Package org.jmol.modelset
Class Atom
- java.lang.Object
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- javajs.util.T3
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- javajs.util.P3
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- org.jmol.util.Point3fi
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- org.jmol.modelset.Atom
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,javajs.api.JSONEncodable
,Node
,SimpleNode
public class Atom extends Point3fi implements Node
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description char
altloc
static int
ATOM_INFRAME
static int
ATOM_INFRAME_NOTHIDDEN
static int
ATOM_NOFLAGS
static int
ATOM_NOTHIDDEN
static int
ATOM_SHAPE_VIS_MASK
static int
ATOM_VISIBLE
static int
ATOM_VISSET
(package private) short
atomicAndIsotopeNumber
byte
atomID
(package private) int
atomSite
javajs.util.BS
atomSymmetry
Bond[]
bonds
MAY BE NULLprivate static int
CHARGE_OFFSET
private static int
CIP_CHIRALITY_MASK
private static int
CIP_CHIRALITY_OFFSET
private static int
CIP_CHIRALITY_RULE_MASK
private static int
CIP_CHIRALITY_RULE_OFFSET
private static int
CIP_MASK
int
clickabilityFlags
short
colixAtom
private static int
FLAG_MASK
private int
formalChargeAndFlags
Group
group
static int
ID_ALL
static int
ID_CHIME
static int
ID_U
static int
ID_XTAL
private static int
IS_HETERO_FLAG
static short
MAD_GLOBAL
short
madAtom
int
nBackbonesDisplayed
private int
nBondsDisplayed
byte
paletteID
static float
RADIUS_GLOBAL
static int
RADIUS_MAX
int
shapeVisibilityFlags
private float
userDefinedVanDerWaalRadius
(package private) byte
valence
private static int
VIBRATION_VECTOR_FLAG
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Constructor Summary
Constructors Constructor Description Atom()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
addDisplayedBond(int stickVisibilityFlag, boolean isVisible)
float
atomPropertyFloat(Viewer vwr, int tokWhat, javajs.util.P3 ptTemp)
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()int
atomPropertyInt(int tokWhat)
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()java.lang.String
atomPropertyString(Viewer vwr, int tokWhat)
javajs.util.T3
atomPropertyTuple(Viewer vwr, int tok, javajs.util.P3 ptTemp)
short
calculateMad(Viewer vwr, RadiusData rd)
boolean
checkVisible()
void
delete(javajs.util.BS bsBonds)
(package private) void
deleteBond(Bond bond)
private void
deleteBondAt(int i)
boolean
equals(java.lang.Object obj)
Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in thisAtom
findAromaticNeighbor(int notAtomIndex)
javajs.util.BS
findAtomsLike(java.lang.String atomExpression)
float
getADPMinMax(boolean isMax)
int
getAtomicAndIsotopeNumber()
java.lang.String
getAtomName()
int
getAtomNumber()
int
getAtomSite()
java.lang.String
getAtomType()
int
getBfactor100()
char
getBioSmilesType()
java.lang.String
getBioStructureTypeName()
Bond
getBond(Atom atomOther)
int
getBondCount()
Get the total number of bonds, including hydrogen bonds.int
getBondedAtomIndex(int bondIndex)
float
getBondingRadius()
int
getCellTranslation(int cellNNN, int[] cellRange, int nOps)
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for thisint
getChainID()
java.lang.String
getChainIDStr()
java.lang.String
getCIPChirality(boolean doCalculate)
Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlagsint
getCIPChiralityCode()
java.lang.String
getCIPChiralityRule()
int
getCovalentBondCount()
Get the total number of covalent bonds, thus not including hydrogen bonds.int
getCovalentBondCountPlusMissingH()
includes actual + missingint
getCovalentHydrogenCount()
boolean
getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
Used by SMILES to get vector of cross-links(package private) int
getCurrentBondCount()
float
getDimensionValue(int dimension)
Edge[]
getEdges()
Get the bond array, including hydrogen bonds.int
getElementNumber()
java.lang.String
getElementSymbol()
java.lang.String
getElementSymbolIso(boolean withIsotope)
int
getExplicitHydrogenCount()
[CH2] for examplefloat
getFloatProperty(java.lang.String property)
int
getFormalCharge()
private float
getFractionalCoord(boolean fixJavaFloat, char ch, boolean ignoreOffset, javajs.util.P3 pt)
javajs.util.P3
getFractionalCoordPt(boolean fixJavaFloat, boolean ignoreOffset, javajs.util.P3 pt)
private float
getFractionalUnitCoord(boolean fixJavaFloat, char ch, javajs.util.P3 pt)
(package private) javajs.util.P3
getFractionalUnitCoordPt(boolean fixJavaFloat, boolean asCartesian, javajs.util.P3 pt)
(package private) float
getFractionalUnitDistance(javajs.util.T3 pt, javajs.util.T3 ptTemp1, javajs.util.T3 ptTemp2)
java.lang.String
getGroup1(char c0)
