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) |
(package private) static java.util.BitSet |
checkAromaticDefined(JmolNode[] jmolAtoms,
java.util.BitSet bsAtoms)
set aromatic atoms based on predefined BOND_AROMATIC definitions
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(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.
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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.
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(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.
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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)
static float getNormalThroughPoints(JmolNode pointA, JmolNode pointB, JmolNode pointC, javax.vecmath.Vector3f vNorm, javax.vecmath.Vector3f vAB, javax.vecmath.Vector3f vAC)
static java.util.BitSet checkAromaticDefined(JmolNode[] jmolAtoms, java.util.BitSet bsAtoms)
jmolAtoms
- bsAtoms
- 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 boolean isAromaticRing(java.util.BitSet bsAromatic, java.util.BitSet bsTest, java.util.BitSet bs, int n)
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)
jmolAtoms
- bsStrict
- growing list of aromatic atomsv5
- v6
- bsRing
- this ring's atomsis5
- private static int countInternalPairs(JmolNode[] jmolAtoms, java.util.BitSet bsRing, boolean is5)
jmolAtoms
- bsRing
- is5
-