From 865382ec80b8b4169133b4dac5ab66187ecdf997 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Wed, 30 Jul 2025 16:24:55 +0100
Subject: [PATCH 01/29] sweep: changed when is the replica is generated for
 virtual sample to avoid redundant iterations

---
 src/supramolsim/analysis/sweep.py | 105 +++++++++++++++---------------
 1 file changed, 54 insertions(+), 51 deletions(-)

diff --git a/src/supramolsim/analysis/sweep.py b/src/supramolsim/analysis/sweep.py
index f3691cdf..81eeffce 100644
--- a/src/supramolsim/analysis/sweep.py
+++ b/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
 
 

From 38b46d9170763de5bd9a85453cf3dbe55feea143 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Fri, 1 Aug 2025 11:43:11 +0100
Subject: [PATCH 02/29] plot in existing axis object

---
 .../generate/molecular_structure.py           | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/src/supramolsim/generate/molecular_structure.py b/src/supramolsim/generate/molecular_structure.py
index e9fe3f14..4dcbe307 100644
--- a/src/supramolsim/generate/molecular_structure.py
+++ b/src/supramolsim/generate/molecular_structure.py
@@ -767,7 +767,8 @@ def show_target_labels(
         axesoff=True,
         show_axis=True,
         with_normals=False,
-        return_plot=False
+        return_plot=False,
+        axis_object=None,
     ):
         """
         Visualize target labels and optionally assembly atoms and reference point.
@@ -798,9 +799,12 @@ def show_target_labels(
         matplotlib.figure.Figure or None
             The figure if return_plot is True, otherwise None.
         """
-        if labelnames is None:
+        if axis_object is not None:
+            ax = axis_object
+        else:
             fig = plt.figure()
             ax = fig.add_subplot(111, projection="3d")
+        if labelnames is None:
             for trgt in list(self.label_targets.keys()):
                 if with_normals:
                     draw_nomral_segments(
@@ -846,11 +850,14 @@ def show_target_labels(
         )
         if axesoff:
             ax.set_axis_off()
-        if return_plot:
-            plt.close()
-            return fig
+        if axis_object is not None:
+            return ax
         else:
-            fig.show
+            if return_plot:
+                plt.close()
+                return fig
+            else:
+                fig.show
 
     def show_assembly_atoms(
         self, assembly_fraction=0.01, view_init=[0, 0, 0], axesoff=True,return_plot=False

From b2867e8da5e7896811ed6631a888becd9745cfb8 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 4 Aug 2025 10:58:41 +0100
Subject: [PATCH 03/29] minor update

---
 src/supramolsim/generate/molecular_structure.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/supramolsim/generate/molecular_structure.py b/src/supramolsim/generate/molecular_structure.py
index 4dcbe307..53a04c13 100644
--- a/src/supramolsim/generate/molecular_structure.py
+++ b/src/supramolsim/generate/molecular_structure.py
@@ -769,6 +769,9 @@ def show_target_labels(
         with_normals=False,
         return_plot=False,
         axis_object=None,
+        target_size = None,
+        atoms_size = None,
+        atoms_alpha = None,
     ):
         """
         Visualize target labels and optionally assembly atoms and reference point.
@@ -806,6 +809,8 @@ def show_target_labels(
             ax = fig.add_subplot(111, projection="3d")
         if labelnames is None:
             for trgt in list(self.label_targets.keys()):
+                if target_size is not None:
+                    self.plotting_params[trgt]["plotsize"] = target_size
                 if with_normals:
                     draw_nomral_segments(
                         [self.get_target_normals(trgt), self.get_target_coords(trgt)],
@@ -824,6 +829,10 @@ def show_target_labels(
             atoms_subset = cif_builder.array_coords_subset(
                 self.assembly_atoms, assembly_fraction
             )
+            if atoms_size is not None:
+                self.plotting_params["assemblyatoms"]["plotsize"] = atoms_size
+            if atoms_alpha is not None:
+                self.plotting_params["assemblyatoms"]["plotalpha"] = atoms_alpha
             add_ax_scatter(
                 ax,
                 format_coordinates(

From 26d15b23b0a9f3969b5523507069ccaaa136ffb8 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 4 Aug 2025 10:58:55 +0100
Subject: [PATCH 04/29] visualisation update

---
 src/supramolsim/generate/labelled_instance.py | 20 ++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/supramolsim/generate/labelled_instance.py b/src/supramolsim/generate/labelled_instance.py
index df658d20..c0dd656a 100644
--- a/src/supramolsim/generate/labelled_instance.py
+++ b/src/supramolsim/generate/labelled_instance.py
@@ -818,6 +818,7 @@ def show_probe(self,
                 xlims = [-100,100],
                 ylims = [-100,100],
                 zlims = None,
+                central_axis=True,
                 **kwargs):
         """
         Visualize the probe structure in 3D.
@@ -868,15 +869,16 @@ def show_probe(self,
                             plotsize=20
                     ),
                 )
-        add_ax_scatter(
-                    ax,
-                        format_coordinates(
-                            centered_axis,
-                            plotmarker="x",
-                            plotcolour="k",
-                            plotsize=20
-                        ),
-                    )
+        if central_axis:
+            add_ax_scatter(
+                        ax,
+                            format_coordinates(
+                                centered_axis,
+                                plotmarker="x",
+                                plotcolour="k",
+                                plotsize=20
+                            ),
+                        )
         ax.set_xlim(xlims)
         ax.set_ylim(ylims)
         if zlims is None:

From a502bd236539cb8a03bb4c8e5fde8eee79020843 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 4 Aug 2025 15:12:29 +0100
Subject: [PATCH 05/29] update labelled structure scaling method

---
 src/supramolsim/generate/labelled_instance.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/supramolsim/generate/labelled_instance.py b/src/supramolsim/generate/labelled_instance.py
index c0dd656a..b19fdb09 100644
--- a/src/supramolsim/generate/labelled_instance.py
+++ b/src/supramolsim/generate/labelled_instance.py
@@ -760,6 +760,10 @@ def scale_coordinates_system(self, new_scale: float):
             if self.secondary[labeltype]["binding"]["distance"]["between_targets"] is not None:
                 self.secondary[labeltype]["binding"]["distance"]["between_targets"] *= probe_scaling_factor
             self.secondary[labeltype]["scale"] = new_scale
+        if self.defects:
+            self.defects_params["d_cluster_params"]["eps1"] *= scaling_factor
+            self.defects_params["d_cluster_params"]["eps2"] *= scaling_factor
+            self.defects_params["xmer_neigh_distance"] *= scaling_factor
 
     # methods to get emitters by target name    
 

From a646025882a8c21b5afb5ecb3c0ac9bade90dac2 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 4 Aug 2025 15:14:20 +0100
Subject: [PATCH 06/29] bugfix on generate_virtual_sample

