emdbva 0.0.1.dev79__tar.gz → 0.0.1.dev81__tar.gz

{emdbva-0.0.1.dev79/emdbva.egg-info → emdbva-0.0.1.dev81}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev79
+Version: 0.0.1.dev81
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev79 → emdbva-0.0.1.dev81/emdbva.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emdbva
-Version: 0.0.1.dev79
+Version: 0.0.1.dev81
 Summary: CryoEM validation toolkit
 Home-page: https://test.pypi.org/project/va/
 Author: Zhe Wang

{emdbva-0.0.1.dev79 → emdbva-0.0.1.dev81}/va/mainva.py

@@ -93,7 +93,7 @@ def allruns(validationobj, runs):
     # Sureface views
     if 'surface' in runs:
         validationobj.surfaces()
-        # validationobj.new_surface_view_chimerax()
+        validationobj.new_surfaces()
 
     # Masks views
     if 'mask' in runs:

{emdbva-0.0.1.dev79 → emdbva-0.0.1.dev81}/va/metrics/phaserandomization.py

@@ -2,11 +2,13 @@ import subprocess
 from va.utils.misc import *
 from distutils.spawn import find_executable
 from va.metrics.contour_level_predicator import *
+from va.utils.ChimeraxViews import *
+from va.utils.misc import find_rawmap_file
 import mrcfile
 
 def create_relion_folders(root, mapname, result_type):
     """
-    Create <mapname>_relion folder in the va directory and subfolders containing mask, fsc and local_resolution
+        Create <mapname>_relion folder in the va directory and subfolders containing mask, fsc and local_resolution
     """
     relion_dir = f'{root}{mapname}_relion'
     mask_dir = f'{relion_dir}/mask'
@@ -67,8 +69,8 @@ def relion_mask(mapone, maptwo, out_dir, relion_mask_executable, mapname=None):
 
     if angpix and max_val_thirty and dilatepx and softpx and input_mrc:
 
-        subprocess.run(f'{relion_mask_executable} --i {original_input_mrc} --o {mask_loose} --ini_threshold {max_val_thirty} '
-                       f'--extend_inimask {dilatepx} --width_soft_edge {softpx} --j {threading_numbers} --lowpass 12', shell=True)
+        # subprocess.run(f'{relion_mask_executable} --i {original_input_mrc} --o {mask_loose} --ini_threshold {max_val_thirty} '
+        #                f'--extend_inimask {dilatepx} --width_soft_edge {softpx} --j {threading_numbers} --lowpass 12', shell=True)
 
         return mask_loose
     else:
@@ -88,8 +90,8 @@ def relion_fsc(mapone, maptwo, out_dir, relion_executable, mapname=None):
 
     if mapone_mrc and maptwo_mrc and mask_file:
 
-        subprocess.run(f"{relion_executable} --i {mapone_mrc} --i2 {maptwo_mrc} --o {out_dir}/fsc"
-                           f" --mask {mask_file} --auto_bfac", shell=True)
+        # subprocess.run(f"{relion_executable} --i {mapone_mrc} --i2 {maptwo_mrc} --o {out_dir}/fsc"
+        #                    f" --mask {mask_file} --auto_bfac", shell=True)
 
         return True
     else:
@@ -116,8 +118,14 @@ def relion_fsc_calculation(mapone, maptwo, root, mapname=None):
         relion_executable = find_executable(relion_executable_name)
         relion_mask_executable = find_executable(relion_mask_executable_name)
         if fsc_dir and mask_dir and relion_mask_executable:
-            relion_mask(mapone, maptwo, mask_dir, relion_mask_executable, mapname)
-            if relion_fsc(mapone, maptwo, fsc_dir, relion_executable, mapname):
+            relion_mask_name = relion_mask(mapone, maptwo, mask_dir, relion_mask_executable, mapname)
+            # Generate Relion mask view with raw map at predicated contour level
+            raw_map_name = find_rawmap_file(root)
+            raw_map_predicated_contour = MapProcessor.predict_contour(f'{root}{raw_map_name}')
+            viewer = ChimeraxViews(va_dir=root)
+            viewer.new_surface_view_chimerax(f'{root}{raw_map_name}', raw_map_predicated_contour, 'relionmask', '', relion_mask_name, 1.0)
+            relion_fsc_result = relion_fsc(mapone, maptwo, fsc_dir, relion_executable, mapname)
+            if relion_fsc_result:
                 return f'{fsc_dir}/fsc.star'
             else:
                 return None