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java.lang.Objectorg.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.AlchemyReader
public class AlchemyReader
TRIPOS simple Alchemy reader. atomtypes based on OpenBabel data/types.txt Somewhat flexible - for 3DNA compatibility. See http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp.alc) Bob Hanson 12/2008
Field Summary | |
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(package private) int |
atomCount
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(package private) int |
bondCount
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
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ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount |
Constructor Summary | |
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AlchemyReader()
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Method Summary | |
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private void |
readAtoms()
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void |
readAtomSetCollection(java.io.BufferedReader reader)
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private void |
readBonds()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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int atomCount
int bondCount
Constructor Detail |
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public AlchemyReader()
Method Detail |
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public void readAtomSetCollection(java.io.BufferedReader reader)
readAtomSetCollection
in class AtomSetCollectionReader
private void readAtoms() throws java.lang.Exception
java.lang.Exception
private void readBonds() throws java.lang.Exception
java.lang.Exception
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