solvent mask: update cctbx-compatible option

rprobe (solvent_radius in cctbx) was changed from 1.11 to 1.1 in Dec 2021
cctbx/cctbx_project@2243cc9

and add more tests

docs/grid.rst

@@ -509,7 +509,7 @@ The parameters of SolventMasker can be inspected and changed:
   >>> masker.atomic_radii_set
   <AtomicRadiiSet.Cctbx: 1>
   >>> masker.rprobe
-  1.11
+  1.1
   >>> masker.rshrink
   0.9
   >>> masker.island_min_volume  # 0 = unused

examples/maskcheck.py

@@ -43,20 +43,24 @@ def maskcheck(mask_path, coor_path, output_diff_map=None, verbose=False):
     grid2.copy_metadata_from(grid)
     masker.put_mask_on_int8_grid(grid2, st[0])
 
-    compare_mask_arrays(grid, grid2)
+    compare_mask_arrays(grid, grid2, verbose)
     if verbose:
         print_nearby_atoms(st, grid, grid2)
     if output_diff_map:
         write_diff_map(grid, grid2, output_diff_map)
 
 
-def compare_mask_arrays(grid1, grid2):
+def compare_mask_arrays(grid1, grid2, verbose):
     arr1 = numpy.array(grid1, copy=False)
     arr2 = numpy.array(grid2, copy=False)
     if arr1.shape != arr2.shape:
         sys.exit('Different grid sizes %s and %s. Exiting.' %
                  (arr1.shape, arr2.shape))
     print('Size: %d x %d x %d,' % arr1.shape, 'total', arr1.size, 'points')
+    if (arr1 == arr2).all():
+        print("Identical.")
+        if not verbose:
+            return
     t = 2 * (arr1 != 0) + (arr2 != 0)
     print('File-Gemmi Count Fraction')
     for (a, b) in [(0, 0), (1, 1), (0, 1), (1, 0)]:

include/gemmi/solmask.hpp

@@ -231,7 +231,7 @@ struct SolventMasker {
         island_min_volume = 0.;
         break;
       case AtomicRadiiSet::Cctbx:
-        rprobe = 1.11;
+        rprobe = 1.1;
         rshrink = 0.9;
         island_min_volume = 0.;
         break;

run-tests.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 # I use this script for building, testing and updating docs.
 
@@ -144,3 +144,15 @@ if [ $1 = w -o $1 = a ]; then
     (cd wasm/mtz && ./compile.sh)
     (cd ../wasm/convert && make clean && make)
 fi
+
+if [ $1 = M -o $1 = a ]; then
+    echo "check bulk solvent mask against cctbx"
+    for code in 1keb 1mru 5oo5 6dd6; do
+        echo Testing mask for $code ...
+        pdb="${PDB_DIR}/structures/divided/pdb/${code:1:2}/pdb${code}.ent.gz"
+        zcat $pdb > /tmp/file.pdb
+        mmtbx.python -m mmtbx.command_line.mask /tmp/file.pdb
+        $PYTHON examples/maskcheck.py mask.ccp4 /tmp/file.pdb
+        /bin/rm mask.ccp4
+    done
+fi

tests/test_examples.py

@@ -79,10 +79,10 @@ def test_maskcheck(self):
 Generating CCTBX-compatible mask ...
 Size: 72 x 72 x 150, total 777600 points
 File-Gemmi Count Fraction
-0-0       511128  65.73%
-1-1       265740  34.17%
-0-1            0   0.00%
-1-0          732   0.09%
+0-0       509676  65.54%
+1-1       265788  34.18%
+0-1         1452   0.19%
+1-0          684   0.09%
 '''
         self.assertEqual(output.splitlines(), expected_output.splitlines())