Field Detail

• chiralClass

  private int chiralClass

• chiralOrder

  int chiralOrder

• atomCount

  int atomCount

• details

  private java.lang.String details

• search

  private SmilesSearch search

• jmolAtoms

  private Node[] jmolAtoms

• directives

  private java.lang.String directives

• DEFAULT

  public static final int DEFAULT

  See Also:

  Constant Field Values

• POLYHEDRAL

  public static final int POLYHEDRAL

  See Also:

  Constant Field Values

• ALLENE

  public static final int ALLENE

  See Also:

  Constant Field Values

• TRIGONAL_PYRAMIDAL

  public static final int TRIGONAL_PYRAMIDAL

  See Also:

  Constant Field Values

• TETRAHEDRAL

  public static final int TETRAHEDRAL

  See Also:

  Constant Field Values

• TRIGONAL_BIPYRAMIDAL

  public static final int TRIGONAL_BIPYRAMIDAL

  See Also:

  Constant Field Values

• OCTAHEDRAL

  public static final int OCTAHEDRAL

  See Also:

  Constant Field Values

• SQUARE_PLANAR

  public static final int SQUARE_PLANAR

  See Also:

  Constant Field Values

• T_SHAPED

  public static final int T_SHAPED

  See Also:

  Constant Field Values

• SEESAW

  public static final int SEESAW

  See Also:

  Constant Field Values

• PERM_TB

  private static final int[] PERM_TB

• PERM_OCT

  private static final int[] PERM_OCT

• PERM_SS

  private static final int[] PERM_SS

• v

  VTemp v

• polyhedralOrders

  private int[][] polyhedralOrders

• isNot

  private boolean isNot

• sorter

  private PolyhedronStereoSorter sorter

Constructor Detail

• SmilesStereo

  SmilesStereo​(int chiralClass,
               int chiralOrder,
               int atomCount,
               java.lang.String details,
               java.lang.String directives)
        throws InvalidSmilesException

  Throws:

  InvalidSmilesException

Method Detail

• getChiralityClass

  private static int getChiralityClass​(java.lang.String xx)

• newStereo

  public static SmilesStereo newStereo​(SmilesSearch search)
                                throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• getChiralClass

  public int getChiralClass​(SmilesAtom sAtom)

• setChiralClass

  private int setChiralClass​(SmilesAtom sAtom)

• fixStereo

  void fixStereo​(SmilesAtom sAtom)
          throws InvalidSmilesException

  Check number of connections and permute them to match a canonical version

  Parameters:

  sAtom -

  Throws:

  InvalidSmilesException

• normalizeClass

  private boolean normalizeClass​(SmilesAtom atom)

  re-order bonds to match standard @ and @@ types

  Parameters:

  atom -

  Returns:

  true if OK

• setTopoCoordinates

  public boolean setTopoCoordinates​(SmilesAtom sAtom0,
                                    SmilesAtom pAtom,
                                    SmilesAtom sAtom2,
                                    Node[] cAtoms,
                                    boolean isNot)

  Parameters:

  sAtom0 - the first target atom

  pAtom - the pattern atom connected to the target atoms

  sAtom2 - allene atom

  cAtoms - the target atoms

  isNot -

  Returns:

• getMappedTopoAtoms

  private int[] getMappedTopoAtoms​(SmilesAtom atom,
                                   SmilesAtom a2,
                                   Node[] cAtoms,
                                   int[] map)

• getTopoMapPt

  private static boolean getTopoMapPt​(int[] map,
                                      int i,
                                      SmilesAtom atom,
                                      SmilesAtom cAtom,
                                      SmilesBond[] bonds,
                                      int n000)

  Parameters:

  map -

  i -

  atom -

  cAtom -

  bonds -

  n000 -

  Returns:

  true if found

• getJmolAtom

  private Node getJmolAtom​(int i)

• sortPolyBondsByStereo

  void sortPolyBondsByStereo​(SimpleNode atom,
                             SimpleNode ref,
                             javajs.util.T3 center,
                             SimpleEdge[] bonds,
                             javajs.util.V3 vTemp)

  Sort bond array as ccw rotation around the axis connecting the atom and the reference point (polyhedron center) as seen from outside the polyhedron looking in. Since we are allowing no branching, all atoms will appear as separate components with only numbers after them. These numbers will be processed and listed in this order.

  Parameters:

  atom -

  ref -

  center -

  bonds -

  vTemp -

• checkStereoChemistry

  boolean checkStereoChemistry​(SmilesSearch search,
                               VTemp v)

• checkStereoForAtom

  public int checkStereoForAtom​(SmilesAtom pAtom,
                                boolean isNot,
                                boolean haveTopo)

• checkPolyHedralWinding

  private boolean checkPolyHedralWinding​(Node a0,
                                         Node[] a)

• getAlleneAtoms

  public Node[] getAlleneAtoms​(SmilesAtom pAtom,
                               SmilesAtom pAtom1)

• addAlleneLonePair

  private void addAlleneLonePair​(SmilesAtom pAtom,
                                 Node[] jn,
                                 int k)

  for allenes, we must check for missing atoms

  Parameters:

  pAtom -

  jn -

  k -

• getStereoFlag

  static java.lang.String getStereoFlag​(SimpleNode atom0,
                                        SimpleNode[] atoms,
                                        int nAtoms,
                                        VTemp v,
                                        boolean is2D)

  Parameters:

  atom0 -

  atoms -

  nAtoms -

  v -

  is2D -

  Returns:

  String

• checkStereochemistryAll

  private static boolean checkStereochemistryAll​(boolean isNot,
                                                 SimpleNode atom0,
                                                 int chiralClass,
                                                 int order,
                                                 SimpleNode atom1,
                                                 SimpleNode atom2,
                                                 SimpleNode atom3,
                                                 SimpleNode atom4,
                                                 SimpleNode atom5,
                                                 SimpleNode atom6,
                                                 VTemp v)

• isDiaxial

  static boolean isDiaxial​(SimpleNode atomA,
                           SimpleNode atomB,
                           SimpleNode atom1,
                           SimpleNode atom2,
                           VTemp v,
                           float f)

• getHandedness

  static int getHandedness​(SimpleNode a,
                           SimpleNode b,
                           SimpleNode c,
                           SimpleNode pt,
                           VTemp v)

  determine the winding of the circuit a--b--c relative to point pt

  Parameters:

  a -

  b -

  c -

  pt -

  v -

  Returns:

  1 for "@", 2 for "@@"

• getPlaneNormals

  private static void getPlaneNormals​(javajs.util.P3 atom1,
                                      javajs.util.P3 atom2,
                                      javajs.util.P3 atom3,
                                      javajs.util.P3 atom4,
                                      VTemp v)

• checkChirality

  static int checkChirality​(SmilesSearch search,
                            java.lang.String pattern,
                            int index,
                            SmilesAtom newAtom)
                     throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• getPolyhedralOrders

  private void getPolyhedralOrders()
                            throws InvalidSmilesException

  experimental Jmol polySMILES

  Throws:

  InvalidSmilesException

• getAtropicStereoFlag

  public static int getAtropicStereoFlag​(Node[] nodes)