modelcraft 3.6.0__tar.gz → 4.0.1__tar.gz

{modelcraft-3.6.0/modelcraft.egg-info → modelcraft-4.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modelcraft
-Version: 3.6.0
+Version: 4.0.1
 Summary: Automated model building pipeline for X-ray crystallography
 Home-page: https://github.com/paulsbond/modelcraft
 Author: Paul Bond

{modelcraft-3.6.0 → modelcraft-4.0.1}/modelcraft/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "3.6.0"
+__version__ = "4.0.1"
 
 from .cell import max_distortion as max_cell_distortion
 from .cell import remove_scale
@@ -11,7 +11,6 @@ from .jobs.buccaneer import Buccaneer
 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 @@ __all__ = [
     "remove_residues",
     "remove_scale",
     "rmsz",
-    "RsrMorph",
     "run",
     "ServalcatNemap",
     "ServalcatRefine",

{modelcraft-3.6.0 → modelcraft-4.0.1}/modelcraft/jobs/coot.py

@@ -29,7 +29,6 @@ class Coot(Job):
             "        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 @@ class FixSideChains(Coot):
         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-3.6.0 → modelcraft-4.0.1}/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-3.6.0 → modelcraft-4.0.1}/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

{modelcraft-3.6.0 → modelcraft-4.0.1}/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-3.6.0 → modelcraft-4.0.1/modelcraft.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modelcraft
-Version: 3.6.0
+Version: 4.0.1
 Summary: Automated model building pipeline for X-ray crystallography
 Home-page: https://github.com/paulsbond/modelcraft
 Author: Paul Bond

{modelcraft-3.6.0 → modelcraft-4.0.1}/modelcraft.egg-info/SOURCES.txt

@@ -32,7 +32,6 @@ modelcraft.egg-info/dependency_links.txt
 modelcraft.egg-info/entry_points.txt
 modelcraft.egg-info/requires.txt
 modelcraft.egg-info/top_level.txt
-modelcraft/coot/morph.py
 modelcraft/coot/prune.py
 modelcraft/coot/sidechains.py
 modelcraft/jobs/__init__.py

{modelcraft-3.6.0 → modelcraft-4.0.1}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as f:
 
 setuptools.setup(
     name="modelcraft",
-    version="3.6.0",
+    version="4.0.1",
     author="Paul Bond",
     author_email="paul.bond@york.ac.uk",
     description="Automated model building pipeline for X-ray crystallography",

modelcraft-3.6.0/modelcraft/coot/morph.py

@@ -1,16 +0,0 @@
-def rsr_morph(imol, imap, local_radius=5, gm_alpha=0.05, blur_b_factor=88):
-    generate_self_restraints(imol, local_radius)
-    set_show_extra_restraints(imol, 0)  # too confusing
-    set_refinement_geman_mcclure_alpha(gm_alpha)
-    set_draw_moving_atoms_restraints(1)  # not useful for non-graphics mode
-    rmsd = map_sigma_py(imap)
-    if rmsd is not None:
-        imap_blurred = sharpen_blur_map(imap, blur_b_factor)
-        set_imol_refinement_map(imap_blurred)
-        set_matrix(15.0 / rmsd)
-        residues = fit_protein_make_specs(imol, "all-chains")
-        if COOT1:
-            coot_utils.with_auto_accept([refine_residues_py, imol, residues])
-        else:
-            with AutoAccept():
-                refine_residues_py(imol, residues)