org.jmol.smiles

Class SmilesAromatic

java.lang.Object

org.jmol.smiles.SmilesAromatic

public class SmilesAromatic
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
SmilesAromatic()

Method Summary

Methods

Modifier and Type	Method and Description
private static boolean	addNormal(javax.vecmath.Vector3f vTemp, javax.vecmath.Vector3f vMean, float maxDev)
private static boolean	checkStandardDeviation(javax.vecmath.Vector3f[] vNorms, javax.vecmath.Vector3f vMean, int n, float cutoff)
(package private) static float	getNormalThroughPoints(JmolNode pointA, JmolNode pointB, JmolNode pointC, javax.vecmath.Vector3f vNorm, javax.vecmath.Vector3f vAB, javax.vecmath.Vector3f vAC)
static boolean	isFlatSp2Ring(JmolNode[] atoms, java.util.BitSet bsSelected, java.util.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,
                    java.util.BitSet bsSelected,
                    java.util.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(javax.vecmath.Vector3f vTemp,
                javax.vecmath.Vector3f vMean,
                float maxDev)

checkStandardDeviation

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

getNormalThroughPoints

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