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)
(package private) static java.util.BitSet	checkAromaticDefined(JmolNode[] jmolAtoms, java.util.BitSet bsAtoms) set aromatic atoms based on predefined BOND_AROMATIC definitions
(package private) static void	checkAromaticStrict(JmolNode[] jmolAtoms, java.util.BitSet bsAromatic, java.util.List<java.lang.Object> v5, java.util.List<java.lang.Object> v6)
private static void	checkAromaticStrict(JmolNode[] jmolAtoms, java.util.BitSet bsStrict, java.util.List<java.lang.Object> v5, java.util.List<java.lang.Object> v6, java.util.BitSet bsRing, boolean is5) uses an MMFF94 strategy for determining aromaticity for a specific ring.
private static boolean	checkStandardDeviation(javax.vecmath.Vector3f[] vNorms, javax.vecmath.Vector3f vMean, int n, float cutoff)
private static int	countInternalPairs(JmolNode[] jmolAtoms, java.util.BitSet bsRing, boolean is5) Counts the electron pairs that are internal to this ring.
(package private) static float	getNormalThroughPoints(JmolNode pointA, JmolNode pointB, JmolNode pointC, javax.vecmath.Vector3f vNorm, javax.vecmath.Vector3f vAB, javax.vecmath.Vector3f vAC)
private static boolean	isAromaticRing(java.util.BitSet bsAromatic, java.util.BitSet bsTest, java.util.BitSet bs, int n)
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)

checkAromaticDefined

static java.util.BitSet checkAromaticDefined(JmolNode[] jmolAtoms,
                                    java.util.BitSet bsAtoms)

set aromatic atoms based on predefined BOND_AROMATIC definitions

Parameters:

jmolAtoms -

bsAtoms -

Returns:

bsAromatic

checkAromaticStrict

static void checkAromaticStrict(JmolNode[] jmolAtoms,
                       java.util.BitSet bsAromatic,
                       java.util.List<java.lang.Object> v5,
                       java.util.List<java.lang.Object> v6)

isAromaticRing

private static boolean isAromaticRing(java.util.BitSet bsAromatic,
                     java.util.BitSet bsTest,
                     java.util.BitSet bs,
                     int n)

checkAromaticStrict

private static void checkAromaticStrict(JmolNode[] jmolAtoms,
                       java.util.BitSet bsStrict,
                       java.util.List<java.lang.Object> v5,
                       java.util.List<java.lang.Object> v6,
                       java.util.BitSet bsRing,
                       boolean is5)

uses an MMFF94 strategy for determining aromaticity for a specific ring.

Parameters:

jmolAtoms -

bsStrict - growing list of aromatic atoms

v5 -

v6 -

bsRing - this ring's atoms

is5 -

countInternalPairs

private static int countInternalPairs(JmolNode[] jmolAtoms,
                     java.util.BitSet bsRing,
                     boolean is5)

Counts the electron pairs that are internal to this ring. Allows for aromatic bond types. Note that Jmol has already determined that the ring is flat so there is no need to worry about hybridization.

Parameters:

jmolAtoms -

bsRing -

is5 -

Returns:

number of pairs