---
 src/supramolsim/experiments.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/supramolsim/experiments.py b/src/supramolsim/experiments.py
index ace99eb5..dbc3138e 100644
--- a/src/supramolsim/experiments.py
+++ b/src/supramolsim/experiments.py
@@ -1138,7 +1138,8 @@ 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,
@@ -1160,6 +1161,7 @@ def generate_virtual_sample(
     random_orientations=False,
     random_placing=False,
     clear_probes=False,
+    clear_experiment = False,
     **kwargs,
 ):
     """
@@ -1223,15 +1225,20 @@ 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

From 0b542b26a2a2f15e8007705a6a2f6bc1bfc7cdd1 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 4 Aug 2025 16:26:14 +0100
Subject: [PATCH 07/29] minor update

---
 src/supramolsim/generate/labelled_instance.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/supramolsim/generate/labelled_instance.py b/src/supramolsim/generate/labelled_instance.py
index b19fdb09..e86cca2a 100644
--- a/src/supramolsim/generate/labelled_instance.py
+++ b/src/supramolsim/generate/labelled_instance.py
@@ -1007,6 +1007,7 @@ def gen_axis_plot(
         source_plotsize=1,
         axis_object=None,
         emitter_plotsize=1,
+        source_plotcolour="#bbbbbb"
     ):
         """
         Generate a 3D axis plot for the labelled instance.
@@ -1055,7 +1056,7 @@ def gen_axis_plot(
                             axis_object,
                             format_coordinates(
                                 self._get_source_coords_normals(labs)["coordinates"],
-                                plotcolour="#bbbbbb",
+                                plotcolour=source_plotcolour,
                                 plotalpha=0.5,
                                 plotsize=source_plotsize,
                             ),

From 84f88f0aa56f4a190023ef646e88e45db5d3cd9c Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Tue, 5 Aug 2025 11:26:03 +0100
Subject: [PATCH 08/29] major fix: probe axis direction vector was not
 calculated but used the point iself

---
 src/supramolsim/workflows.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/supramolsim/workflows.py b/src/supramolsim/workflows.py
index 4640c976..085477d3 100644
--- a/src/supramolsim/workflows.py
+++ b/src/supramolsim/workflows.py
@@ -225,7 +225,10 @@ def particle_from_structure(
                 )
                 if anchor_point.shape == (3,):
                     print("setting new axis")
-                    label_object.set_axis(pivot=anchor_point, direction=direction_point)
+                    print(anchor_point, direction_point)
+                    direction_vector = direction_point - anchor_point
+                    label_object.set_axis(pivot=anchor_point, direction=direction_vector)
+                    print(f'label object axis: {label_object.params["axis"]}')
                 if (
                     probe_epitope["coordinates"] is not None
                     and label_params["as_linker"]
@@ -240,7 +243,7 @@ def particle_from_structure(
                     label_object.set_emitters(probe_emitter_sites)
                 label_params["coordinates"] = label_object.gen_labeling_entity()
                 print(label_params["coordinates"])
-            label_params_list.append(label_params)
+            
             structure.add_label(label_object)
             if label_params["binding"]["distance"]["to_target"] is not None:
                 print("Label is indirect label")
@@ -250,6 +253,7 @@ def particle_from_structure(
             if label_params["binding"]["distance"]["between_targets"] == "estimate":
                 distances = pdist(label_params["coordinates"])
                 label_params["binding"]["distance"]["between_targets"] = np.max(distances)
+            label_params_list.append(label_params)
         inst_builder = structure.create_instance_builder()
         particle = labinstance.create_particle(
             source_builder=inst_builder, label_params_list=label_params_list

From c048a8903881af5d8caff4cade151d6a957ec796 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Tue, 5 Aug 2025 11:26:48 +0100
Subject: [PATCH 09/29] bugfix: translate source points as well for labelled
 structure and update visualisation of probe

---
 src/supramolsim/generate/labelled_instance.py | 26 ++++++++++---------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/supramolsim/generate/labelled_instance.py b/src/supramolsim/generate/labelled_instance.py
index e86cca2a..3bbda448 100644
--- a/src/supramolsim/generate/labelled_instance.py
+++ b/src/supramolsim/generate/labelled_instance.py
@@ -684,6 +684,11 @@ def transform_translate(self, newcenter):
                 self.emitters[labeltype], _ = transform_displace_set(
                     self.get_emitter_by_target(labeltype), self.get_ref_point(), nref
                 )
+                # translate sources as well
+                self.source["targets"][labeltype]["coordinates"], _  = transform_displace_set(
+                    self._get_source_coords_normals(labeltype)["coordinates"], self.get_ref_point(), nref
+                )
+     
         # then replace reference point
         self._set_ref_point(nref)
         self.axis["pivot"] = nref
@@ -753,6 +758,8 @@ def scale_coordinates_system(self, new_scale: float):
             probe_scaling_factor = self.secondary[labeltype]["scale"] / new_scale
             if self.secondary[labeltype]["emitters"] is not None:
                 self.secondary[labeltype]["emitters"] = self.secondary[labeltype]["emitters"].astype('float64') * probe_scaling_factor
+            if self.secondary[labeltype]["minimal_distance"] is not None:
+                self.secondary[labeltype]["minimal_distance"] *= probe_scaling_factor
             if "coordinates" in self.secondary[labeltype].keys():
                 self.secondary[labeltype]["coordinates"] = self.secondary[labeltype]["coordinates"].astype('float64') * probe_scaling_factor
             if self.secondary[labeltype]["binding"]["distance"]["to_target"] is not None:
@@ -856,7 +863,7 @@ def show_probe(self,
             probe_name = self.emitters[first_probe]
         fig = plt.figure()
         ax = fig.add_subplot(111, projection="3d")
-        probe_plotting_params = self._get_label_plotting_params(probe_name)
+        #probe_plotting_params = self._get_label_plotting_params(probe_name)
         total_coordinates = copy.copy(self.labels[probe_name]["emitters"])
         total_number_coordinates = total_coordinates.shape[0]
         center = np.mean(total_coordinates, axis=0)
@@ -869,20 +876,15 @@ def show_probe(self,
                     format_coordinates(
                         centered_emitters, 
                             plotmarker="o",
-                            plotcolour="#984ea3",
-                            plotsize=20
+                            plotsize=20,
+                            **kwargs
                     ),
                 )
         if central_axis:
-            add_ax_scatter(
-                        ax,
-                            format_coordinates(
-                                centered_axis,
-                                plotmarker="x",
-                                plotcolour="k",
-                                plotsize=20
-                            ),
-                        )
+            axis_segment = dict()
+            axis_segment["pivot"] = centered_axis[0]
+            axis_segment["direction"] = centered_axis[1] - centered_axis[0]
+            draw1nomral_segment(axis_segment, ax, lenght=100, colors=["g", "y"])
         ax.set_xlim(xlims)
         ax.set_ylim(ylims)
         if zlims is None:

