public class Atom extends Point3fi implements Node
Modifier and Type | Field and 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 |
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 |
---|---|
(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()
|
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(BS bsBonds) |
(package private) void |
deleteBond(Bond bond) |
private void |
deleteBondAt(int i) |
boolean |
equals(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(String atomExpression) |
float |
getADPMinMax(boolean isMax) |
int |
getAtomicAndIsotopeNumber() |
String |
getAtomName() |
int |
getAtomNumber() |
int |
getAtomSite() |
String |
getAtomType() |
int |
getBfactor100() |
char |
getBioSmilesType() |
String |
getBioStructureTypeName() |
Bond |
getBond(Atom atomOther) |
int |
getBondCount() |
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
|
int |
getChainID() |
String |
getChainIDStr() |
int |
getCovalentBondCount() |
int |
getCovalentBondCountPlusMissingH()
includes actual + missing
|
int |
getCovalentHydrogenCount() |
boolean |
getCrossLinkVector(javajs.util.Lst<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() |
int |
getElementNumber() |
String |
getElementSymbol() |
String |
getElementSymbolIso(boolean withIsotope) |
float |
getFloatProperty(String property) |
int |
getFormalCharge() |
private float |
getFractionalCoord(boolean fixJavaFloat,
char ch,
boolean asAbsolute,
javajs.util.P3 pt) |
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.T3 pt,
javajs.util.T3 ptTemp1,
javajs.util.T3 ptTemp2) |
String |
getGroup1(char c0) |
String |
getGroup3(boolean allowNull) |
void |
getGroupBits(BS bs) |
float |
getHydrophobicity() |
(package private) String |
getIdentity(boolean allInfo) |
String |
getIdentityXYZ(boolean allInfo,
javajs.util.P3 pt) |
int |
getImplicitHydrogenCount()
can be > 0 for PDB model with no H atoms or for SMILES string CCC
|
int |
getIndex() |
String |
getInfo() |
char |
getInsertionCode() |
int |
getIsotopeNumber() |
private float |
getMass() |
int |
getModelIndex()
SMILES only
|
int |
getModelNumber() |
String |
getModelNumberForLabel() |
JmolModulationSet |
getModulation() |
int |
getMoleculeNumber(boolean inModel) |
int |
getOccupancy100() |
int |
getOffsetResidueAtom(String name,
int offset) |
float |
getPartialCharge() |
float |
getRadius() |
int |
getRasMolRadius() |
int |
getResno() |
int |
getSeqID() |
int |
getSurfaceDistance100() |
(package private) 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() |
Object[] |
getTensors() |
int |
getTotalHydrogenCount() |
int |
getTotalValence() |
(package private) SymmetryInterface |
getUnitCell() |
String |
getUnitID(int flags) |
int |
getValence()
return the total bond order for this atom
|
float |
getVanderwaalsRadiusFloat(Viewer vwr,
VDW type) |
private VDW |
getVdwType(VDW type) |
float |
getVib(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() |
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) |
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) |
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() |
String |
toString()
Returns a string that contains the values of this Tuple3f.
|
add, add2, add3, ave, cross, distance, distanceSquared, dot, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON
public static final int ATOM_INFRAME
public static final int ATOM_VISSET
public static final int ATOM_VISIBLE
public static final int ATOM_NOTHIDDEN
public static final int ATOM_NOFLAGS
public static final int ATOM_INFRAME_NOTHIDDEN
public static final int ATOM_SHAPE_VIS_MASK
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)
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 Object[] getTensors()
public int getRasMolRadius()
public int getBondCount()
getBondCount
in interface Node
public void setTranslucent(boolean isTranslucent, float translucentLevel)
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 String getElementSymbolIso(boolean withIsotope)
public String getElementSymbol()
public boolean isHetero()
public boolean hasVibration()
public void setFormalCharge(int charge)
void setVibrationVector()
public int getFormalCharge()
getFormalCharge
in interface Node
public int getOccupancy100()
public boolean isOccupied()
public int getBfactor100()
public float getHydrophobicity()
public boolean setRadius(float radius)
public void delete(BS bsBonds)
public void setValence(int nBonds)
public int getValence()
getValence
in interface Node
public int getCovalentBondCount()
getCovalentBondCount
in interface Node
public int getCovalentHydrogenCount()
getCovalentHydrogenCount
in interface Node
public int getImplicitHydrogenCount()
Node
getImplicitHydrogenCount
in interface Node
public int getTotalHydrogenCount()
getTotalHydrogenCount
in interface Node
public int getTotalValence()
getTotalValence
in interface Node
public int getCovalentBondCountPlusMissingH()
Node
getCovalentBondCountPlusMissingH
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
public void getGroupBits(BS bs)
getGroupBits
in interface Node
public String getAtomName()
getAtomName
in interface Node
public String getAtomType()
getAtomType
in interface Node
public int getAtomNumber()
getAtomNumber
in interface Node
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
- String getSymmetryOperatorList(boolean isAll)
public int getModelIndex()
getModelIndex
in interface Node
public int getMoleculeNumber(boolean inModel)
getMoleculeNumber
in interface Node
private float getFractionalCoord(boolean fixJavaFloat, char ch, boolean asAbsolute, javajs.util.P3 pt)
public 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.T3 pt, javajs.util.T3 ptTemp1, javajs.util.T3 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 String getInfo()
public String getIdentityXYZ(boolean allInfo, javajs.util.P3 pt)
String getIdentity(boolean allInfo)
public char getBioSmilesType()
getBioSmilesType
in interface Node
public boolean isPyrimidine()
isPyrimidine
in interface Node
public boolean isClickable()
public void setClickable(int flag)
public boolean checkVisible()
public boolean isLeadAtom()
isLeadAtom
in interface Node
public int getChainID()
getChainID
in interface Node
public String getChainIDStr()
getChainIDStr
in interface Node
public int getSurfaceDistance100()
public Vibration getVibrationVector()
public JmolModulationSet getModulation()
public String getModelNumberForLabel()
public int getModelNumber()
public String getBioStructureTypeName()
getBioStructureTypeName
in interface Node
public boolean equals(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
- public float getVib(char ch)
private float getMass()
public char getInsertionCode()
getInsertionCode
in interface Node
public javajs.util.T3 atomPropertyTuple(Viewer vwr, int tok, javajs.util.P3 ptTemp)
public int getOffsetResidueAtom(String name, int offset)
getOffsetResidueAtom
in interface Node
public boolean isCrossLinked(Node node)
isCrossLinked
in interface Node
public boolean getCrossLinkVector(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
getCrossLinkVector
in interface Node
public String toString()
javajs.util.T3
toString
in class javajs.util.T3
public BS findAtomsLike(String atomExpression)
findAtomsLike
in interface Node
public String getUnitID(int flags)
public float getFloatProperty(String property)
getFloatProperty
in interface Node
property
- "property_xxxx"