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 Version: v0.2+dev (as of 2016.08.08) is implemented,including: reading atoms, bonds, and DSSP 1.0 secondary structure load =1f88.mmtf filter "DSSP1" [Note that the filter "DSSP1" is required, since mmtf included DSSP 1.0 calculations, while the standard for Jmol itself is DSSP 2.0. These two calculations differ in their treating of helix kinks as one (1.0) or two (2.0) helices.] reading space groups and unit cells, and using those as per other readers load =1crn.mmtf {1 1 1} reading bioassemblies (biomolecules) and applying all symmetry transformations load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P" reading both biomolecules and lattices, and loading course-grained using the filter "BYCHAIN" or "BYSYMOP" load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0; color property symop Many thanks to the MMTF team at RCSB for assistance in this implementation.

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`ac0`
`private int[]`	`atomGroup`
`private Atom[]`	`atomMap`
`private BS[]`	`bsStructures`
`private java.lang.Object[]`	`entities`
`private int`	`fileAtomCount`
`private int`	`groupCount`
`private int[]`	`groupDSSP`
`private int[]`	`groupMap`
`private int[]`	`groupModels`
`private boolean`	`haveStructure`
`private java.lang.String[]`	`labelAsymList`
`private int`	`lastGroup`
`private java.util.Map<java.lang.String,java.lang.Object>`	`map`
`private int`	`opCount`

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

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.readers.cif.MMCifReader
done, htHetero, htSites, isBiomolecule, mident, vBiomolecules

Constructor Summary

Constructors
Constructor Description

MMTFReader()

Constructors
Constructor	Description
`MMTFReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`addHeader()`
`private void`	`addMMTFBonds(int[] bo, int[] bi, int a0, boolean doMulti, boolean isInter)`
`private void`	`addStructureSymmetry()`	We must add groups to the proper bsStructure element
`void`	`applySymmetryAndSetTrajectory()`
`private java.lang.Object`	`decode(java.lang.String key)`
`private void`	`getMMTFAtoms(boolean doMulti)`	set up all atoms, including bonding, within a group
`private void`	`getMMTFBioAssembly()`
`private void`	`getStructure()`	Get and translate the DSSP string from digit format input data
`protected void`	`processBinaryDocument()`
`private void`	`setMMTFSymmetry()`
`protected void`	`setup(java.lang.String fullPath, java.util.Map<java.lang.String,java.lang.Object> htParams, java.lang.Object reader)`	standard set up

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 org.jmol.adapter.readers.cif.CifReader
checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlock

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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

haveStructure
```
private boolean haveStructure
```

map

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

fileAtomCount
```
private int fileAtomCount
```

opCount
```
private int opCount
```

groupModels
```
private int[] groupModels
```

groupMap
```
private int[] groupMap
```

groupDSSP
```
private int[] groupDSSP
```

atomGroup
```
private int[] atomGroup
```

labelAsymList

private java.lang.String[] labelAsymList

atomMap
```
private Atom[] atomMap
```

entities
```
private java.lang.Object[] entities
```

groupCount
```
private int groupCount
```

ac0
```
private int ac0
```

bsStructures
```
private BS[] bsStructures
```

lastGroup
```
private int lastGroup
```

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

applySymmetryAndSetTrajectory
```
public void applySymmetryAndSetTrajectory()
                                   throws java.lang.Exception
```
Overrides:

applySymmetryAndSetTrajectory in class CifReader

Throws:

java.lang.Exception

getMMTFAtoms
```
private void getMMTFAtoms(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

addMMTFBonds

private void addMMTFBonds(int[] bo,
                          int[] bi,
                          int a0,
                          boolean doMulti,
                          boolean isInter)

setMMTFSymmetry
```
private void setMMTFSymmetry()
```

getMMTFBioAssembly
```
private void getMMTFBioAssembly()
```

getStructure
```
private void getStructure()
```
Get and translate the DSSP string from digit format input data

addStructureSymmetry
```
private void addStructureSymmetry()
```
We must add groups to the proper bsStructure element

decode

private java.lang.Object decode(java.lang.String key)

Class MMTFReader

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Detail

haveStructure

map

fileAtomCount

opCount

groupModels

groupMap

groupDSSP

atomGroup

labelAsymList

atomMap

entities

groupCount

ac0

bsStructures

lastGroup

Constructor Detail

MMTFReader

Method Detail

addHeader

setup

processBinaryDocument

applySymmetryAndSetTrajectory

getMMTFAtoms

addMMTFBonds

setMMTFSymmetry

getMMTFBioAssembly

getStructure

addStructureSymmetry

decode