From 3603181efc5be9eae8a2c9da994fa671d495a5b0 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Tue, 5 Aug 2025 14:21:45 +0100
Subject: [PATCH 10/29] update probe_model method

---
 src/supramolsim/workflows.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/supramolsim/workflows.py b/src/supramolsim/workflows.py
index 085477d3..4a7e20ad 100644
--- a/src/supramolsim/workflows.py
+++ b/src/supramolsim/workflows.py
@@ -173,7 +173,7 @@ def probe_model(
     # print(structural_model.label_targets)
     
 
-    return structural_model, target_sites, anchor_point, direction_point, probe_epitope
+    return structural_model, target_sites, np.squeeze(anchor_point, axis=None), np.squeeze(direction_point, axis=None), probe_epitope
 
 
 def particle_from_structure(

From f110db5f4c309bc5d73b5ab89a2641ff0910c838 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Tue, 5 Aug 2025 15:49:50 +0100
Subject: [PATCH 11/29] minor update

---
 src/supramolsim/experiments.py                  | 12 ++++++------
 src/supramolsim/generate/molecular_structure.py |  3 +++
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/supramolsim/experiments.py b/src/supramolsim/experiments.py
index dbc3138e..af3f31c1 100644
--- a/src/supramolsim/experiments.py
+++ b/src/supramolsim/experiments.py
@@ -1149,7 +1149,7 @@ 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,
@@ -1240,9 +1240,9 @@ def generate_virtual_sample(
         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:
@@ -1261,8 +1261,8 @@ 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(
diff --git a/src/supramolsim/generate/molecular_structure.py b/src/supramolsim/generate/molecular_structure.py
index 53a04c13..dec3e431 100644
--- a/src/supramolsim/generate/molecular_structure.py
+++ b/src/supramolsim/generate/molecular_structure.py
@@ -770,6 +770,7 @@ def show_target_labels(
         return_plot=False,
         axis_object=None,
         target_size = None,
+        target_plotcolour = None,
         atoms_size = None,
         atoms_alpha = None,
     ):
@@ -811,6 +812,8 @@ def show_target_labels(
             for trgt in list(self.label_targets.keys()):
                 if target_size is not None:
                     self.plotting_params[trgt]["plotsize"] = target_size
+                if target_plotcolour is not None:
+                    self.plotting_params[trgt]["plotcolour"] = target_plotcolour
                 if with_normals:
                     draw_nomral_segments(
                         [self.get_target_normals(trgt), self.get_target_coords(trgt)],

From 8ff3c1a2184a13ee914b3142913dffaeb3e7929a Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Wed, 6 Aug 2025 11:57:20 +0100
Subject: [PATCH 12/29] minor update

---
 src/supramolsim/experiments.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/supramolsim/experiments.py b/src/supramolsim/experiments.py
index af3f31c1..e8254646 100644
--- a/src/supramolsim/experiments.py
+++ b/src/supramolsim/experiments.py
@@ -956,6 +956,7 @@ 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()
 

From 9f360638ab8950b3ee96f826d74314f4097b4ed2 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Wed, 6 Aug 2025 11:57:41 +0100
Subject: [PATCH 13/29] structure: keep atoms in file

---
 src/supramolsim/generate/molecular_structure.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/supramolsim/generate/molecular_structure.py b/src/supramolsim/generate/molecular_structure.py
index dec3e431..73354305 100644
--- a/src/supramolsim/generate/molecular_structure.py
+++ b/src/supramolsim/generate/molecular_structure.py
@@ -309,6 +309,7 @@ def generate_assembly_reference_point(self):
         """
         # this function could use a small portion of the atoms defined only
         allatoms_defined = self.get_atoms_infile()  # Parse all atoms in file
+        self.atoms_in_file = allatoms_defined
         if self.assembly_operations is None:
             self.generate_assemmbly_operations()
         if self.assymetric_defined:

From f62efdaac943f1dc5e043ac9bc4aa7ebf7492bb9 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Wed, 6 Aug 2025 17:01:02 +0100
Subject: [PATCH 14/29] add option to return volume_activation

---
 src/supramolsim/generate/imaging.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/supramolsim/generate/imaging.py b/src/supramolsim/generate/imaging.py
index 2b0a2156..dcad4fff 100644
--- a/src/supramolsim/generate/imaging.py
+++ b/src/supramolsim/generate/imaging.py
@@ -657,6 +657,14 @@ def generate_imaging(
                         asframes=False,
                     )
                     beads = None
+            elif convolution_type == "raw_volume_activation":
+                    images = conv.generate_frames_volume_convolution(
+                        **field_data,
+                        **psf_data,
+                        asframes=False,
+                        activation_only=True
+                    )
+                    beads = None
             else:
                 images, beads = self.images_by_convolutions(
                     convolution_type, **simparams
@@ -669,7 +677,7 @@ def generate_imaging(
 
             # wrap up the images from a single fluorophore in the channel
             output_per_fluoname[fluo] = dict(images=images, beads=beads)
-        if convolution_type != "raw_volume":
+        if convolution_type not in ["raw_volume", "raw_volume_activation"]:
             timeseries, beadstack = self._add_fluorophore_signals(output_per_fluoname)
             # # # Up to here only the photon information on arrival
             if noise:

From 383a6edda9b0934a740974aac5ee3d9509148a18 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Wed, 6 Aug 2025 17:01:25 +0100
Subject: [PATCH 15/29] return activation volume

---
 src/supramolsim/utils/transform/image_convolution.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/supramolsim/utils/transform/image_convolution.py b/src/supramolsim/utils/transform/image_convolution.py
index 9c60e0de..ad0d646d 100644
--- a/src/supramolsim/utils/transform/image_convolution.py
+++ b/src/supramolsim/utils/transform/image_convolution.py
@@ -77,6 +77,7 @@ def frame_by_volume_convolution(
     kernel3D,
     zfocus_slice,
     projection_depth=2,
+    activation_only=False,
     asframe=True
 ):
     """
@@ -93,6 +94,8 @@ def frame_by_volume_convolution(
     intensity_voxel = voxelize_active_fluorophores_withrange(
         coordinates, photon_vector, ranges, bin_pixelsize=bin_size
     )
+    if activation_only:
+        return intensity_voxel
     if np.sum(photon_vector) > 0:
         convolved_intensity = convolve3D(intensity_voxel, kernel3D)
     else:
@@ -132,6 +135,7 @@ def generate_frames_volume_convolution(
     psf_focus_slice: int,
     psf_pixelsizeXY: float,
     asframes=True,
+    activation_only=False,
     psf_projection_depth=1,
     **kwargs,
 ):
@@ -202,7 +206,8 @@ def generate_frames_volume_convolution(
                 psf_array,
                 psf_focus_slice,
                 projection_depth=psf_projection_depth,
-                asframe=False
+                asframe=asframes,
+                activation_only=activation_only
             )
             volume_frames.append(v_frame)
         return volume_frames

