Remove unused code

docs/source/changelog.rst

@@ -2,6 +2,17 @@
 Changelog
 *********
 
+Upcoming release (TBD)
+======================
+
+Changes
+-------
+
+* Removed the following unused command line options: ``-t``, ``--thermophile``,
+  ``-a``, ``--alignment``, ``-m``, ``--mutation``, ``--mutator``,
+  ``--mutator-option``
+* Removed several unused API functions
+
 Current
 =======
 

docs/source/command.rst

@@ -10,9 +10,9 @@ PROPKA predicts the pKa values of ionizable groups in proteins and
 protein-ligand complexes based in the 3D structure. The
 :program:`propka3` command has the following options::
 
-  propka3 [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS] [-i TITRATE_ONLY] [-t THERMOPHILES] [-a ALIGNMENT] [-m MUTATIONS]
+  propka3 [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS] [-i TITRATE_ONLY]
          [-v VERSION_LABEL] [-p PARAMETERS] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o PH] [-w WINDOW WINDOW WINDOW]
-         [-g GRID GRID GRID] [--mutator MUTATOR] [--mutator-option MUTATOR_OPTIONS] [-d] [-l] [-k] [-q] [--protonate-all]
+         [-g GRID GRID GRID] [-d] [-l] [-k] [-q] [--protonate-all]
          input_pdb
 
 
@@ -47,21 +47,6 @@ protein-ligand complexes based in the 3D structure. The
 	     should be a comma-separated list of "chain:resnum"
 	     values; for  example: ``-i "A:10,A:11"`` (default: None)
 
-.. option::  -t THERMOPHILES, --thermophile THERMOPHILES
-
-             defining a thermophile filename; usually used in
-	     'alignment-mutations' (default: None)
-
-.. option::  -a ALIGNMENT, --alignment ALIGNMENT
-
-             alignment file connecting <filename> and <thermophile>
-	     [<thermophile>.pir] (default: None)
-
-.. option::  -m MUTATIONS, --mutation MUTATIONS
-
-              specifying mutation labels which is used to modify
-	      <filename> according to, e.g. N25R/N181D (default: None)
-
 .. option::  --version
 
 	      show program's version number and exit
@@ -90,16 +75,6 @@ protein-ligand complexes based in the 3D structure. The
             setting the pH-grid to calculate e.g. stability related
 	    properties (default: (0.0, 14.0, 0.1))
 
-.. option::  --mutator MUTATOR
-
-	     setting approach for mutating <filename>
-	     [alignment/scwrl/jackal] (default: None)
-
-.. option::  --mutator-option MUTATOR_OPTIONS
-
-             setting property for mutator [e.g. type="side-chain"]
-	     (default: None)
-
 .. option::  -d, --display-coupled-residues
 
              Displays alternative pKa values due to coupling of

propka/atom.py

@@ -7,8 +7,7 @@
 """
 
 import string
-from typing import cast, List, NoReturn, Optional, TYPE_CHECKING
-import warnings
+from typing import List, Optional, TYPE_CHECKING
 
 from propka.lib import make_tidy_atom_label
 from . import hybrid36
@@ -46,7 +45,6 @@ class Atom:
     group: Optional["Group"] = None
     group_type: Optional[str] = None
     cysteine_bridge: bool = False
-    residue: NoReturn = None  # type: ignore[assignment]
     conformation_container: Optional["ConformationContainer"] = None
     molecular_container: Optional["MolecularContainer"] = None
     is_protonated: bool = False
@@ -87,7 +85,6 @@ def __init__(self, line: Optional[str] = None):
         Args:
             line:  Line from a PDB file to set properties of atom.
         """
-        self.number_of_bonded_elements: NoReturn = cast(NoReturn, {})  # FIXME unused?
         self.bonded_atoms: List[Atom] = []
         self.set_properties(line)
         fmt = "{r.name:3s}{r.res_num:>4d}{r.chain_id:>2s}"
@@ -302,45 +299,6 @@ def make_mol2_line(self, id_):
             atom_label=make_tidy_atom_label(self.name, self.element))
         return str_
 
