modelcraft 5.0.3__py3-none-any.whl → 6.0.0__py3-none-any.whl

modelcraft/tests/ccp4/test_copies.py

@@ -1,4 +1,5 @@
 from modelcraft.scripts.copies import main
+
 from . import ccp4_path, in_temp_directory, insulin_contents
 
 

modelcraft/tests/ccp4/test_ctruncate.py

@@ -1,6 +1,8 @@
 import gemmi
+
 from modelcraft.jobs.ctruncate import CTruncate
 from modelcraft.reflections import DataItem
+
 from . import ccp4_path
 
 

modelcraft/tests/ccp4/test_findwaters.py

@@ -1,6 +1,8 @@
 import gemmi
+
 from modelcraft.jobs.findwaters import FindWaters
 from modelcraft.structure import ModelStats
+
 from . import insulin_refmac
 
 

modelcraft/tests/ccp4/test_freerflag.py

@@ -1,5 +1,7 @@
 import gemmi
+
 from modelcraft.jobs.freerflag import FreeRFlag
+
 from . import ccp4_path
 
 

modelcraft/tests/ccp4/test_libg.py

@@ -1,5 +1,6 @@
 from modelcraft.jobs.libg import Libg
 from modelcraft.structure import read_structure
+
 from . import ccp4_path
 
 

modelcraft/tests/ccp4/test_molrep.py

@@ -1,8 +1,11 @@
 import os
+
 import gemmi
+
 from modelcraft.jobs.molrep import Molrep
 from modelcraft.reflections import DataItem
 from modelcraft.structure import read_structure
+
 from . import ccp4_path
 
 

modelcraft/tests/ccp4/test_monlib.py

@@ -1,61 +1,91 @@
+import math
+
 import gemmi
-from modelcraft.contents import PROTEIN_CODES, DNA_CODES, RNA_CODES
-from modelcraft.monlib import atom_ids, in_library, group, is_protein, is_nucleic
+import pytest
+
+from modelcraft.monlib import MonLib
+from modelcraft.sequence import DNA_CODES, PROTEIN_CODES, RNA_CODES
+
+
+@pytest.fixture(name="monlib", scope="module")
+def monlib_fixture():
+    return MonLib({"COM", "2GP"}, include_standard=True)
 
 
-def test_hoh_ids():
+def test_hoh_ids(monlib: MonLib):
     ids = {"O", "H1", "H2"}
-    assert atom_ids("HOH") == ids
+    assert monlib.atom_ids("HOH") == ids
 
 
-def test_gly_ids():
+def test_gly_ids(monlib: MonLib):
     ids = {"N", "H", "H2", "H3", "CA", "HA3", "HA2", "C", "O", "OXT"}
-    assert atom_ids("GLY") == ids
+    assert monlib.atom_ids("GLY") == ids
 
 
-def test_com_ids():
+def test_com_ids(monlib: MonLib):
     ids = {"C1", "C2", "S1", "S2", "O1S", "O2S", "O3S"}
     ids |= {"H11", "H12", "H21", "H22", "HS1", "HOS3"}
-    assert atom_ids("COM") == ids
+    assert monlib.atom_ids("COM") == ids
 
