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