public final class Atom extends Point3fi implements JmolNode
Modifier and Type | Field and Description |
---|---|
char |
alternateLocationID |
private short |
atomicAndIsotopeNumber |
byte |
atomID |
int |
atomSite |
private BS |
atomSymmetry |
static int |
BACKBONE_VISIBILITY_FLAG |
(package private) Bond[] |
bonds |
int |
clickabilityFlags |
short |
colixAtom |
private static byte |
FLAG_MASK |
private byte |
formalChargeAndFlags |
Group |
group |
private static byte |
IS_HETERO_FLAG |
short |
madAtom |
(package private) int |
nBackbonesDisplayed |
(package private) int |
nBondsDisplayed |
(package private) byte |
paletteID |
static int |
RADIUS_MAX |
int |
shapeVisibilityFlags |
private float |
userDefinedVanDerWaalRadius |
(package private) byte |
valence |
private static byte |
VIBRATION_VECTOR_FLAG |
index, modelIndex, screenDiameter, screenX, screenY, screenZ
Constructor and Description |
---|
Atom(int modelIndex,
int atomIndex,
float x,
float y,
float z,
float radius,
BS atomSymmetry,
int atomSite,
short atomicAndIsotopeNumber,
int formalCharge,
boolean isHetero) |
Modifier and Type | Method and Description |
---|---|
void |
addDisplayedBackbone(int backboneVisibilityFlag,
boolean isVisible) |
(package private) void |
addDisplayedBond(int stickVisibilityFlag,
boolean isVisible) |
static float |
atomPropertyFloat(Viewer viewer,
Atom atom,
int tokWhat)
called by isosurface and int comparator via atomProperty() and also by
getBitsetProperty()
|
static int |
atomPropertyInt(Atom atom,
int tokWhat)
called by isosurface and int comparator via atomProperty()
and also by getBitsetProperty()
|
static java.lang.String |
atomPropertyString(Viewer viewer,
Atom atom,
int tokWhat) |
static Tuple3f |
atomPropertyTuple(Atom atom,
int tok) |
short |
calculateMad(Viewer viewer,
RadiusData rd) |
(package private) void |
clearBonds() |
(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) |
char |
getAlternateLocationID() |
int |
getAtomicAndIsotopeNumber() |
byte |
getAtomID() |
java.lang.String |
getAtomName() |
int |
getAtomNumber() |
int |
getAtomSite() |
BS |
getAtomSymmetry() |
java.lang.String |
getAtomType() |
int |
getBfactor100() |
java.lang.String |
getBioStructureTypeName() |
Bond |
getBond(Atom atomOther) |
int |
getBondedAtomIndex(int bondIndex) |
float |
getBondingRadiusFloat() |
Bond[] |
getBonds() |
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 |
getClickabilityFlags() |
short |
getColix() |
int |
getCovalentBondCount() |
int |
getCovalentHydrogenCount() |
private float |
getCovalentRadiusFloat() |
boolean |
getCrossLinkLeadAtomIndexes(JmolList<java.lang.Integer> vReturn) |
(package private) int |
getCurrentBondCount() |
float |
getDimensionValue(int dimension) |
JmolEdge[] |
getEdges() |
int |
getElementNumber() |
java.lang.String |
getElementSymbol() |
java.lang.String |
getElementSymbolIso(boolean withIsotope) |
int |
getFormalCharge() |
private float |
getFractionalCoord(char ch,
boolean asAbsolute) |
private P3 |
getFractionalCoordPt(boolean asAbsolute) |
private float |
getFractionalUnitCoord(char ch) |
(package private) P3 |
getFractionalUnitCoordPt(boolean asCartesian) |
(package private) float |
getFractionalUnitDistance(P3 pt,
P3 ptTemp1,
P3 ptTemp2) |
Group |
getGroup() |
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) |
int |
getImplicitHydrogenCount() |
int |
getIndex() |
java.lang.String |
getInfo() |
(package private) java.lang.String |
getInfoXYZ(boolean useChimeFormat) |
char |
getInsertionCode() |
int |
getIsotopeNumber() |
private float |
getMass() |
int |
getModelFileIndex() |
int |
getModelFileNumber() |
int |
getModelIndex() |
int |
getModelNumber() |
java.lang.String |
getModelNumberForLabel() |
(package private) int |
getMoleculeNumber(boolean inModel) |
int |
getMonomerIndex() |
int |
getNBackbonesDisplayed() |
int |
getOccupancy100() |
int |
getOffsetResidueAtom(java.lang.String name,
int offset) |
byte |
getPaletteID() |
float |
getPartialCharge() |
int |
getPolymerIndexInModel() |
int |
getPolymerLength() |
EnumStructure |
getProteinStructureSubType() |
java.lang.String |
getProteinStructureTag() |
EnumStructure |
getProteinStructureType() |
float |
getRadius() |
int |
getRasMolRadius() |
int |
getResno() |
int |
getSelectedGroupCountWithinChain() |
int |
getSelectedGroupIndexWithinChain() |
int |
getSelectedMonomerCountWithinPolymer() |
int |
getSelectedMonomerIndexWithinPolymer() |
(package private) int |
getSeqcode() |
java.lang.String |
getSeqcodeString() |
int |
getShapeVisibilityFlags() |
int |
getStrucNo() |
java.lang.String |
getStructureId() |
int |
getSurfaceDistance100() |
(package private) java.lang.String |
getSymmetryOperatorList() |
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 |
getTargetValence() |
Tensor[] |
getTensors() |
int |
getValence() |
float |
getVanderwaalsRadiusFloat(Viewer viewer,
EnumVdw type) |
private EnumVdw |
getVdwType(EnumVdw type) |
float |
getVibrationCoord(char ch) |
V3 |
getVibrationVector() |
(package private) float |
getVolume(Viewer viewer,
EnumVdw vType) |
int |
hashCode()
Returns a hash number based on the data values in this object.
