public class Atom extends Point3fi implements BNode
Modifier and Type | Field and Description |
---|---|
char |
altloc |
private short |
atomicAndIsotopeNumber |
byte |
atomID |
int |
atomSite |
BS |
atomSymmetry |
Bond[] |
bonds
MAY BE NULL
|
int |
clickabilityFlags |
short |
colixAtom |
private static byte |
FLAG_MASK |
private byte |
formalChargeAndFlags |
Group |
group |
private static byte |
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 byte |
VIBRATION_VECTOR_FLAG |
Constructor and Description |
---|
Atom() |
Modifier and Type | Method and Description |
---|---|
void |
addDisplayedBackbone(int backboneVisibilityFlag,
boolean isVisible) |
(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() |
(package private) void |
deleteBond(Bond bond) |
private void |
deleteBondAt(int i) |
void |
deleteBonds(BS bsBonds) |
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 this
|
Atom |
findAromaticNeighbor(int notAtomIndex) |
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() |
java.lang.String |
getBioStructureTypeName() |
Bond |
getBond(Atom atomOther) |
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 this
|
Chain |
getChain() |
int |
getChainID() |
java.lang.String |
getChainIDStr() |
int |
getCovalentBondCount() |
int |
getCovalentHydrogenCount() |
boolean |
getCrossLinkLeadAtomIndexes(javajs.util.Lst<java.lang.Integer> vReturn) |
(package private) int |
getCurrentBondCount() |
float |
getDimensionValue(int dimension) |
Edge[] |
getEdges() |
int |
getElementNumber() |
java.lang.String |
getElementSymbol() |
java.lang.String |
getElementSymbolIso(boolean withIsotope) |
int |
getFormalCharge() |
private float |
getFractionalCoord(boolean fixJavaFloat,
char ch,
boolean asAbsolute,
javajs.util.P3 pt) |
private javajs.util.P3 |
getFractionalCoordPt(boolean fixJavaFloat,
boolean asAbsolute,
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.P3 pt,
javajs.util.P3 ptTemp1,
javajs.util.P3 ptTemp2) |
java.lang.String |
getGroup1(char c0) |
java.lang.String |
getGroup3(boolean allowNull) |
void |
getGroupBits(BS bs) |
short |
getGroupID() |
float |
getGroupParameter(int tok) |
private float |
getHydrophobicity() |
(package private) java.lang.String |
getIdentity(boolean allInfo) |
(package private) java.lang.String |
getIdentityXYZ(boolean allInfo,
javajs.util.P3 pt) |
int |
getImplicitHydrogenCount() |
int |
getIndex() |
java.lang.String |
getInfo() |
java.lang.String |
getInfoXYZ(boolean fixJavaFloat,
boolean useChimeFormat,
javajs.util.P3 pt) |
char |
getInsertionCode() |
int |
getIsotopeNumber() |
private float |
getMass() |
int |
getModelIndex() |
int |
getModelNumber() |
java.lang.String |
getModelNumberForLabel() |
JmolModulationSet |
getModulation() |
float |
getModulationCoord(char ch) |
(package private) int |
getMoleculeNumber(boolean inModel) |
int |
getMonomerIndex() |
int |
getOccupancy100() |
int |
getOffsetResidueAtom(java.lang.String name,
int offset) |
float |
getPartialCharge() |
int |
getPolymerIndexInModel() |
int |
getPolymerLength() |
STR |
getProteinStructureSubType() |
java.lang.String |
getProteinStructureTag() |
STR |
getProteinStructureType() |
float |
getRadius() |
int |
getRasMolRadius() |
int |
getResno() |
int |
getSelectedGroupCountWithinChain() |
int |
getSelectedGroupIndexWithinChain() |
int |
getSelectedMonomerCountWithinPolymer() |
int |
getSelectedMonomerIndexWithinPolymer() |
(package private) int |
getSeqcode() |
java.lang.String |
getSeqcodeString() |
int |
getSeqID() |
int |
getStrucNo() |
java.lang.String |
getStructureId() |
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() |
(package private) SymmetryInterface |
getUnitCell() |
int |
getValence() |
float |
getVanderwaalsRadiusFloat(Viewer vwr,
VDW type) |
private VDW |
getVdwType(VDW type) |
float |
getVibrationCoord(char ch) |
Vibration |
getVibrationVector() |
(package private) float |
getVolume(Viewer vwr,
VDW vType) |
int |
hashCode()
Returns a hash number based on the data values in this object.
