org.jmol.api
Interface JmolBioResolver

All Known Implementing Classes:
Resolver

public interface JmolBioResolver


Method Summary
 void addImplicitHydrogenAtoms(JmolAdapter adapter, int i)
           
 Polymer buildBioPolymer(Group group, Group[] groups, int i, boolean checkPolymerConnections)
           
 void clearBioPolymers(Group[] groups, int groupCount, java.util.BitSet bsModelsExcluded)
           
 Group distinguishAndPropagateGroup(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int maxAtomIndex, int modelIndex, int[] specialAtomIndexes, Atom[] atoms)
           
 void finalizeHydrogens()
           
 void initialize(ModelSet modelSet)
           
 void initializeHydrogenAddition(ModelLoader modelSet, int bondCount)
           
 void setHaveHsAlready(boolean b)
           
 

Method Detail

distinguishAndPropagateGroup

Group distinguishAndPropagateGroup(Chain chain,
                                   java.lang.String group3,
                                   int seqcode,
                                   int firstAtomIndex,
                                   int maxAtomIndex,
                                   int modelIndex,
                                   int[] specialAtomIndexes,
                                   Atom[] atoms)

buildBioPolymer

Polymer buildBioPolymer(Group group,
                        Group[] groups,
                        int i,
                        boolean checkPolymerConnections)

clearBioPolymers

void clearBioPolymers(Group[] groups,
                      int groupCount,
                      java.util.BitSet bsModelsExcluded)

initializeHydrogenAddition

void initializeHydrogenAddition(ModelLoader modelSet,
                                int bondCount)

finalizeHydrogens

void finalizeHydrogens()

setHaveHsAlready

void setHaveHsAlready(boolean b)

addImplicitHydrogenAtoms

void addImplicitHydrogenAtoms(JmolAdapter adapter,
                              int i)

initialize

void initialize(ModelSet modelSet)