org.jmol.adapter.readers.more.MdTopReader

All Implemented Interfaces:: javajs.api.GenericLineReader

public class MdTopReader extends ForceFieldReader

A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file

PDB note: Note that topology format does not include chain designations, chain terminator, chain designator, or element symbol. Chains based on numbering reset just labeled A B C D .... Z a b c d .... z Element symbols based on reasoned guess and properties of hetero groups In principal we could use average atomic mass.

Field Summary

Fields

Modifier and Type

Field

Description

private int

ac

private String[]

atomTypes

(package private) String[]

group3s

private int

nAtoms

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

MdTopReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkLine()

protected void

finalizeSubclassReader()

optional reader-specific method run first.

private void

getAtomNames()

private void

getAtomTypes()

private void

getCharges()

private String[]

getDataBlock()

private void

getMasses()

private void

getPointers()

private void

getResidueLabels()

private void

getResiduePointers()

protected void

initializeReader()

Methods inherited from class org.jmol.adapter.readers.more.ForceFieldReader
deducePdbElementSymbol, getElementSymbol, setUserAtomTypes

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, finalizeModelSet, 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, processBinaryDocument, 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, setup, setupASCR

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

Field Details
- nAtoms
  
  private int nAtoms
- ac
  
  private int ac
- atomTypes
  
  private String[] atomTypes
- group3s
  
  String[] group3s
Constructor Details
- MdTopReader
  
  public MdTopReader()
Method Details
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- finalizeSubclassReader
  
  protected void finalizeSubclassReader() throws Exception
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- getDataBlock
  
  private String[] getDataBlock() throws Exception
  
  Throws:
  
  Exception
- getPointers
  
  private void getPointers() throws Exception
  
  Throws:
  
  Exception
- getAtomTypes
  
  private void getAtomTypes() throws Exception
  
  Throws:
  
  Exception
- getCharges
  
  private void getCharges() throws Exception
  
  Throws:
  
  Exception
- getResiduePointers
  
  private void getResiduePointers() throws Exception
  
  Throws:
  
  Exception
- getResidueLabels
  
  private void getResidueLabels() throws Exception
  
  Throws:
  
  Exception
- getAtomNames
  
  private void getAtomNames() throws Exception
  
  Throws:
  
  Exception
- getMasses
  
  private void getMasses() throws Exception
  
  Throws:
  
  Exception

Class MdTopReader

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.more.ForceFieldReader

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

Methods inherited from class java.lang.Object

Field Details

nAtoms

ac

atomTypes

group3s

Constructor Details

MdTopReader

Method Details

initializeReader

checkLine

finalizeSubclassReader

getDataBlock

getPointers

getAtomTypes

getCharges

getResiduePointers

getResidueLabels

getAtomNames

getMasses