Field Detail

• OS_PI_COUNTS

  private static final int[][] OS_PI_COUNTS

  Index to inner array is covalent bond count (b) + valence (v) + charge (c, carbon only) - 4. Special cases are listed here as -1. -2 indicates not considered aromatic (probably not possible). Many thanks to John May for the excellent visual guide that I have condensed here.

Constructor Detail

• SmilesAromatic

  public SmilesAromatic()

Method Detail

• setAromatic

  static void setAromatic​(int n,
                          Node[] jmolAtoms,
                          BS bsSelected,
                          javajs.util.Lst<java.lang.Object> vR,
                          BS bsAromatic,
                          int strictness,
                          boolean isOpenSMILES,
                          boolean justCheckBonding,
                          boolean checkExplicit,
                          VTemp v,
                          javajs.util.Lst<BS> vOK,
                          javajs.util.Lst<SmilesRing> lstSP2,
                          int[] eCounts,
                          boolean doTestAromatic)

  Main entry point. Note that unless bonds are pre-defined as aromatic, Jmol will first check for a flat ring configuration. This is 3D, after all.

  Parameters:

  n -

  jmolAtoms -

  bsSelected -

  vR -

  bsAromatic -

  strictness -

  isOpenSMILES -

  justCheckBonding -

  checkExplicit -

  v -

  vOK -

  lstSP2 -

  eCounts -

  doTestAromatic -

• checkAromaticDefined

  static void checkAromaticDefined​(Node[] jmolAtoms,
                                   BS bsSelected,
                                   BS bsAromatic)

  Set aromatic atoms based on predefined BOND_AROMATIC definitions. Allows for totally customized creation of aromatic SMILES.

  Parameters:

  jmolAtoms -

  bsSelected -

  bsAromatic -

• isSp2Ring

  private static final boolean isSp2Ring​(int n,
                                         Node[] atoms,
                                         BS bsSelected,
                                         BS bs,
                                         float cutoff,
                                         boolean checkExplicit,
                                         boolean allowSOxide)

  3D-SEARCH aromaticity test. A simple and unambiguous test for aromaticity based on 3D geometry and connectivity only, not Hueckel theory.

  Parameters:

  n -

  atoms - a set of atoms with coordinate positions and associated bonds.

  bs - a bitset of atoms within the set of atoms, defining the ring

  bsSelected - must not be null

  cutoff - an arbitrary value to test the standard deviation against. 0.01 is appropriate here. Use Float.MAX_VALUE to just do bond connectivity check

  checkExplicit - check bonds that are explicit only - for XYZ and QM calcs

  allowSOxide - set TRUE to skip S atoms

  Returns:

  true if standard deviation of vNorm.dot.vMean is less than cutoff

• addNormal

  private static final boolean addNormal​(javajs.util.V3 vTemp,
                                         javajs.util.V3 vMean,
                                         float maxDev)

  adds a normal if similarity is within limits

  Parameters:

  vTemp -

  vMean -

  maxDev -

  Returns:

  true if successful

• checkStandardDeviation

  private static final boolean checkStandardDeviation​(javajs.util.V3[] vNorms,
                                                      javajs.util.V3 vMean,
                                                      int n,
                                                      float cutoff)

  calculates a dot-product standard deviation and reports if it is below a cutoff

  Parameters:

  vNorms -

  vMean -

  n -

  cutoff -

  Returns:

  true if stddev < cutoff

• checkHueckelAromatic

  private static int checkHueckelAromatic​(int nAtoms,
                                          Node[] jmolAtoms,
                                          BS bsAromatic,
                                          BS bsRing,
                                          int strictness,
                                          int[] eCounts)

  For each atom in the ring, look up a unique combination of covalent bond count, valence, and charge for each atom and use that as a key into the PI_COUNTS array. c=X is the only special case. Final trimming will be necesseary if isStrict == true.

  Parameters:

  nAtoms - this ring's size

  jmolAtoms - could also be constructed nodes from a SMILES string

  bsAromatic - at least nominally aromatic atoms

  bsRing - specific atoms of this ring

  strictness - 0 (not) 1 (OpenSMILES), 2 (MMFF94) standard organic chemist's Hueckel interpretation, not allowing c=O

  eCounts -

  Returns:

  -1 if absolutely not possible, 0 if possible but not 4n+2, 1 if 4n+2

• finalizeAromatic

  static void finalizeAromatic​(Node[] jmolAtoms,
                               BS bsAromatic,
                               javajs.util.Lst<BS> lstAromatic,
                               javajs.util.Lst<SmilesRing> lstSP2,
                               int[] eCounts,
                               boolean isOpenNotStrict,
                               boolean isStrict)

  Iteratively trims a set of aromatic atoms that may be initially assigned to be aromatic but because their double bonds extend to non-aromatic atoms must be removed. Checks to see that these atoms really have two adjacent aromatic atoms and are not connected to any nonaromatic atom by a double bond. Could be entered with one of /open/, /open strict/, or /strict/

  Parameters:

  jmolAtoms -

  bsAromatic -

  lstAromatic - all rings passing the sp2 test and (if strict) the Hueckel strict test

  lstSP2 - all rings passing the sp2 test

  eCounts -

  isOpenNotStrict - /open/ option

  isStrict - remove noncyclic double bonds and do not allow bridging aromatic ring systems (/strict/ option)

• removeBridgingRings

  private static void removeBridgingRings​(javajs.util.Lst<BS> lstAromatic,
                                          javajs.util.Lst<SmilesRing> lstSP2)

  check for any two rings with more than two common atoms and remove them from the pool

  Parameters:

  lstAromatic -

  lstSP2 -

• checkBridges

  private static void checkBridges​(javajs.util.Lst<?> lst,
                                   BS bsBad,
                                   javajs.util.Lst<?> lst2,
                                   BS bsBad2,
                                   BS bs)

• checkFusedRings

  private static void checkFusedRings​(javajs.util.Lst<SmilesRing> rings,
                                      int[] eCounts,
                                      javajs.util.Lst<BS> lstAromatic)

  Add fused rings based on the Hueckel 4n+2 rule. Note that this may be reverted later if in a STRICT setting, because in at this point in some cases we will have double bonds to exocyclic nonaromatic atoms. We are being careful here to only group FUSED rings -- that is rings that have only one bond in common.

  Parameters:

  rings -

  eCounts -

  lstAromatic - list to be appended to