Added docs help and cleaning of remove sandbox

biobb_io/api/alphafold.py

@@ -118,6 +118,8 @@ def alphafold(output_pdb_path: str, properties: Optional[dict] = None, **kwargs)
         output_pdb_path=output_pdb_path, properties=properties, **kwargs
     ).launch()
 
+    alphafold.__doc__ = AlphaFold.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/api_binding_site.py

@@ -130,6 +130,8 @@ def api_binding_site(
         output_json_path=output_json_path, properties=properties, **kwargs
     ).launch()
 
+    api_binding_site.__doc__ = ApiBindingSite.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/canonical_fasta.py

@@ -120,6 +120,8 @@ def canonical_fasta(
         output_fasta_path=output_fasta_path, properties=properties, **kwargs
     ).launch()
 
+    canonical_fasta.__doc__ = CanonicalFasta.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/ideal_sdf.py

@@ -118,6 +118,8 @@ def ideal_sdf(output_sdf_path: str, properties: Optional[dict] = None, **kwargs)
         output_sdf_path=output_sdf_path, properties=properties, **kwargs
     ).launch()
 
+    ideal_sdf.__doc__ = IdealSdf.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/ligand.py

@@ -118,6 +118,8 @@ def ligand(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) ->
         output_pdb_path=output_pdb_path, properties=properties, **kwargs
     ).launch()
 
+    ligand.__doc__ = Ligand.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/mddb.py

@@ -153,6 +153,8 @@ def mddb(output_top_path: str, output_trj_path: str, properties: Optional[dict]
         output_top_path=output_top_path, output_trj_path=output_trj_path, properties=properties, **kwargs
     ).launch()
 
+    mddb.__doc__ = MDDB.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/memprotmd_sim.py

@@ -113,6 +113,8 @@ def memprotmd_sim(
         output_simulation=output_simulation, properties=properties, **kwargs
     ).launch()
 
+    memprotmd_sim.__doc__ = MemProtMDSim.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/memprotmd_sim_list.py

@@ -102,6 +102,8 @@ def memprotmd_sim_list(
         output_simulations=output_simulations, properties=properties, **kwargs
     ).launch()
 
+    memprotmd_sim_list.__doc__ = MemProtMDSimList.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/memprotmd_sim_search.py

@@ -113,6 +113,8 @@ def memprotmd_sim_search(
         output_simulations=output_simulations, properties=properties, **kwargs
     ).launch()
 
+    memprotmd_sim_search.__doc__ = MemProtMDSimSearch.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/mmcif.py

@@ -118,6 +118,8 @@ def mmcif(output_mmcif_path: str, properties: Optional[dict] = None, **kwargs) -
         output_mmcif_path=output_mmcif_path, properties=properties, **kwargs
     ).launch()
 
+    mmcif.__doc__ = Mmcif.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/pdb.py

@@ -123,6 +123,8 @@ def pdb(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> in
         output_pdb_path=output_pdb_path, properties=properties, **kwargs
     ).launch()
 
+    pdb.__doc__ = Pdb.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/pdb_cluster_zip.py

@@ -132,7 +132,10 @@ def launch(self) -> int:
         fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
         fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
 
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), unique_dir])
+        self.tmp_files.extend([
+            # self.stage_io_dict.get("unique_dir", ""),
+            unique_dir
+        ])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -150,6 +153,8 @@ def pdb_cluster_zip(
         output_pdb_zip_path=output_pdb_zip_path, properties=properties, **kwargs
     ).launch()
 
+    pdb_cluster_zip.__doc__ = PdbClusterZip.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/pdb_variants.py

@@ -175,6 +175,8 @@ def pdb_variants(
         **kwargs,
     ).launch()
 
+    pdb_variants.__doc__ = PdbVariants.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

biobb_io/api/structure_info.py

@@ -118,6 +118,8 @@ def structure_info(
         output_json_path=output_json_path, properties=properties, **kwargs
     ).launch()
 
+    structure_info.__doc__ = StructureInfo.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""