java.lang.String
getGroup3(boolean allowNull)
void
getGroupBits(javajs.util.BS bs)
float
getHydrophobicity()
(package private) java.lang.String
getIdentity(int mode)
java.lang.String
getIdentityXYZ(javajs.util.P3 pt, int mode)
int
getImplicitHydrogenCount()
can be > 0 for PDB model with no H atoms or for SMILES string CCCint
getIndex()
java.lang.String
getInfo()
char
getInsertionCode()
int
getIsotopeNumber()
float
getMass()
int
getModelIndex()
SMILES onlyint
getModelNumber()
java.lang.String
getModelNumberForLabel()
JmolModulationSet
getModulation()
int
getMoleculeNumber(boolean inModel)
int
getNominalMass()
int
getOccupancy100()
int
getOffsetResidueAtom(java.lang.String name, int offset)
float
getPartialCharge()
float
getRadius()
int
getRasMolRadius()
int
getResno()
int
getSeqID()
int
getSurfaceDistance100()
(package private) java.lang.String
getSymmetryOperatorList(boolean isAll)
int
getSymmetryTranslation(int symop, int[] cellRange, int nOps)
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.(package private) int
getSymOp()
(package private) int
getTargetValence()
java.lang.Object[]
getTensors()
int
getTotalHydrogenCount()
int
getTotalValence()
(package private) SymmetryInterface
getUnitCell()
java.lang.String
getUnitID(int flags)
int
getValence()
return the total bond order for this atomfloat
getVanderwaalsRadiusFloat(Viewer vwr, VDW type)
private VDW
getVdwType(VDW type)
float
getVib(char ch)
Vibration
getVibrationVector()
(package private) float
getVolume(Viewer vwr, VDW vType)
javajs.util.P3
getXYZ()
int
hashCode()
Returns a hash number based on the data values in this object.boolean
hasVibration()
boolean
isBonded(Atom atomOther)
boolean
isClickable()
boolean
isCovalentlyBonded(Atom atomOther)
boolean
isCrossLinked(Node node)
(package private) boolean
isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)
boolean
isDeleted()
boolean
isHetero()
boolean
isLeadAtom()
boolean
isOccupied()
boolean
isPurine()
boolean
isPyrimidine()
boolean
isVisible(int flags)
boolean
modelIsRawPDB()
Atom
setAtom(int modelIndex, int atomIndex, javajs.util.P3 xyz, float radius, javajs.util.BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero)
void
setAtomicAndIsotopeNumber(int n)
void
setCIPChirality(int c)
void
setClickable(int flag)
void
setFormalCharge(int charge)
(package private) void
setFractionalCoord(int tok, float fValue, boolean asAbsolute)
void
setFractionalCoordPt(javajs.util.P3 pt, javajs.util.P3 ptNew, boolean asAbsolute)
(package private) void
setFractionalCoordTo(javajs.util.P3 ptNew, boolean asAbsolute)
void
setMadAtom(Viewer vwr, RadiusData rd)
boolean
setRadius(float radius)
void
setShapeVisibility(int flag, boolean isVisible)
void
setSymop(int isym, boolean andClear)
void
setTranslucent(boolean isTranslucent, float translucentLevel)
void
setValence(int nBonds)
(package private) void
setVibrationVector()
java.lang.String
toString()
Returns a string that contains the values of this Tuple3f.-
Methods inherited from class javajs.util.T3
add, add2, add3, ave, cross, distance, distanceSquared, dot, floatToIntBits, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON
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Field Detail
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ATOM_INFRAME
public static final int ATOM_INFRAME
- See Also:
- Constant Field Values
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ATOM_VISSET
public static final int ATOM_VISSET
- See Also:
- Constant Field Values
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ATOM_VISIBLE
public static final int ATOM_VISIBLE
- See Also:
- Constant Field Values
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ATOM_NOTHIDDEN
public static final int ATOM_NOTHIDDEN
- See Also:
- Constant Field Values
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ATOM_NOFLAGS
public static final int ATOM_NOFLAGS
- See Also:
- Constant Field Values
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ATOM_INFRAME_NOTHIDDEN
public static final int ATOM_INFRAME_NOTHIDDEN
- See Also:
- Constant Field Values
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ATOM_SHAPE_VIS_MASK
public static final int ATOM_SHAPE_VIS_MASK
- See Also:
- Constant Field Values
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RADIUS_MAX
public static final int RADIUS_MAX
- See Also:
- Constant Field Values
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RADIUS_GLOBAL
public static final float RADIUS_GLOBAL
- See Also:
- Constant Field Values
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MAD_GLOBAL
public static short MAD_GLOBAL
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altloc
