v4.0.0 (#45)

CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org).
 
+## [4.0.0] - 2024-03-18
+
+### Removed
+
+- Coot RSR morph
+
 ## [3.6.0] - 2024-03-13
 
 ### Changed

modelcraft/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "3.6.0"
+__version__ = "4.0.0"
 
 from .cell import max_distortion as max_cell_distortion
 from .cell import remove_scale
@@ -11,7 +11,6 @@
 from .jobs.comit import Comit
 from .jobs.coot import FixSideChains
 from .jobs.coot import Prune
-from .jobs.coot import RsrMorph
 from .jobs.ctruncate import CTruncate
 from .jobs.emda import EmdaMapMask
 from .jobs.findwaters import FindWaters
@@ -71,7 +70,6 @@
     "remove_residues",
     "remove_scale",
     "rmsz",
-    "RsrMorph",
     "run",
     "ServalcatNemap",
     "ServalcatRefine",

modelcraft/jobs/coot.py

@@ -29,7 +29,6 @@ def _setup(self) -> None:
             "        COOT1 = False\n",
             "    if COOT1:\n",
             "        from coot import *\n",
-            "        from fitting import fit_protein_make_specs\n",
             "    turn_off_backup(0)\n",
         ]
         for i, structure in enumerate(self.structures):
@@ -103,12 +102,3 @@ def __init__(
         super().__init__(
             script=script, structures=[structure], fphis=[fphi_best, fphi_diff]
         )
-
-
-class RsrMorph(Coot):
-    def __init__(self, structure: gemmi.Structure, fphi_best: DataItem):
-        path = os.path.join(os.path.dirname(__file__), "..", "coot", "morph.py")
-        with open(path) as stream:
-            script = stream.read()
-        script += "rsr_morph(IMOL0, IMAP0)\n"
-        super().__init__(script=script, structures=[structure], fphis=[fphi_best])

modelcraft/tests/ccp4/test_coot.py

@@ -1,4 +1,4 @@
-from modelcraft.jobs.coot import Prune, FixSideChains, RsrMorph
+from modelcraft.jobs.coot import Prune, FixSideChains
 from modelcraft.structure import ModelStats
 from . import insulin_refmac
 
@@ -27,15 +27,3 @@ def test_insulin_fix_side_chains():
     stats_in = ModelStats(refmac.structure)
     stats_out = ModelStats(coot.structure)
     assert stats_out.residues == stats_in.residues
-
-
-def test_insulin_rsr_morph():
-    refmac = insulin_refmac()
-    refmac.structure.remove_alternative_conformations()
-    coot = RsrMorph(
-        structure=refmac.structure,
-        fphi_best=refmac.fphi_best,
-    ).run()
-    stats_in = ModelStats(refmac.structure)
-    stats_out = ModelStats(coot.structure)
-    assert stats_out.residues == stats_in.residues

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="modelcraft",
-    version="3.6.0",
+    version="4.0.0",
     author="Paul Bond",
     author_email="paul.bond@york.ac.uk",
     description="Automated model building pipeline for X-ray crystallography",