Added docs help and cleaning of remove sandbox

Author: gbayarri

biobb_structure_utils/utils/cat_pdb.py

@@ -131,7 +131,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -157,6 +157,8 @@ def cat_pdb(
         **kwargs,
     ).launch()
 
+    cat_pdb.__doc__ = CatPDB.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/closest_residues.py

@@ -208,7 +208,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -232,6 +232,8 @@ def closest_residues(
         **kwargs,
     ).launch()
 
+    closest_residues.__doc__ = ClosestResidues.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/extract_atoms.py

@@ -154,7 +154,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -178,6 +178,8 @@ def extract_atoms(
         **kwargs,
     ).launch()
 
+    extract_atoms.__doc__ = ExtractAtoms.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/extract_chain.py

@@ -151,7 +151,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -191,6 +191,8 @@ def extract_chain(
         **kwargs,
     ).launch()
 
+    extract_chain.__doc__ = ExtractChain.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/extract_heteroatoms.py

@@ -170,7 +170,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -194,6 +194,8 @@ def extract_heteroatoms(
         **kwargs,
     ).launch()
 
+    extract_heteroatoms.__doc__ = ExtractHeteroAtoms.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/extract_model.py

@@ -148,9 +148,10 @@ def launch(self) -> int:
             self.copy_to_host()
 
             # Remove temporal files
-            self.tmp_files.extend(
-                [self.stage_io_dict.get("unique_dir", ""), tmp_folder]
-            )
+            self.tmp_files.extend([
+                # self.stage_io_dict.get("unique_dir", ""),
+                tmp_folder
+            ])
             self.remove_tmp_files()
 
             self.check_arguments(output_files_created=True, raise_exception=False)
@@ -190,6 +191,8 @@ def extract_model(
         **kwargs,
     ).launch()
 
+    extract_model.__doc__ = ExtractModel.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/extract_molecule.py

@@ -146,7 +146,10 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), tmp_folder])
+        self.tmp_files.extend([
+            self.stage_io_dict.get("unique_dir", ""),
+            # tmp_folder
+        ])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -170,6 +173,8 @@ def extract_molecule(
         **kwargs,
     ).launch()
 
+    extract_molecule.__doc__ = ExtractMolecule.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/extract_residues.py

@@ -157,7 +157,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -181,6 +181,8 @@ def extract_residues(
         **kwargs,
     ).launch()
 
+    extract_residues.__doc__ = ExtractResidues.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/remove_ligand.py

@@ -122,7 +122,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -146,6 +146,8 @@ def remove_ligand(
         **kwargs,
     ).launch()
 
+    remove_ligand.__doc__ = RemoveLigand.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/remove_molecules.py

@@ -162,7 +162,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -186,6 +186,8 @@ def remove_molecules(
         **kwargs,
     ).launch()
 
+    remove_molecules.__doc__ = RemoveMolecules.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/remove_pdb_water.py

@@ -95,7 +95,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -119,6 +119,8 @@ def remove_pdb_water(
         **kwargs,
     ).launch()
 
+    remove_pdb_water.__doc__ = RemovePdbWater.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/renumber_structure.py

@@ -177,7 +177,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -203,6 +203,8 @@ def renumber_structure(
         **kwargs,
     ).launch()
 
+    renumber_structure.__doc__ = RenumberStructure.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/sort_gro_residues.py

@@ -94,7 +94,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -118,6 +118,8 @@ def sort_gro_residues(
         **kwargs,
     ).launch()
 
+    sort_gro_residues.__doc__ = SortGroResidues.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/str_check_add_hydrogens.py

@@ -145,7 +145,7 @@ def launch(self) -> int:
         check_output_end(self.io_dict["out"]["output_structure_path"], self.out_log)
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
+        # self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -169,6 +169,8 @@ def str_check_add_hydrogens(
         **kwargs,
     ).launch()
 
+    str_check_add_hydrogens.__doc__ = StrCheckAddHydrogens.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_structure_utils/utils/structure_check.py

@@ -151,7 +151,10 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), tmp_folder])  # type: ignore
+        self.tmp_files.extend([
+            # self.stage_io_dict.get("unique_dir", ""),
+            tmp_folder
+        ])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -175,6 +178,8 @@ def structure_check(
         **kwargs,
     ).launch()
 
+    structure_check.__doc__ = StructureCheck.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""