public char altloc
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atomID
public byte atomID
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atomSite
int atomSite
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group
public Group group
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userDefinedVanDerWaalRadius
private float userDefinedVanDerWaalRadius
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valence
byte valence
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atomicAndIsotopeNumber
short atomicAndIsotopeNumber
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atomSymmetry
public javajs.util.BS atomSymmetry
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formalChargeAndFlags
private int formalChargeAndFlags
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CHARGE_OFFSET
private static final int CHARGE_OFFSET
- See Also:
- Constant Field Values
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FLAG_MASK
private static final int FLAG_MASK
- See Also:
- Constant Field Values
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VIBRATION_VECTOR_FLAG
private static final int VIBRATION_VECTOR_FLAG
- See Also:
- Constant Field Values
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IS_HETERO_FLAG
private static final int IS_HETERO_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_OFFSET
private static final int CIP_CHIRALITY_OFFSET
- See Also:
- Constant Field Values
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CIP_CHIRALITY_MASK
private static final int CIP_CHIRALITY_MASK
- See Also:
- Constant Field Values
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CIP_CHIRALITY_RULE_OFFSET
private static final int CIP_CHIRALITY_RULE_OFFSET
- See Also:
- Constant Field Values
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CIP_CHIRALITY_RULE_MASK
private static final int CIP_CHIRALITY_RULE_MASK
- See Also:
- Constant Field Values
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CIP_MASK
private static final int CIP_MASK
- See Also:
- Constant Field Values
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madAtom
public short madAtom
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colixAtom
public short colixAtom
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paletteID
public byte paletteID
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bonds
public Bond[] bonds
MAY BE NULL
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nBondsDisplayed
private int nBondsDisplayed
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nBackbonesDisplayed
public int nBackbonesDisplayed
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clickabilityFlags
public int clickabilityFlags
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shapeVisibilityFlags
public int shapeVisibilityFlags
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ID_U
public static final int ID_U
- See Also:
- Constant Field Values
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ID_ALL
public static final int ID_ALL
- See Also:
- Constant Field Values
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ID_XTAL
public static final int ID_XTAL
- See Also:
- Constant Field Values
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ID_CHIME
public static final int ID_CHIME
- See Also:
- Constant Field Values
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Method Detail
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setAtom
public Atom setAtom(int modelIndex, int atomIndex, javajs.util.P3 xyz, float radius, javajs.util.BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero)
- Parameters:
modelIndex
-atomIndex
-xyz
-radius
-atomSymmetry
-atomSite
-atomicAndIsotopeNumber
-formalCharge
-isHetero
-- Returns:
- this
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setShapeVisibility
public final void setShapeVisibility(int flag, boolean isVisible)
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isCovalentlyBonded
public boolean isCovalentlyBonded(Atom atomOther)
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isBonded
public boolean isBonded(Atom atomOther)
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addDisplayedBond
void addDisplayedBond(int stickVisibilityFlag, boolean isVisible)
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deleteBond
void deleteBond(Bond bond)
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deleteBondAt
private void deleteBondAt(int i)
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getBondedAtomIndex
public int getBondedAtomIndex(int bondIndex)
- Specified by:
getBondedAtomIndex
in interfaceNode
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setMadAtom
