revamped geo writing

cctbx · Oct 4, 2024 · 1c56922 · 1c56922
1 parent 05c0ab5
commit 1c56922
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Showing 7 changed files with 101 additions and 68 deletions.
diff --git a/cctbx/geometry_restraints/auto_linking_types.py b/cctbx/geometry_restraints/auto_linking_types.py
@@ -29,7 +29,7 @@ def __repr__(self):
                     "Bond angle",
                     "Dihedral angle",
                     "Chirality",
-                    "Plane",
+                    "Planarity",
                     "Parallelity",
                     ]
 
@@ -43,7 +43,7 @@ def __repr__(self):
 
 starting_id = 0
 for link_info in [
-    ['covalent geometry', [0,1,2,3,4,5]], # 0
+    ['covalent geometry', 'covalent geometry', [0,1,2,3,4,5]], # 0
     ['SS BOND', # short desc.
      # complete desc.
      'Disulphide bond for CYS-like sulphur atoms within 3A (default) using '

diff --git a/cctbx/geometry_restraints/linking_class.py b/cctbx/geometry_restraints/linking_class.py
@@ -113,7 +113,10 @@ def get_geo_file_header(self, origin_id_label, internals=None):
     else: return info[0]
 
   def parse_geo_file_header(self, origin_id_label, subheader=None, internals=None):
-    if not origin_id_label in covalent_headers:
+    if origin_id_label in ['Nonbonded']:
+      # special case for Nonbonded
+      return 0, origin_id_label
+    elif not origin_id_label in covalent_headers:
       assert 0, 'origin_id_label "%s" not in %s' % (origin_id_label, covalent_headers)
     info = self.data.get(origin_id_label, None)
     if info:
@@ -136,37 +139,54 @@ def get_origin_label_and_internal(self, query_header, verbose=False):
     if verbose:
       for origin_label, info in self.data.items():
         print('origin_label, info',origin_label,info)
+    if query_header.find('|')==-1: return None
     tmp = query_header.split('|')
-    if len(tmp)==1:
-      oi = 0 # default
-      rc = 'covalent'
-    else:
-      header=tmp[0].strip()
-      subheader=tmp[1].strip()
-      oi, rc = self.parse_geo_file_header(header, subheader=subheader)
-    return oi, rc
+    header=tmp[0].strip()
+    subheader=tmp[1].strip()
+    oi, rc = self.parse_geo_file_header(header, subheader=subheader)
+    tmp = query_header.split(':')
+    num = int(tmp[-1])
+    return oi, rc, num
 