|
boolean |
hasVibration() |
(package private) boolean |
isAlternateLocationMatch(java.lang.String strPattern) |
boolean |
isBonded(Atom atomOther) |
(package private) boolean |
isCarbohydrate() |
boolean |
isClickable() |
boolean |
isCovalentlyBonded(Atom atomOther) |
boolean |
isCrossLinked(JmolNode node) |
(package private) boolean |
isCursorOnTopOf(int xCursor,
int yCursor,
int minRadius,
Atom competitor) |
boolean |
isDeleted() |
boolean |
isDna() |
boolean |
isHetero() |
boolean |
isInFrame() |
boolean |
isLeadAtom() |
boolean |
isNucleic() |
boolean |
isProtein() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
isRna() |
boolean |
isShapeVisible(int shapeVisibilityFlag) |
boolean |
isTranslucent() |
boolean |
isVisible(int flags)
determine if an atom or its PDB group is visible
|
boolean |
isWithinFourBonds(Atom atomOther) |
(package private) boolean |
isWithinStructure(EnumStructure type) |
void |
setAltLoc(char altLoc) |
void |
setAtomicAndIsotopeNumber(int n) |
void |
setAtomSymmetry(BS bsSymmetry) |
void |
setBonds(Bond[] bonds) |
void |
setClickable(int flag) |
void |
setColixAtom(short colixAtom) |
void |
setFormalCharge(int charge) |
(package private) void |
setFractionalCoord(int tok,
float fValue,
boolean asAbsolute) |
void |
setFractionalCoordPt(P3 pt,
P3 ptNew,
boolean asAbsolute) |
(package private) void |
setFractionalCoordTo(P3 ptNew,
boolean asAbsolute) |
(package private) void |
setGroup(Group group) |
void |
setMadAtom(Viewer viewer,
RadiusData rd) |
void |
setPaletteID(byte paletteID) |
boolean |
setRadius(float radius) |
void |
setShapeVisibility(int flag,
boolean isVisible) |
void |
setShapeVisibilityFlags(int flag) |
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.
|
distance, distanceSquared, new3, newP
add, add2, scale, scaleAdd, scaleAdd2, set, setA, setT, sub, sub2
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 char alternateLocationID
public byte atomID
public int atomSite
public Group group
private float userDefinedVanDerWaalRadius
byte valence
private short atomicAndIsotopeNumber
private BS atomSymmetry
private byte formalChargeAndFlags
public short madAtom
public short colixAtom
byte paletteID
Bond[] bonds
int nBondsDisplayed
int nBackbonesDisplayed
public int clickabilityFlags
public int shapeVisibilityFlags
public static final int BACKBONE_VISIBILITY_FLAG
public Atom(int modelIndex, int atomIndex, float x, float y, float z, float radius, BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero)
modelIndex
- atomIndex
- x
- y
- z
- radius
- atomSymmetry
- atomSite
- atomicAndIsotopeNumber
- formalCharge
- isHetero
- public byte getAtomID()
public Bond[] getBonds()
public void setBonds(Bond[] bonds)
public int getNBackbonesDisplayed()
public void setAltLoc(char altLoc)
public final void setShapeVisibilityFlags(int flag)
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)
void clearBonds()
public int getBondedAtomIndex(int bondIndex)
getBondedAtomIndex
in interface JmolNode
public void setMadAtom(Viewer viewer, RadiusData rd)
public short calculateMad(Viewer viewer, RadiusData rd)
public float getADPMinMax(boolean isMax)
public Tensor[] getTensors()
public int getRasMolRadius()
public int getCovalentBondCount()
getCovalentBondCount
in interface JmolNode
public int getCovalentHydrogenCount()
getCovalentHydrogenCount
in interface JmolNode
public void setColixAtom(short colixAtom)
public void setPaletteID(byte paletteID)
public void setTranslucent(boolean isTranslucent, float translucentLevel)
public boolean isTranslucent()
public int getElementNumber()
getElementNumber
in interface JmolNode
public int getIsotopeNumber()
getIsotopeNumber
in interface JmolNode
public int getAtomicAndIsotopeNumber()
getAtomicAndIsotopeNumber
in interface JmolNode
public void setAtomicAndIsotopeNumber(int n)
public java.lang.String getElementSymbolIso(boolean withIsotope)
public java.lang.String getElementSymbol()