public void setMadAtom(Viewer vwr, RadiusData rd)
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calculateMad
public short calculateMad(Viewer vwr, RadiusData rd)
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getADPMinMax
public float getADPMinMax(boolean isMax)
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getTensors
public java.lang.Object[] getTensors()
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getRasMolRadius
public int getRasMolRadius()
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getEdges
public Edge[] getEdges()
Description copied from interface:SimpleNode
Get the bond array, including hydrogen bonds.- Specified by:
getEdges
in interfaceNode
- Specified by:
getEdges
in interfaceSimpleNode
- Returns:
- number of bonds
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getBondCount
public int getBondCount()
Description copied from interface:SimpleNode
Get the total number of bonds, including hydrogen bonds.- Specified by:
getBondCount
in interfaceSimpleNode
- Returns:
- number of bonds
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setTranslucent
public void setTranslucent(boolean isTranslucent, float translucentLevel)
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getElementNumber
public int getElementNumber()
- Specified by:
getElementNumber
in interfaceNode
- Specified by:
getElementNumber
in interfaceSimpleNode
- Returns:
- the atomic number for this aotm
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getIsotopeNumber
public int getIsotopeNumber()
- Specified by:
getIsotopeNumber
in interfaceNode
- Specified by:
getIsotopeNumber
in interfaceSimpleNode
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getAtomicAndIsotopeNumber
public int getAtomicAndIsotopeNumber()
- Specified by:
getAtomicAndIsotopeNumber
in interfaceNode
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setAtomicAndIsotopeNumber
public void setAtomicAndIsotopeNumber(int n)
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getElementSymbolIso
public java.lang.String getElementSymbolIso(boolean withIsotope)
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getElementSymbol
public java.lang.String getElementSymbol()
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isHetero
public boolean isHetero()
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hasVibration
public boolean hasVibration()
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setFormalCharge
public void setFormalCharge(int charge)
- Parameters:
charge
- from -3 to 7
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setVibrationVector
void setVibrationVector()
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getFormalCharge
public int getFormalCharge()
- Specified by:
getFormalCharge
in interfaceNode
- Specified by:
getFormalCharge
in interfaceSimpleNode
- Returns:
- the formal charge for this atom
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getOccupancy100
public int getOccupancy100()
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isOccupied
public boolean isOccupied()
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getBfactor100
public int getBfactor100()
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getHydrophobicity
public float getHydrophobicity()
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setRadius
public boolean setRadius(float radius)
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delete
public void delete(javajs.util.BS bsBonds)
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setValence
public void setValence(int nBonds)
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getValence
public int getValence()
return the total bond order for this atom- Specified by:
getValence
in interfaceNode
- Specified by:
getValence
in interfaceSimpleNode
- Returns:
- the sum of the bond orders for this atom
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getCovalentBondCount
public int getCovalentBondCount()
Description copied from interface:SimpleNode
Get the total number of covalent bonds, thus not including hydrogen bonds.- Specified by:
getCovalentBondCount
in interfaceNode
- Specified by:
getCovalentBondCount
in interfaceSimpleNode
- Returns:
- number of bonds
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getCovalentHydrogenCount
public int getCovalentHydrogenCount()
- Specified by:
getCovalentHydrogenCount
in interfaceNode
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getImplicitHydrogenCount
public int getImplicitHydrogenCount()
Description copied from interface:Node
can be > 0 for PDB model with no H atoms or for SMILES string CCC- Specified by:
getImplicitHydrogenCount
