modelcraft 3.6.0__py3-none-any.whl → 4.0.1__py3-none-any.whl

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/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/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_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/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.dist-info → modelcraft-4.0.1.dist-info}/METADATA

@@ -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.dist-info → modelcraft-4.0.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-modelcraft/__init__.py,sha256=xhMhS18BADwNwceT6stbLcp1ZochelcRfTs_v3RfBj8,2233
+modelcraft/__init__.py,sha256=EShQrPLQTgeHMytTnuJwRw8JFkGsBYMVe-iHAMoy66w,2185
 modelcraft/__main__.py,sha256=0D-TbVRrb0ipPCS-NnUvifaG2kAsBn6mXtWLjyExOXM,77
 modelcraft/arguments.py,sha256=DChFhzk09Fwpsb4ycZ4OBfXxsFJLNiQiao4ZoErB5wA,14606
 modelcraft/cell.py,sha256=mqoQfODyXd43MhLYnGwXxTag42Fx9l2wMH3s-ouXpr0,2057
@@ -10,13 +10,12 @@ 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/monlib.py,sha256=cEiYHKGEKpBlv-fJbKYJ91aZyMu9iAtmwdyuWeZj2F0,1482
 modelcraft/pipeline.py,sha256=2fUmFcCyUG6EmAOxSHtcG91zRHHZmwjRkmJy5Y7Raus,2030
 modelcraft/reflections.py,sha256=w8iV5NBcghUlufXWvxXLtbW8oNHR5Jx9ELKhgKThvkw,6274
 modelcraft/solvent.py,sha256=beGtewZXoXzEdaadG4d0vu3hAL61XZdVue62Xldkw4k,6772
 modelcraft/structure.py,sha256=A0KX9L1hI8Xbk-0dx82BfID3ot_FX2qRBCnWjjL3yko,4122
 modelcraft/utils.py,sha256=1ljfNB-gIdfGjM1-o_U5jrjJc4f0E1213kpAFEVt5qw,192
-modelcraft/coot/morph.py,sha256=rUTQseTBrxriDWYAl4cQdF-7h1cAGuDvdyHWfr0mXPs,754
 modelcraft/coot/prune.py,sha256=-iGv3w8bubRuzZ9JeaSj5JoAiTwMPAZJrCqNLWwrC7g,35851
 modelcraft/coot/sidechains.py,sha256=aOj8MHRGzs90VXsi2LdqUT4KcUDHB0yvSRLFvOuYqnY,1847
 modelcraft/jobs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -24,7 +23,7 @@ modelcraft/jobs/acedrg.py,sha256=nnf1Pe7U5hzY2GJVIluCjmbmQ5V6BayRmZQZD9vMZrs,984
 modelcraft/jobs/acorn.py,sha256=wYyQMY6XoYejCvcIT0rBD0SyBcQ5Ewi01Bjb9totp5E,2465
 modelcraft/jobs/buccaneer.py,sha256=7SintYeB4m4-C_yy5oj7rMwBirugF_ghVjSKCKVPslY,5533
 modelcraft/jobs/comit.py,sha256=peQ5McTlPplTOSqXgkv_W1oB-X9HJ2B3zZQiudx9Ckg,1047
-modelcraft/jobs/coot.py,sha256=XsTdpcMtc-nlNXyW1wMbkVOZ8dS_w4i7CcqMZ8Cg_Hg,4026
+modelcraft/jobs/coot.py,sha256=GPWggYA2CUzVHY0ThsHDiCodyI9Hh8FmgycTWIG6vBI,3581
 modelcraft/jobs/ctruncate.py,sha256=D-aXd6JY2F-XSZOW1Hj8gk1L-BhoRCxbqnUB34wjSVI,1659
 modelcraft/jobs/emda.py,sha256=33Yr_quk-CDne8vkHrjjIUSCCeoRUlBVnhRZFO8wOXA,988
 modelcraft/jobs/findwaters.py,sha256=nh0dRFAYYyBYi-8waLByBlV9xmuMog9kqJ5oSUxj2lQ,1700
@@ -49,7 +48,7 @@ modelcraft/tests/ccp4/test_buccaneer.py,sha256=cNf40Nf_yzqdaaGN_jVBGQIwDxl2kXgNB
 modelcraft/tests/ccp4/test_cell.py,sha256=YrEIxzmUDkYsE1lJRAemBiSQtykhI4XDqMwFSCzhqKE,1057
 modelcraft/tests/ccp4/test_comit.py,sha256=77TQK5-cAK_LCPnhj7sbWQbNXLg_YxuBa-soldURYcs,533
 modelcraft/tests/ccp4/test_contents.py,sha256=da0blxz6SUao2hE5cE1e5aPPHPHkldAxYObujhjTIwQ,6801
-modelcraft/tests/ccp4/test_coot.py,sha256=AZFVOJGtvTo6PE16RnwOFyomc068eXh_TfbDKb-ViPQ,1295
+modelcraft/tests/ccp4/test_coot.py,sha256=59wzv62P2s9oUcmrnhZZmntJrCEwG0kRcrPaanqEkz8,924
 modelcraft/tests/ccp4/test_copies.py,sha256=mU8qMzM0UFN19ASMUX5HWX1yOc5QPhtoEfbuzzj9MOc,315
 modelcraft/tests/ccp4/test_ctruncate.py,sha256=q0QewF2v5-DfEYNrKq2oRluCYi1MDd41rNGFiiTwwlE,2277
 modelcraft/tests/ccp4/test_findwaters.py,sha256=IEzazZXjt0uccLcUSJnacEeJZDrl1c_UmrcQaUJMgCI,1583
@@ -57,7 +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
@@ -75,9 +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-3.6.0.dist-info/LICENSE,sha256=IMF9i4xIpgCADf0U-V1cuf9HBmqWQd3qtI3FSuyW4zE,26526
-modelcraft-3.6.0.dist-info/METADATA,sha256=wO2e_1HY5G1PYX4pQ8n9N8K5xJt241fzQ3cFNH_4Xxk,1893
-modelcraft-3.6.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-modelcraft-3.6.0.dist-info/entry_points.txt,sha256=bWef3WSAihTv1fI39wScTAmrKtn5mOYZ3SEeBpM4RrU,172
-modelcraft-3.6.0.dist-info/top_level.txt,sha256=My5973x4fvPrlRfQOuuFxqultnVzrg_aamczcSijdlQ,11
-modelcraft-3.6.0.dist-info/RECORD,,
+modelcraft-4.0.1.dist-info/LICENSE,sha256=IMF9i4xIpgCADf0U-V1cuf9HBmqWQd3qtI3FSuyW4zE,26526
+modelcraft-4.0.1.dist-info/METADATA,sha256=j5FQa_9CFRpNtBwStccDGNGzfuruNJgw2lgxTzmAHtc,1893
+modelcraft-4.0.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+modelcraft-4.0.1.dist-info/entry_points.txt,sha256=bWef3WSAihTv1fI39wScTAmrKtn5mOYZ3SEeBpM4RrU,172
+modelcraft-4.0.1.dist-info/top_level.txt,sha256=My5973x4fvPrlRfQOuuFxqultnVzrg_aamczcSijdlQ,11
+modelcraft-4.0.1.dist-info/RECORD,,

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)