diff --git a/compechem/ensemble.py b/compechem/ensemble.py
index 5051983..97eba30 100644
--- a/compechem/ensemble.py
+++ b/compechem/ensemble.py
@@ -17,7 +17,7 @@ class Ensemble:
         calculated at various levels of theory
     """
 
-    def __init__(self, molecules_list) -> None:
+    def __init__(self, molecules_list: list) -> None:
         """
         Parameters
         ----------
@@ -53,7 +53,9 @@ def __init__(
             self.electronic = electronic
             self.vibronic = vibronic
 
-    def boltzmann_average(self, method_el, method_vib=None, temperature=297.15):
+    def boltzmann_average(
+        self, method_el: str, method_vib: str = None, temperature: float = 297.15
+    ):
         """Calculates the average free Gibbs energy of the ensemble (in Hartree), weighted for each 
         molecule by its Boltzmann factor.
         
diff --git a/compechem/modules/algorithms.py b/compechem/modules/algorithms.py
index 9a36fea..f4a056a 100644
--- a/compechem/modules/algorithms.py
+++ b/compechem/modules/algorithms.py
@@ -1,7 +1,10 @@
 from compechem.ensemble import Ensemble
+from compechem.molecule import Molecule
 
 
-def calculate_pka(protonated, deprotonated, method_el, method_vib=None):
+def calculate_pka(
+    protonated: Molecule, deprotonated: Molecule, method_el: str, method_vib: str = None
+):
     """Calculates the pKa of a molecule, given the protonated and deprotonated forms.
 
     Parameters
@@ -55,7 +58,9 @@ def calculate_pka(protonated, deprotonated, method_el, method_vib=None):
     return pka
 
 
-def calculate_potential(oxidised, reduced, method_el, method_vib=None, pH=7):
+def calculate_potential(
+    oxidised: Molecule, reduced: Molecule, method_el: str, method_vib: str = None, pH: float = 7.0
+):
     """Calculates the reduction potential of a molecule, given the oxidised and reduced forms.
 
     Parameters
diff --git a/compechem/modules/crest.py b/compechem/modules/crest.py
index 3b8d9dc..f2ce9db 100644
--- a/compechem/modules/crest.py
+++ b/compechem/modules/crest.py
@@ -1,10 +1,11 @@
 import os, copy
 from tempfile import mkdtemp
+from turtle import st
 from compechem.molecule import Molecule
 from compechem.modules import tools
 
 
-def tautomer_search(mol, nproc=1, remove_tdir=True, optionals=""):
+def tautomer_search(mol: Molecule, nproc: int = 1, remove_tdir: bool = True, optionals: str = ""):
     """Tautomer search using CREST.
 
     Parameters
@@ -48,6 +49,10 @@ def tautomer_search(mol, nproc=1, remove_tdir=True, optionals=""):
                 print(
                     f"WARNING: cyclization change spotted for {tautomer.name}. Removing from list."
                 )
+                tools.add_flag(
+                    mol,
+                    f"Cyclization change occurred for {tautomer.name} during conformer search. Conformer was removed.",
+                )
             else:
                 tautomers.append(tautomer)
 
@@ -61,10 +66,11 @@ def tautomer_search(mol, nproc=1, remove_tdir=True, optionals=""):
         tools.process_output(
             mol, "CREST", mol.charge, mol.spin, "tautomers", tdir, remove_tdir, parent_dir
         )
+        tools.add_flag(mol, "No possible tautomers. Tautomer search was ignored.")
         return [mol]
 
 
-def conformer_search(mol, nproc=1, remove_tdir=True, optionals=""):
+def conformer_search(mol: Molecule, nproc: int = 1, remove_tdir: bool = True, optionals: str = ""):
     """Conformer search using CREST.
 
