Class SmilesAromatic

Method Details

• setAromatic

  static void setAromatic(int n, Node[] jmolAtoms, javajs.util.BS bsSelected, javajs.util.Lst<Object> vR, javajs.util.BS bsAromatic, int strictness, boolean isOpenSMILES, boolean justCheckBonding, boolean checkExplicit, VTemp v, javajs.util.Lst<javajs.util.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, javajs.util.BS bsSelected, javajs.util.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, javajs.util.BS bsSelected, javajs.util.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, javajs.util.BS bsAromatic, javajs.util.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, javajs.util.BS bsAromatic, javajs.util.Lst<javajs.util.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<javajs.util.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, javajs.util.BS bsBad, javajs.util.Lst<?> lst2, javajs.util.BS bsBad2, javajs.util.BS bs)

• checkFusedRings

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