From 59c9827eaca359d2639af6707c4cfcc3cd76ba57 Mon Sep 17 00:00:00 2001
From: csbrasnett <c.s.brasnett@rug.nl>
Date: Wed, 9 Oct 2024 18:10:47 +0200
Subject: [PATCH] added test for file coming from itp

---
 polyply/src/apply_modifications.py        |  2 +-
 polyply/tests/test_apply_modifications.py | 31 +++++++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/polyply/src/apply_modifications.py b/polyply/src/apply_modifications.py
index 50184a09..84d39ca5 100644
--- a/polyply/src/apply_modifications.py
+++ b/polyply/src/apply_modifications.py
@@ -75,7 +75,7 @@ def apply_mod(meta_molecule, modifications):
 
         target_residue = meta_molecule.nodes[target_resid - 1]
         # takes care to skip all residues that come from an itp file
-        if not target_residue.get('from_itp', 'False'):
+        if target_residue.get('from_itp'):
             LOGGER.info("meta_molecule has come from itp. Will not attempt to modify.")
             continue
         # checks that the resname is a protein resname as defined above
diff --git a/polyply/tests/test_apply_modifications.py b/polyply/tests/test_apply_modifications.py
index 694ebdfa..1a54069e 100644
--- a/polyply/tests/test_apply_modifications.py
+++ b/polyply/tests/test_apply_modifications.py
@@ -26,6 +26,7 @@
 import polyply.src.ff_parser_sub
 import networkx as nx
 from vermouth.molecule import Interaction
+from polyply.src.meta_molecule import MetaMolecule
 
 
 @pytest.mark.parametrize('input_mods, expected',(
@@ -142,6 +143,36 @@ def test_apply_mod(input_itp, molname, expected, caplog, text):
                                                        meta=interaction.meta)
                             assert _interaction in meta_mol.molecule.interactions[interaction_type]
 
+def test_from_itp(caplog):
+
+    caplog.set_level(logging.INFO)
+    #make the meta molecule from the itp and ff files
+    file_name = TEST_DATA / "itp" / "ALA5.itp"
+
+    ff = vermouth.forcefield.ForceField(name='martini3')
+
+    ff_lines = []
+    for file in ['aminoacids.ff', 'modifications.ff']:
+        with open(TEST_DATA/ "ff" / file) as f:
+            ff_lines += f.readlines()
+    polyply.src.ff_parser_sub.read_ff(ff_lines, ff)
+
+    meta_mol = MetaMolecule.from_itp(ff, file_name, "pALA")
+
+    for node in meta_mol.nodes:
+        meta_mol.nodes[node]['from_itp'] = 'True'
+
+    termini = _patch_protein_termini(meta_mol)
+    apply_mod(meta_mol, termini)
+
+    expected_msg = "meta_molecule has come from itp. Will not attempt to modify."
+    for record in caplog.records:
+        if record.message == expected_msg:
+            assert True
+            break
+        else:
+            continue
+
 @pytest.mark.parametrize('modifications, expected, text',
      (
              (