Fix bug sometimes skipping peptide bond when using bio ccd to infer bonds.

src/chilife/MolSys.py

@@ -569,9 +569,14 @@ def write_cif(self, filename, use_bio_ccd: bool = True):
             else:
                 local_ccd[res.resname] = res_to_ccd(res)
 
+        # Keep the per-residue CCD view for polymer-link detection in struct_conn emission before
+        # join_ccd_info flattens it into the CIF table form.
+        per_res_ccd = local_ccd
         ccd_list = sorted(local_ccd.keys())
         local_ccd = chilife.io.join_ccd_info(ccd_list, local_ccd)
 
+        struct_conn_data = chilife.io.struct_conn_from_bonds(self, ccd_data=per_res_ccd)
+
         cif_data = {
             self.name: {
                 "entry": {"id": self.name},
@@ -659,6 +664,9 @@ def write_cif(self, filename, use_bio_ccd: bool = True):
             }
         }
 
+        if struct_conn_data is not None:
+            cif_data[self.name]["struct_conn"] = struct_conn_data
+
         # Delete empty entries
         del_list = []
         for k1, v1 in cif_data[self.name].items():
@@ -929,6 +937,14 @@ def __init__(
         self.elements = self.atypes
         self.bfactors = self.bs
 
+        # Map to atom index by chain, residue, insertion code, atom name, and altloc code.
+        self.crina = {
+            (str(c), str(r), str(i), str(n), str(a)): ii
+            for ii, (c, r, i, n, a) in enumerate(
+                zip(self.chains, self.resnums, self.icodes, self.names, self.altLocs)
+            )
+        }
+
         self._bonds = None
         self._bond_types = None
         self._bond_mask = np.array([], dtype=bool)
@@ -1135,6 +1151,14 @@ def from_cif(cls, file_name):
             name=name,
             use_ccd=ccd_data,
         )
+
+        # Parse inter-residue bonds from the _struct_conn loop (covale, disulf, metalc).
+        struct_conn = cif_data.get("struct_conn")
+        if struct_conn is not None:
+            sc_bonds, sc_types = chilife.io.parse_struct_conn_bonds(msys, struct_conn)
+            if len(sc_bonds) > 0:
+                msys.add_bonds(sc_bonds, bond_type=sc_types)
+
         msys._cif_data = cif_data
 
         return msys
@@ -2627,6 +2651,11 @@ def struct_to_cif_atom_site(struct):
     ).tolist()
     occupancy = np.tile(struct.occupancies.astype(str), n_frames).tolist()
     B_iso_or_equiv = np.tile(struct.bs.astype(str), n_frames).tolist()
+    formal_charge = np.tile(
+        [f"{charge:.0f}" if not np.isnan(charge) else "?" for charge in struct.charges],
+        n_frames,
+    ).tolist()
+
     auth_seq_id = np.tile(struct.resnums.astype(str), n_frames).tolist()
     auth_asym_id = np.tile(struct.chains, n_frames).tolist()
     pdbx_PDB_model_num = np.concatenate(
@@ -2651,11 +2680,12 @@ def struct_to_cif_atom_site(struct):
         "label_entity_id": label_entity_id,
         "label_seq_id": label_seq_id,
         "pdbx_PDB_ins_code": pdbx_PDB_ins_code,
-        "cartn_x": cartn_x,
-        "cartn_y": cartn_y,
-        "cartn_z": cartn_z,
+        "Cartn_x": cartn_x,
+        "Cartn_y": cartn_y,
+        "Cartn_z": cartn_z,
         "occupancy": occupancy,
         "B_iso_or_equiv": B_iso_or_equiv,
+        "pdbx_formal_charge": formal_charge,
         "auth_seq_id": auth_seq_id,
         "auth_asym_id": auth_asym_id,
         "pdbx_PDB_model_num": pdbx_PDB_model_num,

src/chilife/Topology.py

@@ -422,14 +422,21 @@ def bonds_from_ccd_data(molsys, ccd_data):
 
         if "chem_comp" in ccd_data[res.resname]:
             res_ccd_data = ccd_data[res.resname]["chem_comp"]
-            if (
-                pres := res.previous_residue()
-            ) is not None and "link type" in res_ccd_data:
-                link_type = res_ccd_data["link type"]
+            linkage_key = (
+                "type"
+                if "type" in res_ccd_data
+                else "link type"
+                if "link_type" in res_ccd_data
+                else None
+            )
+            if (pres := res.previous_residue()) is not None and linkage_key:
+                link_type = res_ccd_data["type"].lower()
                 if link_type in POLYMER_LINKAGE_TYPES:
                     a1, a2, btype, bchiral = POLYMER_LINKAGE_TYPES[link_type]
                     i1 = pres.ix[pres.names == a1].flat[0]
                     i2 = res.ix[res.names == a2].flat[0]
+                    if i1 == 0 and i2 == 1255:
+                        print("break")
                     bonds.append([i1, i2])
                     bond_types.append(btype)
                     bond_chiral.append(bchiral)
@@ -477,4 +484,8 @@ def numpyify_ccd(ccd_data):
 
 
 # Linkage data is atom name of the previous residue followed by atom name of the current residue followed by bond type
-POLYMER_LINKAGE_TYPES = {"L-peptide linking": ["C", "N", BondType.SINGLE, "N"]}
+POLYMER_LINKAGE_TYPES = {
+    "l-peptide linking": ["C", "N", BondType.SINGLE, "N"],
+    "peptide linking": ["C", "N", BondType.SINGLE, "N"],
+    "d-peptide linking": ["C", "N", BondType.SINGLE, "N"],
+}

src/chilife/__init__.py

@@ -44,4 +44,4 @@
 # SpinLabel = SpinLabel.SpinLabel
 # dSpinLabel = dSpinLabel.dSpinLabel
 
-__version__ = "1.2.1"
+__version__ = "1.2.2"