org.jmol.smiles
Class SmilesAromatic

java.lang.Object
  extended by org.jmol.smiles.SmilesAromatic

public class SmilesAromatic
extends Object


Constructor Summary
SmilesAromatic()
           
 
Method Summary
private static boolean addNormal(Vector3f vTemp, Vector3f vMean, float maxDev)
           
private static boolean checkStandardDeviation(Vector3f[] vNorms, Vector3f vMean, int n, float cutoff)
           
(package private) static float getNormalThroughPoints(JmolNode pointA, JmolNode pointB, JmolNode pointC, Vector3f vNorm, Vector3f vAB, Vector3f vAC)
           
static boolean isFlatSp2Ring(JmolNode[] atoms, BitSet bsSelected, BitSet bs, float cutoff)
          3D-SEARCH aromaticity test.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SmilesAromatic

public SmilesAromatic()
Method Detail

isFlatSp2Ring

public static final boolean isFlatSp2Ring(JmolNode[] atoms,
                                          BitSet bsSelected,
                                          BitSet bs,
                                          float cutoff)
3D-SEARCH aromaticity test. A simple and unambiguous test for aromaticity based on 3D geometry and connectivity only, not Hueckel theory.

Parameters:
atoms - a set of atoms with coordinate positions and associated bonds.
bs - a bitset of atoms within the set of atoms, defining the ring
bsSelected - must not be null
cutoff - an arbitrary value to test the standard deviation against. 0.01 is appropriate here.
Returns:
true if standard deviation of vNorm.dot.vMean is less than cutoff

addNormal

private static final boolean addNormal(Vector3f vTemp,
                                       Vector3f vMean,
                                       float maxDev)

checkStandardDeviation

private static final boolean checkStandardDeviation(Vector3f[] vNorms,
                                                    Vector3f vMean,
                                                    int n,
                                                    float cutoff)

getNormalThroughPoints

static float getNormalThroughPoints(JmolNode pointA,
                                    JmolNode pointB,
                                    JmolNode pointC,
                                    Vector3f vNorm,
                                    Vector3f vAB,
                                    Vector3f vAC)