org.jmol.adapter.readers.pymol.PyMOLReader

All Implemented Interfaces:: GenericLineReader

public class PyMOLReader extends PdbReader

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

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, CELL_TYPE_SUPER, cellSlop, centroidPacked, checkNearAtoms, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filteredPrecision, filterHetero, floatifyJavaDouble, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isSUPERCELL, isTrajectory, latticeCells, latticeScaling, latticeType, line, lowPrecision, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noMinimize, noPack, optimize2D, out, paramsCentroid, paramsLattice, precision, 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

boolean

compareAtoms(int iPrev, int i)

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

finalizeSubclassReader()

int

getCartoonType(int iAtom)

int

getSequenceNumber(int iAtom)

int

getUniqueID(int iAtom)

double

getVDW(int iAtom)

protected void

initializeReader()

void

processBinaryDocument()

protected void

setAdditionalAtomParameters(Atom atom)

adaptable via subclassing

protected void

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

static Lst<Object>

sublistAt(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, addMoreUnitCellInfo, addSites, addSiteScript, appendLoadNote, 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, fixDoubleA, fixFloatA, fixFloatPt, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getPackingRangeValue, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parsePrecision, 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, setPrecision, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setupASCR, warnSkippingOperation

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

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
  
  Parameters:
  
  atom -
- finalizeSubclassReader
  
  protected void finalizeSubclassReader() throws Exception
  
  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
- sublistAt
  
  public static Lst<Object> sublistAt(Lst<Object> mesh, int... pt)
- getUniqueID
  
  public int getUniqueID(int iAtom)
- getCartoonType
  
  public int getCartoonType(int iAtom)
- getVDW
  
  public double getVDW(int iAtom)
- getSequenceNumber
  
  public int getSequenceNumber(int iAtom)
- compareAtoms
  
  public boolean compareAtoms(int iPrev, int i)

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

Constructor Details

PyMOLReader

Method Details

setup

initializeReader

processBinaryDocument

setAdditionalAtomParameters

finalizeSubclassReader

finalizeModelSet

sublistAt

getUniqueID

getCartoonType

getVDW

getSequenceNumber

compareAtoms