From c31150955f99d6d71f4139d556a68ee2f6ef5a7b Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Thu, 7 Aug 2025 11:02:35 +0100
Subject: [PATCH 16/29] minor update

---
 src/supramolsim/generate/coordinates_field.py | 4 +++-
 src/supramolsim/generate/imaging.py           | 5 ++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/supramolsim/generate/coordinates_field.py b/src/supramolsim/generate/coordinates_field.py
index 532eab6f..21da7f02 100644
--- a/src/supramolsim/generate/coordinates_field.py
+++ b/src/supramolsim/generate/coordinates_field.py
@@ -639,7 +639,7 @@ def get_emitters_by_fluorophores(self):
         return dict(self.fluorophre_emitters)
 
     # methods for visualisation
-    def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, return_fig=False):
+    def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, return_fig=False, axesoff=False):
         """
         Visualize the field and emitters in 3D.
 
@@ -701,6 +701,8 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
             [ub - lb for lb, ub in (getattr(ax, f"get_{a}lim")() for a in "xyz")]
         )
         ax.view_init(elev=view_init[0], azim=view_init[1], roll=view_init[2])
+        if axesoff:
+            ax.set_axis_off()
         if return_fig:
             return fig
         else:
diff --git a/src/supramolsim/generate/imaging.py b/src/supramolsim/generate/imaging.py
index dcad4fff..1bbacc99 100644
--- a/src/supramolsim/generate/imaging.py
+++ b/src/supramolsim/generate/imaging.py
@@ -1076,6 +1076,7 @@ def show_field(
         initial_pos=True,
         reference_pt=False,
         axesoff=False,
+        emitters_plotsize=None,
         return_fig = False
     ):
         """
@@ -1118,7 +1119,7 @@ def show_field(
         zz = yy * 0 + (z_focus * factor)
         fig = plt.figure()
         ax = fig.add_subplot(111, projection="3d")
-        ax.plot_surface(xx, yy, zz, alpha=0.2, cmap="plasma")
+        ax.plot_surface(xx, yy, zz, alpha=0.2)
         # show ROI reference point
         if reference_pt:
             ref_pt = self.get_absoulte_reference_point() * factor
@@ -1127,6 +1128,8 @@ def show_field(
         if self.emitters_by_fluorophore is not None:
             for fname, coords in self.emitters_by_fluorophore.items():
                 # print(fname)
+                if emitters_plotsize is not None:
+                    self.plotting_params[fname]["plotsize"] = emitters_plotsize
                 add_ax_scatter(
                     ax,
                     format_coordinates(coords * factor, **self.plotting_params[fname]),

From d521ce283f73962efdc8ae0ebaffe4e24634aa5c Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Thu, 7 Aug 2025 11:22:20 +0100
Subject: [PATCH 17/29] add projections method for stack visulisation

---
 src/supramolsim/utils/visualisation/matplotlib_plots.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/supramolsim/utils/visualisation/matplotlib_plots.py b/src/supramolsim/utils/visualisation/matplotlib_plots.py
index ccf99b79..55d31718 100644
--- a/src/supramolsim/utils/visualisation/matplotlib_plots.py
+++ b/src/supramolsim/utils/visualisation/matplotlib_plots.py
@@ -138,12 +138,16 @@ def draw_nomral_segments(points_normal, figure, lenght=100, colors=["g", "y"]):
     return figure
 
 
-def stack_projection(stack, angle=45, axes=(1,2), method = "max"):
+def stack_projection(stack, angle=45, axes=(1,2), method = "sd"):
     projection = None
     zstack = copy.copy(stack)
     rotated = rotate(zstack, angle=angle, axes=axes, reshape=False, order=3)  # order=3: cubic interpolation
     if method == "max":
-        projection = np.max(rotated, axis=2) 
+        projection = np.max(rotated, axis=2)
+    elif method == "sd":
+        projection = np.std(rotated, axis=2)
+    elif method == "mean":
+        projection = np.mean(rotated, axis=2)
     return projection
 
 def plot_projection(stack, angle=45, plane="XY", method = "max"):

From 3671b594fd9a9d081131803c2a55a2237a30327c Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Thu, 7 Aug 2025 11:41:00 +0100
Subject: [PATCH 18/29] add sum

---
 src/supramolsim/utils/visualisation/matplotlib_plots.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/supramolsim/utils/visualisation/matplotlib_plots.py b/src/supramolsim/utils/visualisation/matplotlib_plots.py
index 55d31718..928c191b 100644
--- a/src/supramolsim/utils/visualisation/matplotlib_plots.py
+++ b/src/supramolsim/utils/visualisation/matplotlib_plots.py
@@ -148,6 +148,9 @@ def stack_projection(stack, angle=45, axes=(1,2), method = "sd"):
         projection = np.std(rotated, axis=2)
     elif method == "mean":
         projection = np.mean(rotated, axis=2)
+    elif method == "sum":
+        projection = np.sum(rotated, axis=2)
+    
     return projection
 
 def plot_projection(stack, angle=45, plane="XY", method = "max"):

From ba04c600069bfbe2ef48c51407aec41ef10cdf6e Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Thu, 7 Aug 2025 13:38:20 +0100
Subject: [PATCH 19/29] update visualisation in z projections

---
 .../utils/visualisation/matplotlib_plots.py         | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/supramolsim/utils/visualisation/matplotlib_plots.py b/src/supramolsim/utils/visualisation/matplotlib_plots.py
index 928c191b..af91038f 100644
--- a/src/supramolsim/utils/visualisation/matplotlib_plots.py
+++ b/src/supramolsim/utils/visualisation/matplotlib_plots.py
@@ -138,10 +138,16 @@ def draw_nomral_segments(points_normal, figure, lenght=100, colors=["g", "y"]):
     return figure
 
 
-def stack_projection(stack, angle=45, axes=(1,2), method = "sd"):
+def stack_projection(stack, angle=45, axes=(1,2), method = "sd", zdepth = False):
     projection = None
     zstack = copy.copy(stack)
     rotated = rotate(zstack, angle=angle, axes=axes, reshape=False, order=3)  # order=3: cubic interpolation
+    if zdepth:
+        nslices = rotated.shape[2]
+        for i in range(1, nslices):
+            #intensity_factor = np.log(1.8 + ((nslices - i)/(nslices)))
+            intensity_factor = 0.6 * np.exp(((nslices - i)/(nslices)) * (1/(i+1)))
+            rotated[:,:,i] = rotated[:,:,i]*intensity_factor
     if method == "max":
         projection = np.max(rotated, axis=2)
     elif method == "sd":
@@ -150,10 +156,9 @@ def stack_projection(stack, angle=45, axes=(1,2), method = "sd"):
         projection = np.mean(rotated, axis=2)
     elif method == "sum":
         projection = np.sum(rotated, axis=2)
-    
     return projection
 
