read atom serial number from PDB

biasmv · Mar 8, 2016 · 289c076 · 289c076
1 parent 95a93d1
commit 289c076
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/src/io.js b/src/io.js
@@ -267,12 +267,13 @@ PDBReader.prototype = {
     }
     var occupancy = parseFloat(line.substr(54,6).trim());
     var tempFactor = parseFloat(line.substr(60,6).trim());
+    var serial = parseInt(line.substr(6,5).trim(), 10);
     var atom = this._currRes.addAtom(atomName, pos, element, isHetatm,
                                      isNaN(occupancy) ? null : occupancy, 
-                                     isNaN(tempFactor) ? null : tempFactor);
+                                     isNaN(tempFactor) ? null : tempFactor,
+                                     serial);
     // in case parseConect records is set to true, store away the atom serial
     if (this._options.conectRecords) {
-      var serial = parseInt(line.substr(6,5).trim(), 10);
       this._serialToAtomMap[serial] = atom;
     }
     return true;

diff --git a/src/mol/atom.js b/src/mol/atom.js
@@ -65,7 +65,7 @@ AtomBase.prototype = {
 };
 
 function Atom(residue, name, pos, element, index, isHetatm,
-              occupancy, tempFactor) {
+              occupancy, tempFactor, serial) {
   AtomBase.call(this);
   this._properties = {};
   this._residue = residue;
@@ -77,6 +77,7 @@ function Atom(residue, name, pos, element, index, isHetatm,
   this._element = element;
   this._occupancy = occupancy !== undefined ? occupancy : null;
   this._tempFactor = tempFactor !== undefined ? tempFactor : null;
+  this._serial = serial|0;
 }
 
 utils.derive(Atom, AtomBase, {
@@ -104,6 +105,8 @@ utils.derive(Atom, AtomBase, {
 
   tempFactor : function() { return this._tempFactor; },
 
+  serial : function() { return this._serial; },
+
   isHetatm : function() { 
     return this._isHetatm; 
   },
@@ -139,6 +142,7 @@ utils.derive(AtomView, AtomBase, {
   index : function() { return this._atom.index(); },
   occupancy : function() { return this._atom.occupancy(); },
   tempFactor : function() { return this._atom.tempFactor(); },
+  serial : function() { return this._serial; },
   qualifiedName : function() {
     return this._atom.qualifiedName();
   },

diff --git a/src/mol/residue.js b/src/mol/residue.js
@@ -133,10 +133,10 @@ utils.derive(Residue, ResidueBase, {
 
   full : function() { return this; },
 
-  addAtom : function(name, pos, element, isHetatm, occupancy, tempFactor) {
+  addAtom : function(name, pos, element, isHetatm, occupancy, tempFactor, serial) {
     var atom = new Atom(this, name, pos, element, 
                         this.structure().nextAtomIndex(), 
-                        isHetatm, occupancy, tempFactor);
+                        isHetatm, occupancy, tempFactor, serial|0);
     this._atoms.push(atom);
     return atom;
   },