OEAddLigandHighlighting

Highlights atoms and/or bonds of the displayed ligand.

The overloaded versions of the OEAddLigandHighlighting function

Link	Description
OEAddLigandHighlighting(disp, highlight, atompred)	highlights ligand atoms with OEHighlightBase
OEAddLigandHighlighting(adisp, highlight, bondpred)	highlights ligand bonds with OEHighlightBase
OEAddLigandHighlighting(adisp, highlight, atompred, bondpred)	highlights ligand atoms and bonds with OEHighlightBase
OEAddLigandHighlighting(adisp, highlight, match)	highlights ligand atoms and bonds of a match with OEHighlightBase
OEAddLigandHighlighting(adisp, highlight, abset)	highlights ligand atoms and bonds of a set with OEHighlightBase

Parameters :

adisp

The OE2DActiveSiteDisplay object of which ligand atoms add/or ligand bonds being highlighted.

highlight

The OEHighlightBase object that specifies the style of the highlighting.

atompred

OEAddLigandHighlighting function highlights only ligand atoms for which the given atom predicate returns true.

bondpred

OEAddLigandHighlighting function highlights only ligand bonds for which the given bond predicate returns true.

match

OEAddLigandHighlighting function highlights the target atoms and bonds of the OEMatchBase object.

abset

Stores the ligand atoms and bonds being highlighted.

See also

• OEHighlightByColor class

• OEHighlightByCogwheel class

• OEHighlightByBallAndStick class

• OEHighlightByStick class

• OEHighlightByLasso class

1. Highlighting using atom and bond predicates:

   void OEAddLigandHighlighting(OE2DActiveSiteDisplay &adisp, const OEDepict::OEHighlightBase &highlight,
                                const OESystem::OEUnaryPredicate<OEChem::OEAtomBase> &atompred)
   

   Highlights ligand atoms with the style implemented in the given OEHighlightBase object. The atoms being highlighted are specified by given atom predicate.

   void OEAddLigandHighlighting(OE2DActiveSiteDisplay &adisp, const OEDepict::OEHighlightBase &highlight,
                                const OESystem::OEUnaryPredicate<OEChem::OEBondBase> &bondpred)
   

   Highlights ligand bonds with the style implemented in the given OEHighlightBase object. The bonds being highlighted are specified by given bond predicates.

   void OEAddLigandHighlighting(OE2DActiveSiteDisplay &adisp, const OEDepict::OEHighlightBase &highlight,
                                const OESystem::OEUnaryPredicate<OEChem::OEAtomBase> &atompred,
                                const OESystem::OEUnaryPredicate<OEChem::OEBondBase> &bondpred)
   

   Highlights ligand atoms and bonds with the style implemented in the given OEHighlightBase object. The atoms and bonds being highlighted are specified by given atom and bond predicates, respectively.

   Example: (See image generated in Example of highlighting 6-membered rings of a ligand using ‘ball and stick’ style and Example of highlighting 6-membered rings of a ligand using ‘color’ style )

   static class Pred6MemAromAtom extends OEUnaryAtomPred {
       @Override
       public boolean constCall(OEAtomBase atom) {
           return atom.IsAromatic() && oechem.OEAtomIsInAromaticRingSize(atom, 6);
       }
   
       @Override
       public OEUnaryAtomBoolFunc CreateCopy() {
           OEUnaryAtomBoolFunc copy = new Pred6MemAromAtom();
           copy.swigReleaseOwnership();
           return copy;
       }
   }
   
   static class Pred6MemAromBond extends OEUnaryBondPred {
       @Override
       public boolean constCall(OEBondBase bond) {
           return bond.IsAromatic() && oechem.OEBondIsInAromaticRingSize(bond, 6);
       }
   
       @Override
       public OEUnaryBondBoolFunc CreateCopy() {
           OEUnaryBondBoolFunc copy = new Pred6MemAromBond();
           copy.swigReleaseOwnership();
           return copy;
       }
   }
   
   private static void OEAddHighlighting_Predicate(OE2DActiveSiteDisplay adisp) {
       OEHighlightByBallAndStick highlight = new OEHighlightByBallAndStick(oechem.getOEBlueTint());
   
       oegrapheme.OEAddLigandHighlighting(adisp, highlight, new Pred6MemAromAtom());
       oegrapheme.OEAddLigandHighlighting(adisp, highlight, new Pred6MemAromBond());
   }
   
   private static void OEAddHighlighting_AtomAndBondPredicate(OE2DActiveSiteDisplay adisp) {
       OEHighlightByColor highlight = new OEHighlightByColor(oechem.getOEDarkGreen());
       oegrapheme.OEAddLigandHighlighting(adisp, highlight,
                                          new Pred6MemAromAtom(), new Pred6MemAromBond());
   }
   

Example of highlighting 6-membered rings of a ligand using ‘ball and stick’ style

Example of highlighting 6-membered rings of a ligand using ‘color’ style

See also

• Predicate Functors chapter in the OEChem TK manual

1. Highlighting using an OEMatchBase object that is initialized by substructure search or maximum common substructure search:

   void OEAddLigandHighlighting(OE2DActiveSiteDisplay &adisp, const OEDepict::OEHighlightBase &highlight,
                                const OEChem::OEMatchBase &match)
   

   Example: (See image generated in Example of highlighting 6-membered rings of a ligand using ‘lasso’ style)

   private static void OEAddHighlighting_OEMatch(OE2DActiveSiteDisplay adisp) {
       OEMolBase ligand = adisp.GetDisplayedLigand();
       OESubSearch subs = new OESubSearch("a1aaaaa1");
       OEColorIter citer = oechem.OEGetVividColors();
       boolean unique = true;
       for (OEMatchBase match : subs.Match(ligand, unique)) {
           if (citer.hasNext()) {
               OEHighlightByLasso highlight = new OEHighlightByLasso(citer.next());
               highlight.SetConsiderAtomLabelBoundingBox(true);
               oegrapheme.OEAddLigandHighlighting(adisp, highlight, match);
           }
       }
   }
   

Example of highlighting 6-membered rings of a ligand using ‘lasso’ style

1. Highlighting using an OEAtomBondSet object that stores the atoms and bonds being highlighted:

   void OEAddLigandHighlighting(OE2DActiveSiteDisplay &adisp, const OEDepict::OEHighlightBase &highlight,
                                const OEChem::OEAtomBondSet &abset)
   

   Example: (See image generated in Example of highlighting 6-membered rings of a ligand using ‘cogwheel’ style)

   private static void OEAddHighlighting_OEAtomBondSet(OE2DActiveSiteDisplay adisp) {
       OEMolBase ligand = adisp.GetDisplayedLigand();
       OEAtomBondSet abset = new OEAtomBondSet(ligand.GetAtoms(new Pred6MemAromAtom()),
                                               ligand.GetBonds(new Pred6MemAromBond()));
       OEHighlightByCogwheel highlight = new OEHighlightByCogwheel(oechem.getOEPinkTint());
       highlight.SetInnerContour(false);
       oegrapheme.OEAddLigandHighlighting(adisp, highlight, abset);
   }
   

Example of highlighting 6-membered rings of a ligand using ‘cogwheel’ style