Package org.jmol.smiles
Class SmilesStereo
java.lang.Object
org.jmol.smiles.SmilesStereo
This class relates to stereochemical issues
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final int -
Method Summary
Modifier and TypeMethodDescriptionintcheckStereoForAtom(SmilesAtom pAtom, boolean isNot, boolean haveTopo) Node[]getAlleneAtoms(boolean haveTopo, SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom pAtom1) static intgetAtropicStereoFlag(Node[] nodes) intgetChiralClass(SmilesAtom sAtom) static SmilesStereonewStereo(SmilesSearch search) booleansetTopoCoordinates(SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom sAtom2, Node[] cAtoms, boolean isNot)
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Field Details
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DEFAULT
public static final int DEFAULT- See Also:
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POLYHEDRAL
public static final int POLYHEDRAL- See Also:
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ALLENE
public static final int ALLENE- See Also:
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TRIGONAL_PYRAMIDAL
public static final int TRIGONAL_PYRAMIDAL- See Also:
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TETRAHEDRAL
public static final int TETRAHEDRAL- See Also:
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TRIGONAL_BIPYRAMIDAL
public static final int TRIGONAL_BIPYRAMIDAL- See Also:
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OCTAHEDRAL
public static final int OCTAHEDRAL- See Also:
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SQUARE_PLANAR
public static final int SQUARE_PLANAR- See Also:
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T_SHAPED
public static final int T_SHAPED- See Also:
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SEESAW
public static final int SEESAW- See Also:
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Method Details
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newStereo
- Throws:
InvalidSmilesException
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getChiralClass
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setTopoCoordinates
public boolean setTopoCoordinates(SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom sAtom2, Node[] cAtoms, boolean isNot) - Parameters:
sAtom0- the first target atompAtom- the pattern atom connected to the target atomssAtom2- allene atomcAtoms- the target atomsisNot-- Returns:
- true if successful
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checkStereoForAtom
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getAlleneAtoms
public Node[] getAlleneAtoms(boolean haveTopo, SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom pAtom1) - Parameters:
haveTopo-sAtom0-pAtom-pAtom1-- Returns:
- allene atoms
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getAtropicStereoFlag
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