org.jmol.modelset
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 BitSet |
atomSymmetry |
static int |
BACKBONE_VISIBILITY_FLAG |
(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 |
(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,
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 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() |
void |
delete(BitSet bsBonds) |
(package private) void |
deleteBond(Bond bond) |
private void |
deleteBond(int i) |
boolean |
equals(Object obj) |
Atom |
findAromaticNeighbor(int notAtomIndex) |
float |
getADPMinMax(boolean isMax) |
char |
getAlternateLocationID() |
short |
getAtomicAndIsotopeNumber() |
byte |
getAtomID() |
String |
getAtomName() |
int |
getAtomNumber() |
int |
getAtomSite() |
BitSet |
getAtomSymmetry() |
String |
getAtomType() |
int |
getBfactor100() |
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
|
(package private) Chain |
getChain() |
char |
getChainID() |
int |
getClickabilityFlags() |
short |
getColix() |
int |
getCovalentBondCount() |
int |
getCovalentHydrogenCount() |
float |
getCovalentRadiusFloat() |
boolean |
getCrossLinkLeadAtomIndexes(List<Integer> vReturn) |
(package private) int |
getCurrentBondCount() |
float |
getDimensionValue(int dimension) |
JmolEdge[] |
getEdges() |
short |
getElementNumber() |
String |
getElementSymbol() |
String |
getElementSymbol(boolean withIsotope) |
Object[] |
getEllipsoid() |
int |
getFormalCharge() |
private Point3f |
getFractionalCoord(boolean asAbsolute) |
private float |
getFractionalCoord(char ch,
boolean asAbsolute) |
Point3f |
getFractionalUnitCoord(boolean asCartesian) |
private float |
getFractionalUnitCoord(char ch) |
float |
getFractionalUnitDistance(Point3f pt,
Point3f ptTemp1,
Point3f ptTemp2) |
Group |
getGroup() |
String |
getGroup1(char c0) |
String |
getGroup3(boolean allowNull) |
void |
getGroupBits(BitSet bs) |
short |
getGroupID() |
int |
getGroupIndex() |
float |
getGroupParameter(int tok) |
private float |
getHydrophobicity() |
(package private) String |
getIdentity(boolean allInfo) |
(package private) String |
getIdentityXYZ(boolean allInfo) |
int |
getImplicitHydrogenCount() |
int |
getIndex() |
String |
getInfo() |
(package private) String |
getInfoXYZ(boolean useChimeFormat) |
char |
getInsertionCode() |
short |
getIsotopeNumber() |
private float |
getMass() |
int |
getModelFileIndex() |
int |
getModelFileNumber() |
int |
getModelIndex() |
int |
getModelNumber() |
(package private) String |
getModelNumberForLabel() |
int |
getMoleculeNumber(boolean inModel) |
int |
getMonomerIndex() |
int |
getNBackbonesDisplayed() |
int |
getOccupancy100() |
int |
getOffsetResidueAtom(String name,
int offset) |
byte |
getPaletteID() |
float |
getPartialCharge() |
int |
getPolymerIndexInModel() |
int |
getPolymerLength() |
EnumStructure |
getProteinStructureSubType() |
String |
getProteinStructureTag() |
EnumStructure |
getProteinStructureType() |
float |
getRadius() |
int |
getRasMolRadius() |
int |
getResno() |
int |
getSelectedGroupCountWithinChain() |
int |
getSelectedGroupIndexWithinChain() |
int |
getSelectedMonomerCountWithinPolymer() |
int |
getSelectedMonomerIndexWithinPolymer() |
(package private) int |
getSeqcode() |
(package private) String |
getSeqcodeString() |
(package private) int |
getSeqNumber() |
int |
getShapeVisibilityFlags() |
int |
getStrucNo() |
String |
getStructureId() |
int |
getSurfaceDistance100() |
(package private) 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,
EnumVdw type) |
private EnumVdw |
getVdwType(EnumVdw type) |
float |
getVibrationCoord(char ch) |
Vector3f |
getVibrationVector() |
(package private) float |
getVolume(Viewer viewer,
EnumVdw vType) |
int |
hashCode() |
boolean |
hasVibration() |
(package private) boolean |
isAlternateLocationMatch(String strPattern) |
boolean |
isBonded(Atom atomOther) |
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() |
(package private) boolean |
isGroup3(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
|
boolean |
