Merge pull request #110 from Traksewt/add-multiple-residues

add addResidues to MolView
biasmv · Jul 15, 2015 · 0f255c6 · 0f255c6
2 parents ed07279 + 56c1927
commit 0f255c6
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Showing 4 changed files with 82 additions and 24 deletions.
diff --git a/doc/mol.rst b/doc/mol.rst
@@ -236,6 +236,15 @@ Mol (and MolView)
 
   :returns: the newly created :class:`pv.mol.ChainView` instance
 
+.. function:: pv.mol.Mol.addResidues(residues, includeAllAtoms)
+
+  Adds all residues to their respective chain 
+
+  :param residues: list of new residues
+  :param includeAllAtoms: when true, all atoms of the residue are directly added as new AtomViews to the residue. When set to false (the default), a new residue view is created with an empty list of atoms.
+
+  :returns: a map of chain name to chain for the affected chains with new residues.
+
 .. function:: pv.mol.MolView.addAtom(atom)
 
   Adds the given atom to the view. If the atom is already contained in the view, it is not added again. If an atom's residue or chain are not yet part of the view, they are added as well.

diff --git a/src/mol/mol.js b/src/mol/mol.js
@@ -501,6 +501,19 @@ utils.derive(MolView, MolBase, {
     return chain.containsResidue(residue);
   },
 
+  addResidues : function (residues, recurse) {
+    var that = this;
+    var chainsViews = {};
+    residues.forEach(function  (residue) {
+      var chainName = residue.chain().name();
+      if (typeof chainsViews[chainName] === 'undefined') {
+        chainsViews[chainName] = that.addChain(residue.chain(), false); 
+      }
+      chainsViews[chainName].addResidue(residue, recurse);
+    });
+    return chainsViews;
+  },
+
 
   chains : function() { return this._chains; },
 

diff --git a/src/tests/mol/basics.js b/src/tests/mol/basics.js
@@ -252,6 +252,29 @@ test('residue select on structure', function(assert) {
   assert.strictEqual(view.chains().length, 1);
 });
 
+
+test('add residues', function(assert) {
+  var rnums = [268,903,904,905];
+  var firstView = FRAGMENT.select({rnums : rnums });
+  assert.ok(firstView.chain('A')._rnumsOrdered === true);
+  var i, res, res2;
+  for (i = 0; i < rnums.length; ++i) {
+    res = firstView.chain('A').residueByRnum(rnums[i]);
+    assert.strictEqual(res.num(), rnums[i]);
+  }
+  var secondView = FRAGMENT.createEmptyView();
+  var r = [];
+  firstView.eachResidue(function(x) { r.push(x); });
+  secondView.addResidues(r, true);
+  var other = [];
+  secondView.eachResidue(function(x) { other.push(x); });
+  for (i = 0; i < rnums.length; ++i) {
+    res = firstView.chain('A').residueByRnum(rnums[i]);
+    res2 = secondView.chain('A').residueByRnum(rnums[i]);
+    assert.strictEqual(res.num(), res2.num());
+  }
+});
+
 test('atom select on structure', function(assert) {
   var view = FRAGMENT.atomSelect(function(a) { return a.name() === 'CA'; });
   var count = 0;

diff --git a/src/viewer.js b/src/viewer.js
@@ -525,30 +525,43 @@ Viewer.prototype = {
   },
 
   addListener : function(eventName, callback) {
-    var callbacks = this.listenerMap[eventName];
-    if (typeof callbacks === 'undefined') {
-      callbacks = [];
-      this.listenerMap[eventName] = callbacks;
-    }
-    if (callback === 'center') {
-      var cb = utils.bind(this._mouseHandler, 
-                          this._mouseHandler._centerOnClicked);
-      callbacks.push(cb);
-    } else {
-      callbacks.push(callback);
-    }
-    // in case viewer is already initialized, fire viewerReady immediately. 
-    // Otherwise, the callback would never be invoked in this case:
-    //  
-    // document.addEventListener('DOMContentLoaded', function() {
-    //    viewer = pv.Viewer(...);
-    //    viewer.on('viewerReady', function(viewer) {
-    //    });
-    // });
-    if (this._initialized && eventName === 'viewerReady') {
-      // don't use dispatch here, we only want this very callback to be 
-      // invoked.
-      callback(this, null);
+    if (eventName === 'keypress' || 
+        eventName === 'keydown' || 
+        eventName === 'keyup') {
+      // handle keypress events directly onto the parent domElement
+      // mouse downs will make it have focus
+//      this._domElement
+      document.addEventListener(eventName, utils.bind(this, callback),
+          false);
+
+    }
+    else {
+
+      var callbacks = this.listenerMap[eventName];
+      if (typeof callbacks === 'undefined') {
+        callbacks = [];
+        this.listenerMap[eventName] = callbacks;
+      }
+      if (callback === 'center') {
+        var cb = utils.bind(this._mouseHandler, 
+                            this._mouseHandler._centerOnClicked);
+        callbacks.push(cb);
+      } else {
+        callbacks.push(callback);
+      }
+      // in case viewer is already initialized, fire viewerReady immediately. 
+      // Otherwise, the callback would never be invoked in this case:
+      //  
+      // document.addEventListener('DOMContentLoaded', function() {
+      //    viewer = pv.Viewer(...);
+      //    viewer.on('viewerReady', function(viewer) {
+      //    });
+      // });
+      if (this._initialized && eventName === 'viewerReady') {
+        // don't use dispatch here, we only want this very callback to be 
+        // invoked.
+        callback(this, null);
+      }
     }
   },