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, 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, 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, sortAssemblyModels
checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getCifDataParser, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlock
addAtomXYZSymName, 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, setupASCR
private 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 AtomSetCollectionReader
fullPath
- htParams
- reader
- protected void processBinaryDocument() throws java.lang.Exception
processBinaryDocument
in class AtomSetCollectionReader
java.lang.Exception
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
applySymmetryAndSetTrajectory
in class CifReader
java.lang.Exception
private void getMMTFAtoms(boolean doMulti) throws java.lang.Exception
doMulti
- true to add double bondsjava.lang.Exception
private 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)