Package org.jmol.modelset
Class AtomCollection
java.lang.Object
org.jmol.modelset.AtomCollection
- Direct Known Subclasses:
BondCollection
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionint
Atom[]
Object[][]
If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaningprotected Bspf
Binary Space Partitioning Foreststatic final int
static final int
static final int
static final int
static final int
static final int
boolean
protected GData
protected boolean
boolean
protected float
float[]
protected SymmetryInterface
protected boolean
protected int[]
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
BS[]
static String[]
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
P3[][]
calculateHydrogens
(BS bs, int[] nTotal, Lst<Atom> vConnect, int flags) get a list of potential H atom positions based on elemental valence and formal chargeP3[]
calculateSurface
(BS bsSelected, float envelopeRadius) float
calculateVolume
(BS bs, VDW vType) int
chainToUpper
(int chainID) void
void
protected void
deleteModelAtoms
(int firstAtomIndex, int nAtoms, BS bsAtoms) protected void
protected void
protected void
findNearest2
(int x, int y, Atom[] closest, BS bsNot, int min) int
fixFormalCharges
(BS bs) generateCrystalClass
(int atomIndex, P3 pt) getAllAtomTensors
(String type) getAtom
(int iatom) getAtomBitsMDa
(int tokType, Object specInfo, BS bs) general unqualified lookup of atom set typefloat[]
void
getAtomIdentityInfo
(int i, Map<String, Object> info, P3 ptTemp) int[]
getAtomIndices
(BS bs) getAtomInfo
(int i, String format, P3 ptTemp) getAtomPointVector
(BS bs) getAtomsFromAtomNumberInFrame
(int atomNumber) void
getAtomsInFrame
(BS bsAtoms) getAtomsNearPlane
(float distance, P4 plane) getAtomTensor
(int i, String type) Object[]
getAtomTensorList
(int i) String[]
int
int
short[]
float[]
getChainBits
(int chainID) getClickableSet
(boolean forceNew) getElementName
(int i) int
getFirstAtomIndexFromAtomNumber
(int atomNumber, BS bsVisibleFrames) getHybridizationAndAxes
(int atomIndex, int atomicNumber, V3 z, V3 x, String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ, boolean isQuick, T3 ref) float[]
float
int
getMissingHydrogenCount
(Atom atom, boolean allowNegative) getModulation
(int iAtom) float
getOccupancyFloat
(int i) float[]
getQuaternion
(int i, char qtype) protected float
getRadiusVdwJmol
(Atom atom) getSeqcodeBits
(int seqcode, boolean returnEmpty) getSpecNameOrNull
(String name, boolean checkStar) int
getTaintedAtoms
(int type) static int
getUserSettableType
(String dataType) float
getVibCoord
(int atomIndex, char c) also handles modulation infogetVibration
(int atomIndex, boolean forceNew) getVisibleSet
(boolean forceNew) boolean
isAtomHidden
(int iAtom) static boolean
boolean
isModulated
(int i) protected void
mergeAtomArrays
(AtomCollection mergeModelSet) boolean
protected void
void
scaleVectorsToMax
(float max) Scales vibrations and associated vectors such that the maximum length is the given valueprotected void
void
setAtomCoord
(int atomIndex, float x, float y, float z) protected void
setAtomCoord2
(BS bs, int tokType, Object xyzValues) void
setAtomCoordRelative
(int atomIndex, float x, float y, float z) void
setAtomData
(int type, String name, String dataString, boolean isDefault) void
setAtomName
(int atomIndex, String name, boolean doTaint) void
setAtomNumber
(int atomIndex, int atomno, boolean doTaint) protected void
setAtomsCoordRelative
(BS bs, float x, float y, float z) void
setAtomTensors
(int atomIndex, Lst<Object> list) protected void
setBFactor
(int atomIndex, float bfactor, boolean doTaint) protected void
setBondingRadius
(int atomIndex, float radius) void
setBsHidden
(BS bs) void
setElement
(Atom atom, int atomicNumber, boolean doTaint) void
setFormalCharges
(BS bs, int formalCharge) protected void
setOccupancy
(int atomIndex, float occupancy, boolean doTaint) protected void
setPartialCharge
(int atomIndex, float partialCharge, boolean doTaint) void
setPreserveState
(boolean TF) void
void
setTaintedAtoms
(BS bs, int type) protected void
setupAC()
void
setVibrationVector
(int atomIndex, T3 vib) void
taintAtom
(int atomIndex, int type) void
taintAtoms
(BS bsAtoms, int type) void
unTaintAtoms
(BS bs, int type) void
validateBspf
(boolean isValid)
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Field Details
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vwr
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g3d
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bioModelset
If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaning -
at
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ac
public int ac -
trajectory
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pointGroup
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maxBondingRadius
protected float maxBondingRadius -
haveChirality
protected boolean haveChirality -
bspf
Binary Space Partitioning Forest -
preserveState
protected boolean preserveState -
canSkipLoad
public boolean canSkipLoad -
haveStraightness
public boolean haveStraightness -
bsVisible
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bsClickable
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bsModulated
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atomTensorList
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atomTensors
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surfaceDistance100s
protected int[] surfaceDistance100s -
tainted
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userSettableValues
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TAINT_ATOMNAME
public static final int TAINT_ATOMNAME- See Also:
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TAINT_ATOMTYPE
public static final int TAINT_ATOMTYPE- See Also:
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TAINT_COORD
public static final int TAINT_COORD- See Also:
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TAINT_ELEMENT
public static final int TAINT_ELEMENT- See Also:
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TAINT_FORMALCHARGE
public static final int TAINT_FORMALCHARGE- See Also:
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TAINT_HYDROPHOBICITY
public static final int TAINT_HYDROPHOBICITY- See Also:
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TAINT_BONDINGRADIUS
public static final int TAINT_BONDINGRADIUS- See Also:
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TAINT_OCCUPANCY
public static final int TAINT_OCCUPANCY- See Also:
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TAINT_PARTIALCHARGE
public static final int TAINT_PARTIALCHARGE- See Also:
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TAINT_TEMPERATURE
public static final int TAINT_TEMPERATURE- See Also:
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TAINT_VALENCE
public static final int TAINT_VALENCE- See Also:
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TAINT_VANDERWAALS
public static final int TAINT_VANDERWAALS- See Also:
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TAINT_VIBRATION
public static final int TAINT_VIBRATION- See Also:
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TAINT_ATOMNO
public static final int TAINT_ATOMNO- See Also:
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TAINT_SEQID
public static final int TAINT_SEQID- See Also:
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TAINT_RESNO
