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(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.
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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.
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(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.
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public static final boolean isFlatSp2Ring(Node[] atoms, BS bsSelected, BS 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(javajs.util.V3 vTemp, javajs.util.V3 vMean, float maxDev)
private static final boolean checkStandardDeviation(javajs.util.V3[] vNorms, javajs.util.V3 vMean, int n, float cutoff)
static float getNormalThroughPoints(Node pointA, Node pointB, Node pointC, javajs.util.V3 vNorm, javajs.util.V3 vAB, javajs.util.V3 vAC)
static BS checkAromaticDefined(Node[] jmolAtoms, BS bsAtoms)
jmolAtoms
- bsAtoms
- 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)
jmolAtoms
- bsStrict
- growing list of aromatic atomsv5
- v6
- bsRing
- this ring's atomsis5
- private static int countInternalPairs(Node[] jmolAtoms, BS bsRing, boolean is5)
jmolAtoms
- bsRing
- is5
-