public abstract class AtomCollection
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
protected class |
AtomCollection.AtomSorter |
Modifier and Type | Field and Description |
---|---|
(package private) int[] |
aaRet |
int |
ac |
private static float |
almost180 |
Atom[] |
at |
private int |
atomCapacity |
(package private) java.lang.String[] |
atomNames |
(package private) int[] |
atomResnos |
(package private) int[] |
atomSeqIDs |
(package private) int[] |
atomSerials |
java.lang.Object[][] |
atomTensorList |
java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>> |
atomTensors |
(package private) java.lang.String[] |
atomTypes |
private int |
bfactor100Hi |
private int |
bfactor100Lo |
(package private) short[] |
bfactor100s |
BioModelSet |
bioModelset
If any model in the collection is a BioModel, then
it is also indicated here as a "bioModelset", meaning
|
(package private) float[] |
bondingRadii |
javajs.util.BS |
bsClickable |
private javajs.util.BS |
bsHidden |
javajs.util.BS |
bsModulated |
javajs.util.BS |
bsPartialCharges |
protected Bspf |
bspf
Binary Space Partitioning Forest
|
private javajs.util.BS |
bsSurface |
javajs.util.BS |
bsVisible |
boolean |
canSkipLoad |
(package private) float[] |
dssrData |
protected GData |
g3d |
private boolean |
hasBfactorRange |
private boolean |
haveBSClickable |
private boolean |
haveBSVisible |
protected boolean |
haveChirality |
boolean |
haveStraightness |
(package private) float[] |
hydrophobicities |
private LabelToken |
labeler |
protected float |
maxBondingRadius |
private float |
maxVanderwaalsRadius |
private int |
nSurfaceAtoms |
float[] |
occupancies |
(package private) float[] |
partialCharges |
protected SymmetryInterface |
pointGroup |
protected boolean |
preserveState |
private static float |
sqrt3_2 |
protected int[] |
surfaceDistance100s |
private int |
surfaceDistanceMax |
static int |
TAINT_ATOMNAME |
static int |
TAINT_ATOMNO |
static int |
TAINT_ATOMTYPE |
static int |
TAINT_BONDINGRADIUS |
static int |
TAINT_CHAIN |
static int |
TAINT_COORD |
static int |
TAINT_ELEMENT |
static int |
TAINT_FORMALCHARGE |
static int |
TAINT_HYDROPHOBICITY |
static int |
TAINT_MAX |
static int |
TAINT_OCCUPANCY |
static int |
TAINT_PARTIALCHARGE |
static int |
TAINT_RESNO |
static int |
TAINT_SEQID |
static int |
TAINT_TEMPERATURE |
static int |
TAINT_VALENCE |
static int |
TAINT_VANDERWAALS |
static int |
TAINT_VIBRATION |
javajs.util.BS[] |
tainted |
Trajectory |
trajectory |
static java.lang.String[] |
userSettableValues |
Vibration[] |
vibrations |
private static javajs.util.V3 |
vRef |
Viewer |
vwr |
Constructor and Description |
---|
AtomCollection() |
Modifier and Type | Method and Description |
---|---|
void |
addTensor(Tensor t,
java.lang.String type) |
private void |
calcBfactorRange(javajs.util.BS bs) |
private void |
calcSurfaceDistances() |
javajs.util.P3[][] |
calculateHydrogens(javajs.util.BS bs,
int[] nTotal,
boolean doAll,
boolean justCarbon,
javajs.util.Lst<Atom> vConnect)
get a list of potential H atom positions based on
elemental valence and formal charge
|
javajs.util.P3[] |
calculateSurface(javajs.util.BS bsSelected,
float envelopeRadius) |
float |
calculateVolume(javajs.util.BS bs,
VDW vType) |
int |
chainToUpper(int chainID) |
void |
clearBfactorRange() |
void |
clearVisibleSets() |
private void |
deleteAtomTensors(javajs.util.BS bsAtoms) |
protected void |
deleteModelAtoms(int firstAtomIndex,
int nAtoms,
javajs.util.BS bsAtoms) |
protected void |
fillADa(AtomData atomData,
int mode) |
protected void |
findMaxRadii() |
protected void |
findNearest2(int x,
int y,
Atom[] closest,
javajs.util.BS bsNot,
int min) |
private javajs.util.BS |
findNotAttached(int nAttached,
int[][] angles,
int[] ptrs,
int nPtrs) |
int |
fixFormalCharges(javajs.util.BS bs) |
private void |
fixTrajectory(Atom a) |
