From 2ce3ebb232ce6c2fd4bcf4771bcd7bf2494c4a97 Mon Sep 17 00:00:00 2001
From: "Nigel W. Moriarty" <nwmoriarty@lbl.gov>
Date: Thu, 18 Sep 2025 10:28:19 -0700
Subject: [PATCH] start of ION select

---
 iotbx/pdb/atom_selection.py            | 18 ++++++++++++
 mmtbx/monomer_library/linking_setup.py | 39 ++++++++++++++++++++++++++
 2 files changed, 57 insertions(+)

diff --git a/iotbx/pdb/atom_selection.py b/iotbx/pdb/atom_selection.py
index 653aebbfd14..790833ea639 100644
--- a/iotbx/pdb/atom_selection.py
+++ b/iotbx/pdb/atom_selection.py
@@ -192,6 +192,7 @@ class cache(slots_getstate_setstate):
     "nucleotide",
     "single_atom_residue",
     "water",
+    'ion',
     "hetero",
     "backbone",
     "sidechain",
@@ -207,6 +208,7 @@ def __init__(self, root, wildcard_escape_char='\\',
     self.protein = None
     self.nucleotide = None
     self.water = None
+    self.ion = None
     self.hetero = None
     self.backbone = None
     self.sidechain = None
@@ -340,6 +342,17 @@ def get_water(self):
       self.water = (atoms.extract_tmp_as_size_t() == 1).iselection()
     return [self.water]
 
+  def get_ion(self):
+    from mmtbx.monomer_library.linking_setup import ad_hoc_single_metal_residue_element_types
+    if self.ion is None:
+      atoms = self.root.atoms()
+      atoms.set_chemical_element_simple_if_necessary()
+      for atom in atoms:
+        if atom.element.upper() in ad_hoc_single_metal_residue_element_types:
+          atom.tmp=1
+      self.ion = (atoms.extract_tmp_as_size_t() == 1).iselection()
+    return [self.ion]
+
   def get_protein(self):
     if self.protein is None:
       import iotbx.pdb
@@ -524,6 +537,9 @@ def sel_nucleotide(self):
   def sel_water(self):
     return self.union(iselections=self.get_water())
 
+  def sel_ion(self):
+    return self.union(iselections=self.get_ion())
+
   def sel_hetero(self):
     return self.union(iselections=self.get_hetero())
 
@@ -711,6 +727,8 @@ def try_compose_sequence():
           result_stack.append(self.sel_single_atom_residue())
         elif (lword == "water"):
           result_stack.append(self.sel_water())
+        elif (lword == "ion"):
+          result_stack.append(self.sel_ion())
         elif (lword == "hetero") or (lword == "hetatm"):
           result_stack.append(self.sel_hetero())
         elif (lword == "bfactor") or (lword == "occupancy"):
diff --git a/mmtbx/monomer_library/linking_setup.py b/mmtbx/monomer_library/linking_setup.py
index 2fc0aa0845c..cba981714f2 100644
--- a/mmtbx/monomer_library/linking_setup.py
+++ b/mmtbx/monomer_library/linking_setup.py
@@ -1,6 +1,25 @@
 # see iotbx/pdb/common_residue_names.h; additionally here only: U I
 from __future__ import absolute_import, division, print_function
 
+ad_hoc_single_metal_residue_element_types_more_complete = """\
+LI BE
+NA MG
+AL
+K  CA
+SC TI V  CR MN FE CO NI CU ZN
+GA GE AS SE
+RB SR
+Y  ZR NB MO TC RU RH PD AG CD
+IN SN SB TE I
+CS BA
+LA HF TA W  RE OS IR PT AU HG
+TL PB BI PO AT
+FR RA
+AC
+CE PR ND PM SM EU GD TB DY HO ER TM YB LU
+TB PA U  NP PU AM CM BK CF ES FM MD NO LW
+""".split()
+
 ad_hoc_single_metal_residue_element_types = """\
 ZN CA MG NA MN K FE CU CD HG NI CO SR CS PT BA TL PB SM AU RB YB LI
 MO LU CR OS GD TB LA AG HO GA CE W RU RE PR IR EU AL V PD U
@@ -148,5 +167,25 @@ def skip_if_non_linking(lookup, atom1, atom2):
     assert 0
 
 if __name__=="__main__":
+  from libtbx import easy_run
   print(skip_if_both)
   print(skip_if_longer)
+  from mmtbx.monomer_library.pdb_interpretation import ad_hoc_single_atom_residue_element_types
+  s1 = set(ad_hoc_single_metal_residue_element_types_more_complete)
+  s1 = set(ad_hoc_single_atom_residue_element_types)
+  s2 = set(ad_hoc_single_metal_residue_element_types)
+  print(s1)
+  print(s2)
+  print('-'*80)
+  print(s1.difference(s2))
+  print('-'*80)
+  print(s2.difference(s1))
+  print('-'*80)
+  # for e in ad_hoc_single_metal_residue_element_types_more_complete:
+  #   cmd='mmtbx.where_is_that_cif_file %s source=ccd' % e
+  #   print(cmd)
+  #   rc=easy_run.go(cmd)
+  #   print(dir(rc))
+  #   for line in rc.stdout_lines:
+  #     print(line)
+  #   # assert 0