Added docs help and cleaning of remove sandbox

Author: gbayarri

biobb_cmip/cmip/cmip_ignore_residues.py

@@ -113,6 +113,8 @@ def cmip_ignore_residues(input_cmip_pdb_path: str, output_cmip_pdb_path: str, pr
                               output_cmip_pdb_path=output_cmip_pdb_path,
                               properties=properties, **kwargs).launch()
 
+    cmip_ignore_residues.__doc__ = CmipIgnoreResidues.__doc__
+
 
 def main():
     parser = argparse.ArgumentParser(description="Mark residues which charges will be ignored in the CMIP potential calculations.",

biobb_cmip/cmip/cmip_prepare_pdb.py

@@ -111,7 +111,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # remove temporary folder(s)
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
+        # self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -126,6 +126,8 @@ def cmip_prepare_pdb(input_pdb_path: str, output_cmip_pdb_path: str, properties:
                           output_cmip_pdb_path=output_cmip_pdb_path,
                           properties=properties, **kwargs).launch()
 
+    cmip_prepare_pdb.__doc__ = CmipPreparePDB.__doc__
+
 
 def main():
     parser = argparse.ArgumentParser(description="Model the missing atoms in the backbone of a PDB structure.",

biobb_cmip/cmip/cmip_prepare_structure.py

@@ -132,6 +132,8 @@ def cmip_prepare_structure(input_pdb_path: str, output_cmip_pdb_path: str, input
                                 input_topology_path=input_topology_path, properties=properties,
                                 **kwargs).launch()
 
+    cmip_prepare_structure.__doc__ = CmipPrepareStructure.__doc__
+
 
 def main():
     parser = argparse.ArgumentParser(description="Wrapper of the cmip prepare_structure module.",

biobb_cmip/cmip/cmip_run.py

@@ -287,7 +287,10 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # remove temporary folder(s)
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), combined_params_dir])
+        self.tmp_files.extend([
+            # self.stage_io_dict.get("unique_dir", ""),
+            combined_params_dir
+        ])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -312,6 +315,8 @@ def cmip_run(input_pdb_path: str, input_probe_pdb_path: Optional[str] = None, ou
                    input_json_box_path=input_json_box_path, input_json_external_box_path=input_json_external_box_path,
                    properties=properties, **kwargs).launch()
 
+    cmip_run.__doc__ = CmipRun.__doc__
+
 
 def main():
     parser = argparse.ArgumentParser(description="Wrapper of the CMIP cmip module.",

biobb_cmip/cmip/cmip_titration.py

@@ -156,7 +156,10 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # remove temporary folder(s)
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), combined_params_dir])
+        self.tmp_files.extend([
+            # self.stage_io_dict.get("unique_dir", ""),
+            combined_params_dir
+        ])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -173,6 +176,8 @@ def cmip_titration(input_pdb_path: str, output_pdb_path: str,
                          input_vdw_params_path=input_vdw_params_path, input_params_path=input_params_path,
                          properties=properties, **kwargs).launch()
 
+    cmip_titration.__doc__ = CmipTitration.__doc__
+
 
 def main():
     parser = argparse.ArgumentParser(description="Wrapper of the CMIP Titration module.",