-def plot_projection(stack, angle=45, plane="XY", method = "max"):
+def plot_projection(stack, angle=45, plane="XY", method = "max", zdepth=False):
     if plane == "XY":
         axes = (1, 2)
     elif plane == "XZ": 
@@ -162,7 +167,7 @@ def plot_projection(stack, angle=45, plane="XY", method = "max"):
         axes = (0, 1)
     else:
         raise ValueError("Invalid plane. Choose from 'XY', 'XZ', or 'YZ'.")
-    projection = stack_projection(stack, angle=angle, axes=axes, method=method)
+    projection = stack_projection(stack, angle=angle, axes=axes, method=method, zdepth=zdepth)
     plt.imshow(projection, cmap='gray')
     plt.axis('off')
     plt.show()
\ No newline at end of file

From 37cf27462b5b30e43c17356050f8dc7a49f489ef Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Fri, 8 Aug 2025 14:43:09 +0100
Subject: [PATCH 20/29] minor update

---
 src/supramolsim/generate/coordinates_field.py | 21 ++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/src/supramolsim/generate/coordinates_field.py b/src/supramolsim/generate/coordinates_field.py
index 21da7f02..6f4c852c 100644
--- a/src/supramolsim/generate/coordinates_field.py
+++ b/src/supramolsim/generate/coordinates_field.py
@@ -639,7 +639,7 @@ def get_emitters_by_fluorophores(self):
         return dict(self.fluorophre_emitters)
 
     # methods for visualisation
-    def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, return_fig=False, axesoff=False):
+    def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, return_fig=False, axesoff=False, axis_object=None):
         """
         Visualize the field and emitters in 3D.
 
@@ -664,9 +664,13 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
             range(int(dimension_sizes[0])), range(int(dimension_sizes[1]))
         )
         zz = (yy) * 0
-        fig = plt.figure()
-        ax = fig.add_subplot(111, projection="3d")
-        ax.plot_surface(xx, yy, zz, alpha=0.2)
+        if axis_object is not None:
+            ax = axis_object
+            ax.plot_surface(xx, yy, zz, alpha=0.2)
+        else:
+            fig = plt.figure()
+            ax = fig.add_subplot(111, projection="3d")
+            ax.plot_surface(xx, yy, zz, alpha=0.2)
 
         if initial_pos:
             if self.molecules_params["absolute_positions"] is not None:
@@ -703,10 +707,13 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
         ax.view_init(elev=view_init[0], azim=view_init[1], roll=view_init[2])
         if axesoff:
             ax.set_axis_off()
-        if return_fig:
-            return fig
+        if axis_object is not None:
+            return ax
         else:
-            fig.show()
+            if return_fig:
+                return fig
+            else:
+                fig.show()
 
     def expand_isotropically(self, factor):
         """

From ba06ddf943b0fd62f33a91601b4bbf2e22831fda Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 10:33:02 +0100
Subject: [PATCH 21/29] bugfix conjugation sites not being use when adding
 probe to experiment

---
 src/supramolsim/experiments.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/supramolsim/experiments.py b/src/supramolsim/experiments.py
index e8254646..2cb75264 100644
--- a/src/supramolsim/experiments.py
+++ b/src/supramolsim/experiments.py
@@ -942,6 +942,8 @@ 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:

From bd59ca28dcfd824413c2c379372161a37e31fb61 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 10:33:33 +0100
Subject: [PATCH 22/29] minor update

---
 src/supramolsim/generate/labelled_instance.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/supramolsim/generate/labelled_instance.py b/src/supramolsim/generate/labelled_instance.py
index 3bbda448..145f641a 100644
--- a/src/supramolsim/generate/labelled_instance.py
+++ b/src/supramolsim/generate/labelled_instance.py
@@ -918,8 +918,8 @@ def show_instance(
         show_axis=False,
         with_sources=False,
         return_plot=False,
-        source_size=1,
-        emitter_plotsize=1,
+        source_size=None,
+        emitter_plotsize=None,
     ):
         """
         Visualize the labelled instance in 3D.
@@ -955,7 +955,8 @@ def show_instance(
             ax = fig.add_subplot(111, projection="3d")
             for labs in self.labelnames:
                 lab_plotparams = self._get_label_plotting_params(labs)
-                lab_plotparams["plotsize"] = emitter_plotsize
+                if emitter_plotsize is not None:
+                    lab_plotparams["plotsize"] = emitter_plotsize
                 add_ax_scatter(
                     ax,
                     format_coordinates(
@@ -963,6 +964,10 @@ def show_instance(
                     ),
                 )
                 if with_sources:
+                    if source_size is not None:
+                        source_size=source_size
+                    else:
+                        source_size=1
                     add_ax_scatter(
                         ax,
                         format_coordinates(

From b87ccd0a5411899cbc24079966aa4f41b4c8da06 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 13:41:30 +0100
Subject: [PATCH 23/29] show labelled structure with normals

---
 src/supramolsim/generate/labelled_instance.py | 24 +++++++++++++++----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/src/supramolsim/generate/labelled_instance.py b/src/supramolsim/generate/labelled_instance.py
index 145f641a..cd12fce0 100644
--- a/src/supramolsim/generate/labelled_instance.py
+++ b/src/supramolsim/generate/labelled_instance.py
@@ -10,7 +10,7 @@
     transform_displace_set,
 )
 from ..utils.data_format.visualisation import format_coordinates, set_colorplot
-from ..utils.visualisation.matplotlib_plots import add_ax_scatter, draw1nomral_segment
+from ..utils.visualisation.matplotlib_plots import add_ax_scatter, draw1nomral_segment, draw_nomral_segments
 from ..utils.transform.cif_builder import create_instance_label
 from ..utils.transform.defects import xmersubset_byclustering
 from ..utils.data_format.structural_format import builder_format
@@ -1011,10 +1011,12 @@ def gen_axis_plot(
         axesoff=True,
         show_axis=False,
         with_sources=False,
-        source_plotsize=1,
+        source_plotsize=None,
         axis_object=None,
-        emitter_plotsize=1,
-        source_plotcolour="#bbbbbb"
+        emitter_plotsize=None,
+        source_plotcolour="#bbbbbb",
+        with_normals=False,
+        **kwargs
     ):
         """
         Generate a 3D axis plot for the labelled instance.
@@ -1044,7 +1046,8 @@ def gen_axis_plot(
         if labelnames == "All":
             for labs in self.labelnames:
                 lab_plotparams = self._get_label_plotting_params(labs)
-                lab_plotparams["plotsize"] = emitter_plotsize
+                if emitter_plotsize is not None:
+                    lab_plotparams["plotsize"] = emitter_plotsize
                 add_ax_scatter(
                     axis_object,
                     format_coordinates(self.emitters[labs], **lab_plotparams),
@@ -1052,6 +1055,10 @@ def gen_axis_plot(
                 zlims[0] = np.min(self.emitters[labs])
                 zlims[1] = np.max(self.emitters[labs])
                 if with_sources:
+                    if source_plotsize is not None:
+                        source_plotsize = source_plotsize
+                    else:
+                        source_plotsize = 1
                     if self.defects_target_normals is not None:
                         add_ax_scatter(
                             axis_object,
@@ -1076,6 +1083,13 @@ def gen_axis_plot(
                                 plotsize=source_plotsize,
                             ),
                         )
+                    if with_normals:
+                        draw_nomral_segments(
+                            [self.source["targets"][labs]["normals"], self.source["targets"][labs]["coordinates"]],
+                            axis_object,
+                            colors=["grey", "green"],
+                            **kwargs
+                        )
 
