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 javajs.util.BS

bsBytesExcluded

private javajs.util.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<Object>>

mapObjects

private static final int

MIN_RESNO

private int

nModels

private static String

nucleic

private String

objectName

private final javajs.util.P3

ptTemp

private int

pymolFrame

private PyMOLScene

pymolScene

private int

pymolVersion

private javajs.util.BS[]

reps

private javajs.util.Lst<Object>

sceneOrder

private boolean

sourcePNGJ

private Map<String,javajs.util.BS>

ssMapSeq

private int

stateCount

private int

structureCount

private int

totalAtomCount

private int

trajectoryPtr

private javajs.util.P3[]

trajectoryStep

private Hashtable<Integer,javajs.util.Lst<Object>>

uniqueSettings

private Map<String,javajs.util.Lst<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, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor Summary

Constructors

Constructor

Description

PyMOLReader()
Method Summary

Modifier and Type

Method

Description

private javajs.util.P3

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

private void

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

private void

addColors(javajs.util.Lst<Object> colors, boolean isClamped)

Add new colors from the main "colors" map object.

private void

addMolSS(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 String

atomStr(byte[] atomArray, int pt, int offset, String[] lexStr)

private static String

bytesToString(Object object)

private boolean

checkObject(javajs.util.Lst<Object> execObject)

(package private) static int

colorSettingClamped(javajs.util.Lst<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<Object>

fixMovieCommands(javajs.util.Lst<Object> cmds)

Could possibly implement something here that interprets PyMOL script commands.

private static javajs.util.Lst<Object>

fixMovieViews(javajs.util.Lst<Object> views)

Could implement something here that creates a Jmol view.

private javajs.util.Lst<Object>

fixSettings(javajs.util.Lst<Object> settings)

Recent PyMOL files may not have all settings.

(package private) static float

floatAt(javajs.util.Lst<Object> list, int i)

(package private) static float[]

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

private void

getAtomAndStateCount(javajs.util.Lst<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<Object> bonds)

Create the bond set.

private static javajs.util.BS

getBsReps(javajs.util.Lst<Object> list)

int

getCartoonType(int iAtom)

(package private) static int

getColorPt(Object o, javajs.util.P3 ptTemp)

private String

getCStr(byte[] lex, int pt)

private boolean

getFrameScenes(Map<String,Object> map)

remove all scenes that do not define a frame.

private String[]

getLexStr(byte[] lex)

private static javajs.util.Lst<Object>

getMapList(Map<String,Object> map, 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<Object> list, int i)

(package private) static javajs.util.Lst<Object>

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

(package private) static Map<String,javajs.util.Lst<Object>>

listToMap(javajs.util.Lst<Object> list)

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

(package private) static javajs.util.P3

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

private void

process(Map<String,Object> map)

The main processor.

void

processBinaryDocument()

private void

processCGO(javajs.util.Lst<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<Object> pymolObject)

Only process _e_pot objects -- which we need for color settings

private void

processMap(javajs.util.Lst<Object> pymolObject, boolean isObject, boolean isGadget)

Create mapObjects and volumeData; create an ISOSURFACE JmolObject.

private void

processMeasure(javajs.util.Lst<Object> pymolObject)

Create a MEASURE JmolObject.

private void

processMeshes()

Create mesh or mep JmolObjects.

private void

processMolCryst(javajs.util.Lst<Object> cryst)

Pick up the crystal data.

private javajs.util.BS

processMolecule(javajs.util.Lst<Object> pymolObject, int iState)

Create everything necessary to generate a molecule in Jmol.

private void

processMovie(javajs.util.Lst<Object> mov, int frameCount)

Create a JmolObject that will represent the movie.

private void

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

The main object processor.

private void

processSelectionsAndScenes(Map<String,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<Object> list)

Create uniqueSettings from the "unique_settings" map item.

protected void

setup(String fullPath, Map<String,Object> htParams, Object reader)

(package private) static String

stringAt(javajs.util.Lst<Object> list, int i)

static javajs.util.Lst<Object>

sublistAt(javajs.util.Lst<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, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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 Details
- MIN_RESNO
  
  private static final int MIN_RESNO
  See Also:
  
  Constant Field Values
- nucleic
  
  private static 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 javajs.util.BS bsStructureDefined
- bsBytesExcluded
  
  private javajs.util.BS bsBytesExcluded
- atomMap
  
  private int[] atomMap
- ssMapSeq
  
  private Map<String,javajs.util.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 javajs.util.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 String objectName
- volumeData
  
  private Map<String,javajs.util.Lst<Object>> volumeData
- mapObjects
  
  private javajs.util.Lst<javajs.util.Lst<Object>> mapObjects
- haveMeasurements
  
  private boolean haveMeasurements
- frames
  
  private int[] frames
- uniqueSettings
  
  private Hashtable<Integer,javajs.util.Lst<Object>> uniqueSettings
- atoms
  
  private Atom[] atoms
- haveScenes
  
  private boolean haveScenes
- baseModelIndex
  
  private int baseModelIndex
- sceneOrder
  
  private javajs.util.Lst<Object> sceneOrder
- bondCount
  
  private int bondCount
- haveBinaryArrays
  
  private boolean haveBinaryArrays
- ptTemp
  
  private final javajs.util.P3 ptTemp
- aTemp
  
  byte[] aTemp
Constructor Details
- PyMOLReader
  
  public PyMOLReader()
Method Details
- setup
  
  protected void setup(String fullPath, Map<String,Object> htParams, Object reader)
  
