public class MathExt
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private ScriptEval |
e |
private JmolPatternMatcher |
pm |
private java.util.Random |
rand |
private Viewer |
vwr |
Constructor and Description |
---|
MathExt() |
Modifier and Type | Method and Description |
---|---|
private javajs.util.Lst<SV> |
addAllLists(javajs.util.Lst<SV> list,
javajs.util.Lst<SV> l) |
boolean |
evaluate(ScriptMathProcessor mp,
T op,
SV[] args,
int tok) |
private boolean |
evaluateArray(ScriptMathProcessor mp,
SV[] args,
boolean isSelector) |
private boolean |
evaluateBin(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateCache(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateColor(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateCompare(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateConnected(ScriptMathProcessor mp,
SV[] args,
int tok) |
private boolean |
evaluateContact(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateData(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateDotDist(ScriptMathProcessor mp,
SV[] args,
int tok,
int op)
x = y.distance({atoms}) the average distance from elements of y to the
CENTER of {atoms}
x = {atomset1}.distance.min({atomset2}, asAtomSet) If asAtomSet is true,
returns the closest atom in atomset1 to any atom of atomset2; if false or
omitted, returns an array listing the distance of each atom in atomset1 to
the closest atom in atomset2.
|
private boolean |
evaluateFind(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateFormat(ScriptMathProcessor mp,
int intValue,
SV[] args,
boolean isLabel) |
private boolean |
evaluateGetProperty(ScriptMathProcessor mp,
SV[] args,
int tok0,
boolean isAtomProperty)
_ by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo")
$ print _.keys
boundbox group3Counts group3Lists modelLoadNote models properties
someModelsHaveFractionalCoordinates someModelsHaveSymmetry
someModelsHaveUnitcells symmetryRange
_m by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo.models")[_currentFrame]
$ print format("json",_m.unitCellParams)
[ 0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376,
2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN ]
{atomset}._ by itself delivers a subset array of auxiliaryInfo.models for
all models in {atomset}
$ print {*}._..1..aflowInfo
(first model's aflowInfo)
_(key) prepends "auxiliaryInfo.models", delivering a modelCount-length
array of information
$ print _("aflowInfo[SELECT auid WHERE H__eV___VASP_ < 0]")
{atomset}._(key) selects for model Auxiliary info related to models of the
specified atoms
{atomset}.getProperty(key) defaults to atomInfo, but also allows key to
start with "bondInfo"
Examples:
print _("aflowInfo[select sg where volume_cell > 70]")
print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
|
private boolean |
evaluateHelix(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateIn(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateList(ScriptMathProcessor mp,
int tok,
SV[] args) |
private boolean |
evaluateLoad(ScriptMathProcessor mp,
SV[] args,
boolean isFile) |
private boolean |
evaluateMath(ScriptMathProcessor mp,
SV[] args,
int tok) |
private boolean |
evaluateMeasure(ScriptMathProcessor mp,
SV[] args,
int tok) |
private boolean |
evaluateModulation(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluatePlane(ScriptMathProcessor mp,
SV[] args,
int tok)
plane() or intersection()
|
private boolean |
evaluatePoint(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluatePrompt(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateQuaternion(ScriptMathProcessor mp,
SV[] args,
int tok) |
private boolean |
evaluateRandom(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateReplace(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateRowCol(ScriptMathProcessor mp,
SV[] args,
int tok) |
private boolean |
evaluateScript(ScriptMathProcessor mp,
SV[] args,
int tok) |
private boolean |
evaluateSort(ScriptMathProcessor mp,
SV[] args,
int tok)
sort() or sort(n) or count() or count("xxxx")
|
private boolean |
evaluateString(ScriptMathProcessor mp,
int tok,
SV[] args) |
private boolean |
evaluateSubstructure(ScriptMathProcessor mp,
SV[] args,
int tok,
boolean isSelector) |
private boolean |
evaluateSymop(ScriptMathProcessor mp,
SV[] args,
boolean haveBitSet) |
private boolean |
evaluateTensor(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateUnitCell(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateUserFunction(ScriptMathProcessor mp,
java.lang.String name,
SV[] args,
int tok,
boolean isSelector) |
private boolean |
evaluateWithin(ScriptMathProcessor mp,
SV[] args) |
private boolean |
evaluateWrite(ScriptMathProcessor mp,
SV[] args) |
private BS |
getAtomsNearPts(float distance,
javajs.util.T3[] points,
BS bsInclude) |
private BS |
getAtomsNearSurface(float distance,
java.lang.String surfaceId) |
private java.lang.Object |
getHelixData(BS bs,
int tokType) |
java.lang.Object |
getMinMax(java.lang.Object floatOrSVArray,
int tok) |
private java.lang.Object |
getMinMaxPoint(java.lang.Object pointOrSVArray,
int tok)
calculates the statistical value for x, y, and z independently
|
private java.lang.Object |
getMinMaxQuaternion(javajs.util.Lst<SV> svData,
int tok) |
private JmolPatternMatcher |
getPatternMatcher() |
private javajs.util.Lst<SV> |
getSublist(javajs.util.Lst<SV> listIn,
javajs.util.Lst<SV> formatList)
[ {...},{...}...