javajs.util.Lst<javajs.util.P3> |
generateCrystalClass(int atomIndex,
javajs.util.P3 pt) |
javajs.util.Lst<java.lang.Object> |
getAllAtomTensors(java.lang.String type) |
Atom |
getAtom(int iatom) |
javajs.util.BS |
getAtomBitsMDa(int tokType,
java.lang.Object specInfo,
javajs.util.BS bs)
general unqualified lookup of atom set type
|
float[] |
getAtomicCharges() |
void |
getAtomIdentityInfo(int i,
java.util.Map<java.lang.String,java.lang.Object> info,
javajs.util.P3 ptTemp) |
int[] |
getAtomIndices(javajs.util.BS bs) |
java.lang.String |
getAtomInfo(int i,
java.lang.String format,
javajs.util.P3 ptTemp) |
javajs.util.Lst<javajs.util.P3> |
getAtomPointVector(javajs.util.BS bs) |
javajs.util.BS |
getAtomsFromAtomNumberInFrame(int atomNumber) |
void |
getAtomsInFrame(javajs.util.BS bsAtoms) |
javajs.util.BS |
getAtomsNearPlane(float distance,
javajs.util.P4 plane) |
Tensor |
getAtomTensor(int i,
java.lang.String type) |
java.lang.Object[] |
getAtomTensorList(int i) |
java.lang.String[] |
getAtomTypes() |
private Atom[] |
getAttached(Atom atom,
int nMax,
boolean doSort) |
int |
getBfactor100Hi() |
int |
getBfactor100Lo() |
short[] |
getBFactors() |
float[] |
getBondingRadii() |
javajs.util.BS |
getChainBits(int chainID) |
javajs.util.BS |
getClickableSet(boolean forceNew) |
java.lang.String |
getElementName(int i) |
int |
getFirstAtomIndexFromAtomNumber(int atomNumber,
javajs.util.BS bsVisibleFrames) |
java.lang.String |
getHybridizationAndAxes(int atomIndex,
int atomicNumber,
javajs.util.V3 z,
javajs.util.V3 x,
java.lang.String lcaoTypeRaw,
boolean hybridizationCompatible,
boolean doAlignZ) |
private java.lang.String |
getHybridizationAndAxesD(int atomIndex,
javajs.util.V3 z,
javajs.util.V3 x,
java.lang.String lcaoType)
dsp3 (trigonal bipyramidal, see-saw, T-shaped)
or d2sp3 (square planar, square pyramidal, octahedral)
|
float[] |
getHydrophobicity() |
private javajs.util.BS |
getIdentifierOrNull(java.lang.String identifier)
overhauled by RMH Nov 1, 2006.
|
LabelToken |
getLabeler() |
float |
getMaxVanderwaalsRadius() |
int |
getMissingHydrogenCount(Atom atom,
boolean allowNegative) |
JmolModulationSet |
getModulation(int iAtom) |
float[] |
getPartialCharges() |
javajs.util.Quat |
getQuaternion(int i,
char qtype) |
protected float |
getRadiusVdwJmol(Atom atom) |
javajs.util.BS |
getSeqcodeBits(int seqcode,
boolean returnEmpty) |
private javajs.util.BS |
getSpecName(java.lang.String name) |
javajs.util.BS |
getSpecNameOrNull(java.lang.String name,
boolean checkStar) |
(package private) int |
getSurfaceDistance100(int atomIndex) |
int |
getSurfaceDistanceMax() |
javajs.util.BS |
getTaintedAtoms(int type) |
private static java.lang.Object[] |
getTensorList(javajs.util.Lst<java.lang.Object> list) |
static int |
getUserSettableType(java.lang.String dataType) |
float |
getVibCoord(int atomIndex,
char c)
also handles modulation info
|
Vibration |
getVibration(int atomIndex,
boolean forceNew) |
javajs.util.BS |
getVisibleSet(boolean forceNew) |
private float |
getWorkingRadius(Atom atom,
AtomData atomData) |
private boolean |
isAdjacentSp2(Atom atom) |
private boolean |
isAltLoc(char altloc,
java.lang.String strPattern) |
boolean |
isAtomHidden(int iAtom) |
private boolean |
isAtomNameMatch(Atom atom,
java.lang.String strPattern,
boolean checkStar,
boolean allowInitialStar) |
(package private) boolean |
isCursorOnTopOf(Atom contender,
int x,
int y,
int radius,
Atom champion)
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
|
boolean |
isModulated(int i) |
private void |
loadCoordinates(java.lang.String data,
boolean isVibrationVectors,
boolean doTaint) |
protected void |
mergeAtomArrays(AtomCollection mergeModelSet) |
boolean |
modelSetHasVibrationVectors() |
protected void |
releaseModelSetAC() |
private void |
resetPartialCharges() |
void |
scaleVectorsToMax(float max)
