getPossibleMoleculeStructureFromBond: function( a, b ) {
var molA = this.getMolecule( a );
var molB = this.getMolecule( b );
assert && assert( molA !== molB );
return MoleculeStructure.getCombinedMoleculeFromBond( molA, molB, a, b, new Molecule() );
},
bond: function( a, dirAtoB, b ) {
this.lewisDotModel.bond( a, dirAtoB, b );
var molA = this.getMolecule( a );
var molB = this.getMolecule( b );
if ( molA === molB ) {
throw new Error( 'WARNING: loop or other invalid structure detected in a molecule' );
}
var newMolecule = MoleculeStructure.getCombinedMoleculeFromBond( molA, molB, a, b, new Molecule() );
// sanity check and debugging information
if ( !newMolecule.isValid() ) {
// TODO: performance: strip this out for the runtime?
window.console && console.log && console.log( 'invalid molecule!' );
window.console && console.log && console.log( 'bonding: ' + a.symbol + '(' + a.reference + '), ' + dirAtoB + ' ' + b.symbol + ' (' + b.reference + ')' );
window.console && console.log && console.log( 'A' );
window.console && console.log && console.log( molA.getDebuggingDump() );
window.console && console.log && console.log( 'B' );
window.console && console.log && console.log( molB.getDebuggingDump() );
window.console && console.log && console.log( 'combined' );
window.console && console.log && console.log( newMolecule.getDebuggingDump() );
window.console && console.log && console.log( 'found: ' + this.isAllowedStructure( newMolecule ) );
// just exit out for now
return;
}
this.removeMolecule( molA );
this.removeMolecule( molB );
this.addMolecule( newMolecule );
/*---------------------------------------------------------------------------*
* bonding diagnostics and sanity checks
*----------------------------------------------------------------------------*/
var serializedForm = this.getMolecule( a ).toSerial2();
window.console && console.log && console.log( 'created structure: ' + serializedForm );
var structure = this.getMolecule( a );
if ( structure.atoms.length > 2 ) {
structure.bonds.forEach( function( bond ) {
if ( bond.a.hasSameElement( bond.b ) && bond.a.symbol === 'H' ) {
window.console && console.log && console.log( 'WARNING: Hydrogen bonded to another hydrogen in a molecule which is not diatomic hydrogen' );
}
} );
}
assert && assert( this.getMolecule( a ) === this.getMolecule( b ) );
},