|
boolean |
hasVibration() |
(package private) boolean |
isAltLoc(java.lang.String strPattern) |
boolean |
isBonded(Atom atomOther) |
(package private) boolean |
isCarbohydrate() |
boolean |
isClickable() |
boolean |
isCovalentlyBonded(Atom atomOther) |
boolean |
isCrossLinked(BNode node) |
(package private) boolean |
isCursorOnTopOf(int xCursor,
int yCursor,
int minRadius,
Atom competitor) |
boolean |
isDeleted() |
boolean |
isDna() |
boolean |
isHetero() |
boolean |
isLeadAtom() |
boolean |
isNucleic() |
boolean |
isProtein() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
isRna() |
boolean |
isTranslucent() |
boolean |
isVisible(int flags) |
(package private) boolean |
isWithinStructure(STR type) |
Atom |
setAtom(int modelIndex,
int atomIndex,
javajs.util.P3 xyz,
float radius,
BS atomSymmetry,
int atomSite,
short atomicAndIsotopeNumber,
int formalCharge,
boolean isHetero) |
void |
setAtomicAndIsotopeNumber(int n) |
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) |
(package private) void |
setGroup(Group group) |
void |
setMadAtom(Viewer vwr,
RadiusData rd) |
boolean |
setRadius(float radius) |
void |
setShapeVisibility(int flag,
boolean isVisible) |
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.
|
add, add2, add3, ave, cross, distance, distanceSquared, dot, floatToIntBits0, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON
private static final byte VIBRATION_VECTOR_FLAG
private static final byte IS_HETERO_FLAG
private static final byte FLAG_MASK
public static final int RADIUS_MAX
public static final float RADIUS_GLOBAL
public static short MAD_GLOBAL
public char altloc
public byte atomID
public int atomSite
public Group group
private float userDefinedVanDerWaalRadius
byte valence
private short atomicAndIsotopeNumber
public BS atomSymmetry
private byte formalChargeAndFlags
public short madAtom
public short colixAtom
public byte paletteID
public Bond[] bonds
private int nBondsDisplayed
public int nBackbonesDisplayed
public int clickabilityFlags
public int shapeVisibilityFlags
public Atom setAtom(int modelIndex, int atomIndex, javajs.util.P3 xyz, float radius, BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero)
modelIndex
- atomIndex
- xyz
- radius
- atomSymmetry
- atomSite
- atomicAndIsotopeNumber
- formalCharge
- isHetero
- public final void setShapeVisibility(int flag, boolean isVisible)
public boolean isCovalentlyBonded(Atom atomOther)
public boolean isBonded(Atom atomOther)
void addDisplayedBond(int stickVisibilityFlag, boolean isVisible)
public void addDisplayedBackbone(int backboneVisibilityFlag, boolean isVisible)
void deleteBond(Bond bond)
private void deleteBondAt(int i)
public int getBondedAtomIndex(int bondIndex)
getBondedAtomIndex
in interface Node
public void setMadAtom(Viewer vwr, RadiusData rd)
public short calculateMad(Viewer vwr, RadiusData rd)
public float getADPMinMax(boolean isMax)
public java.lang.Object[] getTensors()
public int getRasMolRadius()
public int getCovalentBondCount()
getCovalentBondCount
in interface Node
public int getCovalentHydrogenCount()
getCovalentHydrogenCount
in interface Node
public void setTranslucent(boolean isTranslucent, float translucentLevel)
public boolean isTranslucent()
public int getElementNumber()
getElementNumber
in interface Node
public int getIsotopeNumber()
getIsotopeNumber
in interface Node
public int getAtomicAndIsotopeNumber()
getAtomicAndIsotopeNumber
in interface Node
public void setAtomicAndIsotopeNumber(int n)
public java.lang.String getElementSymbolIso(boolean withIsotope)
public java.lang.String getElementSymbol()
boolean isAltLoc(java.lang.String strPattern)
public boolean isHetero()
public boolean hasVibration()
public void setFormalCharge(int charge)
void setVibrationVector()
public int getFormalCharge()
getFormalCharge
in interface Node
public int getOccupancy100()
public int getBfactor100()
private float getHydrophobicity()
public boolean setRadius(float radius)
public void deleteBonds(BS bsBonds)
public void setValence(int nBonds)
public int getValence()
getValence
in interface Node
public int getImplicitHydrogenCount()
getImplicitHydrogenCount
in interface Node
int getTargetValence()
public float getDimensionValue(int dimension)
private VDW getVdwType(VDW type)
type
- public float getBondingRadius()
int getCurrentBondCount()
public float getRadius()
public int getAtomSite()
getAtomSite
in interface Node
void setGroup(Group group)
public void getGroupBits(BS bs)
getGroupBits
