coordinates retriever for fragment mover

src/idpconfgen/cli_complex.py

@@ -89,6 +89,7 @@
     electropotential_matrix,
     extract_interpairs_from_db,
     extract_intrapairs_from_db,
+    find_ca_coords_fld,
     get_contact_distances,
     process_custom_contacts,
     select_contacts,
@@ -949,13 +950,7 @@ def main(
                         selected_contacts["Y"][contact_type[0]][case].append(y_coords)  # noqa: E501
                         contacts_counter -= len(x_coords)
         log.info(S('done'))
-
-    # TODO extracting distance distributions from database
-    # For custom-contacts we would need to rescan the database for
-    # residue pairs
-    # - Make a d_mtx for every custom contact and align it with
-    #   `cus_inter_res` and `cus_intra_res`
-
+
     # NOTE work with generalizable inter- for IDP-Folded and IDP-IDP before
     # algorithm for intramolecular contacts
     for conf in range(nconfs):
@@ -1079,6 +1074,17 @@ def main(
                     imap = pool.imap(execute, range(1))
                     for _ in imap:
                         pass
+            log.info(S("done"))
+
+            # Move IDP fragments to the desired distance and location
+            fld_contact_coords = []
+            fld_struc = Structure(Path(folded_structure))
+            fld_struc.build()
+            fld_data = fld_struc.data_array
+            for res in res_combos:
+                # First element in res contains our residues of interest
+                coords = find_ca_coords_fld(fld_data, res[0])
+                fld_contact_coords.append(coords)
 
 
 def populate_globals(

src/idpconfgen/libs/libcomplex.py

@@ -12,6 +12,7 @@
     get_substring_characters,
     has_consecutive_match,
     )
+from idpconfgen.libs.libstructure import col_name, col_resSeq, cols_coords
 
 
 contact_type = ["intra", "inter"]
@@ -830,3 +831,33 @@ def get_contact_distances(
         residues = (sub_seq1, sub_seq2)
 
     return distances, residues
+
+
+def find_ca_coords_fld(fld_struc, residues):
+    """
+    Locates CA coordinates in a structure based on residues.
+
+    Parameters
+    ----------
+    fld_struc : np.ndarray
+        data_array property of libstructure.Structure.
+    
+    residues : list or tuple
+        Series of residue numbers for the CA residues of interest.
+    
+    Returns
+    -------
+    coords : list of array
+        [x, y, z] coordinates for each residue's CA.
+    """
+    fld_res = fld_struc[:, col_resSeq].astype(int)
+    fld_coords = fld_struc[:, cols_coords]
+    fld_atom_names = fld_struc[:, col_name]
+    coords = []
+    for r in residues:
+        for i, fr in enumerate(fld_res):
+            atom = fld_atom_names[i]
+            if r == fr and atom == "CA":
+                coords.append(fld_coords[i])
+
+    return coords