Version 3.4.0 (#36)

CHANGELOG.md

@@ -3,6 +3,12 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org).
 
+## [3.4.0] - 2023-09-21
+
+### Added
+
+- Option --mask to provide a custom mask in EM mode instead of using EMDA mapmask
+
 ## [3.3.0] - 2023-08-01
 
 ### Changed

modelcraft/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "3.3.0"
+__version__ = "3.4.0"
 
 from .cell import max_distortion as max_cell_distortion
 from .cell import remove_scale

modelcraft/arguments.py

@@ -237,12 +237,20 @@
     metavar="X",
     help=(
         "Either two half-maps or a single map in MRC format. "
-        "Input maps will be trimmed using Servalcat "
-        "and a mask calculated by EMDA mapmask. "
+        "Input maps will be trimmed using Servalcat. "
         "If two half-maps are provided then Servalcat will be used to calculate "
         "a normalised expected (NE) map for model building."
     ),
 )
+_GROUP.add_argument(
+    "--mask",
+    metavar="X",
+    help=(
+        "Mask with the same grid size and dimensions as the input map(s). "
+        "Servalcat will use this mask when trimming the maps. "
+        "If a mask is not provided then EMDA mapmask will be used to create one."
+    ),
+)
 _GROUP.add_argument(
     "--resolution",
     type=float,
@@ -289,7 +297,7 @@ def _basic_check(args: argparse.Namespace):
 
 
 def _check_paths(args: argparse.Namespace):
-    for arg in ("contents", "data", "map", "model", "restraints"):
+    for arg in ("contents", "data", "map", "mask", "model", "restraints"):
         if hasattr(args, arg):
             attr = getattr(args, arg)
             if isinstance(attr, str):

modelcraft/modelcraftem.py

@@ -60,7 +60,10 @@ def run(self):
 
     def _process_input_maps(self):
         maps = [read_map(path) for path in self.args.map]
-        mask = EmdaMapMask(maps[0]).run(self).mask
+        if self.args.mask is not None:
+            mask = read_map(self.args.mask)
+        else:
+            mask = EmdaMapMask(maps[0]).run(self).mask
         trimmed = ServalcatTrim(mask, maps).run(self)
         self.args.map = trimmed.maps
         if len(maps) == 2:

modelcraft/tests/ccp4/test_buccaneer.py

@@ -22,6 +22,15 @@ def test_insulin():
         freer=freer,
         cycles=1,
     ).run()
+    assert buccaneer.completeness_res > 0
+    assert buccaneer.completeness_chn > 0
+    assert buccaneer.chains_built > 0
+    assert buccaneer.fragments_built > 0
+    assert buccaneer.residues_built > 0
+    assert buccaneer.residues_sequenced > 0
+    assert buccaneer.residues_unique > 0
+    assert buccaneer.longest_fragment > 0
+    assert buccaneer.seconds > 0
     stats = ModelStats(buccaneer.structure)
     assert stats.residues > 0
 

modelcraft/tests/ccpem/test_em.py

@@ -3,7 +3,14 @@
 import pytest
 from modelcraft.scripts.modelcraft import main
 from ..ccp4 import in_temp_directory
-from . import density_path, sequence_path, halfmap1_path, halfmap2_path, structure_path
+from . import (
+    density_path,
+    halfmap1_path,
+    halfmap2_path,
+    mask_path,
+    sequence_path,
+    structure_path,
+)
 
 
 @in_temp_directory
@@ -29,6 +36,7 @@ def test_3488_halfmaps():
     args = ["em"]
     args += ["--contents", sequence_path()]
     args += ["--map", halfmap1_path(), halfmap2_path()]
+    args += ["--mask", mask_path()]
     args += ["--resolution", "3.2"]
     args += ["--cycles", "1"]
     with pytest.raises(SystemExit):

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="modelcraft",
-    version="3.3.0",
+    version="3.4.0",
     author="Paul Bond",
     author_email="paul.bond@york.ac.uk",
     description="Automated model building pipeline for X-ray crystallography",