java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.pdb.PdbReader
  - - org.jmol.adapter.readers.pymol.PyMOLReader

All Implemented Interfaces:

javajs.api.GenericLineReader, PymolAtomReader
```
public class PyMOLReader
extends PdbReader
implements PymolAtomReader
```
PyMOL PSE (binary Python session) file reader. development started Feb 2013 Jmol 13.1.13 reasonably full implementation May 2013 Jmol 13.1.16 PyMOL state --> Jmol model PyMOL object --> Jmol named atom set, isosurface, CGO, or measurement PyMOL group --> Jmol named atom set (TODO: add isosurfaces and measures to these?) PyMOL movie: an initial view and a set of N "frames" PyMOL frame: references (a) a state, (b) a script, and (c) a view PyMOL scene --> Jmol scene, including view, frame, visibilities, colors using set LOGFILE, we can dump this to a readable form. trajectories are not supported yet. Basic idea is as follows: 1) Pickle file is read into a Hashtable. 2) Atoms, bonds, and structures are created, as per other readers, from MOLECULE objects 3) Rendering of atoms and bonds is interpreted as JmolObject objects via PyMOLScene 3) Other objects such as electron density maps, compiled graphical objects, and measures are interpreted, creating more JmolObjects 3) JmolObjects are finalized after file reading takes place by a call from ModelLoader back here to finalizeModelSet(), which runs PyMOLScene.setObjects, which runs JmolObject.finalizeObject. TODO: Handle discrete objects, DiscreteAtmToIdx?

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`ac`
`private int`	`ac0`
`private boolean`	`allowSurface`
`private boolean`	`allStates`
`(package private) byte[]`	`aTemp`
`private int[]`	`atomMap`
`private Atom[]`	`atoms`
`private int`	`baseModelIndex`
`private int`	`bondCount`
`private BS`	`bsBytesExcluded`
`private BS`	`bsStructureDefined`
`private boolean`	`doCache`
`private boolean`	`doResize`
`private int[]`	`frames`
`private boolean`	`haveBinaryArrays`
`private boolean`	`haveMeasurements`
`private boolean`	`haveScenes`
`private boolean`	`isHidden`
`private boolean`	`isMovie`
`private boolean`	`isStateScript`
`private boolean`	`logging`
`private javajs.util.Lst<javajs.util.Lst<java.lang.Object>>`	`mapObjects`
`private static int`	`MIN_RESNO`
`private int`	`nModels`
`private static java.lang.String`	`nucleic`
`private java.lang.String`	`objectName`
`private javajs.util.P3`	`ptTemp`
`private int`	`pymolFrame`
`private PyMOLScene`	`pymolScene`
`private int`	`pymolVersion`
`private BS[]`	`reps`
`private javajs.util.Lst<java.lang.Object>`	`sceneOrder`
`private boolean`	`sourcePNGJ`
`private java.util.Map<java.lang.String,BS>`	`ssMapSeq`
`private int`	`stateCount`
`private int`	`structureCount`
`private int`	`totalAtomCount`
`private int`	`trajectoryPtr`
`private javajs.util.P3[]`	`trajectoryStep`
`private java.util.Hashtable<java.lang.Integer,javajs.util.Lst<java.lang.Object>>`	`uniqueSettings`
`private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>>`	`volumeData`
`private javajs.util.P3`	`xyzMax`
`private javajs.util.P3`	`xyzMin`

Fields inherited from class org.jmol.adapter.readers.pdb.PdbReader
biomtChainAtomCounts, fileAtomIndex, gromacsWideFormat

