buggy write_pdb in network/predict_complex.py

[zsalvet]

predict_complex.py crashes in write_pdb routine due to incorrect handling of -Ls
option (tries to output gaps to PDB and miscalculated positions of residues behind the first gap).
This patch fixes it:

--- RoseTTAFold/network/predict_complex.py.orig 2025-08-22 16:33:14.284501138 +0200
+++ RoseTTAFold_full/RoseTTAFold/network/predict_complex.py    2025-08-22 16:40:44.152420040 +0200
@@ -260,11 +263,13 @@
                     resNo = i+1
                     chain = "A"
                     for i_chain in range(len(Ls)-1,0,-1):
-                        tot_res = sum(Ls[:i_chain])
+                        tot_res = sum(Ls[:i_chain])  + i_chain -1
                         if i+1 > tot_res:
                             chain = chainIDs[i_chain]
-                            resNo = i+1 - tot_res
+                            resNo = i - tot_res
                             break
+                    if i+1 == tot_res+1 :
+                        continue
                     f.write ("%-6s%5s %4s %3s %s%4d    %8.3f%8.3f%8.3f%6.2f%6.2f\n"%(
                             "ATOM", ctr, " CA ", util.num2aa[s],
                              chain, resNo, atoms[i,0], atoms[i,1], atoms[i,2],
@@ -275,11 +280,13 @@
                     resNo = i+1
                     chain = "A"
                     for i_chain in range(len(Ls)-1,0,-1):
-                        tot_res = sum(Ls[:i_chain])
-                        if i+1 > tot_res:
+                        tot_res = sum(Ls[:i_chain]) + i_chain -1
+                        if i+1 > tot_res :
                             chain = chainIDs[i_chain]
-                            resNo = i+1 - tot_res
+                            resNo = i - tot_res
                             break
+                    if i+1 == tot_res+1 :
+                        continue
                     for j,atm_j in enumerate((" N  "," CA "," C  ")):
                         f.write ("%-6s%5s %4s %3s %s%4d    %8.3f%8.3f%8.3f%6.2f%6.2f\n"%(
                                 "ATOM", ctr, atm_j, util.num2aa[s],