pumbing origin_id down to more fundamental functions AND option to di…

…splay rmsd per origin_id

cctbx/geometry_restraints/__init__.py

@@ -1080,14 +1080,15 @@ def get_sorted(self,
     n_not_shown = correct_id_proxies - n_outputted
     return sorted_table, n_not_shown
 
-  def get_outliers(self, sites_cart, sigma_threshold):
+  def get_outliers(self, sites_cart, sigma_threshold, origin_id=None):
     result = []
     from cctbx.geometry_restraints.linking_class import linking_class
     origin_ids = linking_class()
+    if origin_id is None: origin_id=origin_ids.get_origin_id('covalent geometry')
     vals = self.get_sorted(
         by_value="delta",
         sites_cart=sites_cart,
-        origin_id=origin_ids.get_origin_id('covalent geometry'))[0]
+        origin_id=origin_id)[0]
     if(vals is None): return result
     for it in vals:
       i,j = it[0],it[1]
@@ -1539,9 +1540,11 @@ def get_sorted(self,
         site_labels=site_labels, max_items=max_items,
         get_restraints_only=False, origin_id=origin_id)
 
-  def get_outliers(self, sites_cart, sigma_threshold):
+  def get_outliers(self, sites_cart, sigma_threshold, origin_id=0):
     result = []
-    vals = self.get_sorted(by_value="delta", sites_cart=sites_cart)[0]
+    vals = self.get_sorted(by_value="delta",
+                           origin_id=origin_id,
+                           sites_cart=sites_cart)[0]
     if(vals is None): return result
     for it in vals:
       i,j,k = [int(i) for i in it[0]]

cctbx/geometry_restraints/energies.py

@@ -195,25 +195,29 @@ def __init__(self, sites_cart,
     self.finalize_target_and_gradients()
 
   # Not used anymore? -- used in model_statistics.py
-  def get_filtered_n_bond_proxies(self):
-    return self.bond_proxies.simple.proxy_select(origin_id=0).size()
+  def get_filtered_n_bond_proxies(self, origin_id=0):
+    return self.bond_proxies.simple.proxy_select(origin_id=origin_id).size()
 
-  def get_filtered_n_angle_proxies(self):
-    return self.angle_proxies.proxy_select(origin_id=0).size()
+  def get_filtered_n_angle_proxies(self, origin_id=0):
+    return self.angle_proxies.proxy_select(origin_id=origin_id).size()
 
   def get_filtered_n_dihedral_proxies(self):
     return self.dihedral_proxies.proxy_select(origin_id=0).size()
 
   def get_filtered_n_planarity_proxies(self):
     return self.planarity_proxies.proxy_select(origin_id=0).size()
 
-  def get_angle_outliers(self, sites_cart, sigma_threshold=4):
+  def get_angle_outliers(self, sites_cart, sigma_threshold=4, origin_id=0):
     return self.angle_proxies.get_outliers(sites_cart=sites_cart,
-                                           sigma_threshold=sigma_threshold)
+                                           sigma_threshold=sigma_threshold,
+                                           origin_id=origin_id,
+                                           )
 
-  def get_bond_outliers(self, sites_cart, sigma_threshold=4):
-    return self.bond_proxies.get_outliers(sites_cart=sites_cart,
-                                           sigma_threshold=sigma_threshold)
+  def get_bond_outliers(self, sites_cart, sigma_threshold=4, origin_id=0):
+    return self.bond_proxies.get_outliers( sites_cart=sites_cart,
+                                           sigma_threshold=sigma_threshold,
+                                           origin_id=origin_id,
+                                           )
 
   def get_dihedral_outliers(self, sites_cart, sigma_threshold=4):
     return self.dihedral_proxies.get_outliers(sites_cart=sites_cart,
@@ -333,9 +337,9 @@ def angle_deviations_weighted(self):
       else:
         return 0,0,0
 
