Field Detail

• isSmarts

  boolean isSmarts

• top

  SmilesSearch top

• pattern

  java.lang.String pattern

• patternAtoms

  SmilesAtom[] patternAtoms

• targetAtoms

  Node[] targetAtoms

• targetAtomCount

  int targetAtomCount

• bsSelected

  private BS bsSelected

• v

  VTemp v

• aromaticOpen

  boolean aromaticOpen

• aromaticStrict

  boolean aromaticStrict

• aromaticPlanar

  boolean aromaticPlanar

• aromaticDouble

  boolean aromaticDouble

• noAromatic

  boolean noAromatic

• ignoreAtomClass

  boolean ignoreAtomClass

• ignoreStereochemistry

  boolean ignoreStereochemistry

• invertStereochemistry

  boolean invertStereochemistry

• exitFirstMatch

  boolean exitFirstMatch

• groupByModel

  boolean groupByModel

• setAtropicity

  boolean setAtropicity

• patternAromatic

  boolean patternAromatic

  Set in set() to indicate to SmilesMatcher that the string already has aromatic atoms indicated and so no aromaticity model should be applied.

• haveTopo

  boolean haveTopo

• isTopology

  boolean isTopology

• patternBioSequence

  boolean patternBioSequence

• subSearches

  SmilesSearch[] subSearches

• haveSelected

  boolean haveSelected

• haveBondStereochemistry

  boolean haveBondStereochemistry

• stereo

  SmilesStereo stereo

• needRingData

  boolean needRingData

• needAromatic

  boolean needAromatic

• needRingMemberships

  boolean needRingMemberships

• nDouble

  int nDouble

• ringDataMax

  int ringDataMax

• ringSets

  javajs.util.SB ringSets

• ringCount

  int ringCount

• measures

  javajs.util.Lst<SmilesMeasure> measures

• flags

  int flags

• bsAromatic

  BS bsAromatic

• bsAromatic5

  BS bsAromatic5

• bsAromatic6

  BS bsAromatic6

• atropKeys

  java.lang.String atropKeys

• lastChainAtom

  SmilesAtom lastChainAtom

• asVector

  boolean asVector

• getMaps

  boolean getMaps

• isNormalized

  boolean isNormalized

• haveComponents

  boolean haveComponents

• isSilent

  private boolean isSilent

• isRingCheck

  private boolean isRingCheck

• selectedAtomCount

  private int selectedAtomCount

• ringData

  private BS[] ringData

• ringCounts

  private int[] ringCounts

• ringConnections

  private int[] ringConnections

• bsFound

  private BS bsFound

• htNested

  private java.util.Map<java.lang.String,​java.lang.Object> htNested

• nNested

  private int nNested

• nestedBond

  private SmilesBond nestedBond

• vReturn

  private javajs.util.Lst<java.lang.Object> vReturn

• bsReturn

  private BS bsReturn

• bsCheck

  private BS bsCheck

• SUBMODE_NESTED

  private static final int SUBMODE_NESTED

  See Also:

  Constant Field Values

• SUBMODE_RINGCHECK

  private static final int SUBMODE_RINGCHECK

  See Also:

  Constant Field Values

• SUBMODE_OR

  private static final int SUBMODE_OR

  See Also:

  Constant Field Values

Constructor Detail

• SmilesSearch

  public SmilesSearch()

Method Detail

• setTop

  void setTop​(SmilesSearch parent)

• addFlags

  static final int addFlags​(int flags,
                            java.lang.String strFlags)

• setFlags

  void setFlags​(int flags)

• set

  void set()
    throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• setSelected

  void setSelected​(BS bs)

• addAtom

  SmilesAtom addAtom()

• appendAtom

  SmilesAtom appendAtom​(SmilesAtom sAtom)

• addNested

  int addNested​(java.lang.String pattern)

• clear

  void clear()

• clearBsFound

  private void clearBsFound​(int iAtom)

• setNested

  void setNested​(int iNested,
                 java.lang.Object o)

• getNested

  java.lang.Object getNested​(int iNested)

• getMissingHydrogenCount

  int getMissingHydrogenCount()

• setRingData

  void setRingData​(BS bsA,
                   javajs.util.Lst<BS>[] vRings,
                   boolean doProcessAromatic)
            throws InvalidSmilesException

  Sets up all aromatic and ring data. Called from SmilesGenerator.getSmilesComponent and SmilesMatcher.matchPriv.

