Field Detail

• TYPE_UNKNOWN

  public static final int TYPE_UNKNOWN

  See Also:

  Constant Field Values

• TYPE_NONE

  public static final int TYPE_NONE

  See Also:

  Constant Field Values

• TYPE_AROMATIC

  public static final int TYPE_AROMATIC

  See Also:

  Constant Field Values

• TYPE_RING

  public static final int TYPE_RING

  See Also:

  Constant Field Values

• TYPE_ANY

  public static final int TYPE_ANY

  See Also:

  Constant Field Values

• TYPE_BIO_SEQUENCE

  public static final int TYPE_BIO_SEQUENCE

  See Also:

  Constant Field Values

• TYPE_BIO_CROSSLINK

  public static final int TYPE_BIO_CROSSLINK

  See Also:

  Constant Field Values

• ALL_BONDS

  private static final java.lang.String ALL_BONDS

  See Also:

  Constant Field Values

• SMILES_BONDS

  private static final java.lang.String SMILES_BONDS

  See Also:

  Constant Field Values

• atom1

  SmilesAtom atom1

• atom2

  SmilesAtom atom2

• isNot

  boolean isNot

• matchingBond

  Edge matchingBond

• primitives

  private SmilesBond[] primitives

• nPrimitives

  int nPrimitives

• bondsOr

  SmilesBond[] bondsOr

• nBondsOr

  int nBondsOr

• isConnection

  boolean isConnection

• atropType

  int[] atropType

• isChain

  public boolean isChain

Constructor Detail

• SmilesBond

  SmilesBond​(SmilesAtom atom1,
             SmilesAtom atom2,
             int bondType,
             boolean isNot)

  SmilesBond constructor

  Parameters:

  atom1 - First atom

  atom2 - Second atom

  bondType - Bond type

  isNot -

Method Detail

• getBondOrderString

  static java.lang.String getBondOrderString​(int order)

• getBondTypeFromCode

  static int getBondTypeFromCode​(char code)

  Parameters:

  code - Bond code

  Returns:

  Bond type

• set

  void set​(SmilesBond bond)

• setAtropType

  void setAtropType​(int nn)

• setPrimitive

  public SmilesBond setPrimitive​(int i)

• addBondOr

  SmilesBond addBondOr()

• addPrimitive

  SmilesBond addPrimitive()

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object

• set2

  void set2​(int bondType,
            boolean isNot)

• set2a

  void set2a​(SmilesAtom a1,
             SmilesAtom a2)

• setAtom2

  void setAtom2​(SmilesAtom atom,
                SmilesSearch molecule)

  from parse ring

  Parameters:

  atom -

  molecule -

• isFromPreviousTo

  boolean isFromPreviousTo​(SmilesAtom atom)

  Check to see if this is the bond to the previous atom

  Parameters:

  atom -

  Returns:

  TRUE if other atom is previous atom

• isBondType

  static int isBondType​(char ch,
                        boolean isSearch,
                        boolean isBioSequence)
                 throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• getBondType

  int getBondType()

• getValence

  int getValence()

• getOtherAtom

  SmilesAtom getOtherAtom​(SmilesAtom a)

• getAtomIndex1

  public int getAtomIndex1()

  Specified by:

  getAtomIndex1 in class Edge

• getAtomIndex2

  public int getAtomIndex2()

  Specified by:

  getAtomIndex2 in class Edge

• getCovalentOrder

  public int getCovalentOrder()

  Specified by:

  getCovalentOrder in class Edge

• getOtherAtomNode

  public Node getOtherAtomNode​(Node atom)

  Specified by:

  getOtherAtomNode in class Edge

• isCovalent

  public boolean isCovalent()

  Specified by:

  isCovalent in class Edge

• isHydrogen

  public boolean isHydrogen()

  Specified by:

  isHydrogen in class Edge

• switchAtoms

  void switchAtoms()

  Ensure that atom ordering is proper. possibly not fully tested