#8363 – Preserve tail bond length after Arrange as a Ring

api/tests/integration/ref/layout/arrange_ring_tail_length.py.out

@@ -0,0 +1,2 @@
+*** Arrange ring tail length ***
+arrange_ring_tail_length:SUCCEED

api/tests/integration/tests/layout/arrange_ring_tail_length.py

@@ -0,0 +1,51 @@
+import math
+import os
+import sys
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+
+from env_indigo import *  # noqa
+
+indigo = Indigo()
+
+print("*** Arrange ring tail length ***")
+
+library = indigo.loadMonomerLibraryFromFile(
+    dataPath("molecules/basic/monomer_library.ket")
+)
+helm = (
+    "PEPTIDE1{C.C.C.C.C.C.C.C.C.C.C.C.C}$"
+    + "PEPTIDE1,PEPTIDE1,5:R3-8:R3$$$V2.0"
+)
+ket_doc = indigo.loadHelm(helm, library)
+mol = indigo.loadMolecule(ket_doc.json())
+
+for atom in mol.iterateAtoms():
+    if atom.index() >= 4:
+        atom._lib().indigoSelect(atom.id)
+
+mol.layout()
+
+expected = 1.5
+tolerance = 0.05
+tail_pairs = [(7, 8), (8, 9), (9, 10), (10, 11), (11, 12)]
+
+ok = True
+for start_idx, end_idx in tail_pairs:
+    start_atom = mol.getAtom(start_idx)
+    end_atom = mol.getAtom(end_idx)
+    sx, sy, _ = start_atom.xyz()
+    ex, ey, _ = end_atom.xyz()
+    dist = math.sqrt((sx - ex) ** 2 + (sy - ey) ** 2)
+    if abs(dist - expected) > tolerance:
+        ok = False
+        break
+
+if ok:
+    print("arrange_ring_tail_length:SUCCEED")
+else:
+    print("arrange_ring_tail_length:FAILED")

core/indigo-core/layout/src/molecule_layout_graph_assign.cpp

@@ -1252,7 +1252,14 @@ void MoleculeLayoutGraph::_assignFinalCoordinates(float bond_length, const Array
                 }
             }
 
-            _reflectCycleVertices(inner_cycle_vertices, bond_length);
+            if (!sel_vertices.empty())
+            {
+                for (auto vx_idx : sel_vertices)
+                    _layout_vertices[vx_idx].pos.scale(bond_length);
+                selected_centroid.scale(bond_length);
+            }
+
+            _reflectCycleVertices(inner_cycle_vertices, 1.0f);
 
             if (!sel_vertices.empty())
             {