Merge pull request #20 from glycojones/onemodel

Merge onemodel branch into master

.gitignore

@@ -1,4 +1,22 @@
-build/
-.vscode
+# Byte-compiled / optimized / DLL files
 __pycache__/
-PKG-INFO
+*.py[co]
+*$py.class
+
+# Mac meta stuff
+# DS_Store
+.DS_Store
+
+# Ignore build related files
+/dist
+/build
+/.eggs/
+/pyrun/
+
+# Ignore accidental test data
+/*.cif
+/*.pdb
+/*.ent
+/*.json
+/*.mtz
+/*.crd

pyproject.toml

@@ -0,0 +1,44 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "iris_validation"
+dynamic=["version"]
+description = "A package for interactive all-in-one graphical validation of 3D protein model iterations"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.8",
+]
+authors = [
+    { name = "William Rochira", email = "[email protected]" },
+    { name = "Jon Agirre", email = "[email protected]" }
+]
+maintainers = [
+    { name = "Jon Agirre", email = "[email protected]" },
+]
+dependencies = [
+    "svgwrite == 1.3.1"
+]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools_scm]
+version_file = "src/iris_validation/_version.py"
+
+[project.urls]
+Homepage = "https://github.com/glycojones/iris-validation"
+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",
+]

iris_validation/__init__.py → 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,
@@ -27,34 +30,38 @@ def generate_report(
     percentile_bar_range=None,
     wrap_in_html=True,
     output_dir=None,
+    output_name_prefix="report",
+    custom_labels={'Latest':'Latest', 'Previous':'Previous'}
 ):
 
-    model_paths = (previous_model_path, latest_model_path)
-    reflections_paths = (previous_reflections_path, latest_reflections_path)
-    sequence_paths = (previous_sequence_path, latest_sequence_path)
-    distpred_paths = (previous_distpred_path, latest_distpred_path)
-    model_json_paths = (previous_model_metrics_json, latest_model_metrics_json)
+    # sanitise output file name
+    output_name_prefix = output_name_prefix.replace('/','_').replace('.','_')
 
-    model_series = metrics_model_series_from_files(
-        model_paths,
-        reflections_paths,
-        sequence_paths,
-        distpred_paths,
-        run_covariance,
-        run_molprobity,
-        calculate_rama_z,
-        model_json_paths,
-        data_with_percentiles,
-        multiprocessing,
-    )
+    model_series = metrics_model_series_from_files((previous_model_path, latest_model_path),
+                                                   (previous_reflections_path, latest_reflections_path),
+                                                   (previous_sequence_path, latest_sequence_path),
+                                                   (previous_distpred_path, latest_distpred_path),
+                                                   (previous_model_metrics_json, latest_model_metrics_json),
+                                                   run_covariance,
+                                                   run_molprobity,
+                                                   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,
         discrete_metrics_to_display=discrete_metrics_to_display,
         residue_bars_to_display=residue_bars_to_display,
         percentile_bar_label=percentile_bar_label,
         percentile_bar_range=percentile_bar_range,
+        custom_labels=custom_labels
     )
     panel_string = panel.dwg.tostring()
 
@@ -68,5 +75,5 @@ def generate_report(
         os.mkdir(output_dir)
 
     extension = 'html' if wrap_in_html else 'svg'
-    with open(os.path.join(output_dir, f'report.{extension}'), 'w', encoding='utf8') as outfile:
+    with open(os.path.join(output_dir, f"{output_name_prefix}.{extension}"), 'w', encoding='utf8') as outfile:
         outfile.write(panel_string)

iris_validation/graphics/chain.py → src/iris_validation/graphics/chain.py

@@ -5,6 +5,7 @@
 from svgwrite.animate import Animate
 
 from iris_validation._defs import COLORS, CHAIN_VIEW_RINGS, CHAIN_VIEW_GAP_ANGLE
+from iris_validation._version import version_tuple 
 
 
 class ChainView:
@@ -142,21 +143,35 @@ def _draw(self):
 
