rapodaca

import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.io.Molecules;
import com.metamolecular.mx.query.DefaultAtomMatcher;
import junit.framework.TestCase;

public class Test extends TestCase
{
  public void testTolueneQuatDoesntMatchNeopentaneQuat()
  {
    Molecule toluene = Molecules.createToluene();

rapodaca

import com.metamolecular.mx.io.daylight.SMILESReader;
import com.metamolecular.mx.map.Mapper;
import com.metamolecular.mx.map.DefaultMapper;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.query.Node;
import java.util.Map;

import junit.framework.TestCase;

public class Test extends TestCase

rapodaca

import com.metamolecular.mx.io.daylight.SMILESReader;
import com.metamolecular.mx.map.DefaultMapper;
import com.metamolecular.mx.map.Mapper;
import junit.framework.TestCase;

public class Test extends TestCase
{
  public void testSaturatedSulfurDoesntMatchUnsaturatedSulfur()
  {
    Mapper mapper = new DefaultMapper(SMILESReader.read("S-C=O")); 

rapodaca

import com.metamolecular.mx.fingerprint.Fingerprinter;
import com.metamolecular.mx.fingerprint.PathFingerprinter;
import com.metamolecular.mx.io.Molecules;
import junit.framework.TestCase;

import java.util.BitSet;

public class Test extends TestCase
{
  /**

rapodaca

public void testItStopsBranchingWhenMaximumDepthReached()
{
  walker.setMaximumDepth(5);
  when(path.size()).thenReturn(0, 1, 2, 3, 4, 5);
  when(step.hasNextBond()).thenReturn(true, true, true, true, true, false);
  when(step.nextStep(bond)).thenReturn(step);
  when(step.nextBond()).thenReturn(bond);
  doStep();
 
  verify(step, times(5)).nextStep(bond);

rapodaca

private void doStep()
{
  walker.step(step, reporter);
}

rapodaca

public void testItDoesntRequestNextBondWhenMaximumDepthReached()
{
  walker.setMaximumDepth(2);
  when(path.size()).thenReturn(2);
  doStep();
  verify(step, never()).nextBond();
}

rapodaca

241
  -OEChem-07100913442D

 67 72  0  0  1  0            999 V2000
    5.3950   -3.1602    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9853   -3.8822    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4045   -4.6006    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2342   -4.5947    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6482   -3.8727    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2284   -3.1565    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

rapodaca

/**
 * See: http://jsfromhell.com/math/dot-line-length
 *
 * Distance from a point to a line or segment.
 *
 * @param {number} x point's x coord
 * @param {number} y point's y coord
 * @param {number} x0 x coord of the line's A point
 * @param {number} y0 y coord of the line's A point
 * @param {number} x1 x coord of the line's B point

rapodaca

chemtab.browser.FileView.prototype.wiggle = function() {
  goog.dom.classes.add(this.getElement(), 'wiggle');
};