Crystal from PHIL

newsfragments/819.feature

@@ -0,0 +1 @@
+Allow the creation of a simple ``Crystal`` model from PHIL parameters.

src/dxtbx/model/crystal.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import iotbx.phil
 from cctbx.sgtbx import space_group as SG
 from scitbx import matrix
 
@@ -16,6 +17,25 @@
         MosaicCrystalSauter2014,
     )
 
+crystal_phil_scope = iotbx.phil.parse(
+    """
+  crystal
+    .expert_level = 1
+    .short_caption = "Crystal overrides"
+  {
+    unit_cell = None
+      .type = unit_cell
+
+    A_matrix = None
+      .type = floats(size=9)
+      .help = "The crystal setting A=UB matrix. If set, this will override the unit cell."
+
+    space_group = None
+      .type = space_group
+  }
+"""
+)
+
 
 class CrystalFactory:
     @staticmethod
@@ -126,3 +146,35 @@ def from_mosflm_matrix(
         _c = rotate_mosflm_to_imgCIF * c
 
         return Crystal(_a, _b, _c, space_group=space_group)
+
+    @staticmethod
+    def from_phil(
+        params: iotbx.phil.scope_extract,
+        reference: Crystal | None = None,
+    ) -> Crystal:
+        """
+        Convert the phil parameters into a crystal model
+        """
+
+        all_params = [
+            params.crystal.unit_cell,
+            params.crystal.A_matrix,
+            params.crystal.space_group,
+        ]
+        if all_params.count(None) == len(all_params):
+            return None
+
+        if reference is None:
+            crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), "P1")
+        else:
+            crystal = reference
+            crystal.reset_scan_points()
+
+        if params.crystal.unit_cell is not None:
+            crystal.set_unit_cell(params.crystal.unit_cell)
+        if params.crystal.A_matrix is not None:
+            crystal.set_A(params.crystal.A_matrix)
+        if params.crystal.space_group is not None:
+            crystal.set_space_group(params.crystal.space_group.group())
+
+        return crystal

tests/model/test_crystal_model.py

@@ -7,6 +7,7 @@
 
 from cctbx import crystal, sgtbx, uctbx
 from cctbx.sgtbx import change_of_basis_op
+from iotbx.phil import parse
 from libtbx.test_utils import approx_equal
 from scitbx import matrix
 from scitbx.array_family import flex
@@ -18,6 +19,7 @@
     MosaicCrystalKabsch2010,
     MosaicCrystalSauter2014,
 )
+from dxtbx.model.crystal import crystal_phil_scope
 
 from .crystal_model_old import crystal_model_old
 
@@ -639,3 +641,42 @@ def test_recalculated_cell(crystal_class):
     xl.set_recalculated_unit_cell(uctbx.unit_cell((11, 12, 13, 90, 90, 90)))
     assert xl.get_recalculated_cell_parameter_sd() == ()
     assert xl.get_recalculated_cell_volume_sd() == 0
+
+
+def test_from_phil():
+    params = crystal_phil_scope.extract()
+    assert CrystalFactory.from_phil(params) is None
+
+    params = crystal_phil_scope.fetch(
+        parse(
+            """
+    crystal {
+      unit_cell = 10, 20, 30, 90, 90, 90
+      space_group = P222
+    }
+  """
+        )
+    ).extract()
+
+    # Create the crystal
+    crystal = CrystalFactory.from_phil(params)
+    assert crystal.get_unit_cell().parameters() == (10, 20, 30, 90, 90, 90)
+    assert crystal.get_space_group().type().lookup_symbol() == "P 2 2 2"
+
+    params = crystal_phil_scope.fetch(
+        parse(
+            """
+    crystal {
+      A_matrix =  0.0541,  0.0832, -0.0060, 0.0049, -0.0175, -0.0492, -0.0840,  0.0526, -0.0068
+      space_group = P4
+    }
+  """
+        )
+    ).extract()
+
+    # Create the crystal
+    crystal = CrystalFactory.from_phil(params)
+    assert crystal.get_A() == pytest.approx(
+        (0.0541, 0.0832, -0.0060, 0.0049, -0.0175, -0.0492, -0.0840, 0.0526, -0.0068)
+    )
+    assert crystal.get_space_group().type().lookup_symbol() == "P 4"