|
MathExt |
init(java.lang.Object se) |
private T |
opTokenFor(int tok) |
BS |
setContactBitSets(BS bsA,
BS bsB,
boolean localOnly,
float distance,
RadiusData rd,
boolean warnMultiModel) |
private Viewer vwr
private ScriptEval e
private java.util.Random rand
private JmolPatternMatcher pm
public MathExt init(java.lang.Object se)
public boolean evaluate(ScriptMathProcessor mp, T op, SV[] args, int tok) throws ScriptException
ScriptException
private boolean evaluateUnitCell(ScriptMathProcessor mp, SV[] args)
private boolean evaluateArray(ScriptMathProcessor mp, SV[] args, boolean isSelector) throws ScriptException
ScriptException
private boolean evaluateBin(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluateCache(ScriptMathProcessor mp, SV[] args)
private boolean evaluateColor(ScriptMathProcessor mp, SV[] args)
private boolean evaluateCompare(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluateConnected(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException
ScriptException
private boolean evaluateContact(ScriptMathProcessor mp, SV[] args)
private boolean evaluateData(ScriptMathProcessor mp, SV[] args)
private boolean evaluateDotDist(ScriptMathProcessor mp, SV[] args, int tok, int op) throws ScriptException
mp
- args
- tok
- op
- optional .min .max for distanceScriptException
private boolean evaluateHelix(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private java.lang.Object getHelixData(BS bs, int tokType)
private boolean evaluateFind(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluateGetProperty(ScriptMathProcessor mp, SV[] args, int tok0, boolean isAtomProperty) throws ScriptException
mp
- args
- tok0
- isAtomProperty
- ScriptException
private boolean evaluateFormat(ScriptMathProcessor mp, int intValue, SV[] args, boolean isLabel) throws ScriptException
ScriptException
private javajs.util.Lst<SV> getSublist(javajs.util.Lst<SV> listIn, javajs.util.Lst<SV> formatList)
listIn
- formatList
- private boolean evaluateList(ScriptMathProcessor mp, int tok, SV[] args) throws ScriptException
ScriptException
private javajs.util.Lst<SV> addAllLists(javajs.util.Lst<SV> list, javajs.util.Lst<SV> l)
private boolean evaluateLoad(ScriptMathProcessor mp, SV[] args, boolean isFile) throws ScriptException
ScriptException
private boolean evaluateMath(ScriptMathProcessor mp, SV[] args, int tok)
private boolean evaluateMeasure(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException
ScriptException
private boolean evaluateModulation(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluatePlane(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException
mp
- args
- tok
- ScriptException
private boolean evaluatePoint(ScriptMathProcessor mp, SV[] args)
private boolean evaluatePrompt(ScriptMathProcessor mp, SV[] args)
private boolean evaluateQuaternion(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException
ScriptException
private boolean evaluateRandom(ScriptMathProcessor mp, SV[] args)
private boolean evaluateRowCol(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException
ScriptException
private boolean evaluateIn(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluateReplace(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluateScript(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException
ScriptException
private boolean evaluateSort(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException
mp
- args
- tok
- ScriptException
private boolean evaluateString(ScriptMathProcessor mp, int tok, SV[] args) throws ScriptException
ScriptException
private boolean evaluateSubstructure(ScriptMathProcessor mp, SV[] args, int tok, boolean isSelector) throws ScriptException
ScriptException
private boolean evaluateSymop(ScriptMathProcessor mp, SV[] args, boolean haveBitSet) throws ScriptException
ScriptException
private boolean evaluateTensor(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluateUserFunction(ScriptMathProcessor mp, java.lang.String name, SV[] args, int tok, boolean isSelector) throws ScriptException
ScriptException
private boolean evaluateWithin(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private boolean evaluateWrite(ScriptMathProcessor mp, SV[] args) throws ScriptException
ScriptException
private BS getAtomsNearSurface(float distance, java.lang.String surfaceId)
public java.lang.Object getMinMax(java.lang.Object floatOrSVArray, int tok)
private java.lang.Object getMinMaxPoint(java.lang.Object pointOrSVArray, int tok)
pointOrSVArray
- tok
- private java.lang.Object getMinMaxQuaternion(javajs.util.Lst<SV> svData, int tok)
private JmolPatternMatcher getPatternMatcher()
private T opTokenFor(int tok)
public BS setContactBitSets(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel)