From 4c2a379d97a73a1d61962ceb5d10fd4ce2b93062 Mon Sep 17 00:00:00 2001
From: clami66 <claudio.mirabello@scilifelab.se>
Date: Mon, 25 Mar 2024 10:33:47 +0100
Subject: [PATCH] fix src

---
 run_test.sh        |  4 ++--
 src/DockQ/DockQ.py | 18 ------------------
 2 files changed, 2 insertions(+), 20 deletions(-)

diff --git a/run_test.sh b/run_test.sh
index 33faaf6..a30f6ea 100644
--- a/run_test.sh
+++ b/run_test.sh
@@ -3,9 +3,9 @@ set -euo pipefail
 
 # Test that cython version behaves the same as nocython
 coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
-coverage run -a --source=src/ src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
+coverage run -a src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb
 coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
-coverage run -a --source=src/ src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
+coverage run -a src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align
 # Multiple interfaces
 coverage run -a --source='DockQ.DockQ' -m DockQ.DockQ examples/dimer_dimer.model.pdb examples/dimer_dimer.pdb  --short
 # Test on structures with slightly different sequences
diff --git a/src/DockQ/DockQ.py b/src/DockQ/DockQ.py
index de73b9c..a180061 100755
--- a/src/DockQ/DockQ.py
+++ b/src/DockQ/DockQ.py
@@ -52,7 +52,6 @@ def parse_args():
     parser.add_argument(
         "--verbose", "-v", default=False, action="store_true", help="talk a lot!"
     )
-
     parser.add_argument(
         "--use_CA",
         "-ca",
@@ -73,14 +72,6 @@ def parse_args():
         metavar="n_cpu",
         help="Number of cores to use",
     )
-    parser.add_argument(
-        "--chunk_size",
-        default=64,
-        type=int,
-        metavar="chunk_size",
-        help="Size of chunks given to the cores",
-    )
-
     parser.add_argument(
         "--optDockQF1",
         default=False,
@@ -112,15 +103,6 @@ def parse_args():
     return parser.parse_args()
 
 
-def open_file(filename):
-    if filename.endswith(".gz"):
-        with gzip.open(filename) as f:
-            yield f
-    else:
-        with open(filename) as f:
-            yield f
-
-
 @lru_cache
 def get_aligned_residues(chainA, chainB, alignment):
     aligned_resA = []