public final class Atom extends Point3fi implements JmolNode
Modifier and Type | Field and Description |
---|---|
(package private) char |
alternateLocationID |
private short |
atomicAndIsotopeNumber |
byte |
atomID |
(package private) int |
atomSite |
private java.util.BitSet |
atomSymmetry |
(package private) Bond[] |
bonds |
(package private) int |
clickabilityFlags |
(package private) short |
colixAtom |
private static byte |
FLAG_MASK |
private byte |
formalChargeAndFlags |
(package private) 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 |
(package private) int |
shapeVisibilityFlags |
private float |
userDefinedVanDerWaalRadius |
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,
java.util.BitSet atomSymmetry,
int atomSite,
short atomicAndIsotopeNumber,
int formalCharge,
boolean isHetero,
char alternateLocationID) |
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(Atom atom,
int tokWhat) |
static javax.vecmath.Tuple3f |
atomPropertyTuple(Atom atom,
int tok) |
short |
calculateMad(Viewer viewer,
RadiusData rd) |
(package private) void |
clearBonds() |
void |
delete(java.util.BitSet bsBonds) |
(package private) void |
deleteBond(Bond bond) |
private void |
deleteBond(int i) |
boolean |
equals(java.lang.Object obj) |
Atom |
findAromaticNeighbor(int notAtomIndex) |
float |
getADPMinMax(boolean isMax) |
char |
getAlternateLocationID() |
short |
getAtomicAndIsotopeNumber() |
byte |
getAtomID() |
java.lang.String |
getAtomName() |
int |
getAtomNumber() |
int |
getAtomSite() |
java.util.BitSet |
getAtomSymmetry() |
java.lang.String |
getAtomType() |
int |
getBfactor100() |
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
|
(package private) Chain |
getChain() |
char |
getChainID() |
int |
getClickabilityFlags() |
short |
getColix() |
int |
getCovalentBondCount() |
int |
getCovalentHydrogenCount() |
float |
getCovalentRadiusFloat() |
boolean |
getCrossLinkLeadAtomIndexes(java.util.List vReturn) |
(package private) int |
getCurrentBondCount() |
float |
getDimensionValue(int dimension) |
JmolEdge[] |
getEdges() |
short |
getElementNumber() |
java.lang.String |
getElementSymbol() |
java.lang.String |
getElementSymbol(boolean withIsotope) |
java.lang.Object[] |
getEllipsoid() |
int |
getFormalCharge() |
private javax.vecmath.Point3f |
getFractionalCoord(boolean asAbsolute) |
private float |
getFractionalCoord(char ch,
boolean asAbsolute) |
javax.vecmath.Point3f |
getFractionalUnitCoord(boolean asCartesian) |
private float |
getFractionalUnitCoord(char ch) |
float |
getFractionalUnitDistance(javax.vecmath.Point3f pt,
javax.vecmath.Point3f ptTemp1,
javax.vecmath.Point3f ptTemp2) |
Group |
getGroup() |
java.lang.String |
getGroup1(char c0) |
java.lang.String |
getGroup3(boolean allowNull) |
short |
getGroupID() |
int |
getGroupIndex() |
float |
getGroupParameter(int tok) |
java.lang.String |
getGroupType() |
(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() |
short |
getIsotopeNumber() |
int |
getModelFileIndex() |
int |
getModelFileNumber() |
int |
getModelIndex() |
int |
getModelNumber() |
(package private) java.lang.String |
getModelNumberForLabel() |
int |
getMoleculeNumber() |
int |
getMonomerIndex() |
int |
getNBackbonesDisplayed() |
int |
getOccupancy100() |
int |
getOffsetResidueAtom(java.lang.String name,
int offset) |
byte |
getPaletteID() |
float |
getPartialCharge() |
int |
getPolymerIndexInModel() |
int |
getPolymerLength() |
byte |
getProteinStructureSubType() |
java.lang.String |
getProteinStructureTag() |
byte |
getProteinStructureType() |
float |
getRadius() |
int |
getRasMolRadius() |
int |
getResno() |
int |
getSelectedGroupCountWithinChain() |
int |
getSelectedGroupIndexWithinChain() |
int |
getSelectedMonomerCountWithinPolymer() |
int |
getSelectedMonomerIndexWithinPolymer() |
(package private) int |
