Merge pull request #143 from rigdenlab/gemmi_fix

Fixed issue with phaser enantiomorph search and gemmi entities
rigdenlab · Mar 24, 2023 · 476ad55 · 476ad55
2 parents 89570f1 + 5f435fe
commit 476ad55
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Showing 4 changed files with 8 additions and 2 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,11 @@
 Changelog
 =========
 
+0.2.8
+-----
+- Fixed issue with gemmi missing entities
+- Fixed issue with using enantiomorphs in phaser
+
 0.2.7
 -----
 

diff --git a/simbad/mr/phaser_mr.py b/simbad/mr/phaser_mr.py
@@ -307,7 +307,7 @@ def run(self):
 
             if input_mtz_obj.spacegroup_symbol != output_mtz_obj.spacegroup_symbol:
                 mtz_util.reindex(self.hklin, self.hklout,
-                                 "".join(output_mtz_obj.spacegroup_symbol.encode("ascii").split()))
+                                 "".join(output_mtz_obj.spacegroup_symbol.split()))
             else:
                 shutil.copyfile(self.hklin, self.hklout)
 

diff --git a/simbad/util/pdb_util.py b/simbad/util/pdb_util.py
@@ -28,6 +28,7 @@ def from_file(cls, input_file):
         elif input_file.endswith(".ent.gz"):
             struct.structure = gemmi.read_structure(input_file)
         struct.assert_structure()
+        struct.structure.setup_entities()
         return struct
 
     @classmethod

diff --git a/simbad/version.py b/simbad/version.py
@@ -2,7 +2,7 @@
 
 # Maintain sematantic versioning. Further information can
 # be found here [http://semver.org/]
-__version_info__ = (0, 2, 7)
+__version_info__ = (0, 2, 8)
 
 # ======================================================
 # Do __NOT__ change anything below here