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

PyMOLReader()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private javajs.util.P3`	`addAtom(javajs.util.Lst<java.lang.Object> pymolAtoms, int apt, byte[] atomArray, int[] vArray, java.lang.String[] lexStr, int icoord, javajs.util.Lst<java.lang.Object> coords, float[] coordArray, javajs.util.Lst<java.lang.Object> labelPositions, float[] labelArray, BS bsState, int iState)`
`private void`	`addBonds(javajs.util.Lst<Bond> bonds)`
`private void`	`addColors(javajs.util.Lst<java.lang.Object> colors, boolean isClamped)`	Add new colors from the main "colors" map object.
`private void`	`addMolSS(java.lang.String ssType, STR type)`	Secondary structure definition.
`private void`	`addMolStructures()`
`private boolean`	`atomBool(byte[] atomArray, int pt, int offset, int mask)`
`private float`	`atomFloat(byte[] atomArray, int pt, int offset)`
`private int`	`atomInt(byte[] atomArray, int pt, int offset)`
`private java.lang.String`	`atomStr(byte[] atomArray, int pt, int offset, java.lang.String[] lexStr)`
`(package private) static java.lang.String`	`bytesToString(java.lang.Object object)`
`private boolean`	`checkObject(javajs.util.Lst<java.lang.Object> execObject)`
`(package private) static int`	`colorSettingClamped(javajs.util.Lst<java.lang.Object> c, javajs.util.P3 ptTemp)`
`boolean`	`compareAtoms(int iPrev, int i)`
`private void`	`createShapeObjects()`	Create JmolObjects for all the molecular shapes; not executed for a state script.
`private void`	`fillFloatArrayFromBytes(byte[] b, float[] array)`
`private void`	`fillIntArrayFromBytes(byte[] b, int[] array)`
`void`	`finalizeModelSet()`	At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.
`private void`	`finalizeSceneData()`	Make sure atom uniqueID (vectorX) and cartoonType (vectorY) are made permanent
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private static javajs.util.Lst<java.lang.Object>`	`fixMovieCommands(javajs.util.Lst<java.lang.Object> cmds)`	Could possibly implement something here that interprets PyMOL script commands.
`private static javajs.util.Lst<java.lang.Object>`	`fixMovieViews(javajs.util.Lst<java.lang.Object> views)`	Could implement something here that creates a Jmol view.
`private javajs.util.Lst<java.lang.Object>`	`fixSettings(javajs.util.Lst<java.lang.Object> settings)`	Recent PyMOL files may not have all settings.
`(package private) static float`	`floatAt(javajs.util.Lst<java.lang.Object> list, int i)`
`(package private) static float[]`	`floatsAt(javajs.util.Lst<java.lang.Object> a, int pt, float[] data, int len)`
`private void`	`getAtomAndStateCount(javajs.util.Lst<java.lang.Object> names)`	Look through all named objects for molecules, counting atoms and also states; see if trajectories are compatible (experimental).
`private javajs.util.Lst<Bond>`	`getBondList(javajs.util.Lst<java.lang.Object> bonds)`	Create the bond set.
`private static BS`	`getBsReps(javajs.util.Lst<java.lang.Object> list)`
`int`	`getCartoonType(int iAtom)`
`(package private) static int`	`getColorPt(java.lang.Object o, javajs.util.P3 ptTemp)`
`private java.lang.String`	`getCStr(byte[] lex, int pt)`
`private boolean`	`getFrameScenes(java.util.Map<java.lang.String,java.lang.Object> map)`	remove all scenes that do not define a frame.
`private java.lang.String[]`	`getLexStr(byte[] lex)`
`private static javajs.util.Lst<java.lang.Object>`	`getMapList(java.util.Map<java.lang.String,java.lang.Object> map, java.lang.String key)`
`int`	`getSequenceNumber(int iAtom)`
`int`	`getUniqueID(int iAtom)`
`float`	`getVDW(int iAtom)`
`protected void`	`initializeReader()`
`(package private) static int`	`intAt(javajs.util.Lst<java.lang.Object> list, int i)`
`(package private) static javajs.util.Lst<java.lang.Object>`	`listAt(javajs.util.Lst<java.lang.Object> list, int i)`
`(package private) static java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>>`	`listToMap(javajs.util.Lst<java.lang.Object> list)`	return a map of lists of the type: [ [name1,...], [name2,...], ...]
`(package private) static javajs.util.P3`	`pointAt(javajs.util.Lst<java.lang.Object> list, int i, javajs.util.P3 pt)`
`private void`	`process(java.util.Map<java.lang.String,java.lang.Object> map)`	The main processor.
`void`	`processBinaryDocument()`
`private void`	`processCGO(javajs.util.Lst<java.lang.Object> pymolObject)`	Create a CGO JmolObject, just passing on key information.
`private void`	`processDefinitions()`	Create a JmolObject that will define atom sets based on PyMOL objects
`private void`	`processGadget(javajs.util.Lst<java.lang.Object> pymolObject)`	Only process _e_pot objects -- which we need for color settings
`private void`	`processMap(javajs.util.Lst<java.lang.Object> pymolObject, boolean isObject, boolean isGadget)`	Create mapObjects and volumeData; create an ISOSURFACE JmolObject.
`private void`	`processMeasure(javajs.util.Lst<java.lang.Object> pymolObject)`	Create a MEASURE JmolObject.
`private void`	`processMeshes()`	Create mesh or mep JmolObjects.
`private void`	`processMolCryst(javajs.util.Lst<java.lang.Object> cryst)`	Pick up the crystal data.
`private BS`	`processMolecule(javajs.util.Lst<java.lang.Object> pymolObject, int iState)`	Create everything necessary to generate a molecule in Jmol.
`private void`	`processMovie(javajs.util.Lst<java.lang.Object> mov, int frameCount)`	Create a JmolObject that will represent the movie.
`private void`	`processObject(javajs.util.Lst<java.lang.Object> execObject, boolean moleculeOnly, int iState)`	The main object processor.
`private void`	`processSelectionsAndScenes(java.util.Map<java.lang.String,java.lang.Object> map)`	A PyMOL scene consists of one or more of: view frame visibilities, by object colors, by color reps, by type currently just extracts viewpoint
`protected void`	`setAdditionalAtomParameters(Atom atom)`	adaptable via subclassing
`private int`	`setUniqueSettings(javajs.util.Lst<java.lang.Object> list)`	Create uniqueSettings from the "unique_settings" map item.
`protected void`	`setup(java.lang.String fullPath, java.util.Map<java.lang.String,java.lang.Object> htParams, java.lang.Object reader)`
`(package private) static java.lang.String`	`stringAt(javajs.util.Lst<java.lang.Object> list, int i)`
`static javajs.util.Lst<java.lang.Object>`	`sublistAt(javajs.util.Lst<java.lang.Object> mesh, int... pt)`

