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

modelcraft/tests/ccp4/test_xray.py

@@ -1,16 +1,19 @@
 import json
 import os
+
 import gemmi
 import pytest
-from modelcraft.scripts.modelcraft import main
+
 from modelcraft.reflections import write_mtz
+from modelcraft.scripts.modelcraft import main
 from modelcraft.structure import contains_residue, read_structure
+
 from . import (
     ccp4_path,
     in_temp_directory,
     insulin_contents,
-    insulin_fsigf,
     insulin_freer,
+    insulin_fsigf,
     insulin_refmac,
     pdb1rxf_contents,
 )
@@ -33,14 +36,15 @@ def test_insulin_from_phases():
     args += ["--overwrite-directory"]
     with pytest.raises(SystemExit):
         main(args)
-    with open(os.path.join("my_modelcraft_dir", "modelcraft.json")) as report_file:
+    report_path = os.path.join("my_modelcraft_dir", "modelcraft.json")
+    with open(report_path, encoding="utf-8") as report_file:
         report = json.load(report_file)
     assert report["seconds"]["total"] > 0
     assert report["termination_reason"] == "Normal"
     mtz_path = os.path.join("my_modelcraft_dir", "modelcraft.mtz")
     mtz = gemmi.read_mtz_file(mtz_path)
     columns = set(mtz.column_labels())
-    expected = {"FWT", "DELFWT", "FC_ALL_LS", "FOM", "HLACOMB"}
+    expected = {"FWT", "DELFWT", "FC_ALL", "FOM", "HLACOMB"}
     assert expected.issubset(columns)
 
 
@@ -59,7 +63,8 @@ def test_1rxf_from_model():
     args += ["--cycles", "2"]
     with pytest.raises(SystemExit):
         main(args)
-    with open(os.path.join("modelcraft", "modelcraft.json")) as report_file:
+    report_path = os.path.join("modelcraft", "modelcraft.json")
+    with open(report_path, encoding="utf-8") as report_file:
         report = json.load(report_file)
     assert report["seconds"]["total"] > 0
     assert report["termination_reason"] == "Normal"
@@ -80,7 +85,8 @@ def test_toxd():
     args += ["--cycles", "1"]
     with pytest.raises(SystemExit):
         main(args)
-    with open(os.path.join("modelcraft", "modelcraft.json")) as report_file:
+    report_path = os.path.join("modelcraft", "modelcraft.json")
+    with open(report_path, encoding="utf-8") as report_file:
         report = json.load(report_file)
     assert report["seconds"]["total"] > 0
     assert report["termination_reason"] == "Normal"

modelcraft/tests/ccpem/test_em.py

@@ -1,7 +1,10 @@
 import json
 import os
+
 import pytest
+
 from modelcraft.scripts.modelcraft import main
+
 from ..ccp4 import in_temp_directory
 from . import (
     density_path,

modelcraft/tests/ccpem/test_emda.py

@@ -1,6 +1,8 @@
 from os import environ
 from pathlib import Path
+
 import gemmi
+
 from modelcraft.jobs.emda import EmdaMapMask
 from modelcraft.maps import read_map
 

modelcraft/tests/ccpem/test_refmac.py

@@ -1,5 +1,6 @@
 from modelcraft.jobs.refmac import RefmacMapToMtz
 from modelcraft.maps import read_map
+
 from . import density_path
 
 

modelcraft/tests/ccpem/test_servalcat.py

@@ -1,12 +1,13 @@
 from modelcraft.jobs.servalcat import (
+    ServalcatFsc,
     ServalcatNemap,
-    ServalcatTrim,
     ServalcatRefine,
-    ServalcatFsc,
+    ServalcatTrim,
 )
 from modelcraft.maps import read_map
 from modelcraft.structure import read_structure
-from . import halfmap1_path, halfmap2_path, density_path, mask_path, structure_path
+
+from . import density_path, halfmap1_path, halfmap2_path, mask_path, structure_path
 
 
 def test_servalcat_nemap():

modelcraft/utils.py

@@ -1,6 +1,18 @@
-import random
+from random import choice
+from string import ascii_letters, digits
 
+import numpy as np
 
-def random_id(length: int = 10) -> str:
-    chars = "23456789ABCDEFGHJKLMNPQRSTUVWXYZabcdefghijkmnopqrstuvwxyz"
-    return "".join(random.choice(chars) for _ in range(length))
+
+def modified_zscore(a) -> np.ndarray:
+    "Z-score using median and median absolute deviation"
+    median = np.median(a)
+    deviations = a - median
+    mad = np.median(np.abs(deviations))
+    return np.zeros_like(a) if mad == 0 else 0.67449 * deviations / mad
+
+
+def puid(length: int = 10) -> str:
+    "Probably unique identifier"
+    chars = ascii_letters + digits
+    return "".join(choice(chars) for _ in range(length))

