Made a bit more space on the report to have up to 16 chains - will ne…

…ed to work on ... button

pyproject.toml

@@ -37,6 +37,7 @@ Issues = "https://github.com/glycojones/iris-validation/issues"
 [tool.pytest.ini_options]
 markers = [
     "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "simple: a simple test to get output quickly (deselect with '-m \"not simple\"')",
     "tortoize: runs tortoize tests (deselect with '-m \"not tortoize\"')",
     "molprobity: runs molprobity tests (deselect with '-m \"not molprobity\"')",
     "problem",

src/iris_validation/__init__.py

@@ -1,8 +1,11 @@
 import os
+import sys
+import json
 
 from iris_validation.graphics import Panel
 from iris_validation.metrics import metrics_model_series_from_files
 
+PYTEST_RUN = 'pytest' in sys.modules
 
 def generate_report(
     latest_model_path,
@@ -44,7 +47,13 @@ def generate_report(
                                                    calculate_rama_z,
                                                    data_with_percentiles,
                                                    multiprocessing)
+
     model_series_data = model_series.get_raw_data()
+
+    if PYTEST_RUN : 
+        with open(os.path.join(output_dir, output_name_prefix + ".json"), 'w', encoding='utf8') as json_output :
+            json.dump(model_series_data, json_output, indent=2)
+
     panel = Panel(
         model_series_data,
         continuous_metrics_to_display=continuous_metrics_to_display,

src/iris_validation/graphics/js/interaction.js

@@ -294,7 +294,7 @@ function updateSelectedResidue() {
   // Set summary text
   let seqNum = modelData[selectedChain]['residue_seqnos'][selectedVersion][selectedResidue];
   let aaCode = modelData[selectedChain]['residue_codes'][selectedVersion][selectedResidue];
-  residueSummary.textContent = 'Residue ' + seqNum + ' (' + aaCode + ')';
+  residueSummary.textContent = seqNum + ' (' + aaCode + ')';
 };
 
 

src/iris_validation/graphics/panel.py

@@ -142,8 +142,8 @@ def _draw(self):
         middle_gap = 30
         view_border = 10
         view_title_font = 24
-        button_width = 38
-        button_height = 32
+        button_width = 26
+        button_height = 26
         view_width, view_height = [ dim - view_border for dim in self.canvas_size ]
         view_divider_x = round(2/3 * view_width, 2)
         chain_view_bounds = (view_border,
@@ -183,9 +183,15 @@ def _draw(self):
                                    font_size=view_title_font,
                                    font_family='Arial'))
 
-        self.dwg.add(self.dwg.text(text='Residue',
+
+        self.dwg.add(self.dwg.text(text='Amino acid',
                                    insert=(residue_view_bounds[0], residue_view_bounds[1]+view_title_font),
                                    font_size=view_title_font,
+                                   font_family='Arial'))
+
+        self.dwg.add(self.dwg.text(text='',
+                                   insert=(residue_view_bounds[0]+130, residue_view_bounds[1]+view_title_font),
+                                   font_size=16,
                                    font_family='Arial',
                                    id=f'{self.svg_id}-residue-summary'))
 
@@ -200,9 +206,9 @@ def _draw(self):
                                    stroke_width=2))
 
         # Chain selector buttons
-        for chain_index, chain_id in enumerate(self.chain_ids[:12]):
+        for chain_index, chain_id in enumerate(self.chain_ids[:16]):
             selector_color = self.swtich_colors[1] if chain_index == 0 else self.swtich_colors[0]
-            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 50*chain_index, chain_view_bounds[1]),
+            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 30*chain_index, chain_view_bounds[1]+5),
                                        size=(button_width, button_height),
                                        rx=5,
                                        stroke_opacity=0,
@@ -211,13 +217,13 @@ def _draw(self):
                                        id=f'{self.svg_id}-chain-selector-{chain_index}'))
 
             self.dwg.add(self.dwg.text(text=chain_id,
-                                       insert=(chain_view_bounds[0] + 75 + button_width/2 + 50*chain_index, chain_view_bounds[1] + button_height/2),
-                                       font_size=view_title_font,
+                                       insert=(chain_view_bounds[0] + 75 + button_width/2 + 30*chain_index, chain_view_bounds[1] + 5 + button_height/2),
+                                       font_size=16,
                                        font_family='Arial',
                                        text_anchor='middle',
                                        alignment_baseline='central'))
 
