modelcraft 5.0.2__py3-none-any.whl → 6.0.0__py3-none-any.whl

modelcraft/coot/sidechains.py

@@ -1,68 +0,0 @@
-RESIDUES_WITH_SIDECHAINS = {
-    "ARG",
-    "ASN",
-    "ASP",
-    "CYS",
-    "GLN",
-    "GLU",
-    "HIS",
-    "ILE",
-    "LEU",
-    "LYS",
-    "MET",
-    "MSE",
-    "PHE",
-    "PRO",
-    "SER",
-    "THR",
-    "TRP",
-    "TYR",
-    "VAL",
-}
-
-
-def neighbours_specs(residue):
-    specs = [residue.spec]
-    if residue.prev is not None:
-        specs = [residue.prev.spec] + specs
-    if residue.next is not None:
-        specs = specs + [residue.next.spec]
-    return specs
-
-
-def refine(imol, specs):
-    if COOT1:
-        coot_utils.with_auto_accept([refine_residues_py, imol, specs])
-    else:
-        with AutoAccept():
-            refine_residues_py(imol, specs)
-
-
-def fix_side_chain(imol, imap, residue):
-    spec = residue.spec
-    delete_residue_sidechain(imol, spec[0], spec[1], spec[2], 0)
-    neighbours = neighbours_specs(residue)
-    refine(imol, neighbours)
-    fill_partial_residue(imol, *spec)
-    if COOT1:
-        auto_fit_best_rotamer(imol, spec[0], spec[1], spec[2], "", imap, 1, 0.1)
-    else:
-        auto_fit_best_rotamer(spec[1], "", spec[2], spec[0], imol, imap, 1, 0.1)
-    refine(imol, neighbours)
-
-
-def fix_side_chains(imol, imap, imap_diff):
-    model = Model(imol, imap, imap_diff)
-    main_median = median([r.main_chain_correctness for r in model.residues])
-    side_median = median([r.side_chain_correctness for r in model.residues if r.truncatable])
-    if side_median is None:
-        return
-    main_threshold = main_median * 0.25
-    side_threshold = side_median * 0.25
-    for residue in model.residues:
-        if (
-            residue.name in RESIDUES_WITH_SIDECHAINS
-            and residue.main_chain_correctness > main_threshold
-            and ((not residue.truncatable) or (residue.truncatable and residue.side_chain_correctness < side_threshold))
-        ):
-            fix_side_chain(imol, imap, residue)

