add hetatm flag

doc/mol.rst

@@ -128,6 +128,7 @@ The Mol (and MolView) API
   **Available Atom Predicates:**
 
   * *aname* An atom is included iff the atom name it is equal to *aname*. To match against multiple atom names, use the plural forms cnames/chains.
+  * *hetatm* An atom is included iff the atom hetatm flag matches the provided value.
 
   **Examples:**
 
@@ -359,6 +360,11 @@ The Atom (and AtomView) API
 
   The actual coordinates of the atom.
 
+.. function:: mol.Atom.isHetatm()
+              mol.AtomView.isHetatm()
+
+  Returns true when the atom was imported from a HETATM record, false if not. This flag is only meaningful for structures imported from PDB files and will return false for other file formats.
+
 
 The Bond API
 -----------------------------------------------------------------------------------------

src/io.js

@@ -170,6 +170,7 @@ PDBReader.prototype = {
     if (alt_loc !== ' ' && alt_loc !== 'A') {
       return true;
     }
+    var isHetatm = line[0] === 'H';
     var chainName = line[21];
     var resName = line.substr(17, 3).trim();
     var fullAtomName = line.substr(12, 4);
@@ -207,7 +208,7 @@ PDBReader.prototype = {
     if (element === '') {
       element = guessAtomElementFromName(fullAtomName);
     }
-    var atom = this._currRes.addAtom(atomName, pos, element);
+    var atom = this._currRes.addAtom(atomName, pos, element, isHetatm);
     // 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);

src/mol.js

@@ -82,6 +82,9 @@ function _atomPredicates(dict) {
   if (dict.aname !== undefined) {
     predicates.push(function(a) { return a.name() === dict.aname; });
   }
+  if (dict.hetatm !== undefined) {
+    predicates.push(function(a) { return a.isHetatm() === dict.hetatm; });
+  }
   if (dict.anames !== undefined) {
     predicates.push(function(a) { 
       var n = a.name();
@@ -341,7 +344,7 @@ MolBase.prototype = {
     }
     // when what is not one of the simple strings above, we assume what
     // is a dictionary containing predicates which have to be fulfilled.
-    return _dictSelect(this, what);
+    return _dictSelect(this, what || {});
   },
 
   selectWithin : (function() {
@@ -948,9 +951,10 @@ derive(Residue, ResidueBase, {
 
   full : function() { return this; },
 
-  addAtom : function(name, pos, element) {
+  addAtom : function(name, pos, element, isHetatm) {
     var atom = new Atom(this, name, pos, element, 
-                        this.structure().nextAtomIndex());
+                        this.structure().nextAtomIndex(), 
+                        isHetatm);
     this._atoms.push(atom);
     return atom;
   },
@@ -969,10 +973,11 @@ derive(Residue, ResidueBase, {
 
 });
 
-function Atom(residue, name, pos, element, index) {
+function Atom(residue, name, pos, element, index, isHetatm) {
   AtomBase.call(this);
   this._residue = residue;
   this._bonds = [];
+  this._isHetatm = !!isHetatm;
   this._name = name;
   this._pos = pos;
   this._index = index;
@@ -990,7 +995,10 @@ derive(Atom, AtomBase, {
   full : function() { return this; },
   qualifiedName : function() {
     return this.residue().qualifiedName()+'.'+this.name();
-  }
+  },
+  isHetatm : function() { 
+    return this._isHetatm; 
+  },
 });
 
 var Bond = function(atom_a, atom_b) {
@@ -1200,6 +1208,9 @@ derive(AtomView, AtomBase, {
   index : function() { return this._atom.index(); },
   qualifiedName : function() {
     return this._atom.qualifiedName();
+  },
+  isHetatm : function() {
+    return this._atom.isHetatm();
   }
 });
 

tests/all.html

@@ -60,5 +60,6 @@
   <script src="/tests/colors.js"></script>
   <script src="/tests/pdb-io.js"></script>
   <script src="/tests/viewer-render.js"></script>
+  <script src="/tests/mol-select.js"></script>
 </body>
 </html

tests/mol-select.js

@@ -0,0 +1,21 @@
+var SELECT_HETATM='\
+ATOM   3316  C   GLY B 214      24.173   7.911  -3.276  1.00 94.23           C\n\
+ATOM   3317  O   GLY B 214      24.730   8.496  -4.208  1.00 94.94           O\n\
+ATOM   3318  OXT GLY B 214      23.962   8.474  -2.196  1.00 95.71           O\n\
+TER    3319      GLY B 214                                                    \n\
+HETATM 3320  PA  AP5 A 215      18.089  46.955  20.531  1.00 17.77           P\n\
+HETATM 3321  O1A AP5 A 215      17.885  47.954  21.576  1.00 16.47           O\n\
+HETATM 3322  O2A AP5 A 215      18.847  47.325  19.359  1.00 15.16           O\n\
+ATOM   3317  O   GLY A 216      24.730   8.496  -4.208  1.00 94.94           O\n\
+END\n\
+'
+
+test('dict select select by hetatm flag', function(assert) {
+  var structure = io.pdb(HETATM);
+  var view = structure.select({ hetatm: true });
+  assert.strictEqual(view.atomCount(), 3);
+  view = structure.select({ hetatm: false });
+  assert.strictEqual(view.atomCount(), 4);
+
+});
+

tests/pdb-io.js

@@ -111,4 +111,41 @@ test('ignores conect records when conectRecords flag is not set', function(asser
 });
 
 
+var HETATM='\
+ATOM   3316  C   GLY B 214      24.173   7.911  -3.276  1.00 94.23           C\n\
+ATOM   3317  O   GLY B 214      24.730   8.496  -4.208  1.00 94.94           O\n\
+ATOM   3318  OXT GLY B 214      23.962   8.474  -2.196  1.00 95.71           O\n\
+TER    3319      GLY B 214                                                    \n\
+HETATM 3320  PA  AP5 A 215      18.089  46.955  20.531  1.00 17.77           P\n\
+HETATM 3321  O1A AP5 A 215      17.885  47.954  21.576  1.00 16.47           O\n\
+HETATM 3322  O2A AP5 A 215      18.847  47.325  19.359  1.00 15.16           O\n\
+ATOM   3317  O   GLY A 216      24.730   8.496  -4.208  1.00 94.94           O\n\
+END\n\
+'
+
+test('sets HETATM flag', function(assert) {
+  var structure = io.pdb(HETATM);
+  var atoms = [];
+  structure.eachAtom(function(a) { atoms.push(a) });
+  assert.strictEqual(atoms[0].isHetatm(), false);
+  assert.strictEqual(atoms[1].isHetatm(), false);
+  assert.strictEqual(atoms[2].isHetatm(), false);
+  assert.strictEqual(atoms[3].isHetatm(), true);
+  assert.strictEqual(atoms[4].isHetatm(), true);
+  assert.strictEqual(atoms[5].isHetatm(), true);
+  assert.strictEqual(atoms[6].isHetatm(), false);
+
+  // check that accessor also works for views. not strictly an IO test
+  var view = structure.select();
+  atoms = [];
+  view.eachAtom(function(a) { atoms.push(a) });
+  assert.strictEqual(atoms[0].isHetatm(), false);
+  assert.strictEqual(atoms[1].isHetatm(), false);
+  assert.strictEqual(atoms[2].isHetatm(), false);
+  assert.strictEqual(atoms[3].isHetatm(), true);
+  assert.strictEqual(atoms[4].isHetatm(), true);
+  assert.strictEqual(atoms[5].isHetatm(), true);
+  assert.strictEqual(atoms[6].isHetatm(), false);
+
+});