in interfaceNode
- Returns:
- number of missing H atoms
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getTotalHydrogenCount
public int getTotalHydrogenCount()
- Specified by:
getTotalHydrogenCount
in interfaceNode
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getTotalValence
public int getTotalValence()
- Specified by:
getTotalValence
in interfaceNode
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getCovalentBondCountPlusMissingH
public int getCovalentBondCountPlusMissingH()
Description copied from interface:Node
includes actual + missing- Specified by:
getCovalentBondCountPlusMissingH
in interfaceNode
- Returns:
- actual + missing
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getTargetValence
int getTargetValence()
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getDimensionValue
public float getDimensionValue(int dimension)
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getVdwType
private VDW getVdwType(VDW type)
- Parameters:
type
-- Returns:
- if VDW_AUTO, will return VDW_AUTO_JMOL, VDW_AUTO_RASMOL, or VDW_AUTO_BABEL based on the model type
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getBondingRadius
public float getBondingRadius()
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getCurrentBondCount
int getCurrentBondCount()
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getRadius
public float getRadius()
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getIndex
public int getIndex()
- Specified by:
getIndex
in interfaceNode
- Specified by:
getIndex
in interfaceSimpleNode
- Returns:
- the unique ID number associated with this atom (which in Jmol is its position in the atoms[] array
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getAtomSite
public int getAtomSite()
- Specified by:
getAtomSite
in interfaceNode
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getGroupBits
public void getGroupBits(javajs.util.BS bs)
- Specified by:
getGroupBits
in interfaceNode
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getAtomName
public java.lang.String getAtomName()
- Specified by:
getAtomName
in interfaceNode
- Specified by:
getAtomName
in interfaceSimpleNode
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getAtomType
public java.lang.String getAtomType()
- Specified by:
getAtomType
in interfaceNode
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getAtomNumber
public int getAtomNumber()
- Specified by:
getAtomNumber
in interfaceNode
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getSeqID
public int getSeqID()
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isVisible
public boolean isVisible(int flags)
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getPartialCharge
public float getPartialCharge()
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getSymmetryTranslation
public int getSymmetryTranslation(int symop, int[] cellRange, int nOps)
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom. atomSymmetry is a bitset that is created in adapter.smarter.AtomSetCollection It is arranged as follows: |--overall--|---cell1---|---cell2---|---cell3---|... |012..nOps-1|012..nOps-1|012..nOp-1s|012..nOps-1|... If a bit is set, it means that the atom was created using that operator operating on the base file set and translated for that cell. If any bit is set in any of the cell blocks, then the same bit will also be set in the overall block. This allows for rapid determination of special positions and also of atom membership in any operation set. Note that it is not necessarily true that an atom is IN the designated cell, because one can load {nnn mmm 0}, and then, for example, the {-x,-y,-z} operator sends atoms from 555 to 444. Still, those atoms would be marked as cell 555 here, because no translation was carried out. That is, the numbers 444 in symop=3444 do not refer to a cell, per se. What they refer to is the file-designated operator plus a translation of {-1 -1 -1/1}.- Parameters:
symop
- = 0, 1, 2, 3, ....cellRange
- = {444, 445, 446, 454, 455, 456, .... }nOps
- = 2 for x,y,z;-x,-y,-z, for example- Returns:
- cell number such as 565
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getCellTranslation
public int getCellTranslation(int cellNNN, int[] cellRange, int nOps)
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this- Parameters:
cellNNN
-cellRange
-nOps
-- Returns:
- matching cell number, if applicable
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getSymmetryOperatorList
java.lang.String getSymmetryOperatorList(boolean isAll)
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getModelIndex
public int getModelIndex()
SMILES only- Specified by:
getModelIndex
in interfaceNode
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getMoleculeNumber
public int getMoleculeNumber(boolean inModel)
- Specified by:
getMoleculeNumber
in interfaceNode
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getFractionalCoord
private float getFractionalCoord(boolean fixJavaFloat, char ch, boolean ignoreOffset, javajs.util.P3 pt)
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getXYZ
public javajs.util.P3 getXYZ()
- Specified by:
getXYZ
in interfaceNode
- Specified by:
getXYZ
in interfaceSimpleNode
- Returns:
- the position of this atom
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getFractionalCoordPt
public javajs.util.P3 getFractionalCoordPt(boolean fixJavaFloat, boolean ignoreOffset, javajs.util.P3 pt)
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getUnitCell
SymmetryInterface getUnitCell()
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getFractionalUnitCoord
private float getFractionalUnitCoord(boolean fixJavaFloat, char ch, javajs.util.P3 pt)
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getFractionalUnitCoordPt
javajs.util.P3 getFractionalUnitCoordPt(boolean fixJavaFloat, boolean asCartesian, javajs.util.P3 pt)
- Parameters:
fixJavaFloat
- ALWAYS set true for any new references to this method. False is for legacy onlyasCartesian
-pt
-- Returns:
- unit cell coord
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getFractionalUnitDistance
float getFractionalUnitDistance(javajs.util.T3 pt, javajs.util.T3 ptTemp1, javajs.util.T3 ptTemp2)
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setFractionalCoord
void setFractionalCoord(int tok, float fValue, boolean asAbsolute)
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setFractionalCoordTo
void setFractionalCoordTo(javajs.util.P3 ptNew, boolean asAbsolute)
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setFractionalCoordPt
public void setFractionalCoordPt(javajs.util.P3 pt, javajs.util.P3 ptNew, boolean asAbsolute)
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isCursorOnTopOf
boolean isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)
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getInfo
public java.lang.String getInfo()
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getIdentityXYZ
public java.lang.String getIdentityXYZ(javajs.util.P3 pt, int mode)
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getIdentity
java.lang.String getIdentity(int mode)
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getGroup3
public java.lang.String getGroup3(boolean allowNull)
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getBioSmilesType
public char getBioSmilesType()
- Specified by:
getBioSmilesType
in interfaceNode
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isPyrimidine
public boolean isPyrimidine()
- Specified by:
isPyrimidine
in interfaceNode
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isClickable
public boolean isClickable()
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setClickable
public void setClickable(int flag)
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checkVisible
public boolean checkVisible()
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isLeadAtom
public boolean isLeadAtom()
- Specified by:
isLeadAtom
in interfaceNode
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getChainID
public int getChainID()
- Specified by:
getChainID
in interfaceNode
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getChainIDStr
public java.lang.String getChainIDStr()
- Specified by:
getChainIDStr
in interfaceNode
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getSurfaceDistance100
public int getSurfaceDistance100()
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getVibrationVector
public Vibration getVibrationVector()
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getModulation
public JmolModulationSet getModulation()
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getModelNumberForLabel
public java.lang.String getModelNumberForLabel()
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getModelNumber
public int getModelNumber()
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getBioStructureTypeName
public java.lang.String getBioStructureTypeName()
- Specified by:
getBioStructureTypeName
in interfaceNode
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equals
public boolean equals(java.lang.Object obj)
Description copied from class:javajs.util.T3
Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this- Overrides:
equals
in classjavajs.util.T3
- Parameters:
obj
- the vector with which the comparison is made.