Scales vibrations and associated vectors such that the
maximum length is the given value
|
protected void |
setAPa(javajs.util.BS bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list) |
void |
setAtomCoord(int atomIndex,
float x,
float y,
float z) |
protected void |
setAtomCoord2(javajs.util.BS bs,
int tokType,
java.lang.Object xyzValues) |
void |
setAtomCoordRelative(int atomIndex,
float x,
float y,
float z) |
void |
setAtomData(int type,
java.lang.String name,
java.lang.String dataString,
boolean isDefault) |
void |
setAtomName(int atomIndex,
java.lang.String name,
boolean doTaint) |
void |
setAtomNumber(int atomIndex,
int atomno,
boolean doTaint) |
private void |
setAtomResno(int atomIndex,
int resno) |
protected void |
setAtomsCoordRelative(javajs.util.BS bs,
float x,
float y,
float z) |
private void |
setAtomSeqID(int atomIndex,
int seqID) |
void |
setAtomTensors(int atomIndex,
javajs.util.Lst<java.lang.Object> list) |
private void |
setAtomType(int atomIndex,
java.lang.String type) |
private void |
setAtomVibrationVector(int atomIndex,
javajs.util.T3 vib) |
private void |
setBf(int i) |
protected void |
setBFactor(int atomIndex,
float bfactor,
boolean doTaint) |
private void |
setBondingRadius(int atomIndex,
float radius) |
void |
setBsHidden(javajs.util.BS bs) |
(package private) void |
setCapacity(int nAtoms) |
private void |
setChainID(int atomIndex,
java.lang.String id) |
void |
setElement(Atom atom,
int atomicNumber,
boolean doTaint) |
void |
setFormalCharges(javajs.util.BS bs,
int formalCharge) |
private void |
setHydrophobicity(int atomIndex,
float value) |
protected void |
setOccupancy(int atomIndex,
float occupancy,
boolean doTaint) |
protected void |
setPartialCharge(int atomIndex,
float partialCharge,
boolean doTaint) |
void |
setPreserveState(boolean TF) |
void |
setTaintedAtoms(javajs.util.BS bs,
int type) |
protected void |
setupAC() |
protected void |
setVibrationVector(int atomIndex,
javajs.util.T3 vib) |
private void |
setVibrationVector2(int atomIndex,
int tok,
float fValue) |
void |
taintAtom(int atomIndex,
int type) |
void |
taintAtoms(javajs.util.BS bsAtoms,
int type) |
private void |
taintModelCoord(int atomIndex) |
private void |
untaint(int atomIndex,
int type) |
void |
unTaintAtoms(javajs.util.BS bs,
int type) |
void |
validateBspf(boolean isValid) |
(package private) void |
validateBspfForModel(int modelIndex,
boolean isValid) |
private static final float almost180
private static final float sqrt3_2
private static final javajs.util.V3 vRef
public Viewer vwr
protected GData g3d
public BioModelSet bioModelset
public Atom[] at
public int ac
public Trajectory trajectory
protected SymmetryInterface pointGroup
private LabelToken labeler
protected float maxBondingRadius
private float maxVanderwaalsRadius
private boolean hasBfactorRange
private int bfactor100Lo
private int bfactor100Hi
private boolean haveBSVisible
private boolean haveBSClickable
private javajs.util.BS bsSurface
private int nSurfaceAtoms
private int surfaceDistanceMax
protected boolean haveChirality
protected Bspf bspf
protected boolean preserveState
public boolean canSkipLoad
public boolean haveStraightness
private javajs.util.BS bsHidden
public javajs.util.BS bsVisible
public javajs.util.BS bsClickable
public javajs.util.BS bsModulated
public java.lang.Object[][] atomTensorList
public java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>> atomTensors
protected int[] surfaceDistance100s
public javajs.util.BS[] tainted
public static java.lang.String[] userSettableValues
public static final int TAINT_ATOMNAME
public static final int TAINT_ATOMTYPE
public static final int TAINT_COORD
public static final int TAINT_ELEMENT
public static final int TAINT_FORMALCHARGE
public static final int TAINT_HYDROPHOBICITY
public static final int TAINT_BONDINGRADIUS
public static final int TAINT_OCCUPANCY
