[Cctbx-cvs] SF.net SVN: cctbx:[8871] trunk

[<rw...@us...>]

Revision: 8871
          http://cctbx.svn.sourceforge.net/cctbx/?rev=8871&view=rev
Author:   rwgk
Date:     2009-04-04 00:42:54 +0000 (Sat, 04 Apr 2009)

Log Message:
-----------
cctbx/geometry_restraints/nonbonded_sorted.h: nonbonded_sorted_asu_proxies: additional parameter: min_cubicle_edge

Modified Paths:
--------------
    trunk/cctbx/geometry_restraints/__init__.py
    trunk/cctbx/geometry_restraints/manager.py
    trunk/cctbx/geometry_restraints/nonbonded_sorted.h
    trunk/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp
    trunk/cctbx/regression/tst_geometry_restraints_2.py
    trunk/mmtbx/monomer_library/pdb_interpretation.py

Modified: trunk/cctbx/geometry_restraints/__init__.py
===================================================================
--- trunk/cctbx/geometry_restraints/__init__.py	2009-04-03 23:59:09 UTC (rev 8870)
+++ trunk/cctbx/geometry_restraints/__init__.py	2009-04-04 00:42:54 UTC (rev 8871)
@@ -946,7 +946,8 @@
         conformer_indices=None,
         nonbonded_params=None,
         nonbonded_types=None,
-        nonbonded_distance_cutoff_plus_buffer=None):
+        nonbonded_distance_cutoff_plus_buffer=None,
+        min_cubicle_edge=5):
     self.bond_proxies = None
     self.nonbonded_proxies = None
     if (bond_params_table is not None
@@ -972,6 +973,7 @@
         nonbonded_types=nonbonded_types,
         nonbonded_distance_cutoff_plus_buffer=\
           nonbonded_distance_cutoff_plus_buffer,
+        min_cubicle_edge=min_cubicle_edge,
         shell_asu_tables=shell_asu_tables)
 
 class _motif(boost.python.injector, ext.motif):

Modified: trunk/cctbx/geometry_restraints/manager.py
===================================================================
--- trunk/cctbx/geometry_restraints/manager.py	2009-04-03 23:59:09 UTC (rev 8870)
+++ trunk/cctbx/geometry_restraints/manager.py	2009-04-04 00:42:54 UTC (rev 8871)
@@ -28,7 +28,8 @@
         chirality_proxies=None,
         planarity_proxies=None,
         plain_pairs_radius=None,
-        max_reasonable_bond_distance=None):
+        max_reasonable_bond_distance=None,
+        min_cubicle_edge=5):
     if (site_symmetry_table is not None): assert crystal_symmetry is not None
     if (bond_params_table is not None and site_symmetry_table is not None):
       assert bond_params_table.size() == site_symmetry_table.indices().size()
@@ -269,12 +270,14 @@
         self._pair_proxies = geometry_restraints.pair_proxies(
           flags=flags,
           bond_params_table=self.bond_params_table,
+          min_cubicle_edge=self.min_cubicle_edge,
           shell_asu_tables=shell_asu_tables)
       elif (self._pair_proxies is None):
         self.n_updates_pair_proxies += 1
         self._pair_proxies = geometry_restraints.pair_proxies(
           flags=flags,
-          bond_params_table=self.bond_params_table)
+          bond_params_table=self.bond_params_table,
+          min_cubicle_edge=self.min_cubicle_edge)
     elif (sites_cart is not None
           and (self._sites_cart_used_for_pair_proxies is None
                or flags is not None
@@ -374,7 +377,8 @@
           nonbonded_params=self.nonbonded_params,
           nonbonded_types=self.nonbonded_types,
           nonbonded_distance_cutoff_plus_buffer
-            =current_nonbonded_distance_cutoff_plus_buffer)
+            =current_nonbonded_distance_cutoff_plus_buffer,
+          min_cubicle_edge=self.min_cubicle_edge)
         introspection.virtual_memory_info().update_max()
         if (self._pair_proxies.nonbonded_proxies is None):
           break