getSeqcode() |
(package private) java.lang.String |
getSeqcodeString() |
(package private) int |
getSeqNumber() |
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() |
int |
getValence() |
float |
getVanderwaalsRadiusFloat(Viewer viewer,
int iType) |
private int |
getVdwType(int iType) |
float |
getVibrationCoord(char ch) |
javax.vecmath.Vector3f |
getVibrationVector() |
(package private) float |
getVolume(Viewer viewer,
int iType) |
int |
hashCode() |
boolean |
hasVibration() |
(package private) boolean |
isAlternateLocationMatch(java.lang.String strPattern) |
boolean |
isBonded(Atom atomOther) |
boolean |
isCarbohydrate() |
boolean |
isClickable() |
boolean |
isCrossLinked(JmolNode node) |
(package private) boolean |
isCursorOnTopOf(int xCursor,
int yCursor,
int minRadius,
Atom competitor) |
boolean |
isDeleted() |
boolean |
isDna() |
(package private) boolean |
isGroup3(java.lang.String group3) |
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
|
(package private) boolean |
isWithinStructure(byte type) |
void |
setAtomicAndIsotopeNumber(int n) |
void |
setBonds(Bond[] bonds) |
void |
setClickable(int flag) |
void |
setColixAtom(short colixAtom) |
(package private) void |
setFormalCharge(int charge) |
(package private) void |
setFractionalCoord(int tok,
float fValue,
boolean asAbsolute) |
(package private) void |
setFractionalCoord(javax.vecmath.Point3f ptNew,
boolean asAbsolute) |
(package private) void |
setFractionalCoord(javax.vecmath.Point3f pt,
javax.vecmath.Point3f ptNew,
boolean asAbsolute) |
(package private) void |
setGroup(Group group) |
void |
setGroupBits(java.util.BitSet bs) |
void |
setMadAtom(Viewer viewer,
RadiusData rd) |
void |
setPaletteID(byte paletteID) |
boolean |
setRadius(float radius) |
void |
setShapeVisibility(int shapeVisibilityFlag,
boolean isVisible) |
void |
setShapeVisibilityFlags(int flag) |
void |
setTranslucent(boolean isTranslucent,
float translucentLevel) |
void |
setValence(int nBonds) |
(package private) void |
setVibrationVector() |
java.lang.String |
toString() |
distance, distanceL1, distanceLinf, distanceSquared, project
absolute, absolute, add, add, clamp, clamp, clampMax, clampMax, clampMin, clampMin, clone, epsilonEquals, equals, get, get, getX, getY, getZ, interpolate, interpolate, negate, negate, scale, scale, scaleAdd, scaleAdd, set, set, set, set, setX, setY, setZ, sub, sub
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
Group group
private java.util.BitSet atomSymmetry
int atomSite
private float userDefinedVanDerWaalRadius
private short atomicAndIsotopeNumber
private byte formalChargeAndFlags
private byte valence
char alternateLocationID
public byte atomID
public short madAtom
short colixAtom
byte paletteID
Bond[] bonds
int nBondsDisplayed
int nBackbonesDisplayed
int clickabilityFlags
int shapeVisibilityFlags
public Atom(int modelIndex, int atomIndex, float x, float y, float z, float radius, java.util.BitSet atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero, char alternateLocationID)
public byte getAtomID()
public Bond[] getBonds()
public void setBonds(Bond[] bonds)
public int getNBackbonesDisplayed()
public final void setShapeVisibilityFlags(int flag)
public final void setShapeVisibility(int shapeVisibilityFlag, boolean isVisible)
public boolean isBonded(Atom atomOther)
void addDisplayedBond(int stickVisibilityFlag, boolean isVisible)
public void addDisplayedBackbone(int backboneVisibilityFlag, boolean isVisible)
void deleteBond(Bond bond)
private void deleteBond(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 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 short getElementNumber()
getElementNumber
in interface JmolNode
public short getIsotopeNumber()
getIsotopeNumber
in interface JmolNode
public short getAtomicAndIsotopeNumber()
getAtomicAndIsotopeNumber
