Finish building asu bond proxies from .geo file

mmtbx/geometry_restraints/geo_file_parsing.py

@@ -7,6 +7,10 @@
 from libtbx.utils import Sorry
 from cctbx import geometry_restraints
 from cctbx.geometry_restraints.linking_class import linking_class
+from cctbx.array_family import flex
+from cctbx import crystal
+from cctbx.crystal import direct_space_asu
+
 origin_ids = linking_class()
 
 
@@ -37,6 +41,7 @@ def __init__(self,lines,origin_id=0,origin_label="covalent"):
     # Parsing data structures
     self.lines = lines               # raw .geo lines
     self.i_seqs = []                 # list of integer i_seqs (if possible)
+    self.sites_cart = None           # Flex vec3 array, coord for each i_seq if available
     self.atom_labels  = []           # list of string atom label from .geo
     self._numerical = None           # a dict of numerical geo data
     self.origin_id = origin_id
@@ -159,7 +164,19 @@ def has_sym_op(self):
 
   def to_proxy(self):
     if self.has_sym_op:
-      proxy = None
+      asu_mappings = direct_space_asu.non_crystallographic_asu_mappings(
+      sites_cart=self.sites_cart)
+      pair_generator = crystal.neighbors_fast_pair_generator(
+      asu_mappings=asu_mappings,
+      distance_cutoff=5)
+      pair = geometry_restraints.bond_asu_proxy(
+        pair=next(pair_generator),
+        distance_ideal=self.ideal,
+        weight=self.weight,
+        origin_id=self.origin_id)
+      proxy = geometry_restraints.bond_asu_proxy(pair=pair, params=pair)
+      return proxy
+
     else:
       proxy = geometry_restraints.bond_simple_proxy(
               i_seqs=self.i_seqs,
@@ -482,6 +499,7 @@ def __init__(self,geo_lines,model=None,entry_config=None):
     # If model present, add i_seqs
     if self.model:
       self._fill_labels_from_model(self.model)
+      self._fill_sites_cart_from_model(self.model)
 
   @property
   def proxies(self):
@@ -493,6 +511,16 @@ def has_proxies(self):
   def i_seqs_are_available(self):
     return all([entry.i_seqs_are_available() for entry in self.entries_list])
 
+  def _fill_sites_cart_from_model(self,model):
+    # Verify iseqs
+    if not self.i_seqs_are_available():
+      self._fill_labels_from_model(model)
+    # get sites cart
+    sites_cart = model.get_sites_cart()
+    for entry in self.entries_list:
+      entry.sites_cart = sites_cart.select(flex.size_t(entry.i_seqs))
+
+
   def _fill_labels_from_model(self, model):
     """
     Add i_seq attributes for each atom on each entry

mmtbx/geometry_restraints/tst_geo_file_parsing.py

@@ -7,6 +7,7 @@
 from iotbx.data_manager import DataManager
 from cctbx.crystal.tst_super_cell import pdb_str_1yjp
 from mmtbx.geometry_restraints.geo_file_parsing import GeoParser
+from cctbx import geometry_restraints
 from libtbx.test_utils import show_diff
 
 """
@@ -1534,6 +1535,9 @@ def tst_06(model,printing=False):
     geo_container.build_proxies()
   assert geo_container.has_proxies()
   assert len(geo_container.proxies_list) == len(entries)-len(geo_container.entries["Nonbonded"])
+  # Check for successful build of the single asu text proxy
+  proxy_class_list = [type(p) for p in geo_container.proxies_list]
+  assert geometry_restraints.bond_asu_proxy in proxy_class_list
 
   origins = [entry.origin_label for entry in geo_container.entries_list]
   expected_origins = ['covalent geometry', 'Misc.', 'link_ALPHA2-6', 'Disulphide bridge', 'link_NAG-ASN', '-like', 'Metal coordination', 'link_TRANS', 'Custom Glycosidic', 'link_BETA1-6', 'link_BETA1-3', 'User supplied', 'link_BETA1-4', 'covalent geometry', 'link_ALPHA2-6', 'Disulphide bridge', 'link_NAG-ASN', 'Secondary Structure restraints around h-bond', 'link_TRANS', 'Custom Glycosidic', 'link_BETA1-6', 'link_BETA1-3', 'link_BETA1-4', 'covalent geometry', 'C-Beta improper', 'Side chain', 'link_TRANS', 'covalent geometry', 'link_ALPHA2-6', 'link_NAG-ASN', 'link_BETA1-6', 'link_BETA1-3', 'link_BETA1-4', 'covalent geometry', 'link_NAG-ASN', 'link_TRANS', '', 'Stacking parallelity', 'Basepair parallelity']