lines[1] == f"{1:>5d} {2:>5d} {3:>5d} {4:>5d} {1:>5d}"
+        assert lines[2] == f"{2:>5d} {3:>5d} {4:>5d} {5:>5d} {1:>5d} *"
+        assert lines[3] == (
+            f"{5:>5d} {2:>5d} {3:>5d} {4:>5d} {1:>5d} "
+            "# This is a comment."
+        )
+        assert lines[4] == (
+            f"{5:>5d} {2:>5d} {3:>5d} {4:>5d} {1:>5d} * # "
+            "This is a comment."
+        )
+        assert lines[5] == "END"
+
+    def test__get_improper_lines(self):
+        """
+        Test the _get_improper_lines method.
+        """
+        topology = BondedTopology()
+
+        lines = TopologyFileWriter._get_improper_lines(topology)
+        assert lines[0] == "IMPROPERS 0 0 0 0"
+        assert lines[1] == "END"
+
+        improper1 = Dihedral(
+            index1=1,
+            index2=2,
+            index3=3,
+            index4=4,
+            dihedral_type=1,
+            is_improper=True
+        )
+        improper2 = Dihedral(
+            index1=2,
+            index2=3,
+            index3=4,
+            index4=5,
+            dihedral_type=1,
+            is_linker=True,
+            is_improper=True,
+        )
+        improper3 = Dihedral(
+            index1=5,
+            index2=2,
+            index3=3,
+            index4=4,
+            dihedral_type=1,
+            is_improper=True,
+            comment="This is a comment.",
+        )
+        improper4 = Dihedral(
+            index1=5,
+            index2=2,
+            index3=3,
+            index4=4,
+            dihedral_type=1,
+            is_linker=True,
+            is_improper=True,
+            comment="This is a comment."
+        )
+
+        topology.impropers = [improper1, improper2, improper3, improper4]
+
+        lines = TopologyFileWriter._get_improper_lines(topology)
+        assert lines[0] == "IMPROPERS 3 2 2 2"
+        assert lines[1] == f"{1:>5d} {2:>5d} {3:>5d} {4:>5d} {1:>5d}"
+        assert lines[2] == f"{2:>5d} {3:>5d} {4:>5d} {5:>5d} {1:>5d} *"
+        assert lines[3] == (
+            f"{5:>5d} {2:>5d} {3:>5d} {4:>5d} {1:>5d} "
+            "# This is a comment."
+        )
+        assert lines[4] == (
+            f"{5:>5d} {2:>5d} {3:>5d} {4:>5d} {1:>5d} * # "
+            "This is a comment."
+        )
+        assert lines[5] == "END"
+
+    def test__get_shake_lines(self):
+        """
+        Test the _get_shake_lines method.
+        """
+
+        topology = BondedTopology()
+
+        lines = TopologyFileWriter._get_shake_lines(topology)
+        assert lines[0] == "SHAKE 0 0 0"
+        assert lines[1] == "END"
+
+        bond1 = Bond(
+            index1=1,
+            index2=2,
+            equilibrium_distance=1.4,
+            is_shake=True,
+        )
+        bond2 = Bond(
+            index1=2,
+            index2=3,
+            equilibrium_distance=1.4,
+            is_linker=True,
+            is_shake=True
+        )
+        bond3 = Bond(
+            index1=5,
+            index2=2,
+            equilibrium_distance=1.5,
+            is_shake=True,
+            comment="This is a comment.",
+        )
+        bond4 = Bond(
+            index1=5,
+            index2=2,
+            equilibrium_distance=1.5,
+            is_linker=True,
+            is_shake=True,
+            comment="This is a comment."
+        )
+
+        topology.shake_bonds = [bond1, bond2, bond3, bond4]
+
+        lines = TopologyFileWriter._get_shake_lines(topology)
+        assert lines[0] == "SHAKE 3 2 2"
+        assert lines[1] == f"{1:>5d} {2:>5d} {1.4:>16.12f}\t"
+        assert lines[2] == f"{2:>5d} {3:>5d} {1.4:>16.12f}\t*"
+        assert lines[3] == (
+            f"{5:>5d} {2:>5d} {1.5:>16.12f}\t "
+            "# This is a comment."
+        )
+        assert lines[4] == (
+            f"{5:>5d} {2:>5d} {1.5:>16.12f}\t* # "
+            "This is a comment."
+        )
+        assert lines[5] == "END"
diff --git a/tests/topology/test_shakeTopology.py b/tests/topology/test_shakeTopology.py
index 8655c53b..4627e01d 100644
--- a/tests/topology/test_shakeTopology.py
+++ b/tests/topology/test_shakeTopology.py
@@ -127,10 +127,10 @@ def test_write_topology(self, capsys):
 
         captured = capsys.readouterr()
         assert captured.out == """
-SHAKE 3  2  0
-2 1 0.8035533905932738
-3 4 0.8035533905932737
-5 4 1.290569415042095
+SHAKE 3 2 0
+    2     1   0.803553390593\t
+    3     4   0.803553390593\t
+    5     4   1.290569415042\t
 END
 """
 
@@ -141,10 +141,10 @@ def test_write_topology(self, capsys):
 
         captured = capsys.readouterr()
         assert captured.out == """
-SHAKE 3  2  0
-2 1 0.8035533905932738  # test
-3 4 0.8035533905932737  # test2
-5 4 1.290569415042095  # test3
+SHAKE 3 2 0
+    2     1   0.803553390593\t # test
+    3     4   0.803553390593\t # test2
+    5     4   1.290569415042\t # test3
 END
 """
 
@@ -158,9 +158,9 @@ def test_write_topology(self, capsys):
 
         captured = capsys.readouterr()
         assert captured.out == """
-SHAKE 3  2  0
-2 1 0.8035533905932738  # test
-3 4 1.0470614028176843  # test2
-5 4 1.0470614028176843  # test2
+SHAKE 3 2 0
+    2     1   0.803553390593\t # test
+    3     4   1.047061402818\t # test2
+    5     4   1.047061402818\t # test2
 END
 """
diff --git a/tests/utils/__init__.py b/tests/utils/__init__.py
index 0901e3ed..7e3dd4ae 100644
--- a/tests/utils/__init__.py
+++ b/tests/utils/__init__.py
@@ -1,3 +1,7 @@
+"""
+This module is used to test the utils module.
+"""
+
 import pytest
 
 pytestmark = pytest.mark.utils
diff --git a/tests/utils/test_string.py b/tests/utils/test_string.py
new file mode 100644
index 00000000..d050b07b
--- /dev/null
+++ b/tests/utils/test_string.py
@@ -0,0 +1,24 @@
+"""
+Test cases for the string utility functions.
+"""
+
+from PQAnalysis.utils.string import is_comment_line
+
+from . import pytestmark  # pylint: disable=unused-import
+
+
+
+def test_is_comment_line():
+    """
+    Test the is_comment_line function.
+    """
+
+    assert not is_comment_line("This is not a comment line.")
+
+    assert is_comment_line("# This is a comment line.")
+    assert not is_comment_line(" ")
+    assert is_comment_line(" ", empty_line=True)
+
+    assert not is_comment_line("# This is a comment line.", comment_token="!")
+    assert is_comment_line("! This is a comment line.", comment_token="!")
+    assert is_comment_line("     !", comment_token="!", empty_line=False)