public char getAlternateLocationID()
boolean isAlternateLocationMatch(java.lang.String strPattern)
public boolean isHetero()
public boolean hasVibration()
public void setFormalCharge(int charge)
void setVibrationVector()
public int getFormalCharge()
getFormalCharge
in interface JmolNode
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 JmolNode
public int getImplicitHydrogenCount()
getImplicitHydrogenCount
in interface JmolNode
int getTargetValence()
public float getDimensionValue(int dimension)
private EnumVdw getVdwType(EnumVdw type)
type
- private float getCovalentRadiusFloat()
public float getBondingRadiusFloat()
int getCurrentBondCount()
public short getColix()
public byte getPaletteID()
public float getRadius()
public int getAtomSite()
getAtomSite
in interface JmolNode
public void setAtomSymmetry(BS bsSymmetry)
public BS getAtomSymmetry()
void setGroup(Group group)
public Group getGroup()
public void getGroupBits(BS bs)
getGroupBits
in interface JmolNode
public java.lang.String getAtomName()
getAtomName
in interface JmolNode
public java.lang.String getAtomType()
getAtomType
in interface JmolNode
public int getAtomNumber()
public boolean isInFrame()
public int getShapeVisibilityFlags()
public boolean isShapeVisible(int shapeVisibilityFlag)
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()
public int getModelIndex()
getModelIndex
in interface JmolNode
int getMoleculeNumber(boolean inModel)
private float getFractionalCoord(char ch, boolean asAbsolute)
private P3 getFractionalCoordPt(boolean asAbsolute)
private float getFractionalUnitCoord(char ch)
P3 getFractionalUnitCoordPt(boolean asCartesian)
void setFractionalCoord(int tok, float fValue, boolean asAbsolute)
void setFractionalCoordTo(P3 ptNew, boolean asAbsolute)
boolean isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)
public java.lang.String getInfo()
java.lang.String getInfoXYZ(boolean useChimeFormat)
java.lang.String getIdentityXYZ(boolean allInfo)
java.lang.String getIdentity(boolean allInfo)
public java.lang.String getGroup3(boolean allowNull)
boolean isCarbohydrate()
public boolean isPyrimidine()
isPyrimidine
in interface JmolNode
int getSeqcode()
public boolean isClickable()
public int getClickabilityFlags()
public void setClickable(int flag)
public boolean isVisible(int flags)
flags
- public boolean isLeadAtom()
isLeadAtom
in interface JmolNode
public float getGroupParameter(int tok)
public int getChainID()
getChainID
in interface JmolNode
public java.lang.String getChainIDStr()
getChainIDStr
in interface JmolNode
public int getSurfaceDistance100()
public V3 getVibrationVector()
public float getVibrationCoord(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 int getModelFileIndex()
public int getModelFileNumber()
public java.lang.String getBioStructureTypeName()
getBioStructureTypeName
in interface JmolNode
public EnumStructure getProteinStructureType()
public EnumStructure 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)
Tuple3f
public int hashCode()
Tuple3f
public Atom findAromaticNeighbor(int notAtomIndex)
public static int atomPropertyInt(Atom atom, int tokWhat)
atom
- tokWhat
- public static float atomPropertyFloat(Viewer viewer, Atom atom, int tokWhat)
viewer
- atom
- tokWhat
- private float getMass()
public static java.lang.String atomPropertyString(Viewer viewer, Atom atom, int tokWhat)
boolean isWithinStructure(EnumStructure type)
public int getOffsetResidueAtom(java.lang.String name, int offset)
getOffsetResidueAtom
in interface JmolNode
public boolean isCrossLinked(JmolNode node)
isCrossLinked
in interface JmolNode
public boolean getCrossLinkLeadAtomIndexes(JmolList<java.lang.Integer> vReturn)
getCrossLinkLeadAtomIndexes
in interface JmolNode
public java.lang.String toString()
Tuple3f
public boolean isWithinFourBonds(Atom atomOther)
public BS findAtomsLike(java.lang.String atomExpression)
findAtomsLike
in interface JmolNode