-    def make_pdb_line2(self, numb=None, name=None, res_name=None, chain_id=None,
-                       res_num=None, x=None, y=None, z=None, occ=None,
-                       beta=None):
-        """Create a PDB line.
-
-        TODO - this could/should be a @property method/attribute
-        TODO - figure out difference between make_pdb_line, and make_pdb_line2
-
-        Returns:
-            String with PDB line.
-        """
-        warnings.warn("only used by unused function")
-        if numb is None:
-            numb = self.numb
-        if name is None:
-            name = self.name
-        if res_name is None:
-            res_name = self.res_name
-        if chain_id is None:
-            chain_id = self.chain_id
-        if res_num is None:
-            res_num = self.res_num
-        if x is None:
-            x = self.x
-        if y is None:
-            y = self.y
-        if z is None:
-            z = self.z
-        if occ is None:
-            occ = self.occ
-        if beta is None:
-            beta = self.beta
-        str_ = PDB_LINE_FMT2.format(
-            numb=numb, res_name=res_name, chain_id=chain_id, res_num=res_num,
-            x=x, y=y, z=z, occ=occ, beta=beta,
-            atom_label=make_tidy_atom_label(name, self.element)
-        )
-        return str_
-
     def get_tidy_label(self):
         """Returns a 'tidier' atom label for printing the new pdbfile
 
@@ -353,13 +311,3 @@ def get_tidy_label(self):
     def __str__(self):
         """Return an undefined-format string version of this atom."""
         return STR_FMT.format(r=self)
-
-    def set_residue(self, residue: NoReturn):
-        """ Makes a reference to the parent residue
-
-        Args:
-            residue:  the parent residue
-        """
-        raise NotImplementedError("unused")
-        if self.residue is None:
-            self.residue = residue

propka/bonds.py

@@ -87,63 +87,6 @@ def __init__(self):
         self.backbone_atoms = list(self.intra_residue_backbone_bonds.keys())
         self.terminal_oxygen_names = ['OXT', 'O\'\'']
 
-    def find_bonds_for_protein(self, protein):
-        """Bonds proteins based on the way atoms normally bond.
-
-        Args:
-            protein:  the protein to search for bonds
-        """
-        raise NotImplementedError("unused")
-        _LOGGER.info('++++ Side chains ++++')
-        # side chains
-        for chain in protein.chains:
-            for residue in chain.residues:
-                if residue.res_name.replace(' ', '') not in ['N+', 'C-']:
-                    self.find_bonds_for_side_chain(residue.atoms)
-        _LOGGER.info('++++ Backbones ++++')
-        # backbone
-        last_residues = []
-        for chain in protein.chains:
-            for i in range(1, len(chain.residues)):
-                if (chain.residues[i-1].res_name.replace(' ', '')
-                        not in ['N+', 'C-']):
-                    if (chain.residues[i].res_name.replace(' ', '')
-                            not in ['N+', 'C-']):
-                        self.connect_backbone(chain.residues[i-1],
-                                              chain.residues[i])
-                        last_residues.append(chain.residues[i])
-        _LOGGER.info('++++ terminal oxygen ++++')
-        # terminal OXT
-        for last_residue in last_residues:
-            self.find_bonds_for_terminal_oxygen(last_residue)
-        _LOGGER.info('++++ cysteines ++++')
-        # Cysteines
-        for chain in protein.chains:
-            for i in range(0, len(chain.residues)):
-                if chain.residues[i].res_name == 'CYS':
-                    for j in range(0, len(chain.residues)):
-                        if chain.residues[j].res_name == 'CYS' and j != i:
-                            self.check_for_cysteine_bonds(chain.residues[i],
-                                                          chain.residues[j])
-
-    def check_for_cysteine_bonds(self, cys1, cys2):
-        """Looks for potential bonds between two cysteines.
-
-        Args:
-            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:
-                    if atom2.name == 'SG':
-                        dist = propka.calculations.squared_distance(atom1,
-                                                                    atom2)
-                        # TODO - is SS_dist_squared an attribute of this class?
-                        if dist < self.SS_dist_squared:
-                            self.make_bond(atom1, atom2)
-
     def find_bonds_for_terminal_oxygen(self, residue):
         """Look for bonds for terminal oxygen.
 
