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

Modifier and Type	Method and Description
private static boolean	addNormal(javajs.util.V3 vTemp, javajs.util.V3 vMean, float maxDev)
(package private) static BS	checkAromaticDefined(Node[] jmolAtoms, BS bsAtoms) set aromatic atoms based on predefined BOND_AROMATIC definitions
(package private) static void	checkAromaticStrict(Node[] jmolAtoms, BS bsAromatic, javajs.util.Lst<java.lang.Object> v5, javajs.util.Lst<java.lang.Object> v6)
private static void	checkAromaticStrict2(Node[] jmolAtoms, BS bsStrict, javajs.util.Lst<java.lang.Object> v5, javajs.util.Lst<java.lang.Object> v6, BS bsRing, boolean is5) uses an MMFF94 strategy for determining aromaticity for a specific ring.
private static boolean	checkStandardDeviation(javajs.util.V3[] vNorms, javajs.util.V3 vMean, int n, float cutoff)
private static int	countInternalPairs(Node[] jmolAtoms, BS bsRing, boolean is5) Counts the electron pairs that are internal to this ring.
(package private) static float	getNormalThroughPoints(Node pointA, Node pointB, Node pointC, javajs.util.V3 vNorm, javajs.util.V3 vAB, javajs.util.V3 vAC)
private static boolean	isAromaticRing(BS bsAromatic, BS bsTest, BS bs, int n)
static boolean	isFlatSp2Ring(Node[] atoms, BS bsSelected, BS 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(Node[] atoms,
                                          BS bsSelected,
                                          BS 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(javajs.util.V3 vTemp,
                                       javajs.util.V3 vMean,
                                       float maxDev)

checkStandardDeviation

private static final boolean checkStandardDeviation(javajs.util.V3[] vNorms,
                                                    javajs.util.V3 vMean,
                                                    int n,
                                                    float cutoff)

getNormalThroughPoints

static float getNormalThroughPoints(Node pointA,
                                    Node pointB,
                                    Node pointC,
                                    javajs.util.V3 vNorm,
                                    javajs.util.V3 vAB,
                                    javajs.util.V3 vAC)

checkAromaticDefined

static BS checkAromaticDefined(Node[] jmolAtoms,
                               BS bsAtoms)

set aromatic atoms based on predefined BOND_AROMATIC definitions

Parameters:

jmolAtoms -

bsAtoms -

Returns:

bsAromatic

checkAromaticStrict

static void checkAromaticStrict(Node[] jmolAtoms,
                                BS bsAromatic,
                                javajs.util.Lst<java.lang.Object> v5,
                                javajs.util.Lst<java.lang.Object> v6)

isAromaticRing

private static boolean isAromaticRing(BS bsAromatic,
                                      BS bsTest,
                                      BS bs,
                                      int n)

checkAromaticStrict2

private static void checkAromaticStrict2(Node[] jmolAtoms,
                                         BS bsStrict,
                                         javajs.util.Lst<java.lang.Object> v5,
                                         javajs.util.Lst<java.lang.Object> v6,
                                         BS 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(Node[] jmolAtoms,
                                      BS 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