From 8dcbef29c50fadc3f16aeb2357db995aa1a3458b Mon Sep 17 00:00:00 2001
From: clami66 <claudio.mirabello@scilifelab.se>
Date: Mon, 25 Mar 2024 14:17:24 +0100
Subject: [PATCH] NA backbone atoms

---
 run_test.sh        |  4 ++--
 src/DockQ/DockQ.py | 12 +++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/run_test.sh b/run_test.sh
index 78cdf6c..6c59803 100644
--- a/run_test.sh
+++ b/run_test.sh
@@ -9,10 +9,10 @@ else
     binary="DockQ"
 fi
 
-$binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
-diff test testdata/1A2K.dockq
 $binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
 diff test testdata/1A2K.dockq
+$binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+diff test testdata/1A2K.dockq
 
 # Multiple interfaces
 $binary examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short > test
diff --git a/src/DockQ/DockQ.py b/src/DockQ/DockQ.py
index 5fc49dc..c005952 100755
--- a/src/DockQ/DockQ.py
+++ b/src/DockQ/DockQ.py
@@ -165,7 +165,10 @@ def calc_DockQ(
     capri_peptide=False,
     low_memory=False,
 ):
-    atom_for_sup = ("CA", "C", "N", "O", "P")
+    atom_for_sup = ("CA", "C", "N", "O", 
+                    "P", "OP1", "OP2", 
+                    "O2'", "O3'", "O4'", "O5'", 
+                    "C1'",  "C2'",  "C3'", "C4'", "C5'")
     fnat_threshold = 4.0 if capri_peptide else 5.0
     interface_threshold = 8.0 if capri_peptide else 10.0
     clash_threshold = 2.0
@@ -304,7 +307,7 @@ def dockq_formula(fnat, irms, Lrms):
 
 
 @lru_cache
-def align_chains(model_chain, native_chain, use_numbering=False, verbose=False):
+def align_chains(model_chain, native_chain, use_numbering=False):
     """
     Function to align two PDB structures. This can be done by sequence (default) or by
     numbering. If the numbering is used, then each residue number from the pdb structure
@@ -588,7 +591,7 @@ def group_chains(
     chain_clusters = {chain: [] for chain in ref_chains}
 
     for query_chain, ref_chain in alignment_targets:
-        aln = align_chains(query_structure[query_chain], ref_structure[ref_chain])
+        aln = align_chains(query_structure[query_chain], ref_structure[ref_chain], use_numbering=False)
         alignment = format_alignment(aln)
         n_mismatches = alignment["matches"].count(".")
 
@@ -645,13 +648,12 @@ def format_mapping_string(chain_mapping):
     chain1 = ""
     chain2 = ""
 
-    # mapping = sorted([(b, a) for a, b in chain_mapping.items()])
     # Sorting might change LRMSD since the definition of receptor/ligand for equal length depends on order
     mapping = [(b, a) for a, b in chain_mapping.items()]
     for (
         model_chain,
         native_chain,
-    ) in mapping:  # sorted([(b,a) for a,b in chain_mapping.items()]):
+    ) in mapping:
         chain1 += model_chain
         chain2 += native_chain