public interface JmolBioResolver
Modifier and Type | Method and Description |
---|---|
void |
addImplicitHydrogenAtoms(JmolAdapter adapter,
int i,
int nH) |
Group |
distinguishAndPropagateGroup(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int maxAtomIndex,
int modelIndex,
int[] specialAtomIndexes,
