public class Mol2Reader extends ForceFieldReader
http://www.tripos.com/data/support/mol2.pdf PDB note: Note that mol2 format of PDB files is quite minimal. All we get is the PDB atom name, coordinates, residue number, and residue name No chain terminator, not chain designator, no element symbol. Chains based on numbering reset just labeled A B C D .... Z a b c d .... z Element symbols based on reasoned guess and properties of hetero groups So this is just a hack -- trying to guess at all of these.
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private char |
chainID |
private boolean |
isPDB |
private int |
lastSequenceNumber |
private int |
nAtoms |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
Mol2Reader() |
Modifier and Type | Method and Description |
---|---|
boolean |
checkLine() |
protected void |
initializeReader() |
private void |
processMolecule() |
private void |
readAtoms(int atomCount) |
private void |
readBonds(int bondCount) |
private void |
readCrystalInfo() |
private void |
readResInfo(int resCount) |
deducePdbElementSymbol, getElementSymbol, setUserAtomTypes
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private int nAtoms
private int atomCount
private boolean isPDB
private int lastSequenceNumber
private char chainID
protected void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
public boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void processMolecule() throws java.lang.Exception
java.lang.Exception
private void readAtoms(int atomCount) throws java.lang.Exception
java.lang.Exception
private void readBonds(int bondCount) throws java.lang.Exception
java.lang.Exception
private void readResInfo(int resCount) throws java.lang.Exception
java.lang.Exception
private void readCrystalInfo() throws java.lang.Exception
java.lang.Exception