     Parameters
@@ -108,21 +114,26 @@ def conformer_search(mol, nproc=1, remove_tdir=True, optionals=""):
                 print(
                     f"WARNING: cyclization change spotted for {conformer.name}. Removing from list."
                 )
+                tools.add_flag(
+                    mol,
+                    f"Cyclization change occurred for {conformer.name} during conformer search. Conformer was removed.",
+                )
             else:
                 conformers.append(conformer)
 
         tools.process_output(
             mol, "CREST", mol.charge, mol.spin, "conformers", tdir, remove_tdir, parent_dir
         )
-
         return conformers
+
     else:
         print("ERROR: conformer search failed.")
+        tools.add_flag(mol, "Error during conformer search.")
         os.chdir(parent_dir)
-        return None
+        return [mol]
 
 
-def deprotonate(mol, nproc=1, remove_tdir=True, optionals=""):
+def deprotonate(mol: Molecule, nproc: int = 1, remove_tdir: bool = True, optionals: str = ""):
     """Deprotomer search using CREST.
 
     Parameters
@@ -151,7 +162,7 @@ def deprotonate(mol, nproc=1, remove_tdir=True, optionals=""):
     mol.write_xyz("geom.xyz")
 
     os.system(
-        f"crest geom.xyz --alpb water --chrg {mol.charge} --uhf {mol.spin-1} --deprotonate {optionals} -T {nproc} > output.out 2>> output.err"
+        f"crest geom.xyz --alpb water --chrg {mol.charge} --uhf {mol.spin-1} --deprotonate --fstrict {optionals} -T {nproc} > output.out 2>> output.err"
     )
 
     if os.path.exists("deprotonated.xyz"):
@@ -168,6 +179,10 @@ def deprotonate(mol, nproc=1, remove_tdir=True, optionals=""):
                 print(
                     f"WARNING: cyclization change spotted for {deprotomer.name}. Removing from list."
                 )
+                tools.add_flag(
+                    mol,
+                    f"Cyclization change occurred for {deprotomer.name} during deprotomer search. Deprotomer was removed.",
+                )
             else:
                 deprotomers.append(deprotomer)
 
@@ -181,10 +196,8 @@ def deprotonate(mol, nproc=1, remove_tdir=True, optionals=""):
         os.chdir(parent_dir)
         return None
 
-    return deprotomers
-
 
-def protonate(mol, nproc=1, remove_tdir=True, optionals=""):
+def protonate(mol: Molecule, nproc: int = 1, remove_tdir: bool = True, optionals: str = ""):
     """Protomer search using CREST.
 
     Parameters
@@ -213,7 +226,7 @@ def protonate(mol, nproc=1, remove_tdir=True, optionals=""):
     mol.write_xyz("geom.xyz")
 
     os.system(
-        f"crest geom.xyz --alpb water --chrg {mol.charge} --uhf {mol.spin-1} --protonate {optionals} -T {nproc} > output.out 2>> output.err"
+        f"crest geom.xyz --alpb water --chrg {mol.charge} --uhf {mol.spin-1} --protonate --fstrict {optionals} -T {nproc} > output.out 2>> output.err"
     )
 
     if os.path.exists("protonated.xyz"):
@@ -230,8 +243,12 @@ def protonate(mol, nproc=1, remove_tdir=True, optionals=""):
                 print(
                     f"WARNING: cyclization change spotted for {protomer.name}. Removing from list."
                 )
+                tools.add_flag(
+                    mol,
+                    f"Cyclization change occurred for {protomer.name} during deprotomer search. Protomer was removed.",
+                )
             else:
-                protomers.append(deprotomer)
+                protomers.append(protomer)
 
         tools.process_output(
             mol, "CREST", mol.charge, mol.spin, "protomers", tdir, remove_tdir, parent_dir
@@ -243,19 +260,17 @@ def protonate(mol, nproc=1, remove_tdir=True, optionals=""):
         os.chdir(parent_dir)
         return None
 
-    return protomers
-
 
 def qcg_grow(
-    solute,
-    solvent,
-    charge=None,
-    spin=None,
-    method="gfn2",
-    nsolv=0,
-    nproc=1,
-    optionals="",
-    remove_tdir=True,
+    solute: Molecule,
+    solvent: Molecule,
+    charge: int = None,
+    spin: int = None,
+    method: str = "gfn2",
+    nsolv: int = 0,
+    nproc: int = 1,
+    optionals: str = "",
+    remove_tdir: bool = True,
 ):
     """Quantum Cluster Growth using CREST.
 