isWithinFourBonds(Atom atomOther) |
(package private) boolean |
isWithinStructure(EnumStructure type) |
void |
setAtomicAndIsotopeNumber(int n) |
void |
setAtomSymmetry(BitSet 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) |
(package private) void |
setFractionalCoord(Point3f ptNew,
boolean asAbsolute) |
(package private) void |
setFractionalCoord(Point3f pt,
Point3f 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() |
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 BitSet atomSymmetry
int atomSite
private float userDefinedVanDerWaalRadius
private short atomicAndIsotopeNumber
private byte formalChargeAndFlags
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 static final int BACKBONE_VISIBILITY_FLAG
public Atom(int modelIndex, int atomIndex, float x, float y, float z, float radius, BitSet atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero, char alternateLocationID)
public void setAtomSymmetry(BitSet bsSymmetry)
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 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 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 String getElementSymbol(boolean withIsotope)
public String getElementSymbol()
public char getAlternateLocationID()
boolean isAlternateLocationMatch(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 delete(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)
private EnumVdw getVdwType(EnumVdw type)
type
- public float getCovalentRadiusFloat()
public float getBondingRadiusFloat()
int getCurrentBondCount()
public short getColix()
public byte getPaletteID()
public float getRadius()
public int getAtomSite()
getAtomSite
in interface JmolNode
public BitSet getAtomSymmetry()
void setGroup(Group group)
public Group getGroup()
public void getGroupBits(BitSet bs)
getGroupBits
in interface JmolNode
public String getAtomName()
getAtomName
in interface JmolNode
public String getAtomType()
public int getAtomNumber()
public boolean isInFrame()
public int getShapeVisibilityFlags()
public boolean isShapeVisible(int shapeVisibilityFlag)
public float getPartialCharge()
public 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
- String getSymmetryOperatorList()
public int getModelIndex()
getModelIndex
in interface JmolNode
public int getMoleculeNumber(boolean inModel)
private float getFractionalCoord(char ch, boolean asAbsolute)
private float getFractionalUnitCoord(char ch)
private Point3f getFractionalCoord(boolean asAbsolute)
public Point3f getFractionalUnitCoord(boolean asCartesian)
public float getFractionalUnitDistance(Point3f pt, Point3f ptTemp1, Point3f ptTemp2)
void setFractionalCoord(int tok, float fValue, boolean asAbsolute)
void setFractionalCoord(Point3f ptNew, boolean asAbsolute)
boolean isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)
public String getInfo()
String getInfoXYZ(boolean useChimeFormat)
String getIdentityXYZ(boolean allInfo)
String getIdentity(boolean allInfo)
public int getGroupIndex()
boolean isGroup3(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 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()
String getModelNumberForLabel()
public int getModelNumber()
public int getModelFileIndex()
public int getModelFileNumber()
public String getBioStructureTypeName()
getBioStructureTypeName
in interface JmolNode
public EnumStructure getProteinStructureType()
public EnumStructure getProteinStructureSubType()
public int getStrucNo()
public String getStructureId()
public String getProteinStructureTag()
public short getGroupID()
String getSeqcodeString()
int getSeqNumber()
public char getInsertionCode()
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()
boolean isWithinStructure(EnumStructure type)
public int getOffsetResidueAtom(String name, int offset)
getOffsetResidueAtom
in interface JmolNode
public boolean isCrossLinked(JmolNode node)
isCrossLinked
in interface JmolNode
public boolean getCrossLinkLeadAtomIndexes(List<Integer> vReturn)
getCrossLinkLeadAtomIndexes
in interface JmolNode
public boolean isWithinFourBonds(Atom atomOther)