Merge pull request #1746 from TactfulDeity/enh/additional_secondary_s…

…tructures ENH: Additional Secondary Structures
OpenChemistry · Oct 20, 2024 · 7468e5f · 7468e5f
2 parents f0d427e + ac970a9
commit 7468e5f
Show file tree

Hide file tree

Showing 2 changed files with 24 additions and 8 deletions.
diff --git a/avogadro/core/secondarystructure.cpp b/avogadro/core/secondarystructure.cpp
@@ -49,14 +49,26 @@ void SecondaryStructureAssigner::assign(Molecule* mol)
       // check to see how far apart the residues are
       int separation = std::abs(int(hBond->residue - hBond->residuePair));
 
-      // just alpha for now
-      if (separation == 4) {
-        m_molecule->residue(hBond->residue)
-          .setSecondaryStructure(Residue::SecondaryStructure::alphaHelix);
+      switch (separation) {
+        case 3: { // 3-10
+          m_molecule->residue(hBond->residue)
+            .setSecondaryStructure(Residue::SecondaryStructure::helix310);
+          break;
+        }
+        case 4: { // alpha
+          m_molecule->residue(hBond->residue)
+            .setSecondaryStructure(Residue::SecondaryStructure::alphaHelix);
+          break;
+        }
+        case 5: { // pi
+          m_molecule->residue(hBond->residue)
+            .setSecondaryStructure(Residue::SecondaryStructure::piHelix);
+          break;
+        }
+        default: {
+          break;
+        }
       }
-      // TODO
-      // 3-10 helix
-      // pi-helix
     }
   }
 

diff --git a/avogadro/rendering/cartoongeometry.cpp b/avogadro/rendering/cartoongeometry.cpp
@@ -102,6 +102,10 @@ CartoonType secondaryToCartoonType(Residue::SecondaryStructure sec)
       return Arrow;
     case Residue::SecondaryStructure::alphaHelix:
       return Tail;
+    case Residue::SecondaryStructure::helix310:
+      return Tail;
+    case Residue::SecondaryStructure::piHelix:
+      return Tail;
     default:
       return Body;
   }
@@ -132,4 +136,4 @@ void Cartoon::addPoint(const Vector3f& pos, const Vector3ub& color,
   BSplineGeometry::addPoint(pos, color, m_minRadius, group, id);
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::Rendering