                 # add_ax_scatter(ax, format_coordinates(self.emitters[labs]))
         if reference_point:

From 128133930595277d96cab0bc073f8b9d94538ebe Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 13:41:38 +0100
Subject: [PATCH 24/29] minor update

---
 src/supramolsim/utils/visualisation/matplotlib_plots.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/supramolsim/utils/visualisation/matplotlib_plots.py b/src/supramolsim/utils/visualisation/matplotlib_plots.py
index af91038f..9836ab15 100644
--- a/src/supramolsim/utils/visualisation/matplotlib_plots.py
+++ b/src/supramolsim/utils/visualisation/matplotlib_plots.py
@@ -114,7 +114,7 @@ def draw1nomral_segment(points_normal, figure, lenght=100, colors=["g", "y"]):
     figure.scatter(ends[0], ends[1], ends[2], color=colors[1], marker="o")
 
 
-def draw_nomral_segments(points_normal, figure, lenght=100, colors=["g", "y"]):
+def draw_nomral_segments(points_normal, figure, lenght=100, colors=["g", "y"], **kwargs):
     # points_normals is a list of 2 elements
     # first element are the normals
     # second element are ponts in space

From ac63f0f4708c9f081815aab908726ab859339a0a Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 15:32:50 +0100
Subject: [PATCH 25/29] buffix defect parameters

---
 src/supramolsim/generate/labelled_instance.py | 35 +++++++++++--------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/src/supramolsim/generate/labelled_instance.py b/src/supramolsim/generate/labelled_instance.py
index cd12fce0..fa80f0f4 100644
--- a/src/supramolsim/generate/labelled_instance.py
+++ b/src/supramolsim/generate/labelled_instance.py
@@ -503,18 +503,23 @@ def add_defects(
         minsamples : int, optional
             Minimum samples for clustering. Default is 1.
         """
-        d_cluster_params = dict(
-            eps1=eps1,
-            minsamples1=minsamples,
-            eps2=xmer_neigh_distance,
-            minsamples2=minsamples,
-        )
-        self.defects_params["d_cluster_params"] = d_cluster_params
-        self.defects_params["deg_dissasembly"] = deg_dissasembly
-        self.defects_params["xmer_neigh_distance"] = xmer_neigh_distance
-        self.defects_params["fracture"] = fracture
-        self.defects = True
-        self.generate_instance()
+        if deg_dissasembly == 0:
+            self.defects = False
+            self.defects_target_normals = None
+            self.generate_instance()
+        else:
+            d_cluster_params = dict(
+                eps1=eps1,
+                minsamples1=minsamples,
+                eps2=xmer_neigh_distance,
+                minsamples2=minsamples,
+            )
+            self.defects_params["d_cluster_params"] = d_cluster_params
+            self.defects_params["deg_dissasembly"] = deg_dissasembly
+            self.defects_params["xmer_neigh_distance"] = xmer_neigh_distance
+            self.defects_params["fracture"] = fracture
+            self.defects = True
+            self.generate_instance()
 
     def _model_defects(self, target_normals_dictionary):
         """
@@ -899,9 +904,9 @@ def show_probe(self,
         if axesoff:
             ax.set_axis_off()
         else:
-            ax.set_xlabel("X (Angstroms)")
-            ax.set_ylabel("Y (Angstroms)")
-            ax.set_zlabel("Z (Angstroms)")
+            ax.set_xlabel("X (Å)")
+            ax.set_ylabel("Y (Å)")
+            ax.set_zlabel("Z (Å)")
         if return_plot:
             return ax
         else:

From 3729b020b066309bea16cf0b07a338cff000d7c6 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 15:33:10 +0100
Subject: [PATCH 26/29] minor updates

---
 src/supramolsim/generate/coordinates_field.py | 28 +++++++++++++++----
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/supramolsim/generate/coordinates_field.py b/src/supramolsim/generate/coordinates_field.py
index 6f4c852c..aa1223f6 100644
--- a/src/supramolsim/generate/coordinates_field.py
+++ b/src/supramolsim/generate/coordinates_field.py
@@ -639,7 +639,7 @@ def get_emitters_by_fluorophores(self):
         return dict(self.fluorophre_emitters)
 
     # methods for visualisation
-    def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, return_fig=False, axesoff=False, axis_object=None):
+    def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, return_fig=False, axesoff=False, axis_object=None, zoom_in=None, **kwargs):
         """
         Visualize the field and emitters in 3D.
 