@@ -316,6 +331,7 @@ def qcg_grow(
         cluster.update_geometry("grow/cluster.xyz")
     except:
         print("ERROR: cluster growth failed.")
+        tools.add_flag(solute, "Cluster growth failed.")
         os.chdir(parent_dir)
         return None
 
@@ -325,17 +341,17 @@ def qcg_grow(
 
 
 def qcg_ensemble(
-    solute,
-    solvent,
-    charge=None,
-    spin=None,
-    method="gfn2",
-    enslvl="gfn2",
-    ensemble_choice="full_ensemble",
-    nsolv=0,
-    nproc=1,
-    optionals="",
-    remove_tdir=True,
+    solute: Molecule,
+    solvent: Molecule,
+    charge: int = None,
+    spin: int = None,
+    method: st = "gfn2",
+    enslvl: str = "gfn2",
+    ensemble_choice: str = "full_ensemble",
+    nsolv: int = 0,
+    nproc: int = 1,
+    optionals: str = "",
+    remove_tdir: bool = True,
 ):
     """Quantum Cluster Growth + ensemble generation using CREST.
 
@@ -406,6 +422,7 @@ def qcg_ensemble(
 
     except:
         print("ERROR: cluster growth failed.")
+        tools.add_flag(solute, "Cluster growth failed.")
         os.chdir(parent_dir)
         return None
 
diff --git a/compechem/modules/orca.py b/compechem/modules/orca.py
index 91920ea..01f8658 100644
--- a/compechem/modules/orca.py
+++ b/compechem/modules/orca.py
@@ -49,7 +49,14 @@ def __init__(
         self.solvent = solvent
         self.optionals = optionals
 
-    def spe(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
+    def spe(
+        self,
+        mol: Molecule,
+        charge: int = None,
+        spin: int = None,
+        inplace: bool = False,
+        remove_tdir: bool = True,
+    ):
         """Single point energy calculation.
 
         Parameters
@@ -130,7 +137,14 @@ def spe(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
         if inplace is False:
             return newmol
 
-    def opt(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
+    def opt(
+        self,
+        mol: Molecule,
+        charge: int = None,
+        spin: int = None,
+        inplace: bool = False,
+        remove_tdir: bool = True,
+    ):
         """Geometry optimization + frequency analysis.
 
         Parameters
@@ -173,7 +187,7 @@ def opt(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
                 f"%pal nproc {self.nproc} end\n"
                 f"%maxcore {self.maxcore}\n"
                 f"! {self.method} {self.basis_set} {self.optionals}\n"
-                f"! RIJCOSX {self.aux_basis}"
+                f"! RIJCOSX {self.aux_basis}\n"
             )
             if self.solvation is True:
                 inp.write(
@@ -217,9 +231,17 @@ def opt(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
 
         tools.process_output(mol, self.method, charge, spin, "opt", tdir, remove_tdir, parent_dir)
 
-        return newmol
+        if inplace is False:
+            return newmol
 
-    def freq(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
+    def freq(
+        self,
+        mol: Molecule,
+        charge: int = None,
+        spin: int = None,
+        inplace: bool = False,
+        remove_tdir: bool = True,
+    ):
         """Frequency analysis (analytical frequencies).
 
         Note: if the SMD solvation model is detected, defaults to numerical frequencies
@@ -308,7 +330,14 @@ def freq(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
         if inplace is False:
             return newmol
 
-    def nfreq(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
+    def nfreq(
+        self,
+        mol: Molecule,
+        charge: int = None,
+        spin: int = None,
+        inplace: bool = False,
+        remove_tdir: bool = True,
+    ):
         """Frequency analysis (numerical frequencies).
 