in interface JmolNode
public void setAtomicAndIsotopeNumber(int n)
public java.lang.String getElementSymbol(boolean withIsotope)
public java.lang.String getElementSymbol()
public char getAlternateLocationID()
boolean isAlternateLocationMatch(java.lang.String strPattern)
public boolean isHetero()
public boolean hasVibration()
void setFormalCharge(int charge)
void setVibrationVector()
public int getFormalCharge()
getFormalCharge
in interface JmolNode
public int getOccupancy100()
public int getBfactor100()
public boolean setRadius(float radius)
public void delete(java.util.BitSet 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)
public float getVanderwaalsRadiusFloat(Viewer viewer, int iType)
private int getVdwType(int iType)
iType
- public float getCovalentRadiusFloat()
public float getBondingRadiusFloat()
float getVolume(Viewer viewer, int iType)
int getCurrentBondCount()
public short getColix()
public byte getPaletteID()
public float getRadius()
public int getAtomSite()
getAtomSite
in interface JmolNode
public java.util.BitSet getAtomSymmetry()
void setGroup(Group group)
public Group getGroup()
public void setGroupBits(java.util.BitSet bs)
setGroupBits
in interface JmolNode
public java.lang.String getAtomName()
getAtomName
in interface JmolNode
public java.lang.String getAtomType()
public int getAtomNumber()
public boolean isInFrame()
public int getShapeVisibilityFlags()
public boolean isShapeVisible(int shapeVisibilityFlag)
public float getPartialCharge()
public java.lang.Object[] getEllipsoid()
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
public int getMoleculeNumber()
private float getFractionalCoord(char ch, boolean asAbsolute)
private float getFractionalUnitCoord(char ch)
private javax.vecmath.Point3f getFractionalCoord(boolean asAbsolute)
public javax.vecmath.Point3f getFractionalUnitCoord(boolean asCartesian)
public float getFractionalUnitDistance(javax.vecmath.Point3f pt, javax.vecmath.Point3f ptTemp1, javax.vecmath.Point3f ptTemp2)
void setFractionalCoord(int tok, float fValue, boolean asAbsolute)
void setFractionalCoord(javax.vecmath.Point3f ptNew, boolean asAbsolute)
void setFractionalCoord(javax.vecmath.Point3f pt, javax.vecmath.Point3f 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 int getGroupIndex()
public java.lang.String getGroup3(boolean allowNull)
boolean isGroup3(java.lang.String group3)
public 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
- TODOpublic boolean isLeadAtom()
isLeadAtom
in interface JmolNode
public float getGroupParameter(int tok)
public char getChainID()
getChainID
in interface JmolNode
public int getSurfaceDistance100()
public javax.vecmath.Vector3f 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()
Chain getChain()
java.lang.String getModelNumberForLabel()
public int getModelNumber()
public int getModelFileIndex()
public int getModelFileNumber()
public java.lang.String getGroupType()
getGroupType
in interface JmolNode
public byte getProteinStructureType()
public byte getProteinStructureSubType()
public int getStrucNo()
public java.lang.String getStructureId()
public java.lang.String getProteinStructureTag()
public short getGroupID()
java.lang.String getSeqcodeString()
int getSeqNumber()
public char getInsertionCode()
public boolean equals(java.lang.Object obj)
equals
in class javax.vecmath.Tuple3f
public int hashCode()
hashCode
in class javax.vecmath.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
- public static java.lang.String atomPropertyString(Atom atom, int tokWhat)
public static javax.vecmath.Tuple3f atomPropertyTuple(Atom atom, int tok)
boolean isWithinStructure(byte 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(java.util.List vReturn)
getCrossLinkLeadAtomIndexes
in interface JmolNode
public java.lang.String toString()
toString
in class javax.vecmath.Tuple3f