Modified: trunk/cctbx/geometry_restraints/nonbonded_sorted.h
===================================================================
--- trunk/cctbx/geometry_restraints/nonbonded_sorted.h	2009-04-03 23:59:09 UTC (rev 8870)
+++ trunk/cctbx/geometry_restraints/nonbonded_sorted.h	2009-04-04 00:42:54 UTC (rev 8871)
@@ -44,6 +44,7 @@
         geometry_restraints::nonbonded_params const& nonbonded_params,
         af::const_ref<std::string> const& nonbonded_types,
         double nonbonded_distance_cutoff_plus_buffer,
+        double min_cubicle_edge,
         std::vector<crystal::pair_asu_table<> > const& shell_asu_tables)
       :
         nonbonded_sorted_asu_proxies_base(shell_asu_tables[0].asu_mappings()),
@@ -72,7 +73,7 @@
           shell_asu_tables[0].asu_mappings(),
           nonbonded_distance_cutoff_plus_buffer,
           /*minimal*/ false,
-          /*min_cubicle_edge*/ 0); // XXX.XXX.XXX
+          min_cubicle_edge);
         while (!pair_generator.at_end()) {
           direct_space_asu::asu_mapping_index_pair_and_diff<>
             pair = pair_generator.next();

Modified: trunk/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp
===================================================================
--- trunk/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp	2009-04-03 23:59:09 UTC (rev 8870)
+++ trunk/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp	2009-04-04 00:42:54 UTC (rev 8871)
@@ -63,12 +63,14 @@
           nonbonded_params const&,
           af::const_ref<std::string> const&,
           double,
+          double,
           std::vector<crystal::pair_asu_table<> > const&>((
             arg_("model_indices"),
             arg_("conformer_indices"),
             arg_("nonbonded_params"),
             arg_("nonbonded_types"),
             arg_("nonbonded_distance_cutoff_plus_buffer"),
+            arg_("min_cubicle_edge"),
             arg_("shell_asu_tables"))))
         .def_readonly("n_1_3", &w_t::n_1_3)
         .def_readonly("n_1_4", &w_t::n_1_4)

Modified: trunk/cctbx/regression/tst_geometry_restraints_2.py
===================================================================
--- trunk/cctbx/regression/tst_geometry_restraints_2.py	2009-04-03 23:59:09 UTC (rev 8870)
+++ trunk/cctbx/regression/tst_geometry_restraints_2.py	2009-04-04 00:42:54 UTC (rev 8871)
@@ -545,7 +545,7 @@
   vdw_distance: 3.42
 """,
     selections=[range(3), range(138,141), range(303,307), range(347,351),
-      range(372,377), range(400,402), range(-2,0)])
+      range(372,377), range(434,436), range(-2,0)])
   #
   out = StringIO()
   geo.show_interactions(site_labels=site_labels, f=out)
@@ -600,7 +600,7 @@
   vdw_distance: 3.42
 """,
     selections=[range(5), range(230,236), range(560,568), range(648,656),
-      range(689,694), range(717,721), range(-4,0)])
+      range(689,694), range(785,789), range(-4,0)])
   #
   sel0 = geo.simple_edge_list()
   assert len(sel0) == 46

Modified: trunk/mmtbx/monomer_library/pdb_interpretation.py
===================================================================
--- trunk/mmtbx/monomer_library/pdb_interpretation.py	2009-04-03 23:59:09 UTC (rev 8870)
+++ trunk/mmtbx/monomer_library/pdb_interpretation.py	2009-04-04 00:42:54 UTC (rev 8871)
@@ -2417,6 +2417,7 @@
         default_distance=1),
       nonbonded_types=flex.std_string(conformer_indices.size()),
       nonbonded_distance_cutoff_plus_buffer=disulfide_distance_cutoff,
+      min_cubicle_edge=5,
       shell_asu_tables=[pair_asu_table])
     labels = [self.pdb_atoms[i_seq].id_str()
       for i_seq in self.cystein_sulphur_i_seqs]


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