Package org.jmol.smiles
Class SmilesStereo
java.lang.Object
org.jmol.smiles.SmilesStereo
This class relates to stereochemical issues
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
-
Method Summary
Modifier and TypeMethodDescriptionint
checkStereoForAtom
(SmilesAtom pAtom, boolean isNot, boolean haveTopo) Node[]
getAlleneAtoms
(boolean haveTopo, SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom pAtom1) static int
getAtropicStereoFlag
(Node[] nodes) int
getChiralClass
(SmilesAtom sAtom) static SmilesStereo
newStereo
(SmilesSearch search) boolean
setTopoCoordinates
(SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom sAtom2, Node[] cAtoms, boolean isNot)
-
Field Details
-
DEFAULT
public static final int DEFAULT- See Also:
-
POLYHEDRAL
public static final int POLYHEDRAL- See Also:
-
ALLENE
public static final int ALLENE- See Also:
-
TRIGONAL_PYRAMIDAL
public static final int TRIGONAL_PYRAMIDAL- See Also:
-
TETRAHEDRAL
public static final int TETRAHEDRAL- See Also:
-
TRIGONAL_BIPYRAMIDAL
public static final int TRIGONAL_BIPYRAMIDAL- See Also:
-
OCTAHEDRAL
public static final int OCTAHEDRAL- See Also:
-
SQUARE_PLANAR
public static final int SQUARE_PLANAR- See Also:
-
T_SHAPED
public static final int T_SHAPED- See Also:
-
SEESAW
public static final int SEESAW- See Also:
-
-
Method Details
-
newStereo
- Throws:
InvalidSmilesException
-
getChiralClass
-
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
-
checkStereoForAtom
-
getAlleneAtoms
public Node[] getAlleneAtoms(boolean haveTopo, SmilesAtom sAtom0, SmilesAtom pAtom, SmilesAtom pAtom1) - Parameters:
haveTopo
-sAtom0
-pAtom
-pAtom1
-- Returns:
- allene atoms
-
getAtropicStereoFlag
-