bugfixes

src/supramolsim/analysis/sweep.py

@@ -64,6 +64,7 @@ def sweep_vasmples(
             "1XI5",
         ]
     if probes is None:
+        print("Probe list is None. Using default probe")
         probes = [
             default_probe,
         ]
@@ -89,54 +90,56 @@ def sweep_vasmples(
     for struct in structures:
         experiment.structure_id = struct
         experiment._build_structure()
-        for rep in range(repetitions):
-            probe_n = 0
-            for probe in probes:
-                print(f"probe: {probe}")
-                # probe_param_n = 0
-                for probe_param_n, p_param in probe_parameters.items():
-                    # copy p_param?
-                    experiment.remove_probes()
-                    if p_param is None:
-                        experiment.add_probe(
-                            probe_template=probe,
-                        )
-                        #experiment.probe_parameters[probe] = default_params
+        #for rep in range(repetitions):
+        probe_n = 0
+        for probe in probes:
+            print(f"probe: {probe}")
+            # probe_param_n = 0
+            for probe_param_n, p_param in probe_parameters.items():
+                # copy p_param?
+                experiment.remove_probes()
+                if p_param is None:
+                    experiment.add_probe(
+                        probe_template=probe,
+                    )
+                    #experiment.probe_parameters[probe] = default_params
+                else:
+                    p_param_copy = copy.deepcopy(p_param)
+                    p_param_copy["fluorophore_id"] = default_fluorophore
+                    experiment.add_probe(
+                        probe_template=probe,
+                        **p_param_copy
+                    )
+                for defect_n, defects_pars in particle_defects.items():
+                    particle_defects_copy = copy.deepcopy(defects_pars)
+                    for d_key, d_val in particle_defects_copy.items():
+                        if d_key=="defect_small_cluster":
+                            experiment.defect_eps["eps1"] = d_val
+                        if d_key=="defect_large_cluster":
+                            experiment.defect_eps["eps2"] = d_val
+                        if d_key=="defect":
+                            experiment.defect_eps["defect"] = d_val
+                    # print(experiment.defect_eps)
+                    print(experiment.probe_parameters)
+                    experiment._build_particle(keep=True)
+                    if experiment.generators_status("particle"):
+                        if len(experiment.particle.emitters) == 0:
+                            print(f"Skipping {probe}. No emitters were generated")
+                            break
                     else:
-                        p_param_copy = copy.deepcopy(p_param)
-                        p_param_copy["fluorophore_id"] = default_fluorophore
-                        experiment.add_probe(
-                            probe_template=probe,
-                            **p_param_copy
+                        break
+                    #vsample_n = 0
+                    for vsample_n, vsample_pars in virtual_samples.items():
+                        _exported_field = None
+                        # combination += str(vsample_n)
+                        experiment.set_virtualsample_params(
+                            **vsample_pars
                         )
-                    for defect_n, defects_pars in particle_defects.items():
-                        particle_defects_copy = copy.deepcopy(defects_pars)
-                        for d_key, d_val in particle_defects_copy.items():
-                            if d_key=="defect_small_cluster":
-                                experiment.defect_eps["eps1"] = d_val
-                            if d_key=="defect_large_cluster":
-                                experiment.defect_eps["eps2"] = d_val
-                            if d_key=="defect":
-                                experiment.defect_eps["defect"] = d_val
-                        # print(experiment.defect_eps)
-                        print(experiment.probe_parameters)
-                        experiment._build_particle(keep=True)
-                        if experiment.generators_status("particle"):
-                            if len(experiment.particle.emitters) == 0:
-                                print(f"Skipping {probe}. No emitters were generated")
-                                break
-                        else:
-                            break
-                        #vsample_n = 0
-                        for vsample_n, vsample_pars in virtual_samples.items():
-                            _exported_field = None
-                            # combination += str(vsample_n)
-                            experiment.set_virtualsample_params(
-                                **vsample_pars
-                            )
-                            #_exported_field = experiment._build_coordinate_field(
-                            #    keep=False, use_self_particle=True, **vsample_pars
-                            #)
+                        #_exported_field = experiment._build_coordinate_field(
+                        #    keep=False, use_self_particle=True, **vsample_pars
+                        #)
+                        for rep in range(repetitions):
+                            experiment.clear_virtual_sample()
                             experiment.build(modules=["coordinate_field"], use_self_particle=True)
                             _exported_field = experiment.coordinate_field.export_field()
                             combination_n = (
@@ -159,11 +162,11 @@ def sweep_vasmples(
                                 vsample_params[combination_n] = _parameters
                                 vsample_outputs[combination_n] = []
                             vsample_outputs[combination_n].append(_exported_field)
-                            #
-                            #
-                            #vsample_n += 1
-                        # defect_n += 1
-                probe_n += 1
+                        #
+                        #
+                        #vsample_n += 1
+                    # defect_n += 1
+            probe_n += 1
     return experiment, vsample_outputs, vsample_params
 
