improve shouldIntroduceTraceBreak heuristic

In case there is a bond between two residues don't introduce a trace
break. This gives users the option to manually connect amino acids
to avoid trace breaks.

See issue #83 for details.

doc/mol.rst

@@ -449,6 +449,11 @@ Atom (and AtomView)
 
   Returns the temperature factor (aka B-factor) of this atom. In case this value is not available, null will be returned.
 
+.. function pv.mol.Atom.isConnectedTo(otherAtom)
+            pv.mol.AtomView.isConnectedTo(otherAtom)
+
+  Returns true if there is a bond between this atom and other atom, false otherwise. In case otherAtom is null, false is returned.
+
 
 Bond
 -----------------------------------------------------------------------------------------

src/mol/atom.js

@@ -41,7 +41,23 @@ AtomBase.prototype = {
     for (var i = 0, e = bonds.length; i < e; ++i) {
       callback(bonds[i]);
     }
-  }
+  },
+  isConnectedTo: function(otherAtom) {
+    if (otherAtom === null) {
+      return false;
+    }
+    var other = otherAtom.full();
+    var me = this.full();
+    var bonds = this.bonds();
+    for (var i = 0, e = bonds.length; i < e; ++i) {
+      var bond = bonds[i];
+      if ((bond.atom_one() === me && bond.atom_two() === other) ||
+          (bond.atom_one() === other && bond.atom_two() === me)) {
+        return true;
+      }
+    }
+    return false;
+  },
 };
 
 function Atom(residue, name, pos, element, index, isHetatm,

src/mol/chain.js

@@ -125,7 +125,6 @@ ChainBase.prototype  = {
       // binary search our way to heaven
       var startIdx = 
         utils.indexFirstLargerEqualThan(residues, numify(start), rnumComp);
-      console.log(startIdx, start, residues[0].num());
       if (startIdx === -1) {
         return matching;
       }
@@ -172,7 +171,7 @@ function shouldIntroduceTraceBreak(aaStretch, prevResidue, thisResidue) {
   // these checks are on purpose more relaxed than the checks we use in 
   // deriveConnectivity(). We don't really care about correctness of bond 
   // lengths here. The only thing that matters is that the residues are 
-  // more or less close so that they could potentially/ be connected.
+  // more or less close so that they could potentially be connected.
   var prevAtom, thisAtom;
   if (aaStretch) {
     prevAtom = prevResidue.atom('C');
@@ -181,6 +180,11 @@ function shouldIntroduceTraceBreak(aaStretch, prevResidue, thisResidue) {
     prevAtom = prevResidue.atom('O3\'');
     thisAtom = thisResidue.atom('P');
   }
+
+  // in case there is a bond, we don't introduce a chain break
+  if (prevAtom.isConnectedTo(thisAtom)) {
+    return false;
+  }
   var sqrDist = vec3.sqrDist(prevAtom.pos(), thisAtom.pos());
   return (Math.abs(sqrDist - 1.5*1.5) > 1);
 }

src/tests/mol/basics.js

@@ -159,6 +159,20 @@ HETATM 2141  O   HOH A 916     -11.502 -50.640   0.340  1.00 50.23           O
 
 var FRAGMENT = io.pdb(PDB_FRAGMENT);
 
+test('is atom connected to', function(assert) {
+  var atomA = FRAGMENT.atom('A.268.C');
+  var atomB = FRAGMENT.atom('A.268.O');
+  assert.ok(atomA.isConnectedTo(atomB));
+  assert.ok(atomB.isConnectedTo(atomA));
+  assert.ok(!atomB.isConnectedTo(atomB));
+  assert.ok(!atomA.isConnectedTo(atomA));
+
+  var atomC = FRAGMENT.atom('A.268.CB');
+  assert.ok(!atomA.isConnectedTo(atomC));
+  assert.ok(!atomC.isConnectedTo(atomA));
+  assert.ok(!atomC.isConnectedTo(null));
+});
+
 test('get atom by name', function(assert) {
   var oxygen = FRAGMENT.atom('A.905.O1');
   assert.strictEqual(oxygen.name(), 'O1');