 
-def test_in_library():
+def test_in_library(monlib: MonLib):
     for code in PROTEIN_CODES.values():
-        assert in_library(code)
+        assert code in monlib
     for code in DNA_CODES.values():
-        assert in_library(code)
+        assert code in monlib
     for code in RNA_CODES.values():
-        assert in_library(code)
-    assert not in_library("NOT_IN_MONLIB")
-
-
-def test_group():
-    assert group("GLY") == gemmi.ChemComp.Group.Peptide
-    assert group("ALA") == gemmi.ChemComp.Group.Peptide
-    assert group("MSE") == gemmi.ChemComp.Group.Peptide
-    assert group("PRO") == gemmi.ChemComp.Group.PPeptide
-    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():
-    assert is_protein("GLY")
-    assert is_protein("ALA")
-    assert is_protein("MSE")
-    assert is_protein("PRO")
-    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():
-    assert not is_nucleic("GLY")
-    assert not is_nucleic("ALA")
-    assert not is_nucleic("PRO")
-    assert is_nucleic("U")
-    assert is_nucleic("DT")
-    assert not is_nucleic("HOH")
-    assert not is_nucleic("NOT_IN_MONLIB")
+        assert code in monlib
+    assert "NOT_IN_MONLIB" not in monlib
+
+
+def test_group(monlib: MonLib):
+    assert monlib.group("GLY") == gemmi.ChemComp.Group.Peptide
+    assert monlib.group("ALA") == gemmi.ChemComp.Group.Peptide
+    assert monlib.group("MSE") == gemmi.ChemComp.Group.Peptide
+    assert monlib.group("PRO") == gemmi.ChemComp.Group.PPeptide
+    assert monlib.group("U") == gemmi.ChemComp.Group.Rna
+    assert monlib.group("DT") == gemmi.ChemComp.Group.Dna
+    assert monlib.group("HOH") == gemmi.ChemComp.Group.NonPolymer
+    assert monlib.group("NOT_IN_MONLIB") == gemmi.ChemComp.Group.Null
+
+
+def test_protein(monlib: MonLib):
+    assert monlib.is_protein("GLY")
+    assert monlib.is_protein("ALA")
+    assert monlib.is_protein("MSE")
+    assert monlib.is_protein("PRO")
+    assert not monlib.is_protein("U")
+    assert not monlib.is_protein("DT")
+    assert not monlib.is_protein("HOH")
+
+
+def test_nucleic(monlib: MonLib):
+    assert not monlib.is_nucleic("GLY")
+    assert not monlib.is_nucleic("ALA")
+    assert not monlib.is_nucleic("PRO")
+    assert monlib.is_nucleic("U")
+    assert monlib.is_nucleic("DT")
+    assert not monlib.is_nucleic("HOH")
+
+
+@pytest.mark.parametrize("code,expected", [("HOH", 18), ("2GP", 432)])
+def test_volume(monlib: MonLib, code: str, expected: float):
+    assert math.isclose(monlib.volume(code), expected, abs_tol=0.01)
+
+
+def test_not_in_monlib(monlib: MonLib):
+    with pytest.raises(KeyError):
+        monlib["NOT_IN_MONLIB"]
+
+
+@pytest.mark.parametrize(
+    "code,expected",
+    [
+        ("ALA", 89.09),
+        ("ASP", 132.09),
+        ("ASN", 132.12),
+        ("UNK", 103.12),
+    ],
+)
+def test_weight(monlib: MonLib, code: str, expected: float):
+    assert math.isclose(monlib.weight(code), expected, abs_tol=0.01)

modelcraft/tests/ccp4/test_nautilus.py

@@ -1,16 +1,18 @@
 import gemmi
+
 from modelcraft.jobs.freerflag import FreeRFlag
 from modelcraft.jobs.nautilus import Nautilus
 from modelcraft.jobs.refmac import Refmac
 from modelcraft.pipeline import Pipeline
 from modelcraft.reflections import DataItem
-from modelcraft.scripts.contents import _entry_contents
+from modelcraft.scripts.contents import AsuContents
 from modelcraft.structure import (
-    contains_residue,
     ModelStats,
+    contains_residue,
     read_structure,
     remove_residues,
 )
+
 from . import in_temp_directory, pdbe_download
 
 
@@ -27,7 +29,7 @@ def test_102d():
     fsigf = DataItem(mtz, "FP,SIGFP")
     freer = FreeRFlag(fsigf).run().freer
     refmac = Refmac(structure=structure, fsigf=fsigf, freer=freer, cycles=0).run()
-    contents = _entry_contents("102d")
+    contents = AsuContents.from_pdbe("102d")
     pipeline = Pipeline(keep_jobs=True)
     # Test without an input structure
     nautilus = Nautilus(

