emdbva 0.0.1.dev101__tar.gz → 0.0.1.dev102__tar.gz

{emdbva-0.0.1.dev101/emdbva.egg-info → emdbva-0.0.1.dev102}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev101
+Version: 0.0.1.dev102
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev101 → emdbva-0.0.1.dev102/emdbva.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev101
+Version: 0.0.1.dev102
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev101 → emdbva-0.0.1.dev102}/va/mainva.py

@@ -347,7 +347,7 @@ def main():
     # Preparation
     # temp_logger, buffer = setup_temporary_logging()
     prepobj = prep()
-    # path_to_logs = f'{prepobj.dir}/{prepobj.mapname}_va.log'
+    # path_to_logs = f'{prepobj.vadir}/{prepobj.mapname}_va.log'
     # reconfigure_logging(temp_logger, buffer, path_to_logs)
     position = prepobj.args.positions
 

{emdbva-0.0.1.dev101 → emdbva-0.0.1.dev102}/va/metrics/inclusion.py

@@ -18,7 +18,6 @@ class Inclusion:
         self.model = model
         self.workdir = workdir
         self.mapname = os.path.basename(map.fullname)
-        print(self.mapname)
 
     # @execution_time('inclusion')
     # def atom_inclusion(self):

{emdbva-0.0.1.dev101 → emdbva-0.0.1.dev102}/va/preparation.py

@@ -115,7 +115,7 @@ class PreParation:
                         self.evenmap = inputdict_cif.get('even')
                         self.oddmap = inputdict_cif.get('odd')
                         self.resolution = inputdict_cif.get('resolution')
-                        self.method = methoddict.get(inputdict_cif.get('method', '').replace(" ", "").lower())
+                        self.method = methoddict.get(inputdict_cif.get('method', '').replace(" ", ""))
                         if 'mask' in inputdict_cif:
                             mask_path = inputdict_cif['mask'] + 'map'
                             self.masks = {mask_path: 1.0}
@@ -412,14 +412,13 @@ class PreParation:
         block = doc.sole_block()
 
         # Extract resolution and reconstruction method
-        reconstruction_method = block.find_value('_em_experiment.reconstruction_method').replace("'", "") or None
+        reconstruction_method = block.find_value('_em_experiment.reconstruction_method').replace("'", "").lower() or None
         resolution = block.find_value('_em_3d_reconstruction.resolution')
+        resolution = float(resolution) if resolution and resolution != '?' else None
         if resolution is None:
             resolution_loop = block.find_loop('_em_3d_reconstruction.resolution')
             resolution = next(x for x in resolution_loop if x != '?')
 
-        assert resolution is not None, "No resolution can be found."
-
         # Initialize map containers
         map_data = {'primary': {}, 'mask': {}, 'odd': {}, 'even': {}}
 
@@ -428,23 +427,41 @@ class PreParation:
         file_loop = block.find_loop('_em_map.file')
         map_type_loop = block.find_loop('_em_map.type')
 
-        if contour_loop and file_loop:
-            contour_levels = [row for row in contour_loop]
+        # If loops are present
+        if contour_loop and file_loop and map_type_loop:
+            contour_levels = [None if row == '?' else row for row in contour_loop]
             map_files = [row for row in file_loop]
-            map_types = [row.replace("'","") for row in map_type_loop if "'" in row]
-
-            for map_file, contour, map_type in zip(map_files, contour_levels, map_types):
-                map_key = map_file[:-3]  # Strip '.gz'
-                contour = float(contour)
-
-                if map_type == 'primary map':
-                    map_data['primary'] = {'primary': map_key, 'primary_contour': contour}
-                if map_type =='half map' and 'half_map_1' in map_file:
-                    map_data['odd'] = {'odd': map_key, 'odd_contour': contour}
-                if map_type == 'half map' and 'half_map_2' in map_file:
-                    map_data['even'] = {'even': map_key, 'even_contour': contour}
-                if 'msk' in map_file:
-                    map_data['mask'] = {'mask': map_file, 'mask_contour': contour}
+            map_types = [row.replace("'", "") for row in map_type_loop]
+        else:
+            # Check if individual items exist instead
+            try:
+                contour_level = float(block.find_value('_em_map.contour_level'))
+                map_file = block.find_value('_em_map.file')[:-3]
+                map_type = block.find_value('_em_map.type').replace("'", "")  # sanitize string
+
+                contour_levels = [contour_level]
+                map_files = [map_file]
+                map_types = [map_type]
+            except Exception as e:
+                # fallback or log error
+                contour_levels, map_files, map_types = [], [], []
+
+        # Parse combined map data
+        for map_file, contour, map_type in zip(map_files, contour_levels, map_types):
+            map_key = map_file[:-3] if map_file.endswith('.gz') else map_file
+            try:
+                contour = float(contour) if contour is not None else None
+            except:
+                continue  # skip if contour is not valid
+
+            if map_type == 'primary map':
+                map_data['primary'] = {'primary': map_key, 'primary_contour': contour}
+            if map_type == 'half map' and 'half_map_1' in map_file:
+                map_data['odd'] = {'odd': map_key, 'odd_contour': contour}
+            if map_type == 'half map' and 'half_map_2' in map_file:
+                map_data['even'] = {'even': map_key, 'even_contour': contour}
+            if 'msk' in map_file:
+                map_data['mask'] = {'mask': map_file, 'mask_contour': contour}
 
