Field Detail

• atoms

  private Node[] atoms

• ac

  private int ac

• bsSelected

  private BS bsSelected

• bsAromatic

  private BS bsAromatic

• flags

  private int flags

• explicitH

  private boolean explicitH

• ringSets

  private javajs.util.SB ringSets

• vTemp

  private VTemp vTemp

• nPairs

  private int nPairs

• nPairsMax

  private int nPairsMax

• bsBondsUp

  private BS bsBondsUp

• bsBondsDn

  private BS bsBondsDn

• bsToDo

  private BS bsToDo

• prevAtom

  private Node prevAtom

• prevSp2Atoms

  private Node[] prevSp2Atoms

• htRingsSequence

  private java.util.Map<java.lang.String,​java.lang.Object[]> htRingsSequence

• htRings

  private java.util.Map<java.lang.String,​java.lang.Object[]> htRings

• bsRingKeys

  private BS bsRingKeys

• bsIncludingH

  private BS bsIncludingH

• topologyOnly

  private boolean topologyOnly

• getAromatic

  boolean getAromatic

• addAtomComment

  private boolean addAtomComment

• noBioComment

  private boolean noBioComment

• aromaticDouble

  private boolean aromaticDouble

• noStereo

  private boolean noStereo

• openSMILES

  private boolean openSMILES

• polySmilesCenter

  public javajs.util.P3 polySmilesCenter

• smilesStereo

  private SmilesStereo smilesStereo

• isPolyhedral

  private boolean isPolyhedral

• aromaticRings

  private javajs.util.Lst<BS> aromaticRings

• sm

  private SmilesMatcher sm

• iHypervalent

  private int iHypervalent

• atemp

  private Node[] atemp

• chainCheck

  private int chainCheck

Constructor Detail

• SmilesGenerator

  public SmilesGenerator()

Method Detail

• getSmiles

  java.lang.String getSmiles​(SmilesMatcher sm,
                             Node[] atoms,
                             int ac,
                             BS bsSelected,
                             java.lang.String comment,
                             int flags)
                      throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• getBioSmiles

  private java.lang.String getBioSmiles​(BS bsSelected,
                                        java.lang.String comment,
                                        int flags)
                                 throws InvalidSmilesException

  Throws:

  InvalidSmilesException

• addBracketedBioName

  private void addBracketedBioName​(javajs.util.SB sb,
                                   Node atom,
                                   java.lang.String atomName,
                                   boolean addComment)

• getSmilesComponent

  private java.lang.String getSmilesComponent​(Node atom,
                                              BS bs,
                                              boolean allowBioResidues,
                                              boolean allowConnectionsToOutsideWorld,
                                              boolean forceBrackets)
                                       throws InvalidSmilesException

  creates a valid SMILES string from a model. TODO: stereochemistry other than square planar and tetrahedral

  Parameters:

  atom -

  bs -

  allowBioResidues -

  allowConnectionsToOutsideWorld -

  forceBrackets -

  Returns:

  SMILES

  Throws:

  InvalidSmilesException

• generateRingData

  private void generateRingData()
                         throws InvalidSmilesException

  get aromaticity, ringSets, and aromaticRings fields so that we can assign / and \ and also provide inter-aromatic single bond

  Throws:

  InvalidSmilesException

• getBondStereochemistry

  private char getBondStereochemistry​(Edge bond,
                                      Node atomFrom)

  Retrieves the saved character based on the index of the bond. bsBondsUp and bsBondsDown are global fields.

  Parameters:

  bond -

  atomFrom -

  Returns:

  the correct character '/', '\\', '\0' (meaning "no stereochemistry")

• setBondDirections

  private void setBondDirections()

  Creates global BitSets bsBondsUp and bsBondsDown. Noniterative.

• getSmilesAt

  private Node getSmilesAt​(javajs.util.SB sb,
                           Node atom,
                           boolean allowConnectionsToOutsideWorld,
                           boolean allowBranches,
                           boolean forceBrackets)

• swapArray

  private void swapArray​(Node[] a,
                         int i0,
                         int i1,
                         int i2)

  swap slices of an array [i0 i1) with [i1 i2)

  Parameters:

  a -

  i0 -

  i1 -

  i2 -

• getBondOrder

  private java.lang.String getBondOrder​(Edge bondPrev,
                                        int atomIndex,
                                        int prevIndex,
                                        boolean isAromatic)

  Parameters:

  bondPrev -

  atomIndex -

  prevIndex -

  isAromatic -

  Returns:

  "-", "=", "#", "$", or ""

• isSameAromaticRing

  private boolean isSameAromaticRing​(int a1,
                                     int a2)

• sortBonds

  void sortBonds​(Node atom,
                 Node refAtom,
                 javajs.util.P3 center)

• sortInorganic

  private java.lang.String sortInorganic​(Node atom,
                                         javajs.util.Lst<Edge> v,
                                         VTemp vTemp)

  We must sort the bond vector such that a diaxial pair is first and last. Then we assign stereochemistry based on what is left. The assignment is not made if there are no diaxial groups or with octahedral if there are fewer than three or trigonal bipyramidal with no axial ligands.

  Parameters:

  atom -

  v -

  vTemp -

  Returns:

  "@" or "@@" or ""

• checkStereoPairs

  private java.lang.String checkStereoPairs​(Node atom,
                                            int atomIndex,
                                            Node[] stereo,
                                            int stereoFlag)

• addStereoCheck

  private java.lang.String addStereoCheck​(int level,
                                          int atomIndex,
                                          Node atom,
                                          java.lang.String s,
                                          BS bsDone)

  checks a group and either adds a new group to the growing check string or returns null

  Parameters:

  level -

  atomIndex -

  atom -

  s -

  bsDone -

  Returns:

  null if duplicate

• getRingCache

  private java.lang.String getRingCache​(int i0,
                                        int i1,
                                        java.util.Map<java.lang.String,​java.lang.Object[]> ht)

• getRingPointer

  private java.lang.String getRingPointer​(int i)

• dumpRingKeys

  private void dumpRingKeys​(javajs.util.SB sb,
                            java.util.Map<java.lang.String,​java.lang.Object[]> ht)

• getRingKey

  protected static java.lang.String getRingKey​(int i0,
                                               int i1)