Methods inherited from class org.jmol.adapter.readers.pdb.PdbReader
checkLine, checkRemark, deduceElementSymbol, filterPDBAtom, finalizeReaderPDB, fixRadius, model, processAtom, processAtom2

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setupASCR

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MIN_RESNO
```
private static final int MIN_RESNO
```
See Also:

Constant Field Values

nucleic

private static java.lang.String nucleic

allowSurface
```
private boolean allowSurface
```

doResize
```
private boolean doResize
```

doCache
```
private boolean doCache
```

isStateScript
```
private boolean isStateScript
```

sourcePNGJ
```
private boolean sourcePNGJ
```

ac0
```
private int ac0
```

ac
```
private int ac
```

stateCount
```
private int stateCount
```

structureCount
```
private int structureCount
```

isHidden
```
private boolean isHidden
```

bsStructureDefined
```
private BS bsStructureDefined
```

bsBytesExcluded
```
private BS bsBytesExcluded
```

atomMap
```
private int[] atomMap
```

ssMapSeq

private java.util.Map<java.lang.String,BS> ssMapSeq

pymolScene
```
private PyMOLScene pymolScene
```

xyzMin
```
private javajs.util.P3 xyzMin
```

xyzMax
```
private javajs.util.P3 xyzMax
```

nModels
```
private int nModels
```

logging
```
private boolean logging
```

reps
```
private BS[] reps
```

isMovie
```
private boolean isMovie
```

pymolFrame
```
private int pymolFrame
```

allStates
```
private boolean allStates
```

totalAtomCount
```
private int totalAtomCount
```

pymolVersion
```
private int pymolVersion
```

trajectoryStep

private javajs.util.P3[] trajectoryStep

trajectoryPtr
```
private int trajectoryPtr
```

objectName
```
private java.lang.String objectName
```

volumeData

private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>> volumeData

mapObjects

private javajs.util.Lst<javajs.util.Lst<java.lang.Object>> mapObjects

haveMeasurements
```
private boolean haveMeasurements
```

frames
```
private int[] frames
```

uniqueSettings

private java.util.Hashtable<java.lang.Integer,javajs.util.Lst<java.lang.Object>> uniqueSettings

