org.jmol.smiles
Class SmilesAromatic
java.lang.Object
org.jmol.smiles.SmilesAromatic
public class SmilesAromatic
- extends java.lang.Object
Method Summary |
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 |
SmilesAromatic
public SmilesAromatic()
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 ringbsSelected
- must not be nullcutoff
- 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)