public static final int TAINT_PARTIALCHARGE
public static final int TAINT_TEMPERATURE
public static final int TAINT_VALENCE
public static final int TAINT_VANDERWAALS
public static final int TAINT_VIBRATION
public static final int TAINT_ATOMNO
public static final int TAINT_SEQID
public static final int TAINT_RESNO
public static final int TAINT_CHAIN
public static final int TAINT_MAX
java.lang.String[] atomNames
java.lang.String[] atomTypes
int[] atomSerials
int[] atomResnos
int[] atomSeqIDs
float[] dssrData
public Vibration[] vibrations
public float[] occupancies
short[] bfactor100s
float[] partialCharges
float[] bondingRadii
float[] hydrophobicities
public javajs.util.BS bsPartialCharges
int[] aaRet
private int atomCapacity
public Atom getAtom(int iatom)
protected void setupAC()
protected void releaseModelSetAC()
protected void mergeAtomArrays(AtomCollection mergeModelSet)
public javajs.util.Lst<javajs.util.P3> getAtomPointVector(javajs.util.BS bs)
public boolean modelSetHasVibrationVectors()
public java.lang.String[] getAtomTypes()
public float[] getPartialCharges()
public float[] getBondingRadii()
public short[] getBFactors()
public float[] getHydrophobicity()
public void setBsHidden(javajs.util.BS bs)
public boolean isAtomHidden(int iAtom)
public LabelToken getLabeler()
public java.lang.String getAtomInfo(int i, java.lang.String format, javajs.util.P3 ptTemp)
public java.lang.String getElementName(int i)
public javajs.util.Quat getQuaternion(int i, char qtype)
public int getFirstAtomIndexFromAtomNumber(int atomNumber, javajs.util.BS bsVisibleFrames)
public void setFormalCharges(javajs.util.BS bs, int formalCharge)
public float[] getAtomicCharges()
protected float getRadiusVdwJmol(Atom atom)
public float getMaxVanderwaalsRadius()
protected void findMaxRadii()
public void clearBfactorRange()
private void calcBfactorRange(javajs.util.BS bs)
private void setBf(int i)
public int getBfactor100Lo()
public int getBfactor100Hi()
public int getSurfaceDistanceMax()
public float calculateVolume(javajs.util.BS bs, VDW vType)
int getSurfaceDistance100(int atomIndex)
private void calcSurfaceDistances()
public javajs.util.P3[] calculateSurface(javajs.util.BS bsSelected, float envelopeRadius)
protected void setAtomCoord2(javajs.util.BS bs, int tokType, java.lang.Object xyzValues)
private void setAtomVibrationVector(int atomIndex, javajs.util.T3 vib)
public void setAtomCoord(int atomIndex, float x, float y, float z)
private void fixTrajectory(Atom a)
public void setAtomCoordRelative(int atomIndex, float x, float y, float z)
protected void setAtomsCoordRelative(javajs.util.BS bs, float x, float y, float z)
protected void setAPa(javajs.util.BS bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
public float getVibCoord(int atomIndex, char c)
atomIndex
- c
- public Vibration getVibration(int atomIndex, boolean forceNew)
public JmolModulationSet getModulation(int iAtom)
protected void setVibrationVector(int atomIndex, javajs.util.T3 vib)
private void setVibrationVector2(int atomIndex, int tok, float fValue)
public void setAtomName(int atomIndex, java.lang.String name, boolean doTaint)
private void setAtomType(int atomIndex, java.lang.String type)
private void setChainID(int atomIndex, java.lang.String id)
public void setAtomNumber(int atomIndex, int atomno, boolean doTaint)
public void setElement(Atom atom, int atomicNumber, boolean doTaint)
private void resetPartialCharges()
private void setAtomResno(int atomIndex, int resno)
private void setAtomSeqID(int atomIndex, int seqID)
protected void setOccupancy(int atomIndex, float occupancy, boolean doTaint)
protected void setPartialCharge(int atomIndex, float partialCharge, boolean doTaint)
private void setBondingRadius(int atomIndex, float radius)
protected void setBFactor(int atomIndex, float bfactor, boolean doTaint)
private void setHydrophobicity(int atomIndex, float value)