-            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 50*chain_index, chain_view_bounds[1]),
+            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 30*chain_index, chain_view_bounds[1]+5),
                                        size=(button_width, button_height),
                                        rx=5,
                                        stroke_opacity=0,
@@ -228,24 +234,24 @@ def _draw(self):
 
         # Extra chains dropdown
         # TODO: finish this
-        if len(self.chain_ids) > 12:
-            chain_index = 12
+        if len(self.chain_ids) > 16:
+            chain_index = 16
             selector_color = self.swtich_colors[0]
-            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 50*chain_index, chain_view_bounds[1]),
-                                       size=(38, 32),
+            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 30*chain_index, chain_view_bounds[1] +5),
+                                       size=(26, 26),
                                        rx=5,
                                        stroke_opacity=0,
                                        fill_opacity=0.5,
                                        fill=selector_color,
                                        id=f'{self.svg_id}-chain-selector-dropdown'))
 
             self.dwg.add(self.dwg.text(text='...',
-                                       insert=(chain_view_bounds[0] + 85 + 50*chain_index, chain_view_bounds[1]+view_title_font),
-                                       font_size=view_title_font,
+                                       insert=(chain_view_bounds[0] + 80 + 30*chain_index, chain_view_bounds[1]+24),
+                                       font_size=16,
                                        font_family='Arial'))
 
-            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 50*chain_index, chain_view_bounds[1]),
-                                       size=(38, 32),
+            self.dwg.add(self.dwg.rect(insert=(chain_view_bounds[0] + 75 + 30*chain_index, chain_view_bounds[1]+5),
+                                       size=(26, 26),
                                        rx=5,
                                        stroke_opacity=0,
                                        fill_opacity=0,
@@ -255,7 +261,7 @@ def _draw(self):
 
         # Version toggle switch
         self.dwg.add(self.dwg.text(text='Model version',
-                                   insert=(chain_view_bounds[2]-385, chain_view_bounds[1]+20),
+                                   insert=(chain_view_bounds[2]-380, chain_view_bounds[1]+20),
                                    font_size=view_title_font,
                                    font_family='Arial'))
 

src/iris_validation/graphics/residue.py

@@ -145,8 +145,8 @@ def _draw(self):
         self.dwg.add(
             self.dwg.text(
                 self.percentile_bar_label,
-                insert=(self.canvas_size[0] / 2, bar_charts_bounds[3] + 50),
-                font_size=18,
+                insert=((self.canvas_size[0] / 2)+20, bar_charts_bounds[3] + 60),
+                font_size=24,
                 font_family="Arial",
                 fill=COLORS["BLACK"],
                 fill_opacity=1,

src/iris_validation/metrics/__init__.py

@@ -12,7 +12,6 @@
 from iris_validation.metrics.series import MetricsModelSeries
 from iris_validation.metrics.reflections import ReflectionsHandler
 
-PYTEST_RUN = 'pytest' in sys.modules
 
 def _get_minimol_from_path(model_path):
     fpdb = clipper.MMDBfile()
@@ -190,9 +189,7 @@ def _get_tortoize_data(model_path, seq_nums, model_id=None, out_queue=None):
 
     tortoize_output = tortoize_process.communicate()[0]
     tortoize_dict = json.loads(tortoize_output)
-    if PYTEST_RUN : 
-        with open("tortoize.json", "w") as json_output :
-            json.dump(tortoize_dict, json_output, indent=2)
+
     residues = tortoize_dict["model"]["1"]["residues"]
     for res in residues:
         rama_z_data[res['pdb']['strandID']][res['pdb']['seqNum']] = res['ramachandran']['z-score']
@@ -320,8 +317,6 @@ def metrics_model_series_from_files(model_paths,
             else:
                 rama_z_data = _get_tortoize_data(model_path, seq_nums)
 
-        if multiprocessing and PYTEST_RUN : 
-            print (f"\nNumber of data sources queued: {num_queued}")
         all_minimol_data.append(minimol)
         all_covariance_data.append(covariance_data)
         all_molprobity_data.append(molprobity_data)

tests/test_core.py

@@ -10,7 +10,7 @@
 DATASET1_PATH = str(os.path.join(INPUT_DIR, "3atp")) + '{suffix}'
 DATASET2_PATH = str(os.path.join(INPUT_DIR, "8ira")) + '{suffix}'
 
-
+@pytest.mark.simple
 def test_2m2d_noCOV_noMP_noRamaZ_mpro ():
     import iris_validation as iris
     importlib.reload(iris)