From 4106726483bdafc0ad3bf5dd4432b892a3e4573c Mon Sep 17 00:00:00 2001
From: Thomas Holder <thomas.holder@rentschler.de>
Date: Tue, 12 Dec 2023 20:39:59 +0100
Subject: [PATCH] Raise NotImplementedError from unused functions

---
 propka/atom.py              | 3 +++
 propka/bonds.py             | 2 ++
 propka/group.py             | 2 ++
 propka/ligand_pka_values.py | 2 ++
 propka/output.py            | 3 +++
 5 files changed, 12 insertions(+)

diff --git a/propka/atom.py b/propka/atom.py
index 5cb6a4e..fa80997 100644
--- a/propka/atom.py
+++ b/propka/atom.py
@@ -8,6 +8,7 @@ The :class:`Atom` class contains all atom information found in the PDB file.
 
 import string
 from typing import cast, List, NoReturn, Optional, TYPE_CHECKING
+import warnings
 
 from propka.lib import make_tidy_atom_label
 from . import hybrid36
@@ -303,6 +304,7 @@ class Atom:
         Returns:
             String with PDB line.
         """
+        warnings.warn("only used by unused function")
         if numb is None:
             numb = self.numb
         if name is None:
@@ -349,5 +351,6 @@ class Atom:
         Args:
             residue:  the parent residue
         """
+        raise NotImplementedError("unused")
         if self.residue is None:
             self.residue = residue
diff --git a/propka/bonds.py b/propka/bonds.py
index 396ec86..9bc00c0 100644
--- a/propka/bonds.py
+++ b/propka/bonds.py
@@ -93,6 +93,7 @@ class BondMaker:
         Args:
             protein:  the protein to search for bonds
         """
+        raise NotImplementedError("unused")
         _LOGGER.info('++++ Side chains ++++')
         # side chains
         for chain in protein.chains:
@@ -132,6 +133,7 @@ class BondMaker:
             cys1:  one of the cysteines to check
             cys1:  one of the cysteines to check
         """
+        raise NotImplementedError("unused")
         for atom1 in cys1.atoms:
             if atom1.name == 'SG':
                 for atom2 in cys2.atoms:
diff --git a/propka/group.py b/propka/group.py
index 65e09f4..70178cd 100644
--- a/propka/group.py
+++ b/propka/group.py
@@ -167,6 +167,7 @@ class Group:
         Args:
             others:  list of other groups
         """
+        raise NotImplementedError("unused")
         # for each determinant type
         for other in others:
             if other == self:
@@ -1400,6 +1401,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom: Atom) -> Optional[Group]:
             if not o == atom][0]
         atom.marvin_pka = other_oxygen.marvin_pka
         return TitratableLigandGroup(atom)
+    raise NotImplementedError("hydrogen_bonds")
     if atom.element in parameters.hydrogen_bonds.elements:
         return NonTitratableLigandGroup(atom)
     return None
diff --git a/propka/ligand_pka_values.py b/propka/ligand_pka_values.py
index f161d88..5d9adfd 100644
--- a/propka/ligand_pka_values.py
+++ b/propka/ligand_pka_values.py
@@ -13,6 +13,7 @@ import logging
 import os
 import subprocess
 import sys
+import warnings
 from propka.output import write_mol2_for_atoms
 from propka.lib import split_atoms_into_molecules
 
@@ -69,6 +70,7 @@ class LigandPkaValues:
             min_ph:  minimum pH value
             max_ph:  maximum pH value
         """
+        warnings.warn("unused and untested by propka")
         self.get_marvin_pkas_for_molecular_container(
             molecule, num_pkas=num_pkas, min_ph=min_ph, max_ph=max_ph)
 
diff --git a/propka/output.py b/propka/output.py
index db5c311..2f6830e 100644
--- a/propka/output.py
+++ b/propka/output.py
@@ -72,6 +72,7 @@ def write_pdb_for_protein(
         include_hydrogens:  Boolean indicating whether to include hydrogens
         options:  options object
     """
+    raise NotImplementedError("unused")
     if pdbfile is None:
         # opening file if not given
         if filename is None:
@@ -169,6 +170,7 @@ def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.],
         _:  Boolean for verbosity
         options:  options object
     """
+    raise NotImplementedError("unused")
     profile = protein.getTmProfile(
         reference=reference, grid=[0., 14., 0.1], tms=tms, ref=ref,
         options=options)
@@ -358,6 +360,7 @@ def write_jackal_scap_file(mutation_data=None, filename="1xxx_scap.list",
 
     TODO - figure out what this is
     """
+    raise NotImplementedError("unused")
     with open(filename, 'w') as file_:
         for chain_id, _, res_num, code2 in mutation_data:
             str_ = "{chain:s}, {num:d}, {code:s}\n".format(