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hashCode
public int hashCode()
Description copied from class:javajs.util.T3
Returns a hash number based on the data values in this object. Two different Tuple3f objects with identical data values (ie, returns true for equals(Tuple3f) ) will return the same hash number. Two vectors with different data members may return the same hash value, although this is not likely.- Overrides:
hashCode
in classjavajs.util.T3
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findAromaticNeighbor
public Atom findAromaticNeighbor(int notAtomIndex)
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atomPropertyInt
public int atomPropertyInt(int tokWhat)
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()- Parameters:
tokWhat
-- Returns:
- int value or Integer.MIN_VALUE
-
getSymOp
int getSymOp()
-
atomPropertyFloat
public float atomPropertyFloat(Viewer vwr, int tokWhat, javajs.util.P3 ptTemp)
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()- Parameters:
vwr
-tokWhat
-ptTemp
-- Returns:
- float value or value*100 (asInt=true) or throw an error if not found
-
getVib
public float getVib(char ch)
-
getNominalMass
public int getNominalMass()
-
getMass
public float getMass()
- Specified by:
getMass
in interfaceNode
- Specified by:
getMass
in interfaceSimpleNode
- Returns:
- the mass or, if specified, the mass number
-
atomPropertyString
public java.lang.String atomPropertyString(Viewer vwr, int tokWhat)
-
getCIPChirality
public java.lang.String getCIPChirality(boolean doCalculate)
Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags- Specified by:
getCIPChirality
in interfaceNode
- Parameters:
doCalculate
-- Returns:
- one of "", "R", "S", "E", "Z", "r", "s", "?"
-
getCIPChiralityRule
public java.lang.String getCIPChiralityRule()
-
setCIPChirality
public void setCIPChirality(int c)
- Specified by:
setCIPChirality
in interfaceNode
- Specified by:
setCIPChirality
in interfaceSimpleNode
- Parameters:
c
- [0:unknown; 3:none; 1: R; 2: S; 5: Z; 6: E; 9: M, 10: P, +r,s
-
getCIPChiralityCode
public int getCIPChiralityCode()
- Specified by:
getCIPChiralityCode
in interfaceNode
-
getInsertionCode
public char getInsertionCode()
- Specified by:
getInsertionCode
in interfaceNode
-
atomPropertyTuple
public javajs.util.T3 atomPropertyTuple(Viewer vwr, int tok, javajs.util.P3 ptTemp)
-
getOffsetResidueAtom
public int getOffsetResidueAtom(java.lang.String name, int offset)
- Specified by:
getOffsetResidueAtom
in interfaceNode
-
isCrossLinked
public boolean isCrossLinked(Node node)
- Specified by:
isCrossLinked
in interfaceNode
-
getCrossLinkVector
public boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
Used by SMILES to get vector of cross-links- Specified by:
getCrossLinkVector
in interfaceNode
-
toString
public java.lang.String toString()
Description copied from class:javajs.util.T3
Returns a string that contains the values of this Tuple3f. The form is (x,y,z).- Overrides:
toString
in classjavajs.util.T3
- Returns:
- the String representation
-
findAtomsLike
public javajs.util.BS findAtomsLike(java.lang.String atomExpression)
- Specified by:
findAtomsLike
in interfaceNode
-
getUnitID
public java.lang.String getUnitID(int flags)
-
getFloatProperty
public float getFloatProperty(java.lang.String property)
- Specified by:
getFloatProperty
in interfaceNode
- Parameters:
property
- "property_xxxx"- Returns:
- value or Float.NaN
-
modelIsRawPDB
public boolean modelIsRawPDB()
- Specified by:
modelIsRawPDB
in interfaceNode
-
setSymop
public void setSymop(int isym, boolean andClear)
-
getExplicitHydrogenCount
public int getExplicitHydrogenCount()
Description copied from interface:Node
[CH2] for example- Specified by:
getExplicitHydrogenCount
in interfaceNode
- Returns:
- number of H atoms in brackets
-
-