An idiotical tail-counter function covering currently only "sn-*" tails.

Author: comcon1

src/fairmd/lipids/auxiliary/mollib.py

@@ -14,6 +14,7 @@
 
 from fairmd.lipids import FMDL_DATA_PATH
 from fairmd.lipids.core import System
+from fairmd.lipids.molecules import Lipid
 
 
 def uname2element(mapping_name: str) -> str:
@@ -95,3 +96,18 @@ def guess_elements(system: System, u: mda.Universe) -> None:
             selection.atoms.elements = selection.n_atoms * [elname]
         # end mapping loop
     # end molecules loop
+
+
+def get_tails_of_lipid(lipid: Lipid) -> list[str]:
+    """Get the tails of a lipid molecule.
+
+    :param lipid: Lipid molecule
+    :return: List of tails (str-s)
+    """
+    tails = []
+    for props in lipid.mapping_dict.values():
+        if "FRAGMENT" in props and props["FRAGMENT"].startswith("sn-"):
+            tail_id = props["FRAGMENT"]
+            if tail_id not in tails:
+                tails.append(tail_id)
+    return tails

tests/test_misc.py

@@ -192,3 +192,26 @@ def temporary_dir():
         check.is_not_in("Dielectric", line)
         check.is_not_in("ChargeDensity", line)
         check.equal(rcode, RCODE_ERROR)
+
+
+def test_get_tails():
+    """Test Lipid.get_tails function."""
+    from fairmd.lipids.molecules import Lipid
+    from fairmd.lipids.auxiliary.mollib import get_tails_of_lipid
+
+    lipid = Lipid(name="DPPC")
+    lipid.register_mapping("mappingDPPCberger.yaml")
+
+    tails = get_tails_of_lipid(lipid)
+    check.is_instance(tails, list)
+    check.equal(len(tails), 2)
+    check.is_in("sn-1", tails)
+    check.is_in("sn-2", tails)
+
+    lipid = Lipid(name="TOCL")
+    lipid.register_mapping("mappingTOCLcharmm.yaml")
+
+    tails = get_tails_of_lipid(lipid)
+    check.equal(len(tails), 4)
+    check.is_in("sn-1 1", tails)
+    check.is_in("sn-2 1", tails)