December 23, 2011

Chemdoodle web components tricks #1: scaling molecules

I have played around a bit with chemdoodle web compontents. Very nice GPL licensed javascript library for chemical 2D (and 3D if you have a webGL supporting browser).

However, the standard API still is missing some functionality. But you can fix most things by using standard javascript (at least as long as you're only using a standard viewer canvas, without zoom functionality).

Here I will show how you can scale a molecule to the size of the canvas. The standard viewercanvas will not scale molecules to the size of the canvas. So I added this to my code.

Standard canvas with a caffeine molecule and colored atom labels:

And here, the same canvas with the molecule scaled by the size of the canvas:

The javascript code for the standard canvas:

 
  var testmol = new ChemDoodle.ViewerCanvas('testmol', 300, 300);
  testmol.specs.atoms_useJMOLColors = true;
  var caffeineMolFile = 'Molecule Name\n  CHEMDOOD08070920033D 0   0.00000     0.00000     0\n[Insert Comment Here]\n 14 15  0  0  0  0  0  0  0  0  1 V2000\n   -0.3318    2.0000    0.0000   O 0  0  0  1  0  0  0  0  0  0  0  0\n   -0.3318    1.0000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -1.1980    0.5000    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n    0.5342    0.5000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -1.1980   -0.5000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -2.0640    1.0000    0.0000   C 0  0  0  4  0  0  0  0  0  0  0  0\n    1.4804    0.8047    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n    0.5342   -0.5000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -2.0640   -1.0000    0.0000   O 0  0  0  1  0  0  0  0  0  0  0  0\n   -0.3318   -1.0000    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n    2.0640   -0.0000    0.0000   C 0  0  0  2  0  0  0  0  0  0  0  0\n    1.7910    1.7553    0.0000   C 0  0  0  4  0  0  0  0  0  0  0  0\n    1.4804   -0.8047    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n   -0.3318   -2.0000    0.0000   C 0  0  0  4  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  3  2  1  0  0  0  0\n  4  2  1  0  0  0  0\n  3  5  1  0  0  0  0\n  3  6  1  0  0  0  0\n  7  4  1  0  0  0  0\n  4  8  2  0  0  0  0\n  9  5  2  0  0  0  0\n 10  5  1  0  0  0  0\n 10  8  1  0  0  0  0\n  7 11  1  0  0  0  0\n  7 12  1  0  0  0  0\n 13  8  1  0  0  0  0\n 13 11  2  0  0  0  0\n 10 14  1  0  0  0  0\nM  END\n> \n07-08-2009\n';
  var caffeine = ChemDoodle.readMOL(caffeineMolFile);
  testmol.loadMolecule(caffeine);

and the javascript code for the canvas with the scaled molecule:

 
  var testmol2 = new ChemDoodle.ViewerCanvas('testmol2', 300, 300);
  testmol2.specs.atoms_useJMOLColors = true;
  var caffeineMolFile = 'Molecule Name\n  CHEMDOOD08070920033D 0   0.00000     0.00000     0\n[Insert Comment Here]\n 14 15  0  0  0  0  0  0  0  0  1 V2000\n   -0.3318    2.0000    0.0000   O 0  0  0  1  0  0  0  0  0  0  0  0\n   -0.3318    1.0000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -1.1980    0.5000    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n    0.5342    0.5000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -1.1980   -0.5000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -2.0640    1.0000    0.0000   C 0  0  0  4  0  0  0  0  0  0  0  0\n    1.4804    0.8047    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n    0.5342   -0.5000    0.0000   C 0  0  0  1  0  0  0  0  0  0  0  0\n   -2.0640   -1.0000    0.0000   O 0  0  0  1  0  0  0  0  0  0  0  0\n   -0.3318   -1.0000    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n    2.0640   -0.0000    0.0000   C 0  0  0  2  0  0  0  0  0  0  0  0\n    1.7910    1.7553    0.0000   C 0  0  0  4  0  0  0  0  0  0  0  0\n    1.4804   -0.8047    0.0000   N 0  0  0  1  0  0  0  0  0  0  0  0\n   -0.3318   -2.0000    0.0000   C 0  0  0  4  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  3  2  1  0  0  0  0\n  4  2  1  0  0  0  0\n  3  5  1  0  0  0  0\n  3  6  1  0  0  0  0\n  7  4  1  0  0  0  0\n  4  8  2  0  0  0  0\n  9  5  2  0  0  0  0\n 10  5  1  0  0  0  0\n 10  8  1  0  0  0  0\n  7 11  1  0  0  0  0\n  7 12  1  0  0  0  0\n 13  8  1  0  0  0  0\n 13 11  2  0  0  0  0\n 10 14  1  0  0  0  0\nM  END\n> \n07-08-2009\n';
  var caffeine = ChemDoodle.readMOL(caffeineMolFile);
  // get the dimension of the molecule
  var size = caffeine.getDimension();
  // find the scale by taking the minimum of the canvas/size ratios
  var scale = Math.min(testmol2.width/size.x, testmol2.height/size.y);
  // load the molecule first (this function automatically sets scale, so we need to change specs after)
  testmol2.loadMolecule(caffeine);
  // change the specs.scale value to the scale calculated, shrinking it slightly so that text is not cut off
  testmol2.specs.scale = scale*.9;
  // repaint the canvas
  testmol2.repaint(); 

The code for the scaled figure updated after the comment below from Kevin Theisen. So now the code is simpler, but requires a repaint() command instead. Thanks to Kevin for this.