emdbva 0.0.1.dev153__tar.gz → 0.0.1.dev156__tar.gz

{emdbva-0.0.1.dev153/emdbva.egg-info → emdbva-0.0.1.dev156}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev153
+Version: 0.0.1.dev156
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev153 → emdbva-0.0.1.dev156/emdbva.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev153
+Version: 0.0.1.dev156
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev153 → emdbva-0.0.1.dev156}/va/metrics/phenix_locres.py

@@ -222,17 +222,23 @@ def create_local_resolution_views(chimerax, map_path, resolution_map, contour, o
         return '"{}"'.format(os.path.abspath(path).replace('\\', '\\\\').replace('"', '\\"'))
 
     script_path = os.path.join(output_dir, prefix + '_chimerax.cxc')
-    images = {axis: prefix + '_' + axis.upper() + '.png' for axis in ('x', 'y', 'z')}
+    images = {
+        'original': {axis: prefix + '_' + axis.upper() + '.png' for axis in ('x', 'y', 'z')},
+        'scaled': {axis: prefix + '_scaled_' + axis.upper() + '.png' for axis in ('x', 'y', 'z')},
+    }
     with open(script_path, 'w', encoding='utf-8') as script:
         script.write('open {}\nvolume #1 style surface\nvolume #1 step 1\n'.format(quoted(map_path)))
         script.write('volume #1 level {}\n'.format(float(contour)))
         script.write('open {}\nvolume #2 style surface\nvolume #2 step 1\n'.format(quoted(resolution_map)))
         script.write('hide #2 models\nset bgColor #B8B8B8\ncolor sample #1 map #2 palette blue:white:red range full key true\n')
-        script.write('key pos 0.25,0.05 size 0.53,0.015 labelSide right/bottom fontSize 9 border false labelColor black\n')
+        script.write('key pos 0.25,0.12 size 0.53,0.015 labelSide right/bottom fontSize 9 border false labelColor black\n')
         for axis, rotation in (('z', ''), ('x', 'turn y 90\n'), ('y', 'turn x -90\n')):
             script.write('view orient\n' + rotation)
             script.write('view #1 pad 0.25 cofr true\n')
-            script.write('save {} width 1200 height 1200\n'.format(quoted(os.path.join(output_dir, images[axis]))))
+            script.write('save {} width 1200 height 1200\n'.format(
+                quoted(os.path.join(output_dir, images['original'][axis]))))
+            script.write('save {} width 300 height 300\n'.format(
+                quoted(os.path.join(output_dir, images['scaled'][axis]))))
         script.write('exit\n')
     has_display = bool(os.environ.get('DISPLAY') or os.environ.get('WAYLAND_DISPLAY'))
     if sys.platform == 'darwin' and not os.environ.get('SSH_CONNECTION'):
@@ -242,7 +248,10 @@ def create_local_resolution_views(chimerax, map_path, resolution_map, contour, o
         command.extend(['--offscreen', '--nogui'])
     command.append(script_path)
     subprocess.run(command, cwd=output_dir, check=True)
-    missing = [name for name in images.values() if not os.path.isfile(os.path.join(output_dir, name))]
+    missing = [
+        name for size_images in images.values() for name in size_images.values()
+        if not os.path.isfile(os.path.join(output_dir, name))
+    ]
     if missing:
         raise RuntimeError('ChimeraX did not produce images: {}'.format(', '.join(missing)))
     return images
@@ -276,7 +285,10 @@ def create_combined_local_resolution_views(chimerax, map_path, resolution_map, m
         raise ValueError('Residue identifiers and local-resolution values do not match.')
     with open(config_path, 'w', encoding='utf-8') as config_file:
         json.dump({'residues': residue_specs, 'values': values}, config_file, allow_nan=False)
-    images = {axis: prefix + '_' + axis.upper() + '.png' for axis in ('x', 'y', 'z')}
+    images = {
+        'original': {axis: prefix + '_' + axis.upper() + '.png' for axis in ('x', 'y', 'z')},
+        'scaled': {axis: prefix + '_scaled_' + axis.upper() + '.png' for axis in ('x', 'y', 'z')},
+    }
     with open(script_path, 'w', encoding='utf-8') as script:
         script.write('open {}\nvolume #1 style surface\nvolume #1 step 1\n'.format(quoted(map_path)))
         script.write('volume #1 level {}\n'.format(float(contour)))
@@ -291,7 +303,10 @@ def create_combined_local_resolution_views(chimerax, map_path, resolution_map, m
         script.write('set bgColor #B8B8B8\n')
         for axis, rotation in (('z', ''), ('x', 'turn y 90\n'), ('y', 'turn x -90\n')):
             script.write('view orient\n' + rotation + 'view #1 pad 0.25 cofr true\n')
-            script.write('save {} width 1200 height 1200\n'.format(quoted(os.path.join(output_dir, images[axis]))))
+            script.write('save {} width 1200 height 1200\n'.format(
+                quoted(os.path.join(output_dir, images['original'][axis]))))
+            script.write('save {} width 300 height 300\n'.format(
+                quoted(os.path.join(output_dir, images['scaled'][axis]))))
         script.write('exit\n')
     has_display = bool(os.environ.get('DISPLAY') or os.environ.get('WAYLAND_DISPLAY'))
     if sys.platform == 'darwin' and not os.environ.get('SSH_CONNECTION'):
@@ -300,7 +315,10 @@ def create_combined_local_resolution_views(chimerax, map_path, resolution_map, m
     if not has_display:
         command.extend(['--offscreen', '--nogui'])
     subprocess.run(command + [script_path], cwd=output_dir, check=True)
-    missing = [name for name in images.values() if not os.path.isfile(os.path.join(output_dir, name))]
+    missing = [
+        name for size_images in images.values() for name in size_images.values()
+        if not os.path.isfile(os.path.join(output_dir, name))
+    ]
     if missing:
         raise RuntimeError('ChimeraX did not produce images: {}'.format(', '.join(missing)))
     return images

