PyMOLReader

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

All Implemented Interfaces:

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 and Description
`private boolean`	`allowSurface`
`private boolean`	`allStates`
`private int`	`atomCount`
`private int`	`atomCount0`
`private int[]`	`atomMap`
`private Atom[]`	`atoms`
`private int`	`baseAtomIndex`
`private int`	`baseModelIndex`
`private int`	`bondCount`
`private BS`	`bsBytesExcluded`
`private BS`	`bsStructureDefined`
`private boolean`	`doCache`
`private boolean`	`doResize`
`private int[]`	`frames`
`private boolean`	`haveMeasurements`
`private boolean`	`haveScenes`
`private boolean`	`isHidden`
`private boolean`	`isMovie`
`private boolean`	`isStateScript`
`private boolean`	`logging`
`private JmolList<JmolList<java.lang.Object>>`	`mapObjects`
`private static int`	`MIN_RESNO`
`private int`	`nModels`
`private static java.lang.String`	`nucleic`
`private java.lang.String`	`objectName`
`private int`	`pymolFrame`
`private PyMOLScene`	`pymolScene`
`private int`	`pymolVersion`
`private BS[]`	`reps`
`private JmolList<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 P3[]`	`trajectoryStep`
`private java.util.Hashtable<java.lang.Integer,JmolList<java.lang.Object>>`	`uniqueSettings`
`private java.util.Map<java.lang.String,JmolList<java.lang.Object>>`	`volumeData`
`private P3`	`xyzMax`
`private P3`	`xyzMin`

Fields inherited from class org.jmol.adapter.readers.cifpdb.PdbReader
chainAtomCounts, fileAtomIndex, isPQR

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors
Constructor and Description

PyMOLReader()

Constructors
Constructor and Description
`PyMOLReader()`

Method Summary

Methods
Modifier and Type	Method and Description
`private P3`	`addAtom(JmolList<java.lang.Object> pymolAtoms, int apt, int icoord, JmolList<java.lang.Object> coords, JmolList<java.lang.Object> labelPositions, BS bsState, int iState)`
`private void`	`addBonds(JmolList<Bond> bonds)`
`private void`	`addColors(JmolList<java.lang.Object> colors, boolean isClamped)` Add new colors from the main "colors" map object.
`private void`	`addMolSS(java.lang.String ssType, EnumStructure type)` Secondary structure definition.
`private void`	`addMolStructures()`
`private boolean`	`checkObject(JmolList<java.lang.Object> execObject)`
`boolean`	`compareAtoms(int iPrev, int i)`
`private void`	`createShapeObjects()` Create JmolObjects for all the molecular shapes; not executed for a state script.
`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.
`protected void`	`finalizeReader()` optional reader-specific method run first.
`private void`	`finalizeSceneData()` Make sure atom uniqueID (vectorX) and cartoonType (vectorY) are made permanent
`private static JmolList<java.lang.Object>`	`fixMovieCommands(JmolList<java.lang.Object> cmds)` Could possibly implement something here that interprets PyMOL script commands.
`private static JmolList<java.lang.Object>`	`fixMovieViews(JmolList<java.lang.Object> views)` Could implement something here that creates a Jmol view.
`private float`	`floatAt(JmolList<java.lang.Object> a, int i)`
`private void`	`getAtomAndStateCount(JmolList<java.lang.Object> names)` Look through all named objects for molecules, counting atoms and also states; see if trajectories are compatible (experimental).
`private JmolList<Bond>`	`getBondList(JmolList<java.lang.Object> bonds)` Create the bond set.
`private static BS`	`getBsReps(JmolList<java.lang.Object> list)`
`int`	`getCartoonType(int iAtom)`
`private boolean`	`getFrameScenes(java.util.Map<java.lang.String,java.lang.Object> map)` remove all scenes that do not define a frame.
`private static JmolList<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()`
`private static int`	`intAt(JmolList<java.lang.Object> list, int i)`
`private JmolList<java.lang.Object>`	`listAt(JmolList<java.lang.Object> list, int i)`
`private void`	`process(java.util.Map<java.lang.String,java.lang.Object> map)` The main processor.
`void`	`processBinaryDocument(JmolDocument doc)`
`private void`	`processCGO(JmolList<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(JmolList<java.lang.Object> pymolObject)` Only process _e_pot objects -- which we need for color settings
`private void`	`processMap(JmolList<java.lang.Object> pymolObject, boolean isObject, boolean isGadget)` Create mapObjects and volumeData; create an ISOSURFACE JmolObject.
`private void`	`processMeasure(JmolList<java.lang.Object> pymolObject)` Create a MEASURE JmolObject.
`private void`	`processMeshes()` Create mesh or mep JmolObjects.
`private void`	`processMolCryst(JmolList<java.lang.Object> cryst)` Pick up the crystal data.
`private BS`	`processMolecule(JmolList<java.lang.Object> pymolObject, int iState)` Create everything necessary to generate a molecule in Jmol.
`private void`	`processMovie(JmolList<java.lang.Object> mov, int frameCount)` Create a JmolObject that will represent the movie.
`private void`	`processObject(JmolList<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(JmolList<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)`
`private static java.lang.String`	`stringAt(JmolList<java.lang.Object> list, int i)`

