halogen-bond detection and display (PYMOL-3466)

schrodinger · Jan 30, 2024 · ce1fb16 · ce1fb16
1 parent 9c82294
commit ce1fb16
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Showing 11 changed files with 1,948 additions and 18 deletions.
diff --git a/data/setting_help.csv b/data/setting_help.csv
diff --git a/layer1/SettingInfo.h b/layer1/SettingInfo.h
@@ -896,7 +896,12 @@ enum {
   REC_i( 786, cartoon_smooth_cylinder_window          , global    , 2 ),
   REC_i( 787, isosurface_algorithm                    , global    , 0, 0, 2 ),
   REC_b( 788, cell_centered                           , global    , false ),
-
+  REC_f( 789, halogen_bond_distance                       , global    , 3.5f ),
+  REC_f( 790, halogen_bond_as_donor_min_donor_angle       , global    , 140.0f ),
+  REC_f( 791, halogen_bond_as_donor_min_acceptor_angle    , global    , 90.0f ),
+  REC_f( 792, halogen_bond_as_acceptor_min_donor_angle    , global    , 120.0f ),
+  REC_f( 793, halogen_bond_as_acceptor_min_acceptor_angle , global    , 90.0f ),
+  REC_f( 794, halogen_bond_as_acceptor_max_acceptor_angle , global    , 170.0f ),
 
 #ifdef SETTINGINFO_IMPLEMENTATION
 #undef SETTINGINFO_IMPLEMENTATION

diff --git a/layer2/ObjectDist.cpp b/layer2/ObjectDist.cpp
@@ -33,6 +33,7 @@ Z* -------------------------------------------------------------------
 #include"Feedback.h"
 #include"DistSet.h"
 #include"ListMacros.h"
+#include "Interactions.h"
 #ifdef _PYMOL_INCENTIVE
 #endif
 
@@ -449,6 +450,9 @@ ObjectDist *ObjectDistNewFromSele(PyMOLGlobals * G, ObjectDist * oldObj,
           ENDFB(G);
         I->DSet[a] = nullptr;
 #endif
+      } else if (mode == 9) { // 9: halogen-bond interaction
+        I->DSet[a].reset(pymol::FindHalogenBondInteractions(G,
+            I->DSet[a].release(), sele1, state1, sele2, state2, cutoff, &dist));
       } else {
         I->DSet[a].reset(SelectorGetDistSet(
             G, I->DSet[a].release(), sele1, state1, sele2, state2, mode, cutoff, &dist));

diff --git a/layer2/ObjectMolecule.cpp b/layer2/ObjectMolecule.cpp
@@ -846,6 +846,33 @@ void ObjectMoleculeOpRecInit(ObjectMoleculeOpRec * op)
   UtilZeroMem((char *) op, sizeof(ObjectMoleculeOpRec));
 }
 
+bool ObjectMoleculeGetNeighborVector(
+    ObjectMolecule* I, int atom, int state, float* v_result)
+{
+  float v_atom[3] = {0.0, 0.0, 0.0};
+
+  auto const* cs = I->getCoordSet(state);
+  if (cs == nullptr) {
+    return false;
+  }
+
+  if (!CoordSetGetAtomVertex(cs, atom, v_atom)) {
+    return false;
+  }
+
+  for (auto const& neighbor : AtomNeighbors(I, atom)) {
+    auto const a2 = neighbor.atm;
+
+    // ignore hydrogens
+    if (I->AtomInfo[a2].protons != cAN_H &&
+        CoordSetGetAtomVertex(cs, a2, v_result)) {
+      return true;
+    }
+  }
+
+  return false;
+}
+
 /**
  * Returns the most proton-rich element with the lowest priority value (OG1
  * before OG2, CG, HB1)

diff --git a/layer2/ObjectMolecule.h b/layer2/ObjectMolecule.h
@@ -267,6 +267,20 @@ typedef struct {
 void ObjMolPairwiseInit(ObjMolPairwise * pairwise);
 void ObjMolPairwisePurge(ObjMolPairwise * pairwise);
 
+/**
+ * Get neighbor vector
+ *
+ * @param I - ObjectMolecule
+ * @param atom - atom index
+ * @param state - state index
+ * @param v_result - vector result
+ *
+ * @return true if there is a neighbor
+ * @return false if there is no neighbor
+ */
+bool ObjectMoleculeGetNeighborVector(
+    ObjectMolecule* I, int atom, int state, float* v_result);
+
 int ObjectMoleculeGetTopNeighbor(PyMOLGlobals * G,
                                  ObjectMolecule * I, int start, int excluded);
 

diff --git a/layer3/Executive.cpp b/layer3/Executive.cpp
@@ -9538,6 +9538,9 @@ pymol::Result<float> ExecutiveDistance(PyMOLGlobals* G, const char* nam,
     case 8: // "clashes"
       SettingSet(cSetting_dash_color, "0xff8800" /* light red */, obj);
       break;
+    case 9: // "halogen-bonds"
+      SettingSet(cSetting_dash_color, "0xff00ff" /* magenta */, obj);
+      break;
     }
 
       ObjectSetName(obj, nam);