public class MMTFReader extends MMCifReader
| Modifier and Type | Field and Description |
|---|---|
private int |
ac0 |
private int[] |
atomGroup |
private Atom[] |
atomMap |
private javajs.util.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 |
private java.lang.String |
pdbID |
done, htHetero, htSites, isBiomolecule, mident, vBiomoleculesac, 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, useAuthorChainIDaddedData, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, 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 |
|---|---|
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
|
addAssembly, addHetero, addMatrix, checkFilterAssembly, checkPDBModelField, checkSubclassSymmetry, finalizeSubclass, incrementModel, initSubclass, processSubclassAtom, processSubclassEntry, processSubclassLoopBlock, sortAssemblyModelscheckAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getCifDataParser, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlockaddAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, fill3x3, 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, setupASCRprivate boolean haveStructure
private java.lang.String pdbID
private java.util.Map<java.lang.String,java.lang.Object> map
private int fileAtomCount
private int opCount
private int[] groupModels
private int[] groupMap
private int[] groupDSSP
private int[] atomGroup
private java.lang.String[] labelAsymList
private Atom[] atomMap
private java.lang.Object[] entities
private int groupCount
private int ac0
private javajs.util.BS[] bsStructures
private int lastGroup
protected void setup(java.lang.String fullPath,
java.util.Map<java.lang.String,java.lang.Object> htParams,
java.lang.Object reader)
setup in class AtomSetCollectionReaderfullPath - htParams - reader - protected void processBinaryDocument()
throws java.lang.Exception
processBinaryDocument in class AtomSetCollectionReaderjava.lang.Exceptionpublic void applySymmetryAndSetTrajectory()
throws java.lang.Exception
applySymmetryAndSetTrajectory in class CifReaderjava.lang.Exceptionprivate void getMMTFAtoms(boolean doMulti)
throws java.lang.Exception
doMulti - true to add double bondsjava.lang.Exceptionprivate void addMMTFBonds(int[] bo,
int[] bi,
int a0,
boolean doMulti,
boolean isInter)
private void setMMTFSymmetry()
private void getMMTFBioAssembly()
private void getStructure()
private void addStructureSymmetry()
private java.lang.Object decode(java.lang.String key)