         Parameters
diff --git a/compechem/modules/tools.py b/compechem/modules/tools.py
index 80b7b43..c2aee63 100644
--- a/compechem/modules/tools.py
+++ b/compechem/modules/tools.py
@@ -1,13 +1,14 @@
 import os
 import shutil
 import pickle
+from sys import flags
 from rdkit import Chem
 from compechem.molecule import Molecule
 from compechem.modules.orca import r2SCAN
 from compechem.modules.xtb import XtbInput
 
 
-def generate_inchikey(molfile):
+def generate_inchikey(molfile: str):
     """Generates InchiKey from a Mol file.
 
     Parameters
@@ -25,7 +26,7 @@ def generate_inchikey(molfile):
     return inchikey
 
 
-def generate_inchi(molfile):
+def generate_inchi(molfile: str):
     """Generates Inchi from a Mol file.
 
     Parameters
@@ -43,7 +44,21 @@ def generate_inchi(molfile):
     return inchi
 
 
-def info(mol, print_geometry=True):
+def add_flag(mol: Molecule, flag: str):
+    """Adds a warning flag to a Molecule object.
+
+    Parameters
+    ----------
+    mol : Molecule object
+        Molecule object to which the flag will be added
+    flag : str
+        String representing the warning which needs to be added
+    """
+    mol.flags.append(flag)
+    return
+
+
+def info(mol: Molecule, print_geometry: bool = True):
     """Prints information about the molecule
 
     Parameters
@@ -61,6 +76,9 @@ def info(mol, print_geometry=True):
     print(f"\nNumber of atoms: {mol.atomcount}")
     print(f"Charge: {mol.charge}")
     print(f"Spin: {mol.spin}")
+    print("\n--- Warnings ---\n")
+    for warning in mol.flags:
+        print(warning)
     print("\n --- Energies (Eh) --- \n")
     for method in mol.energies:
         print(f"* Method: {method}")
@@ -72,7 +90,7 @@ def info(mol, print_geometry=True):
             print(line, end="")
 
 
-def dump(obj, filename=None):
+def dump(obj, filename: bool = None):
     """Generates a pickle file containing an object 
 
     Parameters
@@ -93,7 +111,7 @@ def dump(obj, filename=None):
     pickle.dump(obj, open(filename, "wb"))
 
 
-def save_ext(ext, output_dir):
+def save_ext(ext: list, output_dir: str):
     """Saves all files matching a certain set of extensions
 
     Parameters
@@ -115,7 +133,16 @@ def save_ext(ext, output_dir):
             shutil.copy(file, output_dir + "/" + file)
 
 
-def process_output(mol, method, charge, spin, calc, tdir, remove_tdir, parent_dir):
+def process_output(
+    mol: Molecule,
+    method: str,
+    charge: int,
+    spin: int,
+    calc: str,
+    tdir: str,
+    remove_tdir: bool,
+    parent_dir: str,
+):
     """Processes the output of a calculation, copying the output files to a safe directory in the
     parent directory tree, and cleans the temporary directory if requested.
 
@@ -156,7 +183,7 @@ def process_output(mol, method, charge, spin, calc, tdir, remove_tdir, parent_di
     os.chdir(parent_dir)
 
 
-def cyclization_check(start_file, end_file):
+def cyclization_check(start_file: str, end_file: str):
     """Checks if a cyclization has occurred (e.g., during a
     geometry optimization), or if a ring opening has occurred.
 
@@ -221,7 +248,7 @@ def dissociation_check():
         return False
 
 
-def split_multixyz(mol, file, suffix, charge=None, spin=None):
+def split_multixyz(mol: Molecule, file: str, suffix: str, charge: int = None, spin: int = None):
     """Splits a .xyz file containing multiple structures into individual structures.
 
     Parameters
@@ -268,7 +295,12 @@ def split_multixyz(mol, file, suffix, charge=None, spin=None):
 
 
 def reorder_energies(
-    molecule_list, nproc=1, maxcore=350, method_opt=None, method_el=None, method_vib=None
+    molecule_list: list,
+    nproc: int = 1,
+    maxcore: int = 350,
+    method_opt: str = None,
+    method_el: str = None,
+    method_vib: str = None,
 ):
     """Reorders a molecule list (generated by a CREST routine such as deprotonation) at a different
     level of theory.
diff --git a/compechem/modules/xtb.py b/compechem/modules/xtb.py
index 55169f0..8327840 100644
--- a/compechem/modules/xtb.py
+++ b/compechem/modules/xtb.py
@@ -38,7 +38,14 @@ def __init__(
         self.solvent = solvent
         self.optionals = optionals
 
-    def spe(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
+    def spe(
+        self,
+        mol: Molecule,
+        charge: int = None,
+        spin: int = None,
+        inplace: bool = False,
+        remove_tdir: bool = True,
+    ):
         """Single point energy calculation.
 
