public class MMTFReader extends MMCifReader
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 |
htHetero, htSites, isBiomolecule, mident, vBiomolecules
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
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 and Description |
---|
MMTFReader() |
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
|
addAssembly, addHetero, addMatrix, checkFilterAssembly, checkPDBModelField, checkSubclassSymmetry, finalizeSubclass, incrementModel, initSubclass, processSubclassAtom, processSubclassEntry, processSubclassLoopBlock, sortAssemblyModels
applySymmetryAndSetTrajectory, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlock
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
private java.util.Map<java.lang.String,java.lang.Object> map
private int fileAtomCount
private int opCount
private int[] groupModels
private java.lang.String[] labelAsymList
private int[] atomMap
protected void setup(java.lang.String fullPath, java.util.Map<java.lang.String,java.lang.Object> htParams, java.lang.Object reader)
setup
in class AtomSetCollectionReader
fullPath
- htParams
- reader
- protected void processBinaryDocument() throws java.lang.Exception
processBinaryDocument
in class AtomSetCollectionReader
java.lang.Exception
private int[] rldecode32(byte[] b, int n)
b
- n
- private int[] rldecode32Delta(byte[] b, int n)
b
- n
- private float[] getFloatsSplit(java.lang.String xyz, float factor)
xyz
- label "x", "y", "z", or "bFactor"factor
- for dividing in the end -- 1000f or 100fprivate float[] splitDelta(byte[] big, byte[] small, int n, float factor)
big
- [n m n m n m...] where n is a "big delta" and m is a number of
"small deltassmall
- array containing the small deltasn
- the size of the final arrayfactor
- to divide the final result by -- 1000f or 100f hereprivate int[] getInts(byte[] b, int nbytes)
b
- nbytes
- 2 (int16) or 4 (int32)private java.lang.String[] bytesTo4CharArray(byte[] b)
b
- a byte arrayprivate void getBonds(boolean doMulti)
private void setSymmetry()
private void getBioAssembly()
private void getAtoms(boolean doMulti) throws java.lang.Exception
doMulti
- true to add double bondsjava.lang.Exception
private void addBond(Bond bond, boolean isInter)
private void getStructure(byte[] a)
a
- input data