From 8dde16f14f9f38e0f25e3edf13837066d6de5457 Mon Sep 17 00:00:00 2001
From: csbrasnett <c.s.brasnett@rug.nl>
Date: Mon, 10 Jun 2024 17:48:57 +0200
Subject: [PATCH] fix error raising for mod not found

need to reset extra for every resspec, otherwise 'success': False gets appended for every non-find and True is never added.
---
 vermouth/processors/annotate_mut_mod.py |  3 +--
 vermouth/tests/test_annotate_mut_mod.py | 35 +++++++++++++++++--------
 2 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/vermouth/processors/annotate_mut_mod.py b/vermouth/processors/annotate_mut_mod.py
index 8994d56c9..d8763f824 100644
--- a/vermouth/processors/annotate_mut_mod.py
+++ b/vermouth/processors/annotate_mut_mod.py
@@ -252,10 +252,9 @@ def annotate_modifications(molecule, modifications, mutations, resspec_counts):
     # Get the name of the chain in the molecule that we're looking at
     residue = {key: residue_graph.nodes[0].get(key)
                for key in 'chain resid resname insertion_code'.split()}
-    chain = residue['chain']
-    extra = False
     for mutmod, key, library in associations:
         for resspec, mod in mutmod:
+            extra = False
             mod_found = _resiter(mod, residue_graph, resspec, library, key, molecule)
             if not mod_found:
                 #if no mod found, return that there's a problem
diff --git a/vermouth/tests/test_annotate_mut_mod.py b/vermouth/tests/test_annotate_mut_mod.py
index 2b37f575a..79ed77e82 100644
--- a/vermouth/tests/test_annotate_mut_mod.py
+++ b/vermouth/tests/test_annotate_mut_mod.py
@@ -304,7 +304,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
     assert found == expected
 
 @pytest.mark.parametrize('node_data, edge_data, mutation, expected', [
-    (
+    (# test 0
         [
             {'chain': 'A', 'resname': 'GLY', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -314,7 +314,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'GLY', 'resid': 1, 'chain': 'A'}, 'MET')],
         False
     ),
-    (
+    (# test 1
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -324,7 +324,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'GLY', 'resid': 1, 'chain': 'A'}, 'MET')],
         True
     ),
-    (
+    (# test 2
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -334,7 +334,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'GLY', 'resid': 1}, 'MET')],
         True
     ),
-    (
+    (# test 3
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -344,7 +344,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'ALA', 'resid': 1}, 'MET')],
         False
     ),
-    (
+    (# test 4
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -357,7 +357,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'ALA', 'chain': 'A'}, 'GLY')],
         False
     ),
-    (
+    (# test 5
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -370,7 +370,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'GLY', 'resid': 1}, 'ALA')],
         True
     ),
-    (
+    (# test 6
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -383,7 +383,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'GLY', 'resid': 1, 'chain': 'A'}, 'ALA')],
         True
     ),
-    (
+    (# test 7
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -396,7 +396,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'ALA', 'resid': 1}, 'GLY')],
         False
     ),
-    (
+    (# test 8
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -409,7 +409,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resname': 'GLY', 'chain': 'A'}, 'ALA')],
         True
     ),
-    (
+    (# test 9
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -422,7 +422,7 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [({'resid': 1, 'resname': 'ASN'}, 'ALA')],
         False
     ),
-        (
+    (# test 10
         [
             {'chain': 'A', 'resname': 'ALA', 'resid': 1},
             {'chain': 'A', 'resname': 'ALA', 'resid': 2},
@@ -434,6 +434,19 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
         [(0, 1), (1, 2), (3, 4), (4, 5)],
         [({'chain':'B', 'resname': 'ASN'}, 'ALA')],
         False
+    ),
+    (  # test 11
+            [
+                {'chain': 'A', 'resname': 'GLY', 'resid': 1},
+                {'chain': 'A', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'A', 'resname': 'SER', 'resid': 3},
+                {'chain': 'B', 'resname': 'GLY', 'resid': 1},
+                {'chain': 'B', 'resname': 'ALA', 'resid': 2},
+                {'chain': 'B', 'resname': 'SER', 'resid': 3}
+            ],
+            [(0, 1), (1, 2), (3, 4), (4, 5)],
+            [({'chain': 'A', 'resname': 'ALA', 'resid': 2}, 'GLY')],
+            False
     )
 ])
 def test_mod_resid_not_correct(caplog, node_data, edge_data, mutation, expected):