  Parameters:

  bsA -

  vRings -

  doProcessAromatic -

  Throws:

  InvalidSmilesException

• getRingData

  void getRingData​(javajs.util.Lst<BS>[] vRings,
                   boolean needRingData,
                   boolean doTestAromatic)
            throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• subsearch

  java.lang.Object subsearch​(SmilesSearch search,
                             int submode)
                      throws InvalidSmilesException

  Parameters:

  search -

  submode -

  Returns:

  Object

  Throws:

  InvalidSmilesException

• search

  java.lang.Object search()
                   throws InvalidSmilesException

  the start of the search. ret will be either a Vector or a BitSet

  Returns:

  BitSet or Vector

  Throws:

  InvalidSmilesException

• search2

  private java.lang.Object search2​(boolean firstAtomOnly)
                            throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• nextPatternAtom

  private boolean nextPatternAtom​(int atomNum,
                                  int iAtom,
                                  boolean firstAtomOnly,
                                  int c)
                           throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• doCheckAtom

  private boolean doCheckAtom​(int j)

• nextTargetAtom

  private final boolean nextTargetAtom​(SmilesAtom patternAtom,
                                       Node jmolAtom,
                                       int atomNum,
                                       int iAtom,
                                       boolean firstAtomOnly,
                                       int c)
                                throws InvalidSmilesException

  Check for a specific match of a model set atom with a pattern position

  Parameters:

  patternAtom - Atom of the pattern that is currently tested.

  jmolAtom -

  atomNum - Current atom of the pattern.

  iAtom - Atom number of the Jmol atom that is currently tested to match patternAtom.

  firstAtomOnly -

  c -

  Returns:

  true to continue or false if oneOnly

  Throws:

  InvalidSmilesException

• checkPrimitiveAtom

  private boolean checkPrimitiveAtom​(SmilesAtom patternAtom,
                                     int iTarget)
                              throws InvalidSmilesException

  Parameters:

  patternAtom -

  iTarget -

  Returns:

  true if a match

  Throws:

  InvalidSmilesException

• checkMatchBond

  private boolean checkMatchBond​(SmilesAtom patternAtom,
                                 SmilesAtom atom1,
                                 SmilesBond patternBond,
                                 int iAtom,
                                 int matchingAtom,
                                 Edge bond)

• checkPrimitiveBond

  private boolean checkPrimitiveBond​(SmilesBond patternBond,
                                     int iAtom1,
                                     int iAtom2,
                                     Edge bond)

• isRingBond

  static boolean isRingBond​(javajs.util.SB ringSets,
                            int i,
                            int j)

• checkStereochemistry

  private boolean checkStereochemistry()

• getAtropIndex

  private int getAtropIndex​(SmilesBond b,
                            boolean isFirst)

• setTopoCoordinates

  private void setTopoCoordinates​(SmilesAtom dbAtom1,
                                  SmilesAtom dbAtom2,
                                  SmilesAtom dbAtom1a,
                                  SmilesAtom dbAtom2a,
                                  int bondType)

• createTopoMap

  void createTopoMap​(BS bsAro)
              throws InvalidSmilesException

  Parameters:

  bsAro - null for molecular formula calculation only

  Throws:

  InvalidSmilesException

• normalizeAromaticity

  static void normalizeAromaticity​(SmilesAtom[] atoms,
                                   BS bsAromatic,
                                   int flags)
                            throws InvalidSmilesException

  create a temporary object to generate the aromaticity in a SMILES pattern for which there is no explicit aromaticity (Kekule) Not applicable to SMARTS

  Parameters:

  atoms -

  bsAromatic -

  flags -

  Throws:

  InvalidSmilesException

• getSelections

  void getSelections()

  htNested may contain $(select xxxx) primitives. We want to clear those up before we start any search.

• getNormalThroughPoints

  static float getNormalThroughPoints​(Node pointA,
                                      Node pointB,
                                      Node pointC,
                                      javajs.util.V3 vNorm,
                                      javajs.util.V3 vAB,
                                      javajs.util.V3 vAC)

  calculates a normal to a plane for three points and returns a signed distance

  Parameters:

  pointA -

  pointB -

  pointC -

  vNorm -

  vAB -

  vAC -

  Returns:

  a signed distance

• findImplicitHydrogen

  Node findImplicitHydrogen​(Node atom)

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object