public static final int TAINT_RESNO- See Also:
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TAINT_CHAIN
public static final int TAINT_CHAIN- See Also:
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TAINT_SITE
public static final int TAINT_SITE- See Also:
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TAINT_MAX
public static final int TAINT_MAX- See Also:
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vibrations
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occupancies
public float[] occupancies -
bsPartialCharges
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CALC_H_DOALL
public static final int CALC_H_DOALL- See Also:
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CALC_H_JUSTC
public static final int CALC_H_JUSTC- See Also:
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CALC_H_HAVEH
public static final int CALC_H_HAVEH- See Also:
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CALC_H_QUICK
public static final int CALC_H_QUICK- See Also:
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CALC_H_IGNORE_H
public static final int CALC_H_IGNORE_H- See Also:
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CALC_H_ALLOW_H
public static final int CALC_H_ALLOW_H- See Also:
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Constructor Details
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AtomCollection
public AtomCollection()
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Method Details
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getAtom
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setupAC
protected void setupAC() -
releaseModelSetAC
protected void releaseModelSetAC() -
mergeAtomArrays
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getAtomPointVector
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modelSetHasVibrationVectors
public boolean modelSetHasVibrationVectors() -
getAtomTypes
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getPartialCharges
public float[] getPartialCharges() -
getBondingRadii
public float[] getBondingRadii() -
getBFactors
public short[] getBFactors() -
getHydrophobicity
public float[] getHydrophobicity() -
setBsHidden
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isAtomHidden
public boolean isAtomHidden(int iAtom) -
getLabeler
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getAtomInfo
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getElementName
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getQuaternion
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getFirstAtomIndexFromAtomNumber
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setFormalCharges
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getAtomicCharges
public float[] getAtomicCharges() -
getRadiusVdwJmol
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getMaxVanderwaalsRadius
public float getMaxVanderwaalsRadius() -
findMaxRadii
protected void findMaxRadii() -
clearBfactorRange
public void clearBfactorRange() -
getBfactor100Lo
public int getBfactor100Lo() -
getBfactor100Hi
public int getBfactor100Hi() -
getSurfaceDistanceMax
public int getSurfaceDistanceMax() -
calculateVolume
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calculateSurface
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setAtomCoord2
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setAtomCoord
public void setAtomCoord(int atomIndex, float x, float y, float z) -
setAtomCoordRelative
public void setAtomCoordRelative(int atomIndex, float x, float y, float z) -
setAtomsCoordRelative
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setAPa
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getVibCoord
public float getVibCoord(int atomIndex, char c) also handles modulation info- Parameters:
atomIndex
-c
- generally x, y, z, but for modulation could be 1, 2, 3, or O (oh, not zero)- Returns:
- value or NaN
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getVibration
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getModulation
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setVibrationVector
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setAtomName
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setAtomNumber
public void setAtomNumber(int atomIndex, int atomno, boolean doTaint) -
setElement
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setSite
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setOccupancy
protected void setOccupancy(int atomIndex, float occupancy, boolean doTaint) -
getOccupancyFloat
public float getOccupancyFloat(int i) -
setPartialCharge
protected void setPartialCharge(int atomIndex, float partialCharge, boolean doTaint) -
setBondingRadius
protected void setBondingRadius(int atomIndex, float radius) -
setBFactor
protected void setBFactor(int atomIndex, float bfactor, boolean doTaint) -
setAtomData
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validateBspf
public void validateBspf(boolean isValid) -
setPreserveState
public void setPreserveState(boolean TF) -
getUserSettableType
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getTaintedAtoms
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taintAtoms
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taintAtom
public void taintAtom(int atomIndex, int type) -
setTaintedAtoms
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unTaintAtoms
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findNearest2
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fillADa
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calculateHydrogens
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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getMissingHydrogenCount
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fixFormalCharges
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getHybridizationAndAxes
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getAtomBitsMDa
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
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chainToUpper
public int chainToUpper(int chainID) -
getSeqcodeBits
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getSpecNameOrNull
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getAtomIndices
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getAtomsNearPlane
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clearVisibleSets
public void clearVisibleSets() -
getAtomsInFrame
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getVisibleSet
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getClickableSet
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isModulated
public boolean isModulated(int i) -
deleteModelAtoms
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getAtomIdentityInfo
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getAtomTensorList
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setAtomTensors
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addTensor
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getAtomTensor
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getAllAtomTensors
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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
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generateCrystalClass
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isDeleted
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