 

src/supramolsim/experiments.py

@@ -483,6 +483,9 @@ def _build_particle(self, lab_eff=1.0, defect_build=None, keep=False):
                         deg_dissasembly=defect,
                     )
                 else:
+                    particle.add_defects(
+                        deg_dissasembly=0,
+                    )
                     print("Particle without defects")
                 if keep:
                     self.particle = particle
@@ -942,6 +945,8 @@ def add_probe(
             probe_configuration["conjugation_target_info"] = (
                 probe_conjugation_target_info
             )
+            probe_configuration["conjugation_sites"]["target"]["type"]= probe_conjugation_target_info["type"]
+            probe_configuration["conjugation_sites"]["target"]["value"]= probe_conjugation_target_info["value"]
         if probe_conjugation_efficiency is not None:
             probe_configuration["conjugation_efficiency"] = probe_conjugation_efficiency
         if probe_seconday_epitope is not None:
@@ -956,6 +961,7 @@ def add_probe(
             probe_configuration["as_linker"] = False
         if probe_steric_hindrance is not None:
             probe_configuration["distance_between_epitope"] = probe_steric_hindrance
+            probe_configuration["binding"]["distance"]["between_targets"] = probe_steric_hindrance
         self.probe_parameters[probe_name] = probe_configuration
         self._update_probes()
 
@@ -1138,7 +1144,8 @@ def current_settings(self, as_string=True, newline="<br>", modalities_acq_params
 
 def generate_virtual_sample(
     structure: str = "1XI5",
-    probe_name: str = None,
+    probe_template: str = "NHS_ester",
+    probe_name:str = None,
     probe_target_type: str = None,
     probe_target_value: str = None,
     probe_distance_to_epitope: float = None,
@@ -1148,7 +1155,7 @@ def generate_virtual_sample(
     probe_conjugation_target_info=None,
     probe_conjugation_efficiency: float = None,
     probe_seconday_epitope=None,
-    probe_wobbling=False,
+    probe_wobble_theta=None,
     labelling_efficiency: float = 1.0,
     defect_small_cluster: float = None,
     defect_large_cluster: float = None,
@@ -1160,6 +1167,7 @@ def generate_virtual_sample(
     random_orientations=False,
     random_placing=False,
     clear_probes=False,
+    clear_experiment = False,
     **kwargs,
 ):
     """
@@ -1223,19 +1231,24 @@ def generate_virtual_sample(
         - ExperimentParametrisation: The experiment containing all modules that were generated to build the virtual sample, and the virtual sample module itself. This experiment can be further used and tweaked for subsequent analysis or branching workflows.
     """
     myexperiment = ExperimentParametrisation()
+    if clear_experiment:
+        myexperiment.clear_experiment()
     # load default configuration for probe
     if not clear_probes:
-        if probe_name is None:
-            probe_name = "NHS_ester"
+        print(probe_template)
         probe_configuration_file = os.path.join(
-            myexperiment.configuration_path, "probes", probe_name + ".yaml"
+            myexperiment.configuration_path, "probes", probe_template + ".yaml"
         )
         probe_configuration = load_yaml(probe_configuration_file)
-        probe_configuration["probe_name"] = probe_name
+        probe_configuration["probe_template"] = probe_template
+        if probe_name is None:
+            probe_name = probe_template
+        else:
+            probe_configuration["label_name"] = probe_name
         if probe_target_type and probe_target_value:
-            probe_configuration["target_info"] = dict(
-                type=probe_target_type, value=probe_target_value
-            )
+            print(probe_target_type, probe_target_value)
+            probe_configuration["probe_target_type"] = probe_target_type
+            probe_configuration["probe_target_value"] = probe_target_value
         if probe_distance_to_epitope is not None:
             probe_configuration["distance_to_epitope"] = probe_distance_to_epitope
         if probe_fluorophore is not None:
@@ -1254,8 +1267,8 @@ def generate_virtual_sample(
             probe_configuration["conjugation_efficiency"] = probe_conjugation_efficiency
         if probe_seconday_epitope is not None:
             probe_configuration["epitope_target_info"] = probe_seconday_epitope
-        if probe_wobbling:
-            probe_configuration["enable_wobble"] = probe_wobbling
+        if probe_wobble_theta is not None:
+            probe_configuration["probe_wobble_theta"] = probe_wobble_theta
         myexperiment.add_probe(**probe_configuration)
     # load default configuration for virtual sample
     virtual_sample_template = os.path.join(