@@ -423,34 +366,3 @@ def make_bond(atom1, atom2):
             atom2.bonded_atoms.append(atom1)
         if atom2 not in atom1.bonded_atoms:
             atom1.bonded_atoms.append(atom2)
-
-    def generate_protein_bond_dictionary(self, atoms):
-        """Generate dictionary of protein bonds.
-
-        Args:
-            atoms:  list of atoms for bonding
-        """
-        for atom in atoms:
-            for bonded_atom in atom.bonded_atoms:
-                resi_i = atom.res_name
-                name_i = atom.name
-                resi_j = bonded_atom.res_name
-                name_j = bonded_atom.name
-                if name_i not in (
-                        self.backbone_atoms
-                        or name_j not in self.backbone_atoms):
-                    if name_i not in (
-                            self.terminal_oxygen_names
-                            and name_j not in self.terminal_oxygen_names):
-                        if resi_i not in list(self.protein_bonds.keys()):
-                            self.protein_bonds[resi_i] = {}
-                        if name_i not in self.protein_bonds[resi_i]:
-                            self.protein_bonds[resi_i][name_i] = []
-                        if name_j not in self.protein_bonds[resi_i][name_i]:
-                            self.protein_bonds[resi_i][name_i].append(name_j)
-                        if resi_j not in list(self.protein_bonds.keys()):
-                            self.protein_bonds[resi_j] = {}
-                        if name_j not in self.protein_bonds[resi_j]:
-                            self.protein_bonds[resi_j][name_j] = []
-                        if name_i not in self.protein_bonds[resi_j][name_j]:
-                            self.protein_bonds[resi_j][name_j].append(name_i)

propka/conformation_container.py

@@ -6,7 +6,7 @@
 """
 import logging
 import functools
-from typing import Callable, Dict, Iterable, Iterator, List, NoReturn, Optional, TYPE_CHECKING, Set
+from typing import Callable, Dict, Iterable, Iterator, List, Optional, TYPE_CHECKING, Set
 
 from propka.lib import Options
 from propka.version import Version
@@ -497,18 +497,6 @@ def get_ions(self):
             group for group in self.groups
             if group.residue_type in self.parameters.ions.keys()]
 
-    def get_group_names(self, group_list: NoReturn) -> NoReturn:  # FIXME unused?
-        """Get names of groups in list.
-
-        Args:
-            group_list:  list to check
-        Returns:
-            list of groups
-        """
-        if TYPE_CHECKING:
-            assert False
-        return [group for group in self.groups if group.type in group_list]
-
     def get_ligand_atoms(self) -> List["Atom"]:
         """Get atoms associated with ligands.
 

propka/group.py

@@ -11,7 +11,7 @@
 """
 import logging
 import math
-from typing import cast, Dict, Iterable, List, NoReturn, Optional
+from typing import Dict, List, Optional
 
 import propka.ligand
 from propka.parameters import Parameters
@@ -119,8 +119,6 @@ def __init__(self, atom: Atom):
             fmt = "{type:<3s}{name:>4s}{chain:>2s}"
             self.label = fmt.format(
                 type=self.residue_type, name=atom.name, chain=atom.chain_id)
-        # container for squared distances
-        self.squared_distances: NoReturn = cast(NoReturn, {})  # FIXME unused?
 
     def couple_covalently(self, other: "Group") -> None:
         """Couple this group with another group.
@@ -162,46 +160,6 @@ def get_non_covalently_coupled_groups(self):
         """
         return self.non_covalently_coupled_groups
 
-    def share_determinants(self, others: Iterable["Group"]) -> None:
-        """Share determinants between this group and others.
-
-        Args:
-            others:  list of other groups
-        """
-        raise NotImplementedError("unused")
-        # for each determinant type
-        for other in others:
-            if other == self:
-                the_other = other
-                continue
-            for type_ in ['sidechain', 'backbone', 'coulomb']:
-                for det in other.determinants[type_]:
-                    self.share_determinant(det, type_)
-        # recalculate pka values
-        self.calculate_total_pka()
-        the_other.calculate_total_pka()
-
-    def share_determinant(self, new_determinant: Determinant, type_: str) -> None:
-        """Add determinant to this group's list of determinants.
-
-        Args:
-            new_determinant:  determinant to add
-            type_:  type of determinant
-        """
-        added = False
-        # first check if we already have a determinant with this label
-        for own_determinant in self.determinants[type_]:
-            if own_determinant.group == new_determinant.group:
-                # if so, find the average value
-                avr = 0.5*(own_determinant.value + new_determinant.value)
-                own_determinant.value = avr
-                new_determinant.value = avr
-                added = True
-        # otherwise we just add the determinant to our list
-        if not added:
-            self.determinants[type_].append(
-                Determinant(new_determinant.group, new_determinant.value))
-
     def __eq__(self, other):
         """Needed for creating sets of groups."""
         if self.atom.type == 'atom':

propka/iterative.py

@@ -202,7 +202,7 @@ def add_iterative_ion_pair(object1: "Iterative", object2: "Iterative",
                 object2.determinants['sidechain'].append(interaction)
 
 
-def add_determinants(iterative_interactions: List[Interaction], version: Version, _=None):
+def add_determinants(iterative_interactions: List[Interaction], version: Version):
     """Add determinants iteratively.
 
     The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'