respect no_altloc in more places

Bio/PDB/internal_coords.py

@@ -555,6 +555,7 @@ def setAtomVw(res, atm):
 
         def setResAtmVws(res):
             for atm in res.get_atoms():
+                # copy not filter so ignore no_altloc
                 if atm.is_disordered():
                     for altAtom in atm.child_dict.values():
                         setAtomVw(res, altAtom)
@@ -641,7 +642,15 @@ def _peptide_check(self, prev: "Residue", curr: "Residue") -> Optional[str]:
         if pNatom is None or pCAatom is None:
             return "previous residue missing N or Ca"
 
-        if not Natom.is_disordered() and not pCatom.is_disordered():
+        if IC_Residue.no_altloc:
+            if Natom.is_disordered():
+                Natom = Natom.selected_child
+            if pCatom.is_disordered():
+                pCatom = pCatom.selected_child
+
+        if IC_Residue.no_altloc or (
+            not Natom.is_disordered() and not pCatom.is_disordered()
+        ):
             dc = self._atm_dist_chk(
                 Natom, pCatom, IC_Chain.MaxPeptideBond, self.sqMaxPeptideBond
             )
@@ -747,7 +756,7 @@ def _set_residues(self, verbose: bool = False) -> None:
             # select only not hetero or accepted hetero
             if res.id[0] == " " or res.id[0] in IC_Residue.accept_resnames:
                 this_res: List["IC_Residue"] = []
-                if 2 == res.is_disordered():
+                if 2 == res.is_disordered() and not IC_Residue.no_altloc:
                     # print('disordered res:', res.is_disordered(), res)
                     for r in res.child_dict.values():
                         if self._add_residue(r, last_res, last_ord_res, verbose):
@@ -807,8 +816,11 @@ def setAtom(res, atm):
         def setResAtms(res):
             for atm in res.get_atoms():
                 if atm.is_disordered():
-                    for altAtom in atm.child_dict.values():
-                        setAtom(res, altAtom)
+                    if IC_Residue.no_altloc:
+                        setAtom(res, atm.selected_child)
+                    else:
+                        for altAtom in atm.child_dict.values():
+                            setAtom(res, altAtom)
                 else:
                     setAtom(res, atm)
 
@@ -1018,9 +1030,12 @@ def _hedraDict2chain(
             initNCaC = []
             for atm in ric.residue.get_atoms():  # n.b. only few PIC spec atoms
                 if 2 == atm.is_disordered():
-                    for altAtom in atm.child_dict.values():
-                        if altAtom.coord is not None:
-                            initNCaC.append(AtomKey(ric, altAtom))
+                    if IC_Residue.no_altloc:
+                        initNCaC.append(AtomKey(ric, atm.selected_child))
+                    else:
+                        for altAtom in atm.child_dict.values():
+                            if altAtom.coord is not None:
+                                initNCaC.append(AtomKey(ric, altAtom))
                 elif atm.coord is not None:
                     initNCaC.append(AtomKey(ric, atm))
             if initNCaC != []:
@@ -3263,6 +3278,8 @@ def _pdb_atom_string(atm: Atom, cif_extend: bool = False) -> str:
             override atom chain id if not None
         """
         if 2 == atm.is_disordered():
+            if IC_Residue.no_altloc:
+                return IC_Residue._pdb_atom_string(atm.selected_child, cif_extend)
             s = ""
             for a in atm.child_dict.values():
                 s += IC_Residue._pdb_atom_string(a, cif_extend)
@@ -3511,7 +3528,7 @@ def _write_PIC(
             col = 0
             for a in sorted(self.residue.get_atoms()):
                 if 2 == a.is_disordered():
-                    if self.alt_ids is None:
+                    if IC_Residue.no_altloc or self.alt_ids is None:
                         s, col = self._write_pic_bfac(a.selected_child, s, col)
                     else:
                         for atm in a.child_dict.values():

Tests/test_PDB_internal_coords.py

@@ -53,6 +53,7 @@ class Rebuild(unittest.TestCase):
     pdb_2XHE2 = PDB_parser.get_structure("2XHE", "PDB/2XHE.pdb")
     pdb_1A8O = PDB_parser.get_structure("1A8O", "PDB/1A8O.pdb")
     cif_3JQH = CIF_parser.get_structure("3JQH", "PDB/3JQH.cif")
+    cif_3JQH2 = CIF_parser.get_structure("3JQH", "PDB/3JQH.cif")
     cif_4CUP = CIF_parser.get_structure("4CUP", "PDB/4CUP.cif")
     cif_4CUP2 = CIF_parser.get_structure("4CUP", "PDB/4CUP.cif")
     cif_4ZHL = CIF_parser.get_structure("4ZHL", "PDB/4ZHL.cif")
@@ -105,6 +106,7 @@ def test_rebuild_disordered_atoms_residues(self):
         """Convert disordered protein to internal coordinates and back."""
         # 3jqh has both disordered residues
         # and disordered atoms in ordered residues
+
         with warnings.catch_warnings(record=True):
             warnings.simplefilter("always", PDBConstructionWarning)
             r = structure_rebuild_test(self.cif_3JQH, False)
@@ -118,6 +120,14 @@ def test_rebuild_disordered_atoms_residues(self):
         self.assertEqual(len(r["chains"]), 1)
         self.assertTrue(r["pass"])
 
+        IC_Residue.no_altloc = True
+        with warnings.catch_warnings(record=True):
+            warnings.simplefilter("always", PDBConstructionWarning)
+            r = structure_rebuild_test(self.cif_3JQH2, verbose=False, quick=True)
+        self.assertEqual(r["aCoordMatchCount"], 167, msg="no_altloc fail")
+        self.assertTrue(r["pass"], msg="no_altloc fail")
+        IC_Residue.no_altloc = False
+
     def test_no_crosstalk(self):
         """Deep copy, change few internal coords, test nothing else changes."""
         # IC_Chain.ParallelAssembleResidues = False