  Overrides:
  
  setup in class AtomSetCollectionReader
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class PdbReader
  
  Throws:
  
  Exception
- processBinaryDocument
  
  public void processBinaryDocument() throws Exception
  
  Overrides:
  
  processBinaryDocument in class AtomSetCollectionReader
  
  Throws:
  
  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 Exception
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class PdbReader
  
  Throws:
  
  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(Map<String,Object> map)
  
  The main processor.
  
  Parameters:
  
  map -
- fixSettings
  
  private javajs.util.Lst<Object> fixSettings(javajs.util.Lst<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(Map<String,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<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<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<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<Object> execObject)
- processMovie
  
  private void processMovie(javajs.util.Lst<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<Object> fixMovieViews(javajs.util.Lst<Object> views)
  
  Could implement something here that creates a Jmol view.
  
  Parameters:
  
  views -
  
  Returns:
  
  new views
- fixMovieCommands
  
  private static javajs.util.Lst<Object> fixMovieCommands(javajs.util.Lst<Object> cmds)
  
  Could possibly implement something here that interprets PyMOL script commands.
  
  Parameters:
  
  cmds -
  
  Returns:
  
  new cmds
- processObject
  
  private void processObject(javajs.util.Lst<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<Object> pymolObject)
  
  Create a CGO JmolObject, just passing on key information.
  
  Parameters:
  
  pymolObject -
- processGadget
  
  private void processGadget(javajs.util.Lst<Object> pymolObject)
  
  Only process _e_pot objects -- which we need for color settings
  
  Parameters:
  
  pymolObject -
- processMap
  
  private void processMap(javajs.util.Lst<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<Object> pymolObject)
  
  Create a MEASURE JmolObject.
  
  Parameters:
  
  pymolObject -
- processMolecule
  
  private javajs.util.BS processMolecule(javajs.util.Lst<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 String[] getLexStr(byte[] lex)
- getCStr
  
  private String getCStr(byte[] lex, int pt)
- processMolCryst
  
  private void processMolCryst(javajs.util.Lst<Object> cryst)
  
  Pick up the crystal data.
  
  Parameters:
  
  cryst -
- getBondList
  
  private javajs.util.Lst<Bond> getBondList(javajs.util.Lst<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<Object> pymolAtoms, int apt, byte[] atomArray, int[] vArray, String[] lexStr, int icoord, javajs.util.Lst<Object> coords, float[] coordArray, javajs.util.Lst<Object> labelPositions, float[] labelArray, javajs.util.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 String atomStr(byte[] atomArray, int pt, int offset, 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(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(Map<String,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<Object> list, int i)
- pointAt
  
  static javajs.util.P3 pointAt(javajs.util.Lst<Object> list, int i, javajs.util.P3 pt)
- floatsAt
  
  static float[] floatsAt(javajs.util.Lst<Object> a, int pt, float[] data, int len)
- floatAt
  
  static float floatAt(javajs.util.Lst<Object> list, int i)
- listAt
  
  static javajs.util.Lst<Object> listAt(javajs.util.Lst<Object> list, int i)
- sublistAt
  
  public static javajs.util.Lst<Object> sublistAt(javajs.util.Lst<Object> mesh, int... pt)
- listToMap
  
  static Map<String,javajs.util.Lst<Object>> listToMap(javajs.util.Lst<Object> list)
  
  return a map of lists of the type: [ [name1,...], [name2,...], ...]
  
  Parameters:
  
  list -
  
  Returns:
  
  Hashtable
- stringAt
  
  static String stringAt(javajs.util.Lst<Object> list, int i)
- bytesToString
  
  private static String bytesToString(Object object)
- colorSettingClamped
  
  static int colorSettingClamped(javajs.util.Lst<Object> c, javajs.util.P3 ptTemp)
- getColorPt
  
  static int getColorPt(Object o, javajs.util.P3 ptTemp)
- getMapList
  
  private static javajs.util.Lst<Object> getMapList(Map<String,Object> map, String key)
- getBsReps
  
  private static javajs.util.BS getBsReps(javajs.util.Lst<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 Details

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 Details

PyMOLReader

Method Details

setup

initializeReader

processBinaryDocument

setAdditionalAtomParameters

finalizeSubclassReader

finalizeModelSet

process

fixSettings

getFrameScenes

setUniqueSettings

addColors

getAtomAndStateCount

checkObject

processMovie

fixMovieViews

fixMovieCommands

processObject

processCGO

processGadget

processMap

processMeasure

processMolecule

getLexStr

getCStr