org.jmol.adapter.readers.cif

Class MMTFReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.cif.CifReader

org.jmol.adapter.readers.cif.MMCifReader

org.jmol.adapter.readers.cif.MMTFReader

All Implemented Interfaces:

javajs.api.GenericLineReader

public class MMTFReader
extends MMCifReader

JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md /full/ specification as of 2016.4.18 is implemented,including: reading atoms, bonds, and DSSR secondary structure load =1f88.mmtf reading space groups and unit cells, and using those as per other readers load =1crn.mmtf {1 1 1} reading bioassemblies (biomolecules) and applying those transformations load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P" reading biomolecules and lattices, and loading course-grained load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0; color property symop Note that the filter "DSSP1" indicates that mmtf included DSSP 1.0 calculation should be used. Otherwise Jmol will use DSSP 2.0 itself.

Field Summary

Fields

Modifier and Type	Field and Description
private int[]	atomMap
private int	fileAtomCount
private int[]	groupModels
private java.lang.String[]	labelAsymList
private java.util.Map<java.lang.String,java.lang.Object>	map
private int	opCount

Fields inherited from class org.jmol.adapter.readers.cif.MMCifReader

htHetero, htSites, isBiomolecule, mident, vBiomolecules

Fields inherited from class org.jmol.adapter.readers.cif.CifReader

ac, col2key, data, FAMILY_ATOM, field, firstChar, haveCellWaveVector, haveHAtoms, htGroup1, iHaveDesiredModel, isCourseGrained, isLigand, isMagCIF, isMMCIF, key, key0, key2col, lastDataSetName, maxSerial, modelMap, nAtoms, nAtoms0, NONE, parser, skipping, thisDataSetName, useAuthorChainID

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 and Description
MMTFReader()

Method Summary

Modifier and Type	Method and Description
private void	addBond(Bond bond, boolean isInter)
protected void	addHeader()
private java.lang.String[]	bytesTo4CharArray(byte[] b) Decode each four bytes as a 1- to 4-character string label
private void	getAtoms(boolean doMulti) set up all atoms, including bonding within a group
private void	getBioAssembly()
private void	getBonds(boolean doMulti)
private float[]	getFloatsSplit(java.lang.String xyz, float factor) Do a split delta to a float[] array
private int[]	getInts(byte[] b, int nbytes) decode a byte array into an int array
private void	getStructure(byte[] a) Get and translate the DSSP string from digit format
protected void	processBinaryDocument()
private int[]	rldecode32(byte[] b, int n) Decode an array of int32 using run-length decoding
private int[]	rldecode32Delta(byte[] b, int n) Decode an array of int32 using run-length decoding of a difference array.
private void	setSymmetry()
protected void	setup(java.lang.String fullPath, java.util.Map<java.lang.String,java.lang.Object> htParams, java.lang.Object reader) standard set up
private float[]	splitDelta(byte[] big, byte[] small, int n, float factor) Do a split delta to a float[] array

Methods inherited from class org.jmol.adapter.readers.cif.MMCifReader

addAssembly, addHetero, addMatrix, checkFilterAssembly, checkPDBModelField, checkSubclassSymmetry, finalizeSubclass, incrementModel, initSubclass, processSubclassAtom, processSubclassEntry, processSubclassLoopBlock, sortAssemblyModels

Methods inherited from class org.jmol.adapter.readers.cif.CifReader

applySymmetryAndSetTrajectory, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlock

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

addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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

map

private java.util.Map<java.lang.String,java.lang.Object> map

fileAtomCount

private int fileAtomCount

opCount

private int opCount

groupModels

private int[] groupModels

labelAsymList

private java.lang.String[] labelAsymList

atomMap

private int[] atomMap

Constructor Detail

MMTFReader

public MMTFReader()

Method Detail

addHeader

protected void addHeader()

Overrides:

addHeader in class CifReader

setup

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

standard set up

Overrides:

setup in class AtomSetCollectionReader

Parameters:

fullPath -

htParams -

reader -

processBinaryDocument

protected void processBinaryDocument()
                              throws java.lang.Exception

Overrides:

processBinaryDocument in class AtomSetCollectionReader

Throws:

java.lang.Exception

rldecode32

private int[] rldecode32(byte[] b,
                         int n)

Decode an array of int32 using run-length decoding

Parameters:

b -

n -

Returns:

array of integers

rldecode32Delta

private int[] rldecode32Delta(byte[] b,
                              int n)

Decode an array of int32 using run-length decoding of a difference array.

Parameters:

b -

n -

Returns:

array of integers

getFloatsSplit

private float[] getFloatsSplit(java.lang.String xyz,
                               float factor)

Do a split delta to a float[] array

Parameters:

xyz - label "x", "y", "z", or "bFactor"

factor - for dividing in the end -- 1000f or 100f

Returns:

float[]

splitDelta

private float[] splitDelta(byte[] big,
                           byte[] small,
                           int n,
                           float factor)

Do a split delta to a float[] array

Parameters:

big - [n m n m n m...] where n is a "big delta" and m is a number of "small deltas

small - array containing the small deltas

n - the size of the final array

factor - to divide the final result by -- 1000f or 100f here

Returns:

float[]

getInts

private int[] getInts(byte[] b,
                      int nbytes)

decode a byte array into an int array

Parameters:

b -

nbytes - 2 (int16) or 4 (int32)

Returns:

int array

bytesTo4CharArray

private java.lang.String[] bytesTo4CharArray(byte[] b)

Decode each four bytes as a 1- to 4-character string label

Parameters:

b - a byte array

Returns:

String[]

getBonds

private void getBonds(boolean doMulti)

setSymmetry

private void setSymmetry()

getBioAssembly

private void getBioAssembly()

getAtoms

private void getAtoms(boolean doMulti)
               throws java.lang.Exception

set up all atoms, including bonding within a group

Parameters:

doMulti - true to add double bonds

Throws:

java.lang.Exception

addBond

private void addBond(Bond bond,
                     boolean isInter)

getStructure

private void getStructure(byte[] a)

Get and translate the DSSP string from digit format

Parameters:

a - input data