-  def angle_deviations(self):
+  def angle_deviations(self, origin_id=0):
     if(self.n_angle_proxies is not None):
-      angle_deltas = self.angle_proxies.proxy_select(origin_id=0).deltas(
+      angle_deltas = self.angle_proxies.proxy_select(origin_id=origin_id).deltas(
           sites_cart=self.sites_cart)
       if len(angle_deltas) > 0:
         a_sq  = angle_deltas * angle_deltas

mmtbx/model/statistics.py

@@ -69,32 +69,36 @@ def _init(self, pdb_hierarchy=None, geometry_restraints_manager=None):
         self.from_restraints.den_residual_sum+
         self.from_restraints.ramachandran_residual_sum)
 
-  def angle(self, return_rmsZ=False):
+  def angle(self, origin_id=0, return_rmsZ=False):
     mi,ma,me,n = 0,0,0,0
     outliers = 0
     if(self.from_restraints is not None):
       if return_rmsZ:
         mi,ma,me = self.from_restraints.angle_deviations_z()
       else:
-        mi,ma,me = self.from_restraints.angle_deviations()
-      n = self.from_restraints.get_filtered_n_angle_proxies()
+        mi,ma,me = self.from_restraints.angle_deviations(origin_id=origin_id)
+      n = self.from_restraints.get_filtered_n_angle_proxies(origin_id=origin_id)
       outliers = self.from_restraints.get_angle_outliers(
         sites_cart = self.pdb_hierarchy.atoms().extract_xyz(),
-        sigma_threshold=4)
+        sigma_threshold=4,
+        origin_id=origin_id,
+        )
     return group_args(min = mi, max = ma, mean = me, n = n, outliers = outliers)
 
-  def bond(self, return_rmsZ=False):
+  def bond(self, origin_id=0, return_rmsZ=False):
     mi,ma,me,n = 0,0,0,0
     outliers = 0
     if(self.from_restraints is not None):
       if return_rmsZ:
         mi,ma,me = self.from_restraints.bond_deviations_z()
       else:
-        mi,ma,me = self.from_restraints.bond_deviations()
-      n = self.from_restraints.get_filtered_n_bond_proxies()
+        mi,ma,me = self.from_restraints.bond_deviations(origin_id=origin_id)
+      n = self.from_restraints.get_filtered_n_bond_proxies(origin_id=origin_id)
       outliers = self.from_restraints.get_bond_outliers(
         sites_cart = self.pdb_hierarchy.atoms().extract_xyz(),
-        sigma_threshold=4)
+        sigma_threshold=4,
+        origin_id=origin_id,
+        )
     return group_args(min = mi, max = ma, mean = me, n = n, outliers = outliers)
 
   def chirality(self):
@@ -311,7 +315,10 @@ def number_of_bonds(self):
     bonds = self.bond()
     return bonds.n
 
-  def show(self, log=None, prefix="", exclude_protein_only_stats=False, uppercase=True):
+  def show(self, log=None, prefix="",
+           exclude_protein_only_stats=False,
+           include_rmsd_details=False,
+           uppercase=True):
     if(log is None): log = sys.stdout
     def fmt(f1,f2,d1,z1=None):
       if f1 is None  : return '   -       -       -  '
@@ -414,6 +421,19 @@ def fmt2(f1):
       result = result.upper()
     print(result, file=log)
 
+    if include_rmsd_details:
+      from cctbx.geometry_restraints.linking_class import linking_class
+      origin_ids = linking_class()
+      print('Details of bonding type rmsd', file=log)
+      for key, i in origin_ids.items():
+        bond_rc=self.bond(origin_id=i)
+        angle_rc=self.angle(origin_id=i)
+        if bond_rc.n:
+          print(f'  {key:20s} : bond  {bond_rc.mean:12.5f} ({bond_rc.n:5d})', file=log)
+        if angle_rc.n:
+          print(f'  {key:20s} : angle {angle_rc.mean:12.3f} ({angle_rc.n:5d})', file=log)
+
+
   def as_cif_block(self, cif_block=None, pdbx_refine_id=''):
     if cif_block is None:
       cif_block = iotbx.cif.model.block()