in interface BNode
public java.lang.String getAtomName()
getAtomName
in interface Node
public java.lang.String getAtomType()
getAtomType
in interface Node
public int getAtomNumber()
public int getSeqID()
public boolean isVisible(int flags)
public float getPartialCharge()
public int getSymmetryTranslation(int symop, int[] cellRange, int nOps)
symop
- = 0, 1, 2, 3, ....cellRange
- = {444, 445, 446, 454, 455, 456, .... }nOps
- = 2 for x,y,z;-x,-y,-z, for examplepublic int getCellTranslation(int cellNNN, int[] cellRange, int nOps)
cellNNN
- cellRange
- nOps
- java.lang.String getSymmetryOperatorList(boolean isAll)
public int getModelIndex()
getModelIndex
in interface Node
int getMoleculeNumber(boolean inModel)
private float getFractionalCoord(boolean fixJavaFloat, char ch, boolean asAbsolute, javajs.util.P3 pt)
private javajs.util.P3 getFractionalCoordPt(boolean fixJavaFloat, boolean asAbsolute, javajs.util.P3 pt)
SymmetryInterface getUnitCell()
private float getFractionalUnitCoord(boolean fixJavaFloat, char ch, javajs.util.P3 pt)
javajs.util.P3 getFractionalUnitCoordPt(boolean fixJavaFloat, boolean asCartesian, javajs.util.P3 pt)
fixJavaFloat
- ALWAYS set true for any new references to this method. False is for legacy onlyasCartesian
- pt
- float getFractionalUnitDistance(javajs.util.P3 pt, javajs.util.P3 ptTemp1, javajs.util.P3 ptTemp2)
void setFractionalCoord(int tok, float fValue, boolean asAbsolute)
void setFractionalCoordTo(javajs.util.P3 ptNew, boolean asAbsolute)
public void setFractionalCoordPt(javajs.util.P3 pt, javajs.util.P3 ptNew, boolean asAbsolute)
boolean isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)
public java.lang.String getInfo()
public java.lang.String getInfoXYZ(boolean fixJavaFloat, boolean useChimeFormat, javajs.util.P3 pt)
java.lang.String getIdentityXYZ(boolean allInfo, javajs.util.P3 pt)
java.lang.String getIdentity(boolean allInfo)
public java.lang.String getGroup3(boolean allowNull)
boolean isCarbohydrate()
public boolean isPyrimidine()
isPyrimidine
in interface BNode
int getSeqcode()
public boolean isClickable()
public void setClickable(int flag)
public boolean checkVisible()
public boolean isLeadAtom()
isLeadAtom
in interface BNode
public float getGroupParameter(int tok)
public int getChainID()
getChainID
in interface BNode
public java.lang.String getChainIDStr()
getChainIDStr
in interface BNode
public int getSurfaceDistance100()
public Vibration getVibrationVector()
public JmolModulationSet getModulation()
public float getVibrationCoord(char ch)
public float getModulationCoord(char ch)
public int getPolymerLength()
public int getPolymerIndexInModel()
public int getMonomerIndex()
public int getSelectedGroupCountWithinChain()
public int getSelectedGroupIndexWithinChain()
public int getSelectedMonomerCountWithinPolymer()
public int getSelectedMonomerIndexWithinPolymer()
public Chain getChain()
public java.lang.String getModelNumberForLabel()
public int getModelNumber()
public java.lang.String getBioStructureTypeName()
getBioStructureTypeName
in interface BNode
public STR getProteinStructureType()
public STR getProteinStructureSubType()
public int getStrucNo()
public java.lang.String getStructureId()
public java.lang.String getProteinStructureTag()
public short getGroupID()
public java.lang.String getSeqcodeString()
public char getInsertionCode()
public boolean equals(java.lang.Object obj)
javajs.util.T3
equals
in class javajs.util.T3
obj
- the vector with which the comparison is made.public int hashCode()
javajs.util.T3
hashCode
in class javajs.util.T3
public Atom findAromaticNeighbor(int notAtomIndex)
public int atomPropertyInt(int tokWhat)
tokWhat
- int getSymOp()
public float atomPropertyFloat(Viewer vwr, int tokWhat, javajs.util.P3 ptTemp)
vwr
- tokWhat
- ptTemp
- private float getMass()
public java.lang.String atomPropertyString(Viewer vwr, int tokWhat)
public javajs.util.T3 atomPropertyTuple(Viewer vwr, int tok, javajs.util.P3 ptTemp)
boolean isWithinStructure(STR type)
public int getOffsetResidueAtom(java.lang.String name, int offset)
getOffsetResidueAtom
in interface BNode
public boolean isCrossLinked(BNode node)
isCrossLinked
in interface BNode
public boolean getCrossLinkLeadAtomIndexes(javajs.util.Lst<java.lang.Integer> vReturn)
getCrossLinkLeadAtomIndexes
in interface BNode
public java.lang.String toString()
javajs.util.T3
toString
in class javajs.util.T3
public BS findAtomsLike(java.lang.String atomExpression)
findAtomsLike
in interface Node