Severe bug fix: arrays of different length were passed into C++ code;…

… it would not crash but produce wrong and very hard to debug results!

mmtbx/refinement/real_space/__init__.py

@@ -172,6 +172,27 @@ def flatten(l):
   if l is None: return None
   return sum(([x] if not (isinstance(x, list) or isinstance(x, flex.size_t)) else flatten(x) for x in l), [])
 
+def get_radii(residue, vdw_radii):
+  atom_names = [a.name.strip() for a in residue.atoms()]
+  converter = iotbx.pdb.residue_name_plus_atom_names_interpreter(
+    residue_name = residue.resname, atom_names = atom_names)
+  mon_lib_names = converter.atom_name_interpretation.mon_lib_names()
+  radii = flex.double()
+  for n in mon_lib_names:
+    try:             radii.append(vdw_radii[n.strip()]-0.25)
+    except KeyError: radii.append(1.5) # XXX U, Uranium, OXT are problems!
+  return radii
+
+def get_radius(atom, vdw_radii):
+  atom_names = [atom.name.strip()]
+  converter = iotbx.pdb.residue_name_plus_atom_names_interpreter(
+    residue_name = atom.parent().resname, atom_names = atom_names)
+  if(converter.atom_name_interpretation is not None):
+    atom_names = converter.atom_name_interpretation.mon_lib_names()
+  n = atom_names[0].strip()
+  try:             return vdw_radii[n.strip()]-0.25
+  except KeyError: return 1.5 # XXX U, Uranium, OXT are problems!
+
 def common_map_values(pdb_hierarchy, unit_cell, map_data):
   d = {}
   for model in pdb_hierarchy.models():
@@ -199,16 +220,8 @@ def mean_filtered(x):
   overall_mean = flex.mean_default(all_vals.select(sel),0)
   for k,v in zip(d.keys(), d.values()):
     sel = mean_filtered(v)
-    if(sel.count(True)>10):
-      result[k] = flex.mean_default(v.select(sel),0)
-    else:
-      result[k] = overall_mean
-      an = key.split("_")[-1][0]
-      mv = flex.mean_default(v,0)
-      if(an=="S"):
-        result[k] = mv
-      else:
-        result[k] = overall_mean
+    if(sel.count(True)>10): result[k] = flex.mean_default(v.select(sel),0)
+    else:                   result[k] = overall_mean
   return result
 
 class side_chain_fit_evaluator(object):

mmtbx/refinement/real_space/fit_residue.py

@@ -7,7 +7,6 @@
 from cctbx import maptbx
 import scitbx.math
 import mmtbx.idealized_aa_residues.rotamer_manager
-import iotbx.pdb
 import collections
 from libtbx import group_args
 
@@ -214,35 +213,34 @@ def fit_side_chain(self, clusters):
       cl = clusters[i]
       axes.append(flex.size_t(cl.axis))
       atr.append(flex.size_t(cl.atoms_to_rotate))
-    sites = self.residue.atoms().extract_xyz()
+    #
     if(self.target_map is not None and self.xyzrad_bumpers is not None):
-      # Get vdW radii
-      offset = 0.25
-      #if(self.residue.resname=="MSE"): offset=0.5
-      radii = flex.double()
-      atom_names = []
+      # Get reference map values
       ref_map_vals = flex.double()
       for a in self.residue.atoms():
-        if(self.rotatable_hd[a.i_seq]): continue # don't include rotatable H
-        atom_names.append(a.name.strip())
         key = "%s_%s_%s"%(
           a.parent().parent().parent().id, a.parent().resname,
           a.name.strip())
         ref_map_vals.append(self.cmv[key])
-      converter = iotbx.pdb.residue_name_plus_atom_names_interpreter(
-        residue_name=self.residue.resname, atom_names = atom_names)
-      mon_lib_names = converter.atom_name_interpretation.mon_lib_names()
-      for n in mon_lib_names:
-        try: radii.append(self.vdw_radii[n.strip()]-offset)
-        except KeyError: radii.append(1.5) # XXX U, Uranium, OXT are problems!
-      #
-      xyzrad_residue = ext.moving(
-        sites_cart       = sites,
+      # Get radii
+      radii = mmtbx.refinement.real_space.get_radii(
+        residue = self.residue, vdw_radii = self.vdw_radii)
+      # Exclude rotatable H from clash calculation
+      tmp = flex.size_t()
+      for i in selection_clash:
+        if(self.rotatable_hd[self.residue.atoms()[i].i_seq]): continue
+        tmp.append(i)
+      selection_clash = tmp[:]
+      # Ad hoc: S or SE have larger peaks!
+      if(self.residue.resname in ["MET","MSE"]): scale=100
+      else:                                      scale=3
+      moving = ext.moving(
+        sites_cart       = self.residue.atoms().extract_xyz(),
         sites_cart_start = sites_cart_start,
         radii            = radii,
         weights          = self.weights,
         bonded_pairs     = self.pairs,
-        ref_map_max      = ref_map_vals * 3,
+        ref_map_max      = ref_map_vals * scale,
         ref_map_min      = ref_map_vals / 10)
       #
       ro = ext.fit(
@@ -251,10 +249,10 @@ def fit_side_chain(self, clusters):
         rotatable_points_indices = atr,
         angles_array             = self.chi_angles,
         density_map              = self.target_map,
-        moving                   = xyzrad_residue,
+        moving                   = moving,
         unit_cell                = self.unit_cell,
         selection_clash          = selection_clash,
-        selection_rsr            = selection_rsr,
+        selection_rsr            = selection_rsr, # select atoms to compute map target
         sin_table                = self.sin_cos_table.sin_table,
         cos_table                = self.sin_cos_table.cos_table,
         step                     = self.sin_cos_table.step,
@@ -266,7 +264,7 @@ def fit_side_chain(self, clusters):
         rotatable_points_indices = atr,
         angles_array             = self.chi_angles,
         density_map              = self.target_map,
-        all_points               = sites,
+        all_points               = self.residue.atoms().extract_xyz(),
         unit_cell                = self.unit_cell,
         selection                = selection_rsr,
         sin_table                = self.sin_cos_table.sin_table,

mmtbx/refinement/real_space/fit_residues.py

@@ -127,8 +127,8 @@ def get_nonbonded_bumpers(self, residue, radius):
     for i in selection_around_residue_minus_residue_minus_rotatableH:
       atom = self.atoms[i]
       an = atom.name.strip()
-      try:             rad = self.vdw_radii[an]-0.25
-      except KeyError: rad = 1.5 # XXX U, Uranium, OXT are problems!
+      rad = mmtbx.refinement.real_space.get_radius(
+        atom = atom, vdw_radii = self.vdw_radii)
       good = True
       if(self.diff_map_data is not None):
         sf = self.crystal_symmetry.unit_cell().fractionalize(atom.xyz)