         Parameters
@@ -116,7 +123,14 @@ def spe(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
         if inplace is False:
             return newmol
 
-    def opt(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
+    def opt(
+        self,
+        mol: Molecule,
+        charge: int = None,
+        spin: int = None,
+        inplace: bool = False,
+        remove_tdir: bool = True,
+    ):
         """Geometry optimization + frequency analysis.
 
         Parameters
@@ -169,10 +183,16 @@ def opt(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
 
         if tools.dissociation_check() is True:
             print(f"ERROR: dissociation spotted for {mol.name}.")
+            tools.add_flag(
+                mol, f"Dissociation occurred during geometry optimization with {self.method}."
+            )
             os.chdir(parent_dir)
             return None
         elif tools.cyclization_check(f"{mol.name}.xyz", "xtbopt.xyz") is True:
             print(f"ERROR: cyclization change spotted for {mol.name}.")
+            tools.add_flag(
+                mol, f"Cyclization change occurred during geometry optimization with {self.method}."
+            )
             os.chdir(parent_dir)
             return None
         else:
@@ -209,7 +229,14 @@ def opt(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
             if inplace is False:
                 return newmol
 
-    def freq(self, mol, charge=None, spin=None, inplace=False, remove_tdir=True):
+    def freq(
+        self,
+        mol: Molecule,
+        charge: int = None,
+        spin: int = None,
+        inplace: bool = False,
+        remove_tdir: bool = True,
+    ):
         """Frequency analysis.
 
         Parameters
diff --git a/compechem/molecule.py b/compechem/molecule.py
index 3c4ccae..f14d080 100644
--- a/compechem/molecule.py
+++ b/compechem/molecule.py
@@ -19,9 +19,11 @@ class Molecule:
     energies : dict
         dictionary containing the electronic/vibronic energies of the molecule,
         calculated at various levels of theory
+    flags : list
+        list containing all "warning" flags which might be encountered during calculations.
     """
 
-    def __init__(self, xyz_file, charge=0, spin=1) -> None:
+    def __init__(self, xyz_file: str, charge: int = 0, spin: int = 1) -> None:
         """
         Parameters
         ----------
@@ -38,6 +40,7 @@ def __init__(self, xyz_file, charge=0, spin=1) -> None:
         self.spin: int = spin
         self.atomcount: int = None
         self.geometry: list = []
+        self.flags: list = []
 
         self.energies: dict = {}
 
@@ -73,7 +76,7 @@ def __init__(
         def __str__(self):
             return f"method: {self.method}, el={self.electronic}, vib={self.vibronic}"
 
-    def write_xyz(self, xyz_file):
+    def write_xyz(self, xyz_file: str):
         """Writes the current geometry to a .xyz file.
 
         Parameters
@@ -87,7 +90,7 @@ def write_xyz(self, xyz_file):
             for line in self.geometry:
                 file.write(line)
 
-    def update_geometry(self, xyz_file):
+    def update_geometry(self, xyz_file: str):
         """Updates the current geometry from an external .xyz file
 
         Parameters
diff --git a/meta.yaml b/meta.yaml
index 0a74292..26fa9a7 100644
--- a/meta.yaml
+++ b/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "GES-comp-echem" %}
-{% set version = "0.1.22a" %}
+{% set version = "0.1.23a" %}
 
 
 
diff --git a/setup.py b/setup.py
index bf51ca7..239912d 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 
 setuptools.setup(
     name="GES-comp-echem",
-    version="0.1.22a",
+    version="0.1.23a",
     description="",
     long_description="",
     packages=["compechem"],