public void setAtomData(int type, java.lang.String name, java.lang.String dataString, boolean isDefault)
private void loadCoordinates(java.lang.String data, boolean isVibrationVectors, boolean doTaint)
public void validateBspf(boolean isValid)
void validateBspfForModel(int modelIndex, boolean isValid)
public void setPreserveState(boolean TF)
public static int getUserSettableType(java.lang.String dataType)
public javajs.util.BS getTaintedAtoms(int type)
public void taintAtoms(javajs.util.BS bsAtoms, int type)
public void taintAtom(int atomIndex, int type)
private void taintModelCoord(int atomIndex)
private void untaint(int atomIndex, int type)
public void setTaintedAtoms(javajs.util.BS bs, int type)
public void unTaintAtoms(javajs.util.BS bs, int type)
protected void findNearest2(int x, int y, Atom[] closest, javajs.util.BS bsNot, int min)
boolean isCursorOnTopOf(Atom contender, int x, int y, int radius, Atom champion)
contender
- x
- y
- radius
- champion
- protected void fillADa(AtomData atomData, int mode)
public javajs.util.P3[][] calculateHydrogens(javajs.util.BS bs, int[] nTotal, boolean doAll, boolean justCarbon, javajs.util.Lst<Atom> vConnect)
bs
- nTotal
- doAll
- -- whether we add to C that already have H or not.justCarbon
- vConnect
- private boolean isAdjacentSp2(Atom atom)
public int getMissingHydrogenCount(Atom atom, boolean allowNegative)
public int fixFormalCharges(javajs.util.BS bs)
public java.lang.String getHybridizationAndAxes(int atomIndex, int atomicNumber, javajs.util.V3 z, javajs.util.V3 x, java.lang.String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ)
private java.lang.String getHybridizationAndAxesD(int atomIndex, javajs.util.V3 z, javajs.util.V3 x, java.lang.String lcaoType)
atomIndex
- z
- x
- lcaoType
- private javajs.util.BS findNotAttached(int nAttached, int[][] angles, int[] ptrs, int nPtrs)
public javajs.util.BS getAtomBitsMDa(int tokType, java.lang.Object specInfo, javajs.util.BS bs)
tokType
- specInfo
- bs
- - to be filledpublic javajs.util.BS getChainBits(int chainID)
public int chainToUpper(int chainID)
private boolean isAltLoc(char altloc, java.lang.String strPattern)
public javajs.util.BS getSeqcodeBits(int seqcode, boolean returnEmpty)
private javajs.util.BS getIdentifierOrNull(java.lang.String identifier)
identifier
- private javajs.util.BS getSpecName(java.lang.String name)
public javajs.util.BS getSpecNameOrNull(java.lang.String name, boolean checkStar)
private boolean isAtomNameMatch(Atom atom, java.lang.String strPattern, boolean checkStar, boolean allowInitialStar)
public int[] getAtomIndices(javajs.util.BS bs)
public javajs.util.BS getAtomsNearPlane(float distance, javajs.util.P4 plane)
public void clearVisibleSets()
public void getAtomsInFrame(javajs.util.BS bsAtoms)
public javajs.util.BS getVisibleSet(boolean forceNew)
public javajs.util.BS getClickableSet(boolean forceNew)
public boolean isModulated(int i)
protected void deleteModelAtoms(int firstAtomIndex, int nAtoms, javajs.util.BS bsAtoms)
public void getAtomIdentityInfo(int i, java.util.Map<java.lang.String,java.lang.Object> info, javajs.util.P3 ptTemp)
public java.lang.Object[] getAtomTensorList(int i)
private void deleteAtomTensors(javajs.util.BS bsAtoms)
void setCapacity(int nAtoms)
public void setAtomTensors(int atomIndex, javajs.util.Lst<java.lang.Object> list)
public void addTensor(Tensor t, java.lang.String type)
private static java.lang.Object[] getTensorList(javajs.util.Lst<java.lang.Object> list)
public Tensor getAtomTensor(int i, java.lang.String type)
public javajs.util.Lst<java.lang.Object> getAllAtomTensors(java.lang.String type)
public void scaleVectorsToMax(float max)
max
- public javajs.util.BS getAtomsFromAtomNumberInFrame(int atomNumber)
public javajs.util.Lst<javajs.util.P3> generateCrystalClass(int atomIndex, javajs.util.P3 pt)