public class CIPData
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
(package private) SimpleNode[] |
atoms
all application atoms referenced by bit sets
|
(package private) javajs.util.BS |
bsAromatic
Jmol's definition of aromatic
|
(package private) javajs.util.BS |
bsAtoms
bit set of all atoms to process
|
(package private) javajs.util.BS |
bsAtropisomeric
bit set of all biphenyl-like connections
"[!H](.t1:-20,20)a{a(.t2:-20,20)-a}a[!H]"
|
(package private) javajs.util.BS |
bsAzacyclic
all N atoms that are sp3-hybridized and at small ring fusions
|
(package private) javajs.util.BS |
bsEnes
all sp2-hybridized atoms that are not Kekule-ambiguous
|
(package private) javajs.util.BS |
bsHelixM
aromatic atoms at the end of a negative helical turn
"A{a}(.t:-10,-40)a(.t:-10,-40)aaa"
|
(package private) javajs.util.BS |
bsHelixP
aromatic atoms at the end of a positive helical turn
"A{a}(.t:10,40)a(.t:10,40)aaa"
|
(package private) javajs.util.BS |
bsKekuleAmbiguous
atoms that need specially-calculated element number in Rule 1a
|
(package private) javajs.util.BS |
bsMolecule
atoms in all molecules containing the atoms of interest
|
(package private) javajs.util.BS |
bsNegativeAromatic
[a-]
|
(package private) javajs.util.BS |
bsXAromatic
excluded aromatics
[r5d3n+0,r5d2o+0]
|
(package private) javajs.util.BS[] |
lstSmallRings
all 3- to 7-membered rings; used to exclude E/Z and N-SP3 descriptors
|
boolean |
testRule6Full
A flag that, if set, returns rr for bicyclo[2.2.2]octane
|
(package private) static float |
TRIGONALITY_MIN
measure of planarity in a trigonal system, in Angstroms
|
protected javajs.util.V3 |
vNorm |
protected javajs.util.V3 |
vTemp |
(package private) Viewer |
vwr
Jmol's viewer class
|
Constructor and Description |
---|
CIPData() |
Modifier and Type | Method and Description |
---|---|
private void |
addAzacyclicN(int i) |
private int |
checkEne(javajs.util.BS bsAllEnes,
javajs.util.BS bsPath,
int iLast,
int iAtom,
int order,
javajs.util.BS bsEneAtom1)
Look for a path that contains this ene in a fully conjugated pattern
|
(package private) int |
checkHandedness(CIPChirality.CIPAtom a)
Determine the ordered CIP winding of this atom.
|
(package private) int |
couldBeChiralAlkene(SimpleNode a,
SimpleEdge edge)
Allow double bonds only if trivalent and first-row atom.
|
(package private) boolean |
couldBeChiralAtom(SimpleNode a)
Determine whether an atom is one we need to consider.
|
private void |
getAzacyclic()
Identify bridgehead nitrogens, as these may need to be given chirality
designations.
|
(package private) int |
getBondOrder(SimpleEdge bond) |
(package private) void |
getEneKekule()
Look for conjugated loops of any size that have atoms not already in aromatic rings
|
protected javajs.util.BS[] |
getList(java.lang.String smarts)
Retrieve an array of bit sets that match a given SMARTS
|
(package private) java.lang.String |
getRootTrackerResult(CIPChirality.CIPAtom root)
CIPDataTracker only
|
(package private) float |
getTrigonality(SimpleNode a,
javajs.util.V3 vNorm)
Determine the trigonality of an atom in order to determine whether it might
have a lone pair.
|
protected void |
init()
initializer -- called also by CIPDataSmiles
|
(package private) int |
isCis(CIPChirality.CIPAtom a,
CIPChirality.CIPAtom b,
CIPChirality.CIPAtom c,
CIPChirality.CIPAtom d)
Check cis vs.