modelcraft/validation.py

@@ -0,0 +1,101 @@
+from collections import defaultdict
+
+import gemmi
+import numpy as np
+import pandas as pd
+
+from .geometry import per_residue_geometry_rmsz
+from .jobs.refmac import RefmacResult
+from .monlib import MonLib
+from .reflections import DataItem
+from .utils import modified_zscore
+
+
+def validate(
+    structure: gemmi.Structure,
+    fphi_best: DataItem,
+    fphi_diff: DataItem,
+    fphi_calc: DataItem,
+    monlib: MonLib,
+    model_index: int = 0,
+) -> pd.DataFrame:
+    best_map = fphi_best.map(spacing=1.0)
+    diff_map = fphi_diff.map(size=best_map.shape)
+    calc_map = fphi_calc.map(size=best_map.shape)
+
+    bfac = _bfac(structure[model_index])
+    rscc, diff = _rscc_diff(structure, best_map, diff_map, calc_map, model_index)
+    geom = per_residue_geometry_rmsz(structure, monlib, model_index)
+
+    data = {
+        "Chain": [],
+        "SeqId": [],
+        "Name": [],
+        "BFac": [],
+        "RSCC": [],
+        "Diff": [],
+        "Geom": [],
+    }
+    for chain in structure[model_index]:
+        for residue in chain:
+            if monlib.is_protein(residue.name):
+                key = (chain.name, str(residue.seqid))
+                data["Chain"].append(chain.name)
+                data["SeqId"].append(str(residue.seqid))
+                data["Name"].append(residue.name)
+                data["BFac"].append(bfac[key])
+                data["RSCC"].append(rscc[key])
+                data["Diff"].append(diff[key])
+                data["Geom"].append(geom[key])
+
+    df = pd.DataFrame(data)
+    df["BFac"] = -modified_zscore(df["BFac"])
+    df["RSCC"] = modified_zscore(df["RSCC"])
+    df["Diff"] = -modified_zscore(df["Diff"])
+    df["Geom"] = -modified_zscore(df["Geom"])
+    density_score = (df["BFac"] + df["RSCC"] + df["Diff"]) / 3
+    df["Score"] = modified_zscore((density_score + df["Geom"]) / 2)
+    return df
+
+
+def validate_refmac(result: RefmacResult, monlib: MonLib) -> pd.DataFrame:
+    return validate(
+        result.structure, result.fphi_best, result.fphi_diff, result.fphi_calc, monlib
+    )
+
+
+def _bfac(model: gemmi.Model) -> dict:
+    return {
+        (chain.name, str(residue.seqid)): np.mean([a.b_iso for a in residue])
+        for chain in model
+        for residue in chain
+    }
+
+
+def _rscc_diff(
+    structure: gemmi.Structure,
+    best_map: gemmi.FloatGrid,
+    diff_map: gemmi.FloatGrid,
+    calc_map: gemmi.FloatGrid,
+    model_index: int,
+) -> dict:
+    search = gemmi.NeighborSearch(structure, max_radius=3, model_index=model_index)
+    search.populate(include_h=False)
+    best_values = defaultdict(list)
+    diff_values = defaultdict(list)
+    calc_values = defaultdict(list)
+    for point in best_map.masked_asu():
+        position = best_map.point_to_position(point)
+        mark = search.find_nearest_atom(position, radius=3)
+        if mark is not None:
+            cra = mark.to_cra(structure[model_index])
+            key = (cra.chain.name, str(cra.residue.seqid))
+            best_values[key].append(point.value)
+            diff_values[key].append(diff_map.get_value(point.u, point.v, point.w))
+            calc_values[key].append(calc_map.get_value(point.u, point.v, point.w))
+    rscc = {}
+    diff = {}
+    for key, best_value in best_values.items():
+        rscc[key] = np.corrcoef(best_value, calc_values[key])[0, 1]
+        diff[key] = np.sqrt(np.mean(np.square(diff_values[key])))
+    return rscc, diff