atoms
```
private Atom[] atoms
```

haveScenes
```
private boolean haveScenes
```

baseModelIndex
```
private int baseModelIndex
```

sceneOrder

private javajs.util.Lst<java.lang.Object> sceneOrder

bondCount
```
private int bondCount
```

haveBinaryArrays
```
private boolean haveBinaryArrays
```

ptTemp
```
private final javajs.util.P3 ptTemp
```

aTemp
```
byte[] aTemp
```

Constructor Detail
- PyMOLReader
```
public PyMOLReader()
```

Method Detail

setup

protected void setup(java.lang.String fullPath,
                     java.util.Map<java.lang.String,java.lang.Object> htParams,
                     java.lang.Object reader)

Overrides:: setup in class AtomSetCollectionReader

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:: initializeReader in class PdbReader
Throws:: java.lang.Exception

processBinaryDocument
```
public void processBinaryDocument()
                           throws java.lang.Exception
```
Overrides:

processBinaryDocument in class AtomSetCollectionReader

Throws:

java.lang.Exception

setAdditionalAtomParameters
```
protected void setAdditionalAtomParameters(Atom atom)
```
Description copied from class: PdbReader

adaptable via subclassing

Overrides:

setAdditionalAtomParameters in class PdbReader

finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class PdbReader

Throws:

java.lang.Exception

finalizeModelSet
```
public void finalizeModelSet()
```
At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.

Overrides:

finalizeModelSet in class AtomSetCollectionReader

process

private void process(java.util.Map<java.lang.String,java.lang.Object> map)

The main processor.

Parameters:: map -

fixSettings
```
private javajs.util.Lst<java.lang.Object> fixSettings(javajs.util.Lst<java.lang.Object> settings)
```
Recent PyMOL files may not have all settings. For now, we just add null values;

Parameters:

settings -

Returns:

settings

getFrameScenes
```
private boolean getFrameScenes(java.util.Map<java.lang.String,java.lang.Object> map)
```
remove all scenes that do not define a frame.

Parameters:

map -

Returns:

true if there are scenes that define a frame

setUniqueSettings
```
private int setUniqueSettings(javajs.util.Lst<java.lang.Object> list)
```
Create uniqueSettings from the "unique_settings" map item. This will be used later in processing molecule objects.

Parameters:

list -

Returns:

max id

addColors
```
private void addColors(javajs.util.Lst<java.lang.Object> colors,
                       boolean isClamped)
```
Add new colors from the main "colors" map object. Not 100% clear how color clamping works.

Parameters:

colors -

isClamped -

getAtomAndStateCount
```
private void getAtomAndStateCount(javajs.util.Lst<java.lang.Object> names)
```
Look through all named objects for molecules, counting atoms and also states; see if trajectories are compatible (experimental).

Parameters:

names -

checkObject

private boolean checkObject(javajs.util.Lst<java.lang.Object> execObject)

processMovie
```
private void processMovie(javajs.util.Lst<java.lang.Object> mov,
                          int frameCount)
```
Create a JmolObject that will represent the movie. For now, only process unscripted movies without views.

Parameters:

mov -

frameCount -

fixMovieViews

private static javajs.util.Lst<java.lang.Object> fixMovieViews(javajs.util.Lst<java.lang.Object> views)

Could implement something here that creates a Jmol view.

Parameters:: views -
Returns:: new views

fixMovieCommands
```
private static javajs.util.Lst<java.lang.Object> fixMovieCommands(javajs.util.Lst<java.lang.Object> cmds)
```
Could possibly implement something here that interprets PyMOL script commands.

