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Showing 254 of 254 total issues

Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self, pdbblock: str,
Severity: Minor
Found in fragmenstein/laboratory/_base.py - About 45 mins to fix

    Consider simplifying this complex logical expression.
    Open

                if ringcore_first and atom_a.HasProp('_current_is') and not atom_b.HasProp('_current_is'):
                ringcore = ai
                other = bi
                pairing = f'{ringcore}-{other}'
            elif ringcore_first and atom_b.HasProp('_current_is') and not atom_a.HasProp('_current_is'):
    Severity: Major
    Found in fragmenstein/monster/_collapse_ring.py - About 40 mins to fix

      Consider simplifying this complex logical expression.
      Open

              if isinstance(map, list) and isinstance(map[0], tuple) and isinstance(map[0][0], tuple):
            return [(h, f) for h, f in map if f >= 0 and h >= 0]
        elif isinstance(map, list) and isinstance(map[0], list):
            return [self._remove_negatives(m) for m in map]
        elif isinstance(map, list) and isinstance(map[0], dict):
      Severity: Major
      Found in fragmenstein/monster/_place_modes/_no_blending.py - About 40 mins to fix

        Function __call__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def __call__(self,
        Severity: Minor
        Found in fragmenstein/monster/mcs_mapping/compare_atom.py - About 35 mins to fix

          Function from_pdbblock has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def from_pdbblock(cls,
          Severity: Minor
          Found in fragmenstein/igor/_igor_init.py - About 35 mins to fix

            Function _join_atoms has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def _join_atoms(self,
            Severity: Minor
            Found in fragmenstein/monster/_join_neighboring.py - About 35 mins to fix

              Function _restore_bond has 5 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def _restore_bond(self, mol: Chem.RWMol,
              Severity: Minor
              Found in fragmenstein/monster/_collapse_ring.py - About 35 mins to fix

                Function check_possible_distances has 5 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                    def check_possible_distances(self, other, possible_map, combined, combined_map, cutoff=2.5):
                Severity: Minor
                Found in fragmenstein/monster/unmerge_mapper.py - About 35 mins to fix

                  Function get_mod_FastRelax has 5 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                      def get_mod_FastRelax(self,
                  Severity: Minor
                  Found in fragmenstein/igor/_igor_min.py - About 35 mins to fix

                    Function draw has 5 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                    def draw(mol, color_map, x=200, y=200, **kwargs):
                    Severity: Minor
                    Found in fragmenstein/monster/_util_compare.py - About 35 mins to fix

                      Function relax_with_ED has 5 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                          def relax_with_ED(cls, pose,
                      Severity: Minor
                      Found in fragmenstein/igor/_igor_utils.py - About 35 mins to fix

                        Function _gpm_distance has 5 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                            def _gpm_distance(cls, mols: List[Chem.Mol], confs: [Chem.Conformer], i, j, dummy_w_dummy=True) \
                        Severity: Minor
                        Found in fragmenstein/monster/positional_mapping.py - About 35 mins to fix

                          Function from_pdbfile has 5 arguments (exceeds 4 allowed). Consider refactoring.
                          Open

                              def from_pdbfile(cls,
                          Severity: Minor
                          Found in fragmenstein/igor/_igor_init.py - About 35 mins to fix

                            Function _add_bond_regardlessly has 5 arguments (exceeds 4 allowed). Consider refactoring.
                            Open

                                def _add_bond_regardlessly(self, mol, first: Chem.Atom, second: Chem.Atom, bond_type, provenance='other_novel'):
                            Severity: Minor
                            Found in fragmenstein/monster/_communal.py - About 35 mins to fix

                              Function restrain has 5 arguments (exceeds 4 allowed). Consider refactoring.
                              Open

                                  def restrain(self, system: mm.System, pdb: Union[mma.PDBFile, mma.Modeller],
                              Severity: Minor
                              Found in fragmenstein/openmm/fritz.py - About 35 mins to fix

                                Function _pipe_set_up has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                Open

                                    def _pipe_set_up(self, output, cutoff, quick, suffix, **kwargs):
                                Severity: Minor
                                Found in fragmenstein/cli/pipeline.py - About 35 mins to fix

                                  Function closest_hit has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                  Open

                                      def closest_hit(cls, pdb_filenames: List[str],
                                  Severity: Minor
                                  Found in fragmenstein/victor/_victor_utils.py - About 35 mins to fix

                                    Function add_neighbors has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                    Open

                                        def add_neighbors(self, selection: str, comp_id: int = 0, radius: float = 5, style: str = 'hyperball',
                                    Severity: Minor
                                    Found in fragmenstein/ngl_display.py - About 35 mins to fix

                                      Function flatten_trio has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                      Open

                                          def flatten_trio(self, mol_idx: int, atom_idcs: Tuple[int, int, int],
                                      Severity: Minor
                                      Found in fragmenstein/walton/_advmoves.py - About 35 mins to fix

                                        Function distance_hits has 5 arguments (exceeds 4 allowed). Consider refactoring.
                                        Open

                                            def distance_hits(cls, pdb_filenames: List[str],
                                        Severity: Minor
                                        Found in fragmenstein/victor/_victor_utils.py - About 35 mins to fix
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