emdbva 0.0.1.dev131__tar.gz → 0.0.1.dev134__tar.gz

{emdbva-0.0.1.dev131/emdbva.egg-info → emdbva-0.0.1.dev134}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev131
+Version: 0.0.1.dev134
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev131 → emdbva-0.0.1.dev134/emdbva.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev131
+Version: 0.0.1.dev134
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev131 → emdbva-0.0.1.dev134}/va/metrics/phaserandomization.py

@@ -183,8 +183,8 @@ def calculate_pixels(angpix):
     """
 
     if angpix != 0:
-        dilatepx = 10 / angpix
-        softpx = 5 / angpix
+        dilatepx = 10 * angpix
+        softpx = 5 * angpix
         return dilatepx, softpx
     else:
         print('No hard and soft radius for mask as voxel value is 0.')

{emdbva-0.0.1.dev131 → emdbva-0.0.1.dev134}/va/preparation.py

@@ -774,6 +774,29 @@ class PreParation:
                 if db_name == 'PDB' and accession_code:
                     db_info['accession'] = accession_code
 
+        # Fallback: if no PDB id found in _database_2, try _em_db_reference
+        if 'accession' not in db_info:
+            em_access = block.find_value('_em_db_reference.access_code')
+            em_dbname = block.find_value('_em_db_reference.db_name')
+
+            # Case 1: _em_db_reference is a single (non-loop) category
+            if em_access and str(em_access).strip() not in ('?', '.', ''):
+                if em_dbname and str(em_dbname).strip().upper() == 'PDB':
+                    db_info['PDB'] = str(em_access).strip().strip("'").strip('"')
+
+            # Case 2: _em_db_reference is looped (multiple references)
+            else:
+                em_access_col = block.find_loop('_em_db_reference.access_code')
+                em_dbname_col = block.find_loop('_em_db_reference.db_name')
+
+                if em_access_col and em_dbname_col:
+                    for acc, name in zip(em_access_col, em_dbname_col):
+                        acc_s = str(acc).strip().strip("'").strip('"')
+                        name_s = str(name).strip().strip("'").strip('"')
+                        if name_s.upper() == 'PDB' and acc_s not in ('', '?', '.'):
+                            db_info['PDB'] = acc_s
+                            break  # take first PDB accession found
+
         # Final merge and return
         result = {
             'resolution': resolution,

{emdbva-0.0.1.dev131 → emdbva-0.0.1.dev134}/va/utils/stars.py

@@ -66,10 +66,16 @@ class GetStars:
 
     def bfactor_sharpen(self):
         """
-            Get the resolution value that Relion is use for the phase randomization calculation
+            Get the B-factor value that Relion is use for the sharpening of the map in postprocess
         """
         return float(self.data_general_block()['_rlnBfactorUsedForSharpening'])
 
+    def guinier_correlation(self):
+        """
+            Get the correlation value of the Guinier plot
+        """
+        return float(self.data_general_block()['_rlnCorrelationFitGuinierPlot'])
+
     def data_fsc_block(self):
         """
         Get the data_fsc block
@@ -222,6 +228,7 @@ class GetStars:
         phase_rand = data_fsc_block.get('CorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps', None)
         randomise_from = self.randomise_from()
         sharpen_bfactor = self.bfactor_sharpen()
+        guinier_correlation = self.guinier_correlation()
 
         x_gold, y_gold = interpolated_intercept(x, correlation, gold)
         x_half, y_half = interpolated_intercept(x, correlation, half)
@@ -289,7 +296,8 @@ class GetStars:
             'phase_randomized_half': {'x': x_phase_half, 'y': y_phase_half},
             'phase_randomized_halfbit': {'x': x_phase_halfbit, 'y': y_phase_halfbit},
             'randomise_from': randomise_from,
-            'sharpen_bfactor': sharpen_bfactor
+            'sharpen_bfactor': sharpen_bfactor,
+            'guinier_correlation': guinier_correlation
         }
         }
 

{emdbva-0.0.1.dev131 → emdbva-0.0.1.dev134}/va/version.py

@@ -18,5 +18,5 @@ under the License.
 
 """
 
-__version__ = '0.0.1.dev131'
+__version__ = '0.0.1.dev134'
 __em_statistics_version__ = '202505.v01'