modelcraft/tests/ccp4/test_nucleofind.py

@@ -0,0 +1,62 @@
+import shutil
+
+import gemmi
+import pytest
+
+from modelcraft.jobs.freerflag import FreeRFlag
+from modelcraft.jobs.nucleofind import NucleoFindBuild, NucleoFindPredict
+from modelcraft.jobs.refmac import Refmac
+from modelcraft.pipeline import Pipeline
+from modelcraft.reflections import DataItem
+from modelcraft.scripts.contents import AsuContents
+from modelcraft.structure import (
+    ModelStats,
+    contains_residue,
+    read_structure,
+    remove_residues,
+)
+
+from . import in_temp_directory, pdbe_download
+
+
+@pytest.mark.skipif(not shutil.which("nucleofind"), reason="NucleoFind not installed")
+@in_temp_directory
+def test_102d():
+    # Prepare input data
+    pdbe_download("102d.cif")
+    structure = read_structure("102d.cif")
+    pdbe_download("r102dsf.ent")
+    doc = gemmi.cif.read("r102dsf.ent")
+    rblocks = gemmi.as_refln_blocks(doc)
+    cif2mtz = gemmi.CifToMtz()
+    mtz = cif2mtz.convert_block_to_mtz(rblocks[0])
+    fsigf = DataItem(mtz, "FP,SIGFP")
+    freer = FreeRFlag(fsigf).run().freer
+    refmac = Refmac(structure=structure, fsigf=fsigf, freer=freer, cycles=0).run()
+    contents = AsuContents.from_pdbe("102d")
+    pipeline = Pipeline(keep_jobs=True)
+    # Test without an input structure
+    prediction = NucleoFindPredict(fphi=refmac.fphi_best).run(pipeline)
+    build_result = NucleoFindBuild(
+        contents=contents,
+        fphi=refmac.fphi_best,
+        prediction=prediction,
+    ).run(pipeline)
+    stats = ModelStats(build_result.structure)
+    assert stats.residues > 12
+    # Test with an input structure
+    remove_residues(structure, ["HOH"])
+    build_result = NucleoFindBuild(
+        contents=contents,
+        fphi=refmac.fphi_best,
+        prediction=prediction,
+        structure=structure,
+    ).run(pipeline)
+    stats = ModelStats(build_result.structure)
+    assert contains_residue(build_result.structure, "DT")
+    assert stats.residues > 22
+    assert build_result.fragments_built > 2
+    assert build_result.residues_built > 22
+    assert build_result.residues_sequenced > 20
+    assert build_result.longest_fragment > 11
+    # TODO: assert contains_residue(nautilus.structure, "TNT")

modelcraft/tests/ccp4/test_parrot.py

@@ -1,7 +1,9 @@
 import gemmi
-from modelcraft.reflections import DataItem
+
 from modelcraft.contents import AsuContents
 from modelcraft.jobs.parrot import Parrot
+from modelcraft.reflections import DataItem
+
 from . import ccp4_path
 
 

modelcraft/tests/ccp4/test_phasematch.py

@@ -1,8 +1,10 @@
 import gemmi
+
 from modelcraft.jobs.phasematch import PhaseMatch
 from modelcraft.jobs.refmac import Refmac
 from modelcraft.reflections import DataItem
 from modelcraft.structure import read_structure
+
 from . import ccp4_path
 
 

modelcraft/tests/ccp4/test_prune.py

@@ -0,0 +1,17 @@
+from ...prune import prune
+from ...structure import ModelStats
+from . import insulin_refmac
+
+
+def test_insulin_prune():
+    refmac = insulin_refmac()
+    pruned = prune(
+        structure=refmac.structure,
+        fphi_best=refmac.fphi_best,
+        fphi_diff=refmac.fphi_diff,
+        fphi_calc=refmac.fphi_calc,
+        residue_threshold=-2,
+    )
+    stats_in = ModelStats(refmac.structure)
+    stats_out = ModelStats(pruned)
+    assert stats_out.residues < stats_in.residues

modelcraft/tests/ccp4/test_reflections.py

@@ -1,9 +1,118 @@
 from typing import List
+
 import gemmi
-from modelcraft.reflections import DataItem, convert_to_fsigf_and_phifom
+import pytest
+
+from modelcraft.reflections import (
+    DataItem,
+    column_refs,
+    contract_label,
+    convert_to_fsigf_and_phifom,
+    expand_label,
+)
+
 from . import ccp4_path
 
 
+@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, label in enumerate(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 == label
+        assert refs2[i].label == label
+
+
 def search_test(
     mtz: gemmi.Mtz, types: str, expected: List[str], sequential: bool = True
 ) -> None:

modelcraft/tests/ccp4/test_refmac.py

@@ -1,8 +1,11 @@
 import math
+
 import gemmi
+
 from modelcraft.jobs.refmac import Refmac
 from modelcraft.reflections import DataItem
 from modelcraft.structure import read_structure
+
 from . import ccp4_path
 