modelcraft/jobs/acorn.py

@@ -1,114 +0,0 @@
-# from .job import Job
-
-
-# class Acorn(Job):
-#     def __init__(self):
-#         super().__init__()
-#         self.finish()
-
-
-# /home/paul/Programs/ccp4-7.0/bin/mtzdump \
-# HKLIN "/home/paul/Desktop/tmp.mtz" \
-# << EOF
-# END
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/unique \
-# HKLOUT "/tmp/paul/TEST_2_2_mtz.tmp" \
-# << EOF
-# cell 40.4450 42.6790 56.6510 90.0000 90.0000 90.0000
-# symmetry 'P 21 21 21'
-# resolution 1.0
-# title [No title given]
-# labout  F=F_unique SIGF=SIGF_unique
-# end
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/cad \
-# HKLIN1 "/home/paul/Desktop/tmp.mtz" \
-# HKLIN2 "/tmp/paul/TEST_2_2_mtz.tmp" \
-# HKLOUT "/tmp/paul/TEST_2_5_mtz.tmp" \
-# << EOF
-# LABIN FILE 1 ALL
-# LABIN FILE 2 ALL
-# END
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/mtzutils \
-# HKLIN "/tmp/paul/TEST_2_5_mtz.tmp" \
-# HKLOUT "/tmp/paul/TEST_2_7_mtz.tmp" \
-# << EOF
-# EXCL F_unique SIGF_unique
-# END
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/phaser \
-# << EOF
-# MODE MR_ANO
-# HKLIN "/tmp/paul/TEST_2_7_mtz.tmp"
-# LABIN FP=FP SIGFP=SIGFP
-# ROOT "/home/paul/Desktop/TEST_2"
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/ecalc \
-# HKLIN "/home/paul/Desktop/TEST_2.mtz" \
-# HKLOUT "/home/paul/Desktop/tmp_ecalc1.mtz" \
-# << EOF
-# title [No title given]
-# labin  FP=FP_ISO SIGFP=SIGFP_ISO
-# labout  FECALC=F_ECALC E=E_ISO SIGE=SIGE_ISO
-# spacegroup 'P 21 21 21'
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/acorn \
-# HKLIN "/home/paul/Desktop/tmp_ecalc1.mtz" \
-# HKLOUT "/home/paul/Desktop/tmp_acorn1.mtz" \
-# << EOF
-# title [No title given]
-# labin  FP=FP_ISO SIGFP=SIGFP_ISO E=E_ISO PHIN=hltofom.Phi_fom.phi WTIN=hltofom.Phi_fom.fom
-# labout  PHIOUT=PHIOUT WTOUT=WTOUT
-
-# #General ACORN keywords
-
-# #Select Reflection Data
-# EXTEND
-
-# #Select Model Parameters
-
-# #ACORN-MR keywords
-
-# #ACORN-PHASE keywords
-# NTRY 10
-
-# END
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/fft \
-# HKLIN "/home/paul/Desktop/tmp_acorn1.mtz" \
-# MAPOUT "/tmp/paul/TEST_2_11_map.tmp" \
-# << EOF
-# title [No title given]
-# labin -
-#    F1=E_ISO SIG1=SIGE_ISO PHI=PHIOUT W=WTOUT
-# end
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/mapmask \
-# MAPIN "/tmp/paul/TEST_2_11_map.tmp" \
-# MAPOUT "/tmp/paul/TEST_2.map" \
-# << EOF
-# SYMMETRY 'P 21 21 21'
-# XYZLIM ASU
-# EOF
-
-# /home/paul/Programs/ccp4-7.0/bin/peakmax \
-# MAPIN "/tmp/paul/TEST_2.map" \
-# XYZOUT "/home/paul/Desktop/TEST_2.pdb" \
-# XYZFRC "/home/paul/Desktop/TEST_2.ha" \
-# << EOF
-# threshhold -
-#     rms -
-#     5.0
-# numpeaks 40
-# output brookhaven frac
-# EOF

modelcraft/jobs/coot.py

@@ -1,104 +0,0 @@
-import dataclasses
-import os
-import gemmi
-from ..job import Job
-from ..reflections import DataItem, write_mtz
-from ..structure import read_structure, write_mmcif
-
-
-@dataclasses.dataclass
-class CootResult:
-    structure: gemmi.Structure
-    seconds: float
-
-
-class Coot(Job):
-    def __init__(self, script: str, structures: list, fphis: list):
-        super().__init__("coot")
-        self.script = script
-        self.structures = structures
-        self.fphis = fphis
-
-    def _setup(self) -> None:
-        script_lines = [
-            "try:\n",
-            "    COOT1 = True\n",
-            "    try:\n",
-            "        import coot_utils\n",
-            "    except NameError:\n",
-            "        COOT1 = False\n",
-            "    if COOT1:\n",
-            "        from coot import *\n",
-            "    turn_off_backup(0)\n",
-        ]
-        for i, structure in enumerate(self.structures):
-            write_mmcif(self._path(f"xyzin{i}.cif"), structure)
-            script_lines += [
-                f"    IMOL{i} = handle_read_draw_molecule('xyzin{i}.cif')\n"
-            ]
-        for i, fphi in enumerate(self.fphis):
-            write_mtz(self._path(f"hklin{i}.mtz"), [fphi])
-            script_lines += [
-                f"    IMAP{i} = make_and_draw_map('hklin{i}.mtz', "
-                f"'{fphi.label(0)}', '{fphi.label(1)}', '', 0, 0)\n"
-            ]
-        script_lines += ["    set_imol_refinement_map(IMAP0)\n"]
-        for line in self.script.split("\n"):
-            script_lines += [f"    {line}\n"]
-        script_lines += [
-            "    write_cif_file(IMOL0, 'xyzout.cif')\n",
-            "    coot_real_exit(0)\n",
-            "except:\n",
-            "    import traceback\n",
-            "    traceback.print_exc()\n",
-            "    coot_real_exit(1)\n",
-        ]
-        with open(self._path("script.py"), "w") as script_file:
-            script_file.writelines(script_lines)
-        self._args += ["--no-graphics"]
-        self._args += ["--no-guano"]
-        self._args += ["--no-state-script"]
-        self._args += ["--script", "script.py"]
-
-    def _result(self) -> CootResult:
-        self._check_files_exist("xyzout.cif")
-        return CootResult(
-            structure=read_structure(self._path("xyzout.cif")),
-            seconds=self._seconds,
-        )
-
-
-class Prune(Coot):
-    def __init__(
-        self,
-        structure: gemmi.Structure,
-        fphi_best: DataItem,
-        fphi_diff: DataItem,
-        chains_only: bool = False,
-    ):
-        path = os.path.join(os.path.dirname(__file__), "..", "coot", "prune.py")
-        with open(path) as stream:
-            script = stream.read()
-        if chains_only:
-            script += "prune(IMOL0, IMAP0, IMAP1, residues=False, sidechains=False)\n"
-        else:
-            script += "prune(IMOL0, IMAP0, IMAP1)\n"
-        super().__init__(
-            script=script, structures=[structure], fphis=[fphi_best, fphi_diff]
-        )
-
-
-class FixSideChains(Coot):
-    def __init__(
-        self, structure: gemmi.Structure, fphi_best: DataItem, fphi_diff: DataItem
-    ):
-        path = os.path.join(os.path.dirname(__file__), "..", "coot", "prune.py")
-        with open(path) as stream:
-            script = stream.read()
-        path = os.path.join(os.path.dirname(__file__), "..", "coot", "sidechains.py")
-        with open(path) as stream:
-            script += "\n\n%s\n" % stream.read()
-        script += "fix_side_chains(IMOL0, IMAP0, IMAP1)\n"
-        super().__init__(
-            script=script, structures=[structure], fphis=[fphi_best, fphi_diff]
-        )