|
(package private) int |
isPositiveTorsion(CIPChirality.CIPAtom a,
CIPChirality.CIPAtom b,
CIPChirality.CIPAtom c,
CIPChirality.CIPAtom d)
Checks the torsion angle and returns true if it is positive
|
(package private) boolean |
isSmiles()
Subclass identifier
|
protected boolean |
isTracker()
Subclass identifier
|
protected javajs.util.BS |
match(java.lang.String smarts)
Return a bit set corresponding to a SMARTS
|
CIPData |
set(Viewer vwr,
javajs.util.BS bsAtoms)
Actual constructor.
|
(package private) boolean |
setCoord(SimpleNode atom1,
CIPChirality.CIPAtom[] atoms)
set the coordinate -- SMILES only
|
void |
setRule6Full(boolean rrrr) |
(package private) void |
track(CIPChirality cip,
CIPChirality.CIPAtom a,
CIPChirality.CIPAtom b,
int sphere,
int finalScore,
boolean trackTerminal)
Track this decision - CIPDataTracker only
|
static final float TRIGONALITY_MIN
public boolean testRule6Full
Viewer vwr
SimpleNode[] atoms
javajs.util.BS bsAtoms
javajs.util.BS bsMolecule
javajs.util.BS bsAromatic
javajs.util.BS bsXAromatic
javajs.util.BS bsNegativeAromatic
javajs.util.BS bsAzacyclic
javajs.util.BS bsAtropisomeric
javajs.util.BS bsHelixM
javajs.util.BS bsHelixP
javajs.util.BS[] lstSmallRings
javajs.util.BS bsKekuleAmbiguous
javajs.util.BS bsEnes
protected javajs.util.V3 vNorm
protected javajs.util.V3 vTemp
protected boolean isTracker()
boolean isSmiles()
public CIPData set(Viewer vwr, javajs.util.BS bsAtoms)
vwr
- Jmol viewerbsAtoms
- selected atomsprotected void init()
protected javajs.util.BS[] getList(java.lang.String smarts) throws java.lang.Exception
smarts
- java.lang.Exception
protected javajs.util.BS match(java.lang.String smarts) throws java.lang.Exception
smarts
- java.lang.Exception
void getEneKekule()
private int checkEne(javajs.util.BS bsAllEnes, javajs.util.BS bsPath, int iLast, int iAtom, int order, javajs.util.BS bsEneAtom1)
bsAllEnes
- all ene carbonsbsPath
- current path to loop intoiLast
- the last atomiAtom
- this atomorder
- expected next order, alternating 2,1,2,1,...bsEneAtom1
- alternating atoms; first of double bondprivate void getAzacyclic()
private void addAzacyclicN(int i)
boolean couldBeChiralAtom(SimpleNode a)
a
- int couldBeChiralAlkene(SimpleNode a, SimpleEdge edge)
a
- edge
- optional bondfloat getTrigonality(SimpleNode a, javajs.util.V3 vNorm)
a
- vNorm
- a vector returned with the normal from the atom to the base planeint isCis(CIPChirality.CIPAtom a, CIPChirality.CIPAtom b, CIPChirality.CIPAtom c, CIPChirality.CIPAtom d)
a
- b
- c
- d
- int isPositiveTorsion(CIPChirality.CIPAtom a, CIPChirality.CIPAtom b, CIPChirality.CIPAtom c, CIPChirality.CIPAtom d)
a
- b
- c
- d
- int getBondOrder(SimpleEdge bond)
boolean setCoord(SimpleNode atom1, CIPChirality.CIPAtom[] atoms)
atom1
- atoms
- int checkHandedness(CIPChirality.CIPAtom a)
a
- void track(CIPChirality cip, CIPChirality.CIPAtom a, CIPChirality.CIPAtom b, int sphere, int finalScore, boolean trackTerminal)
cip
- a
- b
- sphere
- finalScore
- trackTerminal
- java.lang.String getRootTrackerResult(CIPChirality.CIPAtom root)
root
- public void setRule6Full(boolean rrrr)