modelcraft 4.0.0__py3-none-any.whl → 4.0.2__py3-none-any.whl

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/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/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/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.dist-info → modelcraft-4.0.2.dist-info}/METADATA

@@ -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
@@ -16,7 +16,7 @@ Classifier: Programming Language :: Python :: 3.9
 Requires-Python: ~=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: gemmi >=0.5.4
+Requires-Dist: gemmi>=0.5.4
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: requests

{modelcraft-4.0.0.dist-info → modelcraft-4.0.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-modelcraft/__init__.py,sha256=MzPNDe7aO3iAb2tZ58zt84wAOx2RUiY-q-E2aBtUemM,2185
+modelcraft/__init__.py,sha256=b6kF56OszYiw4E6RCSy1Ezv0CChodB7w0N3DmWJrgu8,2185
 modelcraft/__main__.py,sha256=0D-TbVRrb0ipPCS-NnUvifaG2kAsBn6mXtWLjyExOXM,77
 modelcraft/arguments.py,sha256=DChFhzk09Fwpsb4ycZ4OBfXxsFJLNiQiao4ZoErB5wA,14606
 modelcraft/cell.py,sha256=mqoQfODyXd43MhLYnGwXxTag42Fx9l2wMH3s-ouXpr0,2057
@@ -9,8 +9,8 @@ modelcraft/geometry.py,sha256=ofgIgZ4G2W56vofldJVrkTjuxAbDhzOtsJckv-kCP_A,1218
 modelcraft/job.py,sha256=RpM8UfIPH0uNf_yuwBTq4GLp2aY-4_yvJEQd7r3aL4o,4104
 modelcraft/maps.py,sha256=Lyv3YjKNdUgi6vaLmQ8CcZFKq39EPL4NDC5qO_kCd0A,354
 modelcraft/modelcraftem.py,sha256=x2o2b_uD91mr-gJHK9CrODVAdp9FCJF9kIC1GrofMLI,5133
-modelcraft/modelcraftxray.py,sha256=l73CSdLkEjgf1MdEZgp6tJnTwtkTvp5lvkxSA-mCSWU,12791
-modelcraft/monlib.py,sha256=WZqfxPMv9kygvOipTsDNFBR87khpYGTUVNYjbw3JVRE,1425
+modelcraft/modelcraftxray.py,sha256=tRzxvhcC5opUiy24GeQaMLG2ZT_qvlcdq6ObFpA9nnM,13121
+modelcraft/monlib.py,sha256=cEiYHKGEKpBlv-fJbKYJ91aZyMu9iAtmwdyuWeZj2F0,1482
 modelcraft/pipeline.py,sha256=2fUmFcCyUG6EmAOxSHtcG91zRHHZmwjRkmJy5Y7Raus,2030
 modelcraft/reflections.py,sha256=w8iV5NBcghUlufXWvxXLtbW8oNHR5Jx9ELKhgKThvkw,6274
 modelcraft/solvent.py,sha256=beGtewZXoXzEdaadG4d0vu3hAL61XZdVue62Xldkw4k,6772
@@ -56,7 +56,7 @@ modelcraft/tests/ccp4/test_freerflag.py,sha256=2Z4nRka3VbXSx89qj-vIbAZ9m12Tl_O2s
 modelcraft/tests/ccp4/test_geometry.py,sha256=LFeCGHqALgWoiP5X2p1oRbsK8Mbk8p5ICk4CDbGAbKI,556
 modelcraft/tests/ccp4/test_libg.py,sha256=JHGOeg3jSriWUH96H8aAVd3K9SrrE3qwHPMjpmv3vJg,256
 modelcraft/tests/ccp4/test_molrep.py,sha256=ooyYNXtN5sNkpF-j59vJzRD4f1CEQkMQkVdatzIhA10,1318
-modelcraft/tests/ccp4/test_monlib.py,sha256=Ov1RMXMHZShaMefzRTWz2r0H30HT_wQPji_-5VGILrI,1621
+modelcraft/tests/ccp4/test_monlib.py,sha256=vuU0EMNVBGqegF6JinUhw3FPJ6KB1Zdik8NV2p0gbJ0,1792
 modelcraft/tests/ccp4/test_nautilus.py,sha256=rytNdr27fAtXajZk52fs3eYVi1_8WJbubeXnWd2XXOw,1946
 modelcraft/tests/ccp4/test_parrot.py,sha256=0Qug6Q3UjH54DokA3C_vKyur7UiLyhyGK3w7Cfjfpxs,792
 modelcraft/tests/ccp4/test_phasematch.py,sha256=mSWA2eBsipDe3xWyj5iRn7Yj8Gpav0Iva1DaGOHWYa8,1143
@@ -74,9 +74,9 @@ modelcraft/tests/ccpem/test_servalcat.py,sha256=3FQVpo-Vf9MStV-dZD-ZVzGin7YefgTG
 modelcraft/tests/unittests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 modelcraft/tests/unittests/test_contents.py,sha256=aAHha4pQYMyKes7OiOZ11_-9z-BVqh4OSmAL8gRUX_Y,3153
 modelcraft/tests/unittests/test_reflections.py,sha256=xshb_2QcAko2l98-Pd1LuEjMZAVv-O7LkhtzGRnrbM4,3674
-modelcraft-4.0.0.dist-info/LICENSE,sha256=IMF9i4xIpgCADf0U-V1cuf9HBmqWQd3qtI3FSuyW4zE,26526
-modelcraft-4.0.0.dist-info/METADATA,sha256=LEhWmHIc3N46f3vqGzxpIv2sF1IjzrqCBmF4U-8WIKY,1893
-modelcraft-4.0.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-modelcraft-4.0.0.dist-info/entry_points.txt,sha256=bWef3WSAihTv1fI39wScTAmrKtn5mOYZ3SEeBpM4RrU,172
-modelcraft-4.0.0.dist-info/top_level.txt,sha256=My5973x4fvPrlRfQOuuFxqultnVzrg_aamczcSijdlQ,11
-modelcraft-4.0.0.dist-info/RECORD,,
+modelcraft-4.0.2.dist-info/LICENSE,sha256=IMF9i4xIpgCADf0U-V1cuf9HBmqWQd3qtI3FSuyW4zE,26526
+modelcraft-4.0.2.dist-info/METADATA,sha256=MHumkhjTRqsPqeRIq6f2VRVnDl1ij3TxHQUgReCUocU,1892
+modelcraft-4.0.2.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+modelcraft-4.0.2.dist-info/entry_points.txt,sha256=bWef3WSAihTv1fI39wScTAmrKtn5mOYZ3SEeBpM4RrU,172
+modelcraft-4.0.2.dist-info/top_level.txt,sha256=My5973x4fvPrlRfQOuuFxqultnVzrg_aamczcSijdlQ,11
+modelcraft-4.0.2.dist-info/RECORD,,

{modelcraft-4.0.0.dist-info → modelcraft-4.0.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any