modelcraft/tests/ccp4/test_coot.py

@@ -1,29 +0,0 @@
-from modelcraft.jobs.coot import Prune, FixSideChains
-from modelcraft.structure import ModelStats
-from . import insulin_refmac
-
-
-def test_insulin_prune():
-    refmac = insulin_refmac()
-    refmac.structure.remove_alternative_conformations()
-    coot = Prune(
-        structure=refmac.structure,
-        fphi_best=refmac.fphi_best,
-        fphi_diff=refmac.fphi_diff,
-    ).run()
-    stats_in = ModelStats(refmac.structure)
-    stats_out = ModelStats(coot.structure)
-    assert stats_out.residues < stats_in.residues
-
-
-def test_insulin_fix_side_chains():
-    refmac = insulin_refmac()
-    refmac.structure.remove_alternative_conformations()
-    coot = FixSideChains(
-        structure=refmac.structure,
-        fphi_best=refmac.fphi_best,
-        fphi_diff=refmac.fphi_diff,
-    ).run()
-    stats_in = ModelStats(refmac.structure)
-    stats_out = ModelStats(coot.structure)
-    assert stats_out.residues == stats_in.residues

modelcraft/tests/ccp4/test_geometry.py

@@ -1,20 +0,0 @@
-import gemmi
-from modelcraft.structure import read_structure
-from modelcraft.geometry import rmsz
-from . import ccp4_path
-
-
-def test_standard():
-    path = ccp4_path("examples", "data", "2eck.pdb")
-    structure = read_structure(path)
-    assert 0 < rmsz(structure) < 2
-
-
-def test_with_unl():
-    path = ccp4_path("examples", "data", "2eck.pdb")
-    structure = read_structure(path)
-    residue = gemmi.Residue()
-    residue.name = "UNL"
-    residue.seqid = gemmi.SeqId(999, " ")
-    structure[0][0].add_residue(residue)
-    assert 0 < rmsz(structure) < 2

