modelcraft 4.0.0__tar.gz → 4.0.2__tar.gz

{modelcraft-4.0.0/modelcraft.egg-info → modelcraft-4.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modelcraft
-Version: 4.0.0
+Version: 4.0.2
 Summary: Automated model building pipeline for X-ray crystallography
 Home-page: https://github.com/paulsbond/modelcraft
 Author: Paul Bond

{modelcraft-4.0.0 → modelcraft-4.0.2}/modelcraft/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "4.0.0"
+__version__ = "4.0.2"
 
 from .cell import max_distortion as max_cell_distortion
 from .cell import remove_scale

{modelcraft-4.0.0 → modelcraft-4.0.2}/modelcraft/modelcraftxray.py

@@ -123,6 +123,8 @@ class ModelCraftXray(Pipeline):
     def run_buccaneer_and_nautilus(self):
         buccaneer = self.buccaneer()
         nautilus = self.nautilus()
+        if buccaneer is None and nautilus is None:
+            self.terminate(reason="No residues built")
         if buccaneer is None or nautilus is None:
             self.update_current_from_refmac_result(buccaneer or nautilus)
         else:
@@ -132,7 +134,7 @@ class ModelCraftXray(Pipeline):
 
     def buccaneer(self):
         if not self.args.contents.proteins:
-            return
+            return None
         result = Buccaneer(
             contents=self.args.contents,
             fsigf=self.args.fmean,
@@ -147,12 +149,14 @@ class ModelCraftXray(Pipeline):
             cycles=3 if self.cycle == 1 else 2,
             threads=self.args.threads,
         ).run(self)
+        if result.structure is None or ModelStats(result.structure).residues == 0:
+            return None
         write_mmcif(self.path("current.cif"), result.structure)
         return self.run_refmac(result.structure, cycles=10)
 
     def nautilus(self):
         if not (self.args.contents.rnas or self.args.contents.dnas):
-            return
+            return None
         result = Nautilus(
             contents=self.args.contents,
             fsigf=self.args.fmean,
@@ -161,6 +165,8 @@ class ModelCraftXray(Pipeline):
             freer=self.args.freer,
             structure=self.current_structure,
         ).run(self)
+        if result.structure is None or ModelStats(result.structure).residues == 0:
+            return None
         write_mmcif(self.path("current.cif"), result.structure)
         return self.run_refmac(result.structure, cycles=10)
 

{modelcraft-4.0.0 → modelcraft-4.0.2}/modelcraft/monlib.py

@@ -29,10 +29,12 @@ def in_library(code: str) -> bool:
 
 @functools.lru_cache(maxsize=None)
 def group(code: str) -> gemmi.ChemComp.Group:
-    doc = gemmi.cif.read(_path(code))
-    monlib = gemmi.MonLib()
-    monlib.read_monomer_doc(doc)
-    return monlib.monomers[code].group
+    if in_library(code):
+        doc = gemmi.cif.read(_path(code))
+        monlib = gemmi.MonLib()
+        monlib.read_monomer_doc(doc)
+        return monlib.monomers[code].group
+    return None
 
 
 @functools.lru_cache(maxsize=None)

{modelcraft-4.0.0 → modelcraft-4.0.2}/modelcraft/tests/ccp4/test_monlib.py

@@ -26,6 +26,7 @@ def test_in_library():
         assert in_library(code)
     for code in RNA_CODES.values():
         assert in_library(code)
+    assert not in_library("NOT_IN_MONLIB")
 
 
 def test_group():
@@ -36,6 +37,7 @@ def test_group():
     assert group("U") == gemmi.ChemComp.Group.Rna
     assert group("DT") == gemmi.ChemComp.Group.Dna
     assert group("HOH") == gemmi.ChemComp.Group.NonPolymer
+    assert group("NOT_IN_MONLIB") is None
 
 
 def test_protein():
@@ -46,6 +48,7 @@ def test_protein():
     assert not is_protein("U")
     assert not is_protein("DT")
     assert not is_protein("HOH")
+    assert not is_protein("NOT_IN_MONLIB")
 
 
 def test_nucleic():
@@ -55,3 +58,4 @@ def test_nucleic():
     assert is_nucleic("U")
     assert is_nucleic("DT")
     assert not is_nucleic("HOH")
+    assert not is_nucleic("NOT_IN_MONLIB")

{modelcraft-4.0.0 → modelcraft-4.0.2/modelcraft.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modelcraft
-Version: 4.0.0
+Version: 4.0.2
 Summary: Automated model building pipeline for X-ray crystallography
 Home-page: https://github.com/paulsbond/modelcraft
 Author: Paul Bond

{modelcraft-4.0.0 → modelcraft-4.0.2}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as f:
 
 setuptools.setup(
     name="modelcraft",
-    version="4.0.0",
+    version="4.0.2",
     author="Paul Bond",
     author_email="paul.bond@york.ac.uk",
     description="Automated model building pipeline for X-ray crystallography",