Merge pull request #705 from haddocking/input_to_json

Input to json

Author: mgiulini

src/haddock/modules/__init__.py

@@ -241,15 +241,14 @@ def confirm_installation(self):
         """
         return
 
-    def export_output_models(self, faulty_tolerance=0):
+    def export_io_models(self, faulty_tolerance=0):
         """
-        Export output to the ModuleIO interface.
+        Export input/output to the ModuleIO interface.
 
-        Modules that generate PDBs that other models should take as input,
-        should export those PDBs registries through the ModuleIO interface.
+        Modules that do not perform any operation on PDB files should have
+         input = output.
 
-        This function implements a common interface for all modules requiring
-        this feature.
+        This function implements a common interface for all modules.
 
         Parameters
         ----------
@@ -260,6 +259,9 @@ def export_output_models(self, faulty_tolerance=0):
         """
         assert self.output_models, "`self.output_models` cannot be empty."
         io = ModuleIO()
+        # add the input models
+        io.add(self.previous_io.output, "i")
+        # add the output models
         io.add(self.output_models, "o")
         faulty = io.check_faulty()
         if faulty > faulty_tolerance:

src/haddock/modules/_template_cat/_template_mod/__init__.py

@@ -128,10 +128,10 @@ def _run(self):
 
         # final section
         self.output_models = list_of_created_models
-        self.export_output_models()
+        self.export_io_models()
         # in case your module considers possible tolerance for generated models,
         # you can use:
-        # self.export_output_models(faulty_tolerance=self.params["tolerance"])
+        # self.export_io_models(faulty_tolerance=self.params["tolerance"])
 
 
 # Finally, the haddock module's class inherit from BaseHaddockModule. It is

src/haddock/modules/analysis/caprieval/__init__.py

@@ -99,4 +99,4 @@ def _run(self):
         # Send models to the next step,
         #  no operation is done on them
         self.output_models = models
-        self.export_output_models()
+        self.export_io_models()

src/haddock/modules/analysis/clustfcc/__init__.py

@@ -247,4 +247,4 @@ def _run(self):
             log.warning('No clusters were found')
             self.output_models = models_to_cluster
 
-        self.export_output_models()
+        self.export_io_models()

src/haddock/modules/analysis/clustrmsd/__init__.py

@@ -211,7 +211,7 @@ def _run(self):
         with open(output_fname, 'w') as out_fh:
             out_fh.write(output_str)
 
-        self.export_output_models()
+        self.export_io_models()
         # sending matrix to next step of the workflow
         matrix_io = ModuleIO()
         matrix_io.add(self.matrix_json.input[0])

src/haddock/modules/analysis/rmsdmatrix/__init__.py

@@ -160,7 +160,7 @@ def _run(self):
 
         # Sending models to the next step of the workflow
         self.output_models = models
-        self.export_output_models()
+        self.export_io_models()
         # Sending matrix path to the next step of the workflow
         matrix_io = ModuleIO()
         rmsd_matrix_file = RMSDFile(

src/haddock/modules/analysis/seletop/__init__.py

@@ -53,4 +53,4 @@ def _run(self):
 
         # select the models based on the parameter
         self.output_models = models_to_select[:self.params['select']]
-        self.export_output_models()
+        self.export_io_models()

src/haddock/modules/analysis/seletopclusts/__init__.py

@@ -94,4 +94,4 @@ def _run(self):
                 model.path = str(Path(self.path).resolve())
 
         self.output_models = models_to_export
-        self.export_output_models()
+        self.export_io_models()

src/haddock/modules/refinement/emref/__init__.py

@@ -125,4 +125,4 @@ def _run(self):
                 haddock_score = haddock_model.calc_haddock_score(**weights)
                 pdb.score = haddock_score
 
-        self.export_output_models(faulty_tolerance=self.params["tolerance"])
+        self.export_io_models(faulty_tolerance=self.params["tolerance"])

src/haddock/modules/refinement/flexref/__init__.py

@@ -128,4 +128,4 @@ def _run(self):
                 pdb.score = haddock_score
 
         # Save module information
-        self.export_output_models(faulty_tolerance=self.params["tolerance"])
+        self.export_io_models(faulty_tolerance=self.params["tolerance"])