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

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processDOM, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, 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
```

atomCount0
```
private int atomCount0
```

atomCount
```
private int atomCount
```

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 P3 xyzMin
```

xyzMax
```
private 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 P3[] trajectoryStep
```

trajectoryPtr
```
private int trajectoryPtr
```

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

volumeData

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

mapObjects

private JmolList<JmolList<java.lang.Object>> mapObjects

haveMeasurements
```
private boolean haveMeasurements
```

frames
```
private int[] frames
```

uniqueSettings

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

atoms
```
private Atom[] atoms
```

haveScenes
```
private boolean haveScenes
```

baseAtomIndex
```
private int baseAtomIndex
```

baseModelIndex
```
private int baseModelIndex
```

sceneOrder

private JmolList<java.lang.Object> sceneOrder

bondCount
```
private int bondCount
```

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(JmolDocument doc)
                           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
- finalizeReader
```
protected void finalizeReader()
                       throws java.lang.Exception
```
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeReader 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 -
- 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(JmolList<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(JmolList<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(JmolList<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(JmolList<java.lang.Object> execObject)
```
- processMovie
```
private void processMovie(JmolList<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 JmolList<java.lang.Object> fixMovieViews(JmolList<java.lang.Object> views)
```
  Could implement something here that creates a Jmol view.
  
  Parameters:
  views -
  
  Returns:
  new views
- fixMovieCommands
```
private static JmolList<java.lang.Object> fixMovieCommands(JmolList<java.lang.Object> cmds)
```
  Could possibly implement something here that interprets PyMOL script commands.
  
  Parameters:
  cmds -
  
  Returns:
  new cmds
- processObject
```
private void processObject(JmolList<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(JmolList<java.lang.Object> pymolObject)
```
  Create a CGO JmolObject, just passing on key information.
  
  Parameters:
  pymolObject -
- processGadget
```
private void processGadget(JmolList<java.lang.Object> pymolObject)
```
  Only process _e_pot objects -- which we need for color settings
  
  Parameters:
  pymolObject -
- processMap
```
private void processMap(JmolList<java.lang.Object> pymolObject,
              boolean isObject,
              boolean isGadget)
```
  Create mapObjects and volumeData; create an ISOSURFACE JmolObject.
  
  Parameters:
  pymolObject -
  isObject -
  isGadget -
- processMeasure
```
private void processMeasure(JmolList<java.lang.Object> pymolObject)
```
  Create a MEASURE JmolObject.
  
  Parameters:
  pymolObject -
- processMolecule
```
private BS processMolecule(JmolList<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.
- processMolCryst
```
private void processMolCryst(JmolList<java.lang.Object> cryst)
```
  Pick up the crystal data.
  
  Parameters:
  cryst -
- getBondList
```
private JmolList<Bond> getBondList(JmolList<java.lang.Object> bonds)
```
  Create the bond set.
  
  Parameters:
  bonds -
  
  Returns:
  list of bonds
- addAtom
```
private P3 addAtom(JmolList<java.lang.Object> pymolAtoms,
         int apt,
         int icoord,
         JmolList<java.lang.Object> coords,
         JmolList<java.lang.Object> labelPositions,
         BS bsState,
         int iState)
```
  Parameters:
  pymolAtoms - list of atom details
  apt - array pointer into pymolAtoms
  icoord - array pointer into coords (/3)
  coords - coordinates array
  labelPositions -
  bsState - this state -- Jmol atomIndex
  iState -
  
  Returns:
  true if successful
- addBonds
```
private void addBonds(JmolList<Bond> bonds)
```
- addMolStructures
```
private void addMolStructures()
```
- addMolSS
```
private void addMolSS(java.lang.String ssType,
            EnumStructure 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
```
private static int intAt(JmolList<java.lang.Object> list,
        int i)
```
- stringAt
```
private static java.lang.String stringAt(JmolList<java.lang.Object> list,
                        int i)
```
- getMapList
```
private static JmolList<java.lang.Object> getMapList(java.util.Map<java.lang.String,java.lang.Object> map,
                                    java.lang.String key)
```
- getBsReps
```
private static BS getBsReps(JmolList<java.lang.Object> list)
```
- floatAt
```
private float floatAt(JmolList<java.lang.Object> a,
            int i)
```
- listAt
```
private JmolList<java.lang.Object> listAt(JmolList<java.lang.Object> list,
                                int i)
```
- 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.cifpdb.PdbReader

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.cifpdb.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

atomCount0

atomCount

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

baseAtomIndex

baseModelIndex

sceneOrder

bondCount

Constructor Detail

PyMOLReader

Method Detail

setup

initializeReader

processBinaryDocument

setAdditionalAtomParameters

finalizeReader

finalizeModelSet

process

getFrameScenes

setUniqueSettings

addColors

getAtomAndStateCount

checkObject

processMovie

fixMovieViews

fixMovieCommands

processObject

processCGO

processGadget

processMap

processMeasure

processMolecule

processMolCryst

getBondList

addAtom

addBonds

addMolStructures