         # Extract database cross-references
         db_ids = block.find_loop('_database_2.database_id')

{emdbva-0.0.1.dev101 → emdbva-0.0.1.dev102}/va/validationanalysis.py

@@ -220,7 +220,8 @@ class ValidationAnalysis:
             self.workdir = workdir
         self.check_dir = create_directory(f'{self.workdir}/checks/')
         self.get_resolution()
-        self.relion_mask = self.get_relion_mask()
+        if self.rawmap:
+            self.relion_mask = self.get_relion_mask()
         # make a symbolic link for relion_mask in the va folder
         if self.relion_mask:
             mask_name = os.path.basename(self.relion_mask)
@@ -228,9 +229,10 @@ class ValidationAnalysis:
             create_symbolic_link(self.relion_mask, link_name)
             self.relion_mask = link_name
         # The read masked raw map here is only used in line 455 for produce the masked raw map glow image
-        maskedrawmap = MapProcessor.mask_map(self.rawmap._iostream.name, self.relion_mask)
-        self.masked_rawmap = mrcfile.mmap(maskedrawmap, mode='r+')
-        self.masked_rawmap.fullname = maskedrawmap
+        if self.rawmap and self.relion_mask:
+            maskedrawmap = MapProcessor.mask_map(self.rawmap._iostream.name, self.relion_mask)
+            self.masked_rawmap = mrcfile.mmap(maskedrawmap, mode='r+')
+            self.masked_rawmap.fullname = maskedrawmap
 
 
     def get_resolution(self):
@@ -2207,7 +2209,8 @@ class ValidationAnalysis:
         # Primary map surface view
         primary_input_map = f'{self.workdir}{self.mapname}'
         primary_input_contour = self.cl
-        viewer.new_surface_view_chimerax(primary_input_map, primary_input_contour)
+        if primary_input_contour is not None and self.met != 'tomo':
+            viewer.new_surface_view_chimerax(primary_input_map, primary_input_contour)
 
         # Raw map surface view
         if self.hmodd is not None and self.hmeven is not None:
@@ -4802,31 +4805,30 @@ class ValidationAnalysis:
     @staticmethod
     def compute_surface_area_two(mrc_file, contour_level):
         """
-            Compute the surface area of a 3D cryo-EM density map at a given contour level.
-        - mrc_file (str): Path to the .mrc file.
-        - contour_level (float): The density threshold to define the surface.
-
+        Compute the surface area of a 3D cryo-EM density map at a given contour level.
         Returns:
-        - float: Surface area in arbitrary units.
+            float: Surface area in arbitrary units, or None if failed.
         """
+        try:
+            with mrcfile.open(mrc_file, permissive=True) as mrc:
+                volume = mrc.data.astype(np.float32)
+                voxel_size = mrc.voxel_size['x']
 
-        with mrcfile.open(mrc_file, permissive=True) as mrc:
-            volume = mrc.data.astype(np.float32)
-            voxel_size = mrc.voxel_size['x']
-
-        # Apply Marching Cubes algorithm to extract surface mesh
-        verts, faces, _, _ = measure.marching_cubes(volume, level=contour_level)
-
-        # Compute surface area by summing the area of all mesh triangles
-        def triangle_area(v1, v2, v3):
-            return 0.5 * np.linalg.norm(np.cross(v2 - v1, v3 - v1))
+            verts, faces, _, _ = measure.marching_cubes(volume, level=contour_level)
 
-        surface_area = sum(triangle_area(verts[f[0]], verts[f[1]], verts[f[2]]) for f in faces)
+            def triangle_area(v1, v2, v3):
+                return 0.5 * np.linalg.norm(np.cross(v2 - v1, v3 - v1))
 
-        # Convert area to real space (scaling by voxel size squared)
-        surface_area *= (voxel_size ** 2)
+            surface_area = sum(triangle_area(verts[f[0]], verts[f[1]], verts[f[2]]) for f in faces)
+            surface_area *= (voxel_size ** 2)
+            return surface_area
 
-        return surface_area
+        except MemoryError:
+            print("Error: Not enough memory to compute surface area.")
+            sys.exit(1)
+        except Exception as e:
+            print(f"Error during surface area computation: {e}")
+            return None
 
     def compute_surface_ratios_two(self, map_one, map_two):
         """

{emdbva-0.0.1.dev101 → emdbva-0.0.1.dev102}/va/version.py

@@ -28,4 +28,4 @@ under the License.
 
 """
 
-__version__ = '0.0.1.dev101'
+__version__ = '0.0.1.dev102'