Parameters:

cmds -

Returns:

new cmds

processObject

private void processObject(javajs.util.Lst<java.lang.Object> execObject,
                           boolean moleculeOnly,
                           int iState)

The main object processor. Not implemented: ALIGNMENT, CALLBACK, SLICE, SURFACE

Parameters:: execObject -; moleculeOnly -; iState -

processCGO
```
private void processCGO(javajs.util.Lst<java.lang.Object> pymolObject)
```
Create a CGO JmolObject, just passing on key information.

Parameters:

pymolObject -

processGadget
```
private void processGadget(javajs.util.Lst<java.lang.Object> pymolObject)
```
Only process _e_pot objects -- which we need for color settings

Parameters:

pymolObject -

processMap

private void processMap(javajs.util.Lst<java.lang.Object> pymolObject,
                        boolean isObject,
                        boolean isGadget)

Create mapObjects and volumeData; create an ISOSURFACE JmolObject.

Parameters:: pymolObject -; isObject -; isGadget -

processMeasure

private void processMeasure(javajs.util.Lst<java.lang.Object> pymolObject)

Create a MEASURE JmolObject.

Parameters:: pymolObject -

processMolecule
```
private BS processMolecule(javajs.util.Lst<java.lang.Object> pymolObject,
                           int iState)
```
Create everything necessary to generate a molecule in Jmol.

Parameters:

pymolObject -

iState -

Returns:

atom set only if this is a trajectory.

getLexStr

private java.lang.String[] getLexStr(byte[] lex)

getCStr

private java.lang.String getCStr(byte[] lex,
                                 int pt)

processMolCryst

private void processMolCryst(javajs.util.Lst<java.lang.Object> cryst)

Pick up the crystal data.

Parameters:: cryst -

getBondList

private javajs.util.Lst<Bond> getBondList(javajs.util.Lst<java.lang.Object> bonds)

Create the bond set.

Parameters:: bonds -
Returns:: list of bonds

fillIntArrayFromBytes

private void fillIntArrayFromBytes(byte[] b,
                                   int[] array)

fillFloatArrayFromBytes

private void fillFloatArrayFromBytes(byte[] b,
                                     float[] array)

addAtom

private javajs.util.P3 addAtom(javajs.util.Lst<java.lang.Object> pymolAtoms,
                               int apt,
                               byte[] atomArray,
                               int[] vArray,
                               java.lang.String[] lexStr,
                               int icoord,
                               javajs.util.Lst<java.lang.Object> coords,
                               float[] coordArray,
                               javajs.util.Lst<java.lang.Object> labelPositions,
                               float[] labelArray,
                               BS bsState,
                               int iState)

Parameters:: pymolAtoms - list of atom details; apt - array pointer into pymolAtoms; atomArray -; vArray -; lexStr -; icoord - array pointer into coords (/3); coords - coordinates array; coordArray -; labelPositions -; labelArray -; bsState - this state -- Jmol atomIndex; iState -
Returns:: true if successful

atomBool

private boolean atomBool(byte[] atomArray,
                         int pt,
                         int offset,
                         int mask)

atomFloat

private float atomFloat(byte[] atomArray,
                        int pt,
                        int offset)

atomStr

private java.lang.String atomStr(byte[] atomArray,
                                 int pt,
                                 int offset,
                                 java.lang.String[] lexStr)

atomInt

private int atomInt(byte[] atomArray,
                    int pt,
                    int offset)

addBonds

private void addBonds(javajs.util.Lst<Bond> bonds)

addMolStructures
```
private void addMolStructures()
```

addMolSS

private void addMolSS(java.lang.String ssType,
                      STR type)

Secondary structure definition.