 if __name__=='__main__':
   lc = linking_class()
   print(lc)
-  for line in [ 'Bond restraints',
-                'Bond | Misc. | restraints',
-                'Bond | link_BETA1-4 | restraints',
-                'Bond | link_TRANS | restraints',
-                'Bond angle restraints',
-                'Bond angle | link_BETA1-4 | restraints',
-                'Bond angle | link_TRANS | restraints',
-                'Dihedral angle restraints',
-                'Dihedral angle | C-Beta improper | restraints',
-                'Dihedral angle | link_TRANS | restraints',
-                'Chirality restraints',
-                'Chirality | link_BETA1-4 | restraints',
-                'Planarity restraints',
-                'Plane | link_TRANS | restraints',
-
-                "Bond | Bond-like | restraints",
-                "Bond angle | Secondary Structure restraints around h-bond | restraints",
-                "Parallelity | Stacking parallelity | restraints",
-                "Parallelity | Basepair parallelity | restraints",
+  for line in [ 'Bond | covalent geometry | restraints: -1',
+                'Bond | Misc. | restraints: -1',
+                'Bond | link_BETA1-4 | restraints: -1',
+                'Bond | link_TRANS | restraints: -1',
+                'Bond angle | covalent geometry | restraints: -1',
+                'Bond angle | link_BETA1-4 | restraints: -1',
+                'Bond angle | link_TRANS | restraints: -1',
+                'Dihedral angle | covalent geometry | restraints: -1',
+                'Dihedral angle | C-Beta improper | restraints: -1',
+                'Dihedral angle | link_TRANS | restraints: -1',
+                'Chirality | covalent geometry | restraints: -1',
+                'Chirality | link_BETA1-4 | restraints: -1',
+                'Planarity | covalent geometry | restraints: -1',
+                'Planarity | link_TRANS | restraints: -1',
+
+                "Bond | Bond-like | restraints: -1",
+                "Bond angle | Secondary Structure restraints around h-bond | restraints: -1",
+                "Parallelity | Stacking parallelity | restraints: -1",
+                "Parallelity | Basepair parallelity | restraints: -1",
+                'random line',
+
+                #148L
+                'Bond | covalent geometry | restraints: 1390',
+                'Bond | Misc. | restraints: 4',
+                'Bond | link_BETA1-4 | restraints: 1',
+                'Bond | link_TRANS | restraints: 1',
+                'Bond angle | covalent geometry | restraints: 1868',
+                'Bond angle | link_BETA1-4 | restraints: 3',
+                'Bond angle | link_TRANS | restraints: 3',
+                'Dihedral angle | covalent geometry | restraints: 563',
+                'Dihedral angle | C-Beta improper | restraints: 308',
+                'Dihedral angle | link_TRANS | restraints: 3',
+                'Chirality | covalent geometry | restraints: 210',
+                'Chirality | link_BETA1-4 | restraints: 1',
+                'Planarity | covalent geometry | restraints: 238',
+                'Planarity | link_TRANS | restraints: 1',
+                'Nonbonded | unspecified | interactions: 15086',
     ]:
     print('.........',line, lc.get_origin_label_and_internal(line))
diff --git a/cctbx/geometry_restraints/manager.py b/cctbx/geometry_restraints/manager.py
@@ -1633,7 +1633,8 @@ def show_sorted(self,
         f=None):
     from cctbx.geometry_restraints.auto_linking_types import covalent_headers
     from cctbx.geometry_restraints.auto_linking_types import internal_labels
-    default_origin_id = origin_ids.get_origin_id('covalent geometry')
+    covalent_key = 'covalent geometry'
+    default_origin_id = origin_ids.get_origin_id(covalent_key)
     if (f is None): f = sys.stdout
     pair_proxies = self.pair_proxies(flags=flags, sites_cart=sites_cart)
     if (sites_cart is None):
@@ -1643,7 +1644,7 @@ def show_sorted(self,
       #
       # write covalent bonds
       #
-      label=covalent_headers[0]
+      label='%s | %s |' % (covalent_headers[0], covalent_key)
       tempbuffer = StringIO()
       pair_proxies.bond_proxies.show_sorted(
           by_value="residual",
@@ -1656,6 +1657,7 @@ def show_sorted(self,
       #
       # write bonds with other origin_id
       #
+      label=covalent_headers[0]
       for key in origin_ids.get_bond_origin_id_labels():
         origin_id=origin_ids.get_origin_id(key)
         if origin_id==default_origin_id: continue
@@ -1673,51 +1675,54 @@ def show_sorted(self,
     #
     # write of the other internals for each origin_id
     #
-    for i, (proxies, i_label, keys, start) in enumerate([
+    for i, (proxies, keys, start) in enumerate([
       (
        self.angle_proxies, # self.get_all_angle_proxies(),
-       '',
        origin_ids.get_angle_origin_id_labels(),
        11),
       (
        self.dihedral_proxies, # self.get_dihedral_proxies(),
-       '', #'torsion',
        origin_ids.get_dihedral_origin_id_labels(),
        15),
       (
        self.chirality_proxies,
-       '',
        origin_ids.get_chiral_origin_id_labels(),
        10),
       (
        self.planarity_proxies,
-       '',
        origin_ids.get_plane_origin_id_labels(),
        10),
       (
        self.parallelity_proxies,
-       '',
        origin_ids.get_parallelity_origin_id_labels(),
        12),
       ]):
       p_label=covalent_headers[i+1]
       internals=internal_labels[i+1]
       if (proxies is not None):
+        #
+        # "covalent" original ids
+        #
         if p_label not in ['Parallelity']: # not default origin for parallelity
+          tempbuffer = StringIO()
           proxies.show_sorted(
             by_value="residual",
             sites_cart=sites_cart,
             site_labels=site_labels,
-            f=f,
+            f=tempbuffer,
             origin_id=default_origin_id)
-          print(file=f)
-        for key in keys: #origin_ids.get_dihedral_origin_id_labels():
+          print('%s | %s | %s' % (tempbuffer.getvalue()[:start-1],
+                                  covalent_key,
+                                  tempbuffer.getvalue()[start:]),
+                file=f)
+        #
+        # other origin ids
+        #
+        for key in keys:
           origin_id=origin_ids.get_origin_id(key)
           if origin_id==default_origin_id: continue
           label=origin_ids.get_geo_file_header(key, internals=internals)
           if label is None: continue
-          # label = '%s - %s' % (p_label, label)
-          if i_label: label = '%s %s' % (label, i_label)
           tempbuffer = StringIO()
           proxies.show_sorted(
               by_value="residual",
@@ -1748,11 +1753,17 @@ def show_sorted(self,
     # Here should be showing DEN manager...
     #
     if (pair_proxies.nonbonded_proxies is not None):
+      tempbuffer = StringIO()
       pair_proxies.nonbonded_proxies.show_sorted(
         by_value="delta",
-        sites_cart=sites_cart, site_labels=site_labels, f=f,
+        sites_cart=sites_cart, site_labels=site_labels,
+        f=tempbuffer,
         suppress_model_minus_vdw_greater_than=None)
-      print(file=f)
+      start=10
+      print('%s| unspecified | %s' % (tempbuffer.getvalue()[:start],
+                                      tempbuffer.getvalue()[start:]
+                                     ),
+            file=f)
 
 # This should be in model class?
 #  def nb_overlaps_info(

diff --git a/cctbx/regression/tst_geometry_restraints_2.py b/cctbx/regression/tst_geometry_restraints_2.py
@@ -395,7 +395,7 @@ def exercise_non_crystallographic_conserving_bonds_and_angles():
   sio = StringIO()
   geo.show_sorted(sites_cart=sites_cart_noise, f=sio)
   expected_first_part = """\
-Bond restraints: 5
+Bond | covalent geometry | restraints: 5
 Sorted by residual:
 bond 2
      3
@@ -420,7 +420,7 @@ def exercise_non_crystallographic_conserving_bonds_and_angles():
 
 """
   assert not show_diff(sio.getvalue(), expected_first_part + """\
-Nonbonded interactions: 0
+Nonbonded | unspecified | interactions: 0
 
 """)
   #
@@ -438,7 +438,7 @@ def exercise_non_crystallographic_conserving_bonds_and_angles():
   sio = StringIO()
   geo.show_sorted(sites_cart=sites_cart_noise, f=sio)
   assert not show_diff(sio.getvalue(), expected_first_part + """\
-Nonbonded interactions: 2
+Nonbonded | unspecified | interactions: 2
 Sorted by model distance:
 nonbonded 0
           4
@@ -598,10 +598,11 @@ def exercise_na_restraints_output_to_geo(verbose=False):
         print("This portion was not found:\n%s\n=====End of portion." % portion)
         assert 0, "the portion above does not match expected portion."
   # check .geo output
-  geo_identical_portions = ["Bond restraints: 87",
-      "Bond angle restraints: 130", "Dihedral angle restraints: 33",
-      "Chirality restraints: 15",
-      "Planarity restraints: 4"]
+  geo_identical_portions = ["Bond | covalent geometry | restraints: 87",
+      "Bond angle | covalent geometry | restraints: 130",
+      "Dihedral angle | covalent geometry | restraints: 33",
+      "Chirality | covalent geometry | restraints: 15",
+      "Planarity | covalent geometry | restraints: 4"]
   ss_geo_portions = [
       # "Bond-like restraints: 6",
       "Bond | Bond-like | restraints: 6",
@@ -611,12 +612,12 @@ def exercise_na_restraints_output_to_geo(verbose=False):
       # 'Basepair parallelity restraints: 2',
       'Parallelity | Stacking parallelity | restraints: 2',
       'Parallelity | Basepair parallelity | restraints: 2',
-      "Nonbonded interactions: 504"]
+      "Nonbonded | unspecified | interactions: 504"]
   non_ss_geo_portions = [
       #"Bond-like restraints: 0",
       #'Secondary Structure restraints around h-bond angle restraints: 0',
       # "Parallelity restraints: 0", removed because zero
-      "Nonbonded interactions: 526"]
+      "Nonbonded | unspecified | interactions: 526"]
   acp = processed_pdb_file.all_chain_proxies
   sites_cart = acp.sites_cart_exact()
   site_labels = [atom.id_str() for atom in acp.pdb_atoms]

diff --git a/mmtbx/monomer_library/tst_linking.py b/mmtbx/monomer_library/tst_linking.py
@@ -2441,7 +2441,8 @@
   "linking_test_CD_GHE_A_B.pdb" : [0,0],             #4],
   "linking_test_XYP_XYP.pdb" : [18,19],
   "linking_test_ALY_MCM.pdb" : [11,12], # links AA with quasi-AA
-  "linking_test_cyclic_side_chain.pdb" : [67,68], # side chain cross link
+  # cross link not working
+  "linking_test_cyclic_side_chain.pdb" : [67,67], # side chain cross link
   "linking_test_cyclic_main_chain.pdb" : [34,35], # main chain cyclic
   "linking_test_over_valence.pdb" : [6,6],
   "linking_test_c2_c6.pdb" : [21,22],
@@ -2481,7 +2482,7 @@ def run_and_test(cmd, pdb, i, skip_links=False):
       assert lines.find('link_TRANS | restraints: 1')>-1
   bonds = 0
   for line in lines.splitlines():
-    for bond_like in ["Bond restraints:",
+    for bond_like in ["Bond | covalent geometry | restraints:",
                       'Bond-like restraints:',
                       'Bond | Metal coordination | restraints',
                       'Bond | User supplied | restraints',

diff --git a/mmtbx/monomer_library/tst_paral_geo.py b/mmtbx/monomer_library/tst_paral_geo.py
@@ -704,7 +704,7 @@ def test_geo(result, opposite=False):
 
 def main():
   write_and_run(large_pdb)
-  result = '''Plane | Basepair planarity | restraints: 5
+  result = '''Planarity | Basepair planarity | restraints: 5
 Sorted by residual:
                                delta    sigma   weight rms_deltas residual
 plane pdb=" C1'  DC C   7 "   -0.366 1.76e-01 3.23e+01   1.84e-01 2.28e+01

diff --git a/mmtbx/regression/tst_origin_ids.py b/mmtbx/regression/tst_origin_ids.py
@@ -3,13 +3,13 @@
 from iotbx.data_manager import DataManager
 
 count_1yjp = {
-              'Bond restraints': 59,
-              'Bond angle restraints': 79,
-              'Dihedral angle restraints': 22,
+              'Bond | covalent geometry | restraints': 59,
+              'Bond angle | covalent geometry | restraints': 79,
+              'Dihedral angle | covalent geometry | restraints': 22,
               '    harmonic':  7,
               '  sinusoidal': 15,
-              'Planarity restraints': 13,
-              'Chirality restraints': 6,
+              'Planarity | covalent geometry | restraints': 13,
+              'Chirality | covalent geometry | restraints': 6,
               # 'C-Beta improper torsion angle restraints': 12,
               'Dihedral angle | C-Beta improper | restraints': 12,
               # 'Parallelity restraints': 0,
@@ -24,12 +24,12 @@
               #'Metal coordination restraints': 0,
               #'Disulphide bridge angle restraints': 0,
               #'Disulphide bridge restraints': 0,
-              'Nonbonded interactions': 990,
+              'Nonbonded | unspecified | interactions': 990,
               #
               # 'Bond | User supplied | restraints': -1,
               }
 count_1yjp_with_waters = count_1yjp.copy()
-count_1yjp_with_waters['Nonbonded interactions'] = 1178
+count_1yjp_with_waters['Nonbonded | unspecified | interactions'] = 1178
 
 edits = '''
 refinement.geometry_restraints.edits {
@@ -76,7 +76,7 @@ def main():
   model = dm.get_model()
   rc = model.restraints_as_geo(force=True)
   rc = check_geo(rc)
-  assert rc == count_1yjp_with_waters, rc
+  assert rc == count_1yjp_with_waters, '%s != %s' % (count_1yjp_with_waters, rc)
 
   params = model.get_default_pdb_interpretation_params()
   edits_1yjp = params.geometry_restraints.edits
@@ -93,7 +93,7 @@ def main():
   current = count_1yjp_with_waters.copy()
   # current['User supplied restraints'] = 1
   current['Bond | User supplied | restraints'] = 1
-  current['Nonbonded interactions']   = 1176
+  current['Nonbonded | unspecified | interactions']   = 1176
   assert rc == current, check_diff(rc, current)
 
   edits_1yjp.angle[0].action='add'
@@ -109,7 +109,7 @@ def main():
   current = count_1yjp_with_waters.copy()
   current['Bond | User supplied | restraints'] = 1
   current['Bond angle | User supplied | restraints'] = 1
-  current['Nonbonded interactions']   = 1176
+  current['Nonbonded | unspecified | interactions']   = 1176
   assert rc == current, check_diff(rc, current)
 
   edits_1yjp.dihedral[0].action='add'
@@ -129,7 +129,7 @@ def main():
   current['Bond angle | User supplied | restraints'] = 1
   current['Dihedral angle | User supplied | restraints'] = 1
   #current['  sinusoidal'] = 16
-  current['Nonbonded interactions']   = 1176
+  current['Nonbonded | unspecified | interactions']   = 1176
   assert rc == current, check_diff(rc, current)
   print('OK')