public class SmilesAromatic
extends java.lang.Object
Constructor and Description |
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SmilesAromatic() |
Modifier and Type | Method and Description |
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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.
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public static final boolean isFlatSp2Ring(JmolNode[] atoms, java.util.BitSet bsSelected, java.util.BitSet bs, float cutoff)
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.private static final boolean addNormal(javax.vecmath.Vector3f vTemp, javax.vecmath.Vector3f vMean, float maxDev)
private static final boolean checkStandardDeviation(javax.vecmath.Vector3f[] vNorms, javax.vecmath.Vector3f vMean, int n, float cutoff)