Remove code duplication in precision_rmsd. Fixes issue #11

salilab · Jan 6, 2022 · 80bfbf4 · 80bfbf4
1 parent 1e6994b
commit 80bfbf4
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Showing 2 changed files with 17 additions and 77 deletions.
diff --git a/pyext/src/exhaust.py b/pyext/src/exhaust.py
@@ -388,16 +388,10 @@ def main():
 
             # get superposition of each model to cluster center and the
             # RMSD between the two
-            if args.symmetry_groups:
-                rmsd, superposed_ps, trans = \
-                    precision_rmsd.get_particles_from_superposed_amb(
-                        conforms[model_index], conform_0, args.align, ps,
-                        trans, symm_groups)
-            else:
-                rmsd, superposed_ps, trans = \
+            rmsd, superposed_ps, trans = \
                     precision_rmsd.get_particles_from_superposed(
                         conforms[model_index], conform_0, args.align,
-                        ps, trans)
+                        ps, trans, symm_groups)
 
             model.update()  # why not?
 

diff --git a/pyext/src/precision_rmsd.py b/pyext/src/precision_rmsd.py
@@ -16,20 +16,30 @@ def parse_custom_ranges(ranges_file):
 
 
 def get_particles_from_superposed(
-        cluster_conform_i, cluster_conform_0, align, ps, trans):
+        cluster_conform_i, cluster_conform_0, align, ps, trans,
+        symm_groups=None):
     def _to_vector3ds(numpy_array):
         # No need to fit the whole array - we only need 4 non-coplanar points,
         # so 100 should be plenty
         return [IMP.algebra.Vector3D(c) for c in numpy_array[:100]]
 
     if align:
+        calculator_name = "QCP_SERIAL_CALCULATOR"
+    else:
+        calculator_name = "NOSUP_SERIAL_CALCULATOR"
+
+    conforms = numpy.array([cluster_conform_0, cluster_conform_i])
+
+    if symm_groups is None:
         calculator = pyRMSD.RMSDCalculator.RMSDCalculator(
-            "QCP_SERIAL_CALCULATOR",
-            numpy.array([cluster_conform_0, cluster_conform_i]))
+            calculator_name,
+            conforms)
     else:
         calculator = pyRMSD.RMSDCalculator.RMSDCalculator(
-            "NOSUP_SERIAL_CALCULATOR",
-            numpy.array([cluster_conform_0, cluster_conform_i]))
+            calculator_name,
+            fittingCoordsets=conforms,
+            calcSymmetryGroups=symm_groups,
+            fitSymmetryGroups=symm_groups)
 
     rmsd, superposed_fit = calculator.pairwise(
         0, 1, get_superposed_coordinates=True)
@@ -48,70 +58,6 @@ def _to_vector3ds(numpy_array):
 
     return rmsd, ps, trans
 
-
-def get_particles_from_superposed_amb(
-        cluster_conform_i, cluster_conform_0, align, ps, trans, symm_groups):
-
-    '''Modified superposed function to work with symmetric copies'''
-
-    def _to_vector3ds(numpy_array):
-        # No need to fit the whole array - we only need 4 non-coplanar points,
-        # so 100 should be plenty
-        return [IMP.algebra.Vector3D(c) for c in numpy_array[:100]]
-
-    min_rmsd = 10000.0
-
-    superposed_final_coords = []
-
-    for perm in pyRMSD.symmTools.symm_permutations(symm_groups):
-        # for each permutation
-
-        new_cluster_conform_i = cluster_conform_i
-
-        for sg in perm:  # for each symmetric group in perm
-
-            for [particle0, particle1] in sg:
-                # swap the particles if they are in non-standard order
-                # in this permutation
-                if particle0 > particle1:
-                    pyRMSD.symmTools.swap_atoms(
-                        new_cluster_conform_i, particle0, particle1)
-
-        if align:
-            calculator = pyRMSD.RMSDCalculator.RMSDCalculator(
-                "QCP_SERIAL_CALCULATOR",
-                numpy.array([cluster_conform_0, new_cluster_conform_i]))
-        else:
-            calculator = pyRMSD.RMSDCalculator.RMSDCalculator(
-                "NOSUP_SERIAL_CALCULATOR",
-                numpy.array([cluster_conform_0, new_cluster_conform_i]))
-
-        rmsd, superposed_fit = calculator.pairwise(
-            0, 1, get_superposed_coordinates=True)
-
-        if rmsd < min_rmsd:
-            min_rmsd = rmsd
-            superposed_final_coords = superposed_fit
-
-    # Get transformation from pyRMSD reference on the first call.
-    # This is somewhat inefficient (since we are essentially repeating
-    # the pyRMSD calculation) but pyRMSD doesn't appear to make its
-    # reference orientation available.
-    if trans is None:
-        trans = IMP.algebra.get_transformation_aligning_first_to_second(
-            _to_vector3ds(superposed_final_coords[0]),
-            _to_vector3ds(cluster_conform_0))
-
-    for particle_index in range(len(superposed_final_coords[1])):
-
-        # Transform from pyRMSD back to original reference
-        IMP.core.XYZ(ps[particle_index]).set_coordinates(
-            trans * IMP.algebra.Vector3D(
-                superposed_final_coords[1][particle_index]))
-
-    return min_rmsd, ps, trans
-
-
 class GetModelDensity(object):
     """Compute mean density maps from structures.
     Keeps a dictionary of density maps,