modelcraft/tests/unittests/test_reflections.py

@@ -1,101 +0,0 @@
-import pytest
-from modelcraft.reflections import column_refs, expand_label, contract_label
-
-
-@pytest.mark.parametrize(
-    "label,expanded",
-    [
-        ("HL", "HLA,HLB,HLC,HLD"),
-        ("HLanom", "HLanomA,HLanomB,HLanomC,HLanomD"),
-        ("HLABCD.F_sigF", "HLABCD.F_sigF.F,HLABCD.F_sigF.sigF"),
-        ("parrot.ABCD", "parrot.ABCD.A,parrot.ABCD.B,parrot.ABCD.C,parrot.ABCD.D"),
-        ("parrot.F_phi", "parrot.F_phi.F,parrot.F_phi.phi"),
-        ("FreeR_flag", "FreeR_flag"),
-        ("prefix.HL", "prefix.HLA,prefix.HLB,prefix.HLC,prefix.HLD"),
-        ("prefix.label", "prefix.label"),
-        ("prefix_ABCD", "prefix_ABCD.A,prefix_ABCD.B,prefix_ABCD.C,prefix_ABCD.D"),
-        ("prefix_HL", "prefix_HLA,prefix_HLB,prefix_HLC,prefix_HLD"),
-        ("x.y.HL", "x.y.HLA,x.y.HLB,x.y.HLC,x.y.HLD"),
-        ("prefix.FreeR_flag", "prefix.FreeR_flag"),
-        ("prefix.I_sigI", "prefix.I_sigI.I,prefix.I_sigI.sigI"),
-        ("prefix.phi_fom", "prefix.phi_fom.phi,prefix.phi_fom.fom"),
-    ],
-)
-def test_expand_label(label: str, expanded: str):
-    assert expand_label(label) == expanded
-
-
-@pytest.mark.parametrize(
-    "label,contracted",
-    [
-        ("FreeR_flag", "FreeR_flag"),
-        ("prefix.FreeR_flag", "prefix.FreeR_flag"),
-        ("prefix.F_phi.F,prefix.F_phi.phi", "prefix.F_phi"),
-        ("prefix.F_sigF.F,prefix.F_sigF.sigF", "prefix.F_sigF"),
-        ("prefix.I_sigI.I,prefix.I_sigI.sigI", "prefix.I_sigI"),
-        ("prefix.phi_fom.phi,prefix.phi_fom.fom", "prefix.phi_fom"),
-        ("prefix.ABCD.A,prefix.ABCD.B,prefix.ABCD.C,prefix.ABCD.D", "prefix.ABCD"),
-    ],
-)
-def test_contract_label(label: str, contracted: str):
-    assert contract_label(label) == contracted
-
-
-@pytest.mark.parametrize(
-    "columns,project,crystal,dataset,label",
-    [
-        ("label", "", "", "", "label"),
-        ("/label", "", "", "", "label"),
-        ("/label/", "", "", "", "label"),
-        ("[label]", "", "", "", "label"),
-        ("[[label]]", "", "", "", "label"),
-        ("/*/*/*/*/*/*/*/*/*/[[label]]//", "", "", "", "label"),
-        ("dataset/label", "", "", "dataset", "label"),
-        ("crystal/dataset/label", "", "crystal", "dataset", "label"),
-        ("project/crystal/dataset/label", "project", "crystal", "dataset", "label"),
-    ],
-)
-def test_single_column_ref(
-    columns: str, project: str, crystal: str, dataset: str, label: str
-):
-    refs = column_refs(columns)
-    assert refs[0].project == project
-    assert refs[0].crystal == crystal
-    assert refs[0].dataset == dataset
-    assert refs[0].label == label
-
-
-@pytest.mark.parametrize(
-    "columns",
-    [
-        ("label1,label2"),
-        ("[label1,label2]"),
-        ("/*/*/*/label1,label2"),
-        ("/*/*/*/[label1,label2]"),
-    ],
-)
-def test_multiple_column_refs(columns: str):
-    refs = column_refs(columns)
-    for ref in refs:
-        assert ref.project == ""
-        assert ref.crystal == ""
-        assert ref.dataset == ""
-    assert refs[0].label == "label1"
-    assert refs[1].label == "label2"
-
-
-def test_column_refs_with_duplicate_labels():
-    refs1 = column_refs("/xtal/peak/[F(+),SIGF(+),F(-),SIGF(-)]")
-    refs2 = column_refs("/xtal/infl/[F(+),SIGF(+),F(-),SIGF(-)]")
-    labels = ["F(+)", "SIGF(+)", "F(-)", "SIGF(-)"]
-    assert len(refs1) == len(labels)
-    assert len(refs2) == len(labels)
-    for i in range(len(labels)):
-        assert refs1[i].project == ""
-        assert refs2[i].project == ""
-        assert refs1[i].crystal == "xtal"
-        assert refs2[i].crystal == "xtal"
-        assert refs1[i].dataset == "peak"
-        assert refs2[i].dataset == "infl"
-        assert refs1[i].label == labels[i]
-        assert refs2[i].label == labels[i]