Parameters:: ssType -; type -

createShapeObjects
```
private void createShapeObjects()
```
Create JmolObjects for all the molecular shapes; not executed for a state script.

processMeshes
```
private void processMeshes()
```
Create mesh or mep JmolObjects. Caching the volumeData, because it will be needed by org.jmol.jvxl.readers.PyMOLMeshReader

processDefinitions
```
private void processDefinitions()
```
Create a JmolObject that will define atom sets based on PyMOL objects

processSelectionsAndScenes
```
private void processSelectionsAndScenes(java.util.Map<java.lang.String,java.lang.Object> map)
```
A PyMOL scene consists of one or more of: view frame visibilities, by object colors, by color reps, by type currently just extracts viewpoint

Parameters:

map -

finalizeSceneData
```
private void finalizeSceneData()
```
Make sure atom uniqueID (vectorX) and cartoonType (vectorY) are made permanent

intAt

static int intAt(javajs.util.Lst<java.lang.Object> list,
                 int i)

pointAt

static javajs.util.P3 pointAt(javajs.util.Lst<java.lang.Object> list,
                              int i,
                              javajs.util.P3 pt)

floatsAt

static float[] floatsAt(javajs.util.Lst<java.lang.Object> a,
                        int pt,
                        float[] data,
                        int len)

floatAt

static float floatAt(javajs.util.Lst<java.lang.Object> list,
                     int i)

listAt

static javajs.util.Lst<java.lang.Object> listAt(javajs.util.Lst<java.lang.Object> list,
                                                int i)

sublistAt

public static javajs.util.Lst<java.lang.Object> sublistAt(javajs.util.Lst<java.lang.Object> mesh,
                                                          int... pt)

listToMap

static java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object>> listToMap(javajs.util.Lst<java.lang.Object> list)

return a map of lists of the type: [ [name1,...], [name2,...], ...]

Parameters:: list -
Returns:: Hashtable

stringAt

static java.lang.String stringAt(javajs.util.Lst<java.lang.Object> list,
                                 int i)

bytesToString

static java.lang.String bytesToString(java.lang.Object object)

colorSettingClamped

static int colorSettingClamped(javajs.util.Lst<java.lang.Object> c,
                               javajs.util.P3 ptTemp)

getColorPt

static int getColorPt(java.lang.Object o,
                      javajs.util.P3 ptTemp)

getMapList

private static javajs.util.Lst<java.lang.Object> getMapList(java.util.Map<java.lang.String,java.lang.Object> map,
                                                            java.lang.String key)

getBsReps

private static BS getBsReps(javajs.util.Lst<java.lang.Object> list)

getUniqueID
```
public int getUniqueID(int iAtom)
```
Specified by:

getUniqueID in interface PymolAtomReader

getCartoonType
```
public int getCartoonType(int iAtom)
```
Specified by:

getCartoonType in interface PymolAtomReader

getVDW
```
public float getVDW(int iAtom)
```
Specified by:

getVDW in interface PymolAtomReader

getSequenceNumber
```
public int getSequenceNumber(int iAtom)
```
Specified by:

getSequenceNumber in interface PymolAtomReader

compareAtoms

public boolean compareAtoms(int iPrev,
                            int i)

Specified by:: compareAtoms in interface PymolAtomReader

Class PyMOLReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.pdb.PdbReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.pdb.PdbReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Detail

MIN_RESNO

nucleic

allowSurface

doResize

doCache

isStateScript

sourcePNGJ

ac0

ac

stateCount

structureCount

isHidden

bsStructureDefined

bsBytesExcluded

atomMap

ssMapSeq

pymolScene

xyzMin

xyzMax

nModels

logging

reps

isMovie

pymolFrame

allStates

totalAtomCount

pymolVersion

trajectoryStep

trajectoryPtr

objectName

volumeData

mapObjects

haveMeasurements

frames

uniqueSettings

atoms

haveScenes

baseModelIndex

sceneOrder

bondCount

haveBinaryArrays

ptTemp

aTemp

Constructor Detail

PyMOLReader

Method Detail

setup

initializeReader

processBinaryDocument

setAdditionalAtomParameters

finalizeSubclassReader

finalizeModelSet

process

fixSettings

getFrameScenes

setUniqueSettings

addColors

getAtomAndStateCount

checkObject

processMovie

fixMovieViews

fixMovieCommands

processObject

processCGO

processGadget

processMap

processMeasure

processMolecule

getLexStr

getCStr