@@ -659,11 +659,23 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
         matplotlib.figure.Figure or None
             The figure if return_fig is True, otherwise None.
         """
-        dimension_sizes = self.get_field_param("dimension_sizes")
-        xx, yy = np.meshgrid(
-            range(int(dimension_sizes[0])), range(int(dimension_sizes[1]))
-        )
-        zz = (yy) * 0
+        dimension_sizes = copy.copy(self.get_field_param("dimension_sizes"))
+        if zoom_in and zoom_in>0.2 and zoom_in<1:
+            x_to_remove = dimension_sizes[0]*zoom_in
+            x_size = dimension_sizes[0] - x_to_remove
+            y_to_remove = dimension_sizes[1]*zoom_in
+            y_size = dimension_sizes[1] - y_to_remove
+            xx, yy = np.meshgrid(
+                range(int(x_size)), range(int(y_size))
+            )
+            xx = xx + (x_to_remove/2)
+            yy = yy + (y_to_remove/2)
+            zz = (yy) * 0
+        else:
+            xx, yy = np.meshgrid(
+                range(int(dimension_sizes[0])), range(int(dimension_sizes[1]))
+            )
+            zz = (yy) * 0
         if axis_object is not None:
             ax = axis_object
             ax.plot_surface(xx, yy, zz, alpha=0.2)
@@ -707,6 +719,10 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
         ax.view_init(elev=view_init[0], azim=view_init[1], roll=view_init[2])
         if axesoff:
             ax.set_axis_off()
+        else:
+            ax.set_xlabel("X (Å)")
+            ax.set_ylabel("Y (Å)")
+            ax.set_zlabel("Z (Å)")
         if axis_object is not None:
             return ax
         else:

From 918b34ad168e078752ed22a588ea3484e160e156 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 15:35:38 +0100
Subject: [PATCH 27/29] update defects at experiment

---
 src/supramolsim/experiments.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/supramolsim/experiments.py b/src/supramolsim/experiments.py
index 2cb75264..746fdc79 100644
--- a/src/supramolsim/experiments.py
+++ b/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

From 2ef0a51eb06f1e4cdfe2949964688a04cd7c1777 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 18:36:01 +0100
Subject: [PATCH 28/29] tests update

---
 tests/test_feature_defects.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/test_feature_defects.py b/tests/test_feature_defects.py
index 6fa8a5fa..5c993d67 100644
--- a/tests/test_feature_defects.py
+++ b/tests/test_feature_defects.py
@@ -13,4 +13,7 @@ def test_add_defects(defect, experiment_7r5k_base):
         xmer_neigh_distance=600,
         deg_dissasembly=defect,
     )
-    assert experiment_7r5k_base.particle.defects_target_normals is not None
+    if defect == 0:
+        assert experiment_7r5k_base.particle.defects_target_normals is None
+    else:
+        assert experiment_7r5k_base.particle.defects_target_normals is not None

From a50074a5af350af49b3c73ed2825a9cd7da48b06 Mon Sep 17 00:00:00 2001
From: Damian Martinez <jdmartinezigc@gmail.com>
Date: Mon, 11 Aug 2025 18:36:38 +0100
Subject: [PATCH 29/29] format coordinates field module

---
 src/supramolsim/generate/coordinates_field.py | 113 ++++++++++--------
 1 file changed, 66 insertions(+), 47 deletions(-)

diff --git a/src/supramolsim/generate/coordinates_field.py b/src/supramolsim/generate/coordinates_field.py
index aa1223f6..1c824266 100644
--- a/src/supramolsim/generate/coordinates_field.py
+++ b/src/supramolsim/generate/coordinates_field.py
@@ -112,7 +112,9 @@ def init_from_file(self, field_yaml):
         # set molecules params
         self.set_molecules_params(**molecules)
 
-    def create_minimal_field(self, nmolecules=1, random_placing=False, random_orientations=False, **kwargs):
+    def create_minimal_field(
+        self, nmolecules=1, random_placing=False, random_orientations=False, **kwargs
+    ):
         """
         Create a minimal field with a specified number of molecules and placement options.
 
@@ -158,7 +160,7 @@ def create_minimal_field(self, nmolecules=1, random_placing=False, random_orient
             }
         else:
             # if none of the above, this is the case of a single particle in the center
-            #point = self.get_field_param("absolute_reference_point")
+            # point = self.get_field_param("absolute_reference_point")
             self.set_molecule_param("nMolecules", 1)
             if random_placing:
                 self.random_placing = True
@@ -169,8 +171,6 @@ def create_minimal_field(self, nmolecules=1, random_placing=False, random_orient
         self._set_fluo_plotting_params(fluo_name)
         self.random_orientations = random_orientations
 
-
-
     def calculate_absolute_reference(self):
         """
         Calculate and set the absolute reference point based on the relative reference and dimension sizes.
@@ -296,7 +296,9 @@ def generate_random_positions(self):
         # print(f"Total positions: {npositions}")
         # this can only work after the size of field has been established
         if self.molecules_params["minimal_distance"] is not None:
-            print(f"distributing with minimal distance: {self.molecules_params['minimal_distance']}")
+            print(
+                f"distributing with minimal distance: {self.molecules_params['minimal_distance']}"
+            )
             self._random_pos_minimal_dist(npositions)
         else:
             print("Generating unconstrained random positions")
@@ -318,7 +320,7 @@ def generate_random_orientations(self):
             orientations.append(np.array(sampl.sample_spherical_normalised(1, ndim=3)))
         self.set_molecule_param("orientations", orientations)
 
-    def generate_global_orientation(self, global_orientation = None):
+    def generate_global_orientation(self, global_orientation=None):
         """
         Set a global orientation for all molecules.
 
@@ -372,19 +374,19 @@ def _random_pos_minimal_dist(self, n):
                 # print(np.linalg.norm(new - selected_positions[pos]))
                 if np.linalg.norm(new - selected_positions[pos]) < minimal_distance:
                     is_available = 0
-                    #break
+                    # break
             if is_available:
                 selected_positions.append(new)
         for abs_pos in selected_positions:
             rel_pos = abs_pos
-            rel_pos[0] = abs_pos[0]/maxabs_posx
-            rel_pos[1] = abs_pos[1]/maxabs_posy
-            rel_pos[2] = abs_pos[2]/maxabs_posz
+            rel_pos[0] = abs_pos[0] / maxabs_posx
+            rel_pos[1] = abs_pos[1] / maxabs_posy
+            rel_pos[2] = abs_pos[2] / maxabs_posz
             selected_relative.append(rel_pos)
         # print(f"end flag : {flag}")
         self.molecules_params["relative_positions"] = selected_relative
-        #self.set_molecule_param("absolute_positions", selected_positions)
-        #self.absolute_pos = selected_positions
+        # self.set_molecule_param("absolute_positions", selected_positions)
+        # self.absolute_pos = selected_positions
 
     def _calculate_absolute_position(self, relative_pos):
         fieldsizes = self.get_field_param("dimension_sizes")
@@ -444,9 +446,7 @@ def create_molecules_from_InstanceObject(self, InstancePrototype: LabeledInstanc
         particle_copy.scale_coordinates_system(self.get_field_param("scale"))
         self.molecules_default_orientation = particle_copy.get_axis()
         if self.molecules_params["minimal_distance"] is None:
-            self._set_molecule_minimal_distance(
-                dist=particle_copy.radial_hindance
-            )
+            self._set_molecule_minimal_distance(dist=particle_copy.radial_hindance)
         if self.random_placing:
             self.generate_random_positions()
         self._gen_abs_from_rel_positions()
@@ -468,7 +468,6 @@ def create_molecules_from_InstanceObject(self, InstancePrototype: LabeledInstanc
             self.generate_random_orientations()
             # self.relabel_molecules()
         self.relabel_molecules()
-        
 
     def _create_instances_from_pdb(self, cif_f, structure_id, label_file):
         # this is exactly the same as the high level function
@@ -513,7 +512,7 @@ def relabel_molecules(self):
             for mol in self.molecules:
                 mol.generate_instance()
                 # mol.show_instance()
-                #mol.scale_coordinates_system(self.get_field_param("scale"))
+                # mol.scale_coordinates_system(self.get_field_param("scale"))
 
     def relocate_molecules(self):
         """
@@ -578,9 +577,11 @@ def construct_static_field(self, relocate=True, reorient=True):
             self._construct_channels_by_fluorophores()
         else:
             default_fluorophore = "AF647"
-            #self.get_molecule_param("absolute_positions")
+            # self.get_molecule_param("absolute_positions")
             self.fluorophre_emitters = {}
-            self.fluorophre_emitters[default_fluorophore] = self.get_molecule_param("absolute_positions")
+            self.fluorophre_emitters[default_fluorophore] = self.get_molecule_param(
+                "absolute_positions"
+            )
 
     def _construct_channels_by_fluorophores(self):
         """
@@ -639,7 +640,18 @@ def get_emitters_by_fluorophores(self):
         return dict(self.fluorophre_emitters)
 
     # methods for visualisation
-    def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, return_fig=False, axesoff=False, axis_object=None, zoom_in=None, **kwargs):
+    def show_field(
+        self,
+        fluo_type="all",
+        view_init=[30, 0, 0],
+        initial_pos=True,
+        return_fig=False,
+        axesoff=False,
+        axis_object=None,
+        zoom_in=None,
+        emitters_plotsize=None,
+        **kwargs,
+    ):
         """
         Visualize the field and emitters in 3D.
 
@@ -660,16 +672,14 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
             The figure if return_fig is True, otherwise None.
         """
         dimension_sizes = copy.copy(self.get_field_param("dimension_sizes"))
-        if zoom_in and zoom_in>0.2 and zoom_in<1:
-            x_to_remove = dimension_sizes[0]*zoom_in
+        if zoom_in and zoom_in > 0.2 and zoom_in < 1:
+            x_to_remove = dimension_sizes[0] * zoom_in
             x_size = dimension_sizes[0] - x_to_remove
-            y_to_remove = dimension_sizes[1]*zoom_in
+            y_to_remove = dimension_sizes[1] * zoom_in
             y_size = dimension_sizes[1] - y_to_remove
-            xx, yy = np.meshgrid(
-                range(int(x_size)), range(int(y_size))
-            )
-            xx = xx + (x_to_remove/2)
-            yy = yy + (y_to_remove/2)
+            xx, yy = np.meshgrid(range(int(x_size)), range(int(y_size)))
+            xx = xx + (x_to_remove / 2)
+            yy = yy + (y_to_remove / 2)
             zz = (yy) * 0
         else:
             xx, yy = np.meshgrid(
@@ -699,6 +709,8 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
             print("Showing all fluorophores")
             for fname in self.fluorophre_emitters.keys():
                 print(fname)
+                if emitters_plotsize is not None:
+                    self.plotting_params[fname]["plotsize"] = emitters_plotsize
                 add_ax_scatter(
                     ax,
                     format_coordinates(
@@ -706,6 +718,8 @@ def show_field(self, fluo_type="all", view_init=[30, 0, 0], initial_pos=True, re
                     ),
                 )
         else:
+            if emitters_plotsize is not None:
+                    self.plotting_params[fname]["plotsize"] = emitters_plotsize
             add_ax_scatter(
                 ax,
                 format_coordinates(
@@ -797,7 +811,13 @@ def export_field(self):
         return export_field
 
 
-def create_min_field(number_of_particles=1, random_placing=False, random_orientations=False, prints=False, **kwargs):
+def create_min_field(
+    number_of_particles=1,
+    random_placing=False,
+    random_orientations=False,
+    prints=False,
+    **kwargs,
+):
     """
     Create a minimal field with a specified number of particles.
 
@@ -822,19 +842,21 @@ def create_min_field(number_of_particles=1, random_placing=False, random_orienta
     if prints:
         print("Initialising default field")
     coordinates_field = Field()
-    #if molecule_pars:
+    # if molecule_pars:
     #    for key, value in molecule_pars.items():
     #        coordinates_field.molecules_params[key] = value
     coordinates_field.create_minimal_field(
         nmolecules=number_of_particles,
-        random_placing=random_placing, 
+        random_placing=random_placing,
         random_orientations=random_orientations,
-        **kwargs
+        **kwargs,
     )
     return coordinates_field
 
 
-def gen_positions_from_image(img, mode="mask", pixelsize = None, min_distance = None, **kwargs):
+def gen_positions_from_image(
+    img, mode="mask", pixelsize=None, min_distance=None, **kwargs
+):
     """
     Generate relative positions from an image using either a mask or local maxima.
 
@@ -859,7 +881,7 @@ def gen_positions_from_image(img, mode="mask", pixelsize = None, min_distance =
     if min_distance is None:
         min_distance = 1
     else:
-        min_dist_pixels = min_distance/pixelsize
+        min_dist_pixels = min_distance / pixelsize
         min_distance = math.ceil(min_dist_pixels)
     npixels = list(img.shape)
     image_physical_size = np.zeros(shape=(2))
@@ -871,9 +893,7 @@ def gen_positions_from_image(img, mode="mask", pixelsize = None, min_distance =
         else:
             npositions = kwargs["npositions"]
         pixel_positions = sampl.get_random_pixels(
-            img, 
-            num_pixels=npositions, 
-            min_distance=min_distance
+            img, num_pixels=npositions, min_distance=min_distance
         )
     elif mode == "localmaxima":
         if "background" not in kwargs.keys():
@@ -889,14 +909,13 @@ def gen_positions_from_image(img, mode="mask", pixelsize = None, min_distance =
         else:
             threshold = kwargs["threshold"]
         pixel_positions, img_processed = metrics.local_maxima_positions(
-            img, 
-            min_distance=min_distance, 
-            threshold=threshold, 
-            sigma=sigma, 
-            background=background)
-    xyz_relative = metrics.pixel_positions_to_relative(
-            pixel_positions,
-            image_sizes=image_physical_size,
-            pixelsize=pixelsize
+            img,
+            min_distance=min_distance,
+            threshold=threshold,
+            sigma=sigma,
+            background=background,
         )
-    return xyz_relative, image_physical_size
\ No newline at end of file
+    xyz_relative = metrics.pixel_positions_to_relative(
+        pixel_positions, image_sizes=image_physical_size, pixelsize=pixelsize
+    )
+    return xyz_relative, image_physical_size