modelcraft-6.0.0.dist-info/METADATA

@@ -0,0 +1,76 @@
+Metadata-Version: 2.4
+Name: modelcraft
+Version: 6.0.0
+Summary: Automated model-building pipeline for X-ray crystallography and cryo-EM
+Author-email: Paul Bond <paul.bond@york.ac.uk>
+Maintainer-email: Paul Bond <paul.bond@york.ac.uk>
+Project-URL: Source, https://github.com/paulsbond/modelcraft
+Project-URL: Issues, https://github.com/paulsbond/modelcraft/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: gemmi>=0.5.5
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: requests
+Requires-Dist: scipy
+Requires-Dist: tabulate
+
+![](https://github.com/paulsbond/modelcraft/blob/691b8a0d72dbf48b8d8a431bdb193298a397e1bb/modelcraft.png)
+
+# ModelCraft
+
+ModelCraft is an automated model-building pipeline
+that builds proteins and nucleic acids
+into X-ray crystallography and cryo-EM maps.
+It combines the previous Buccaneer and Nautilus pipelines and adds new steps
+for density modification, refinement, validation and pruning.
+
+## Installation
+
+ModelCraft is distributed with CCP4.
+Please obtain the latest version from the
+[CCP4 download page](https://www.ccp4.ac.uk/download).
+
+## Graphical interfaces
+
+For X-ray crystallography, ModelCraft can be used through
+[CCP4i2](https://ccp4i2.gitlab.io/rstdocs/tasks/modelcraft/index.html) or
+[CCP4 Cloud](https://cloud.ccp4.ac.uk/manuals/html-taskref/doc.task.ModelCraft.html).
+For cryo-EM, it is available in
+[CCP-EM Doppio](https://www.ccpem.ac.uk/docs/doppio/user_guide.html).
+
+## Command-line interface
+
+The first argument must be either
+`xray` for X-ray crystallography or `em` for cryo-EM SPA.
+The command line documentation has detailed information on individual arguments.
+
+```bash
+modelcraft xray --help
+```
+
+```bash
+modelcraft em --help
+```
+
+## Links
+
+- [Source (latest)](https://github.com/paulsbond/modelcraft)
+- [Source (releases)](https://github.com/paulsbond/modelcraft/releases)
+- [Issues (e.g. bugs and feature requests)](https://github.com/paulsbond/modelcraft/issues)
+- [PyPI (Python Package Index)](https://pypi.org/project/modelcraft)
+
+## Citations
+
+- [ModelCraft](https://doi.org/10.1107/S2059798322007732)
+- [Buccaneer](https://doi.org/10.1107/S0907444906022116)
+- [EMDA](https://doi.org/10.1016/j.jsb.2021.107826)
+- [Nautilus](https://doi.org/10.1107/S2052252514019290)
+- [Parrot](https://doi.org/10.1107/S090744490903947X)
+- [Refmac](https://doi.org/10.1107/S2059798318000979)
+- [Servalcat](https://doi.org/10.1107/S2059798321009475)
+- [Sheetbend](https://doi.org/10.1107/S2059798320013170)

modelcraft-6.0.0.dist-info/RECORD

@@ -0,0 +1,85 @@
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+modelcraft/maps.py,sha256=Lyv3YjKNdUgi6vaLmQ8CcZFKq39EPL4NDC5qO_kCd0A,354
+modelcraft/modelcraftem.py,sha256=Ru4sjfERIdOENIQDYwzyh2dnL84rlo3oH5ZSq2-MfdE,7559
+modelcraft/modelcraftxray.py,sha256=eKwRVBouQfVreHvXOgc2hW5wsBB2GvN2E9ST6LEZsK8,15061
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+modelcraft/tests/ccpem/__init__.py,sha256=fY53G_EEc9LG4FmZ-IfQEhmEsNg5FZfxFwOCUQj019c,656
+modelcraft/tests/ccpem/test_em.py,sha256=eS7qdlqCQlBizmaqnEHvTsUJ2-z2w1DRcUX-1acrExY,1532
+modelcraft/tests/ccpem/test_emda.py,sha256=nNseLsi0C8vu4UjYIP6OtalwKHyeHxMUfu9BV2HOOO8,401
+modelcraft/tests/ccpem/test_refmac.py,sha256=g3evpenT47aZuSkSwVVHLSfSJZe2QK_YYttDOnsYMnU,326
+modelcraft/tests/ccpem/test_servalcat.py,sha256=jWrPCoq2TlAiHW6x5SPtkH8o-JcSdwRWvt2ZU1ZvSYA,1436
+modelcraft-6.0.0.dist-info/METADATA,sha256=_4gQqy7CG6sz36YsXv_ZUH_BlpVWfZ2hys1Vsfs1s64,2741
+modelcraft-6.0.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+modelcraft-6.0.0.dist-info/entry_points.txt,sha256=KTN5D1dIVxOdag4aue-o2vdEq3VSWHLp5o0Jcm98rv4,286
+modelcraft-6.0.0.dist-info/top_level.txt,sha256=My5973x4fvPrlRfQOuuFxqultnVzrg_aamczcSijdlQ,11
+modelcraft-6.0.0.dist-info/RECORD,,

{modelcraft-5.0.2.dist-info → modelcraft-6.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{modelcraft-5.0.2.dist-info → modelcraft-6.0.0.dist-info}/entry_points.txt

@@ -2,3 +2,5 @@
 modelcraft = modelcraft.scripts.modelcraft:main
 modelcraft-contents = modelcraft.scripts.contents:main
 modelcraft-copies = modelcraft.scripts.copies:main
+modelcraft-sidechains = modelcraft.scripts.sidechains:main
+modelcraft-validate = modelcraft.scripts.validate:main