         # Draw center text
         self.dwg.add(self.dwg.text(text='Iris',
-                                   insert=(self.center[0], self.center[1]-24),
-                                   font_size=1.5*16,
+                                   insert=(self.center[0], self.center[1]-22),
+                                   font_size=1.5*18,
                                    font_family='Arial',
                                    font_weight='bold',
                                    text_anchor='middle',
                                    alignment_baseline='central'))
+        self.dwg.add(self.dwg.text(text='Release ' + '.'.join(map(str, version_tuple[:3])),
+                                   insert=(self.center[0], self.center[1]),
+                                   font_size=14,
+                                   font_family='Arial',
+                                   text_anchor='middle',
+                                   alignment_baseline='central'))
         self.dwg.add(self.dwg.text(text='Chain ' + self.data['chain_id'],
-                                   insert=(self.center[0], self.center[1]+16),
+                                   insert=(self.center[0], self.center[1]+18),
                                    font_size=16,
                                    font_family='Arial',
                                    text_anchor='middle',
                                    alignment_baseline='central'))
         if self.data['has_molprobity']:
             self.dwg.add(self.dwg.text(text='MolProbity',
-                                       insert=(self.center[0], self.center[1]+48),
+                                       insert=(self.center[0], self.center[1]+50),
+                                       font_size=16,
+                                       font_family='Arial',
+                                       text_anchor='middle',
+                                       alignment_baseline='central',
+                                       fill=COLORS['L_GREY']))
+        elif self.data['has_rama_z']:
+            self.dwg.add(self.dwg.text(text='Tortoize',
+                                       insert=(self.center[0], self.center[1]+50),
                                        font_size=16,
                                        font_family='Arial',
                                        text_anchor='middle',

iris_validation/graphics/js/constants.js → src/iris_validation/graphics/js/constants.js

@@ -1,4 +1,5 @@
 const modelData = {model_data};
+const numVersions = {num_versions};
 const numChains = {num_chains};
 const boxMetricIDs = {box_metric_ids};
 const barMetricIDs = {bar_metric_ids};

iris_validation/graphics/js/interaction.js → src/iris_validation/graphics/js/interaction.js

@@ -1,4 +1,4 @@
-let selectedVersion = 1;
+let selectedVersion = numVersions - 1;
 let selectedChain = 0;
 let selectedResidue = 0;
 
@@ -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 + ')';
 };
 
 

iris_validation/graphics/panel.py → src/iris_validation/graphics/panel.py

@@ -33,9 +33,11 @@ def __init__(
         residue_bars_to_display=None,
         percentile_bar_label=None,
         percentile_bar_range=None,
+        custom_labels={'Latest':'Latest', 'Previous':'Previous'}
     ):
         self.data = data
         self.canvas_size = canvas_size
+        self.custom_labels = custom_labels
         self.chain_view_rings = CHAIN_VIEW_RINGS
         if continuous_metrics_to_display:
             self.chain_view_rings = self.get_chain_view_rings(
@@ -91,6 +93,7 @@ def _verify_chosen_metrics(self):
 
     def _generate_javascript(self):
         json_data = json.dumps(self.data)
+        num_versions = self.num_models
         num_chains = len(self.chain_ids)
         bar_metric_ids = [metric["id"] for metric in self.residue_view_bars]
         box_metric_ids = [ metric['id'] for metric in RESIDUE_VIEW_BOXES ]
@@ -106,6 +109,7 @@ def _generate_javascript(self):
 
         js_constants = js_constants.format(
             model_data=json_data,
+            num_versions=num_versions,
             num_chains=num_chains,
             bar_metric_ids=bar_metric_ids,
             box_metric_ids=box_metric_ids,
@@ -138,8 +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,
@@ -179,9 +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'))
 
@@ -196,9 +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,
@@ -207,13 +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,
@@ -224,24 +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,
@@ -250,12 +260,17 @@ def _draw(self):
                                        onclick=f'toggleDropdown();'))
 
         # Version toggle switch
-        self.dwg.add(self.dwg.text(text='Previous',
+        self.dwg.add(self.dwg.text(text='Model version',
+                                   insert=(chain_view_bounds[2]-380, chain_view_bounds[1]+20),
+                                   font_size=view_title_font,
+                                   font_family='Arial'))
+
+        self.dwg.add(self.dwg.text(text=self.custom_labels['Previous'],
                                    insert=(chain_view_bounds[2]-215, chain_view_bounds[1]+20),
                                    font_size=16,
                                    font_family='Arial'))
 
-        self.dwg.add(self.dwg.text(text='Latest',
+        self.dwg.add(self.dwg.text(text=self.custom_labels['Latest'],
                                    insert=(chain_view_bounds[2]-55, chain_view_bounds[1]+20),
                                    font_size=16,
                                    font_family='Arial'))

iris_validation/graphics/residue.py → 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,