 

modelcraft/tests/{unittests/test_contents.py → ccp4/test_sequence.py}

@@ -1,10 +1,6 @@
 import pytest
-from modelcraft.contents import (
-    code1_to_code3,
-    guess_sequence_type,
-    PolymerType,
-    sequences_in_file,
-)
+
+from modelcraft.sequence import PolymerType, sequences_in_file
 
 
 @pytest.mark.parametrize(
@@ -18,8 +14,8 @@ from modelcraft.contents import (
         ("GGGG", PolymerType.PROTEIN),
     ],
 )
-def test_guess_sequence_type(sequence: str, expected: PolymerType):
-    assert guess_sequence_type(sequence) == expected
+def test_polymer_type(sequence: str, expected: PolymerType):
+    assert PolymerType.guess(sequence) == expected
 
 
 @pytest.mark.parametrize(
@@ -27,19 +23,16 @@ def test_guess_sequence_type(sequence: str, expected: PolymerType):
     [
         ("A", PolymerType.PROTEIN, "ALA"),
         ("B", PolymerType.PROTEIN, "ASX"),
-        ("J", PolymerType.PROTEIN, "UNK"),
         ("X", PolymerType.PROTEIN, "UNK"),
         ("Z", PolymerType.PROTEIN, "GLX"),
         ("A", PolymerType.RNA, "A"),
-        ("J", PolymerType.RNA, "N"),
         ("X", PolymerType.RNA, "N"),
         ("A", PolymerType.DNA, "DA"),
-        ("J", PolymerType.DNA, "DN"),
         ("X", PolymerType.DNA, "DN"),
     ],
 )
 def test_code1_to_code3(code1: str, polymer_type: PolymerType, expected: str):
-    assert code1_to_code3(code1, polymer_type) == expected
+    assert polymer_type.codes[code1] == expected
 
 
 @pytest.mark.parametrize(

modelcraft/tests/ccp4/test_servalcat.py

@@ -0,0 +1,52 @@
+import gemmi
+
+from modelcraft.jobs.servalcat import ServalcatFw
+from modelcraft.reflections import DataItem
+
+from . import ccp4_path
+
+
+def ianom_test(path: str, label: str) -> None:
+    mtz = gemmi.read_mtz_file(path)
+    observations = DataItem(mtz, label)
+    servalcat = ServalcatFw(observations=observations).run()
+    assert servalcat.fmean.nreflections == observations.nreflections
+    assert servalcat.fanom.nreflections == observations.nreflections
+    assert servalcat.imean.nreflections == observations.nreflections
+
+
+def imean_test(path: str, label: str) -> None:
+    mtz = gemmi.read_mtz_file(path)
+    observations = DataItem(mtz, label)
+    servalcat = ServalcatFw(observations=observations).run()
+    assert servalcat.fmean.nreflections == observations.nreflections
+    assert servalcat.fanom is None
+    assert servalcat.imean is None
+
+
+def test_1rxf():
+    path = ccp4_path("examples", "data", "1rxf.mtz")
+    imean_test(path, "I,SIGI")
+
+
+def test_ianom():
+    path = ccp4_path("examples", "data", "1vr7_lr_i.mtz")
+    imean_test(path, "IMEAN,SIGIMEAN")
+    ianom_test(path, "I(+),SIGI(+),I(-),SIGI(-)")
+
+
+def test_deuterolysin():
+    path = ccp4_path("examples", "data", "deuterolysin.mtz")
+    imean_test(path, "IMEAN,SIGIMEAN")
+    ianom_test(path, "I(+),SIGI(+),I(-),SIGI(-)")
+
+
+def test_gere():
+    path = ccp4_path("examples", "data", "gere.mtz")
+    imean_test(path, "IMEAN,SIGIMEAN")
+    ianom_test(path, "I(+),SIGI(+),I(-),SIGI(-)")
+
+
+def test_insulin():
+    path = ccp4_path("examples", "data", "insulin.mtz")
+    imean_test(path, "IMEAN,SIGIMEAN")

modelcraft/tests/ccp4/test_sheetbend.py

@@ -1,7 +1,9 @@
 import gemmi
+
 from modelcraft.jobs.sheetbend import Sheetbend
 from modelcraft.reflections import DataItem
-from modelcraft.structure import ModelStats, read_structure
+from modelcraft.structure import read_structure
+
 from . import ccp4_path
 