{emdbva-0.0.1.dev153 → emdbva-0.0.1.dev156}/va/utils/chimerax_combined_locres.py

@@ -44,21 +44,20 @@ def color_combined_view(session, config):
         lower, upper = lower - 0.01, upper + 0.01
 
     run(session, 'color sample #1 map #2 palette blue:white:red range {},{} key true'.format(lower, upper))
-    run(session, 'key blue: white: red: pos 0.25,0.08 size 0.5,0.02 border false')
-    for label, limits, text_y, arrow_start, arrow_end in (
-        ('Map', (map_lower, map_upper), 0.073, 0.074, 0.08),
-        ('Model', (model_lower, model_upper), 0.110, 0.110, 0.10),
+    run(session, 'key blue: white: red: pos 0.25,0.14 size 0.5,0.02 '
+        'labelSide right/bottom fontSize 9 labelColor black border false')
+    for label, limits, text_y in (
+        ('Map', (map_lower, map_upper), 0.105),
+        ('Model', (model_lower, model_upper), 0.185),
     ):
-        run(session, '2dlabels text "{}" color black size 9 xpos 0.16 ypos {}'.format(label, text_y))
+        run(session, '2dlabels text "{}" color black size 6 xpos 0.16 ypos {}'.format(label, text_y))
         values = (limits[0], (limits[0] + limits[1]) / 2, limits[1])
         for value in sorted(set(values)):
             xpos = 0.25 + 0.5 * (value - lower) / (upper - lower)
-            run(session, '2dlabels arrow start {},{} end {},{} color black weight 0.3 headStyle pointer'.format(
-                xpos, arrow_start, xpos, arrow_end))
             label_x = xpos
             if label == 'Map' and value == map_lower:
                 label_x = 0.25 + 0.5 * (model_lower - lower) / (upper - lower)
-            run(session, '2dlabels text "{:.2f}" color black size 9 xpos {} ypos {}'.format(
+            run(session, '2dlabels text "{:.2f}" color black size 6 xpos {} ypos {}'.format(
                 value, max(0.0, label_x - 0.012), text_y))
     colors = []
     for spec, value in zip(config['residues'], config['values']):

{emdbva-0.0.1.dev153 → emdbva-0.0.1.dev156}/va/version.py

@@ -18,5 +18,5 @@ under the License.
 
 """
 
-__version__ = '0.0.1.dev153'
+__version__ = '0.0.1.dev156'
 __em_statistics_version__ = '202505.v01'