 
@@ -12,5 +14,4 @@ def test_1rxf():
     freer = DataItem(mtz, "FreeR_flag")
     pdb_path = ccp4_path("examples", "data", "1rxf_randomise.pdb")
     structure = read_structure(pdb_path)
-    sheetbend = Sheetbend(structure=structure, fsigf=fsigf, freer=freer).run()
-    assert ModelStats(structure) == ModelStats(sheetbend.structure)
+    Sheetbend(structure=structure, fsigf=fsigf, freer=freer).run()

modelcraft/tests/ccp4/test_sidechains.py

@@ -0,0 +1,25 @@
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+import gemmi
+
+from modelcraft.reflections import write_mtz
+from modelcraft.scripts.sidechains import any_missing_side_chains
+from modelcraft.scripts.sidechains import main as fix_side_chains
+from modelcraft.structure import write_mmcif
+
+from . import insulin_refmac
+
+
+def test_insulin():
+    refmac = insulin_refmac()
+    assert any_missing_side_chains(refmac.structure)
+    with TemporaryDirectory() as tempdir:
+        xyzin = str(Path(tempdir, "input.cif"))
+        hklin = str(Path(tempdir, "input.mtz"))
+        xyzout = str(Path(tempdir, "output.cif"))
+        write_mmcif(xyzin, refmac.structure)
+        write_mtz(hklin, [refmac.fphi_best], ["FWT,PHWT"])
+        fix_side_chains([xyzin, hklin, xyzout])
+        structure = gemmi.read_structure(xyzout)
+        assert not any_missing_side_chains(structure)

modelcraft/tests/ccp4/test_solvent.py

@@ -1,30 +1,16 @@
-import math
+import gemmi
 import pytest
-from modelcraft.contents import Polymer, PolymerType
-from modelcraft.solvent import _library_volume, _library_weight, _polymer_weight
 
+from modelcraft.contents import AsuContents
+from modelcraft.solvent import solvent_fraction
 
-@pytest.mark.parametrize(
-    "code,expected",
-    [
-        ("ALA", 89.09),
-        ("ASP", 132.09),
-        ("ASN", 132.12),
-        ("UNK", 103.12),
-    ],
-)
-def test_library_weight(code: str, expected: float):
-    weight = _library_weight(code)
-    assert math.isclose(weight, expected, abs_tol=0.01)
 
-
-@pytest.mark.parametrize("code,expected", [("HOH", 18), ("2GP", 432)])
-def test_library_volume(code: str, expected: float):
-    volume = _library_volume(code)
-    assert math.isclose(volume, expected, abs_tol=0.01)
-
-
-def test_polymer_weight():
-    polymer = Polymer("GG", polymer_type=PolymerType.PROTEIN)
-    weight = _polymer_weight(polymer)
-    assert math.isclose(weight, 132.12, abs_tol=0.01)
+def test_1o6a():
+    contents = AsuContents.from_pdbe("1o6a")
+    cell = gemmi.UnitCell(61.481, 61.481, 113.148, 90, 90, 90)
+    spacegroup = gemmi.SpaceGroup("P 41 21 2")
+    fraction = solvent_fraction(contents, cell, spacegroup, resolution=1.85)
+    assert fraction == pytest.approx(0.5, abs=0.1)
+    contents.copies = None
+    guessed = solvent_fraction(contents, cell, spacegroup, resolution=1.85)
+    assert guessed == fraction

modelcraft/tests/ccp4/test_structure.py

@@ -1,4 +1,5 @@
 import pytest
+
 from ...structure import read_structure
 from . import ccp4_path
 

modelcraft/tests/ccp4/test_validation.py

@@ -0,0 +1,19 @@
+import math
+
+import numpy as np
+
+from ...monlib import MonLib
+from ...validation import validate_refmac
+from . import insulin_refmac
+
+
+def test_insulin():
+    refmac = insulin_refmac()
+    monlib = MonLib(refmac.structure[0].get_all_residue_names())
+    metrics = validate_refmac(refmac, monlib)
+    assert len(metrics) > 0
+    assert math.isclose(np.median(metrics["BFac"]), 0)
+    assert math.isclose(np.median(metrics["RSCC"]), 0)
+    assert math.isclose(np.median(metrics["Diff"]), 0)
+    assert math.isclose(np.median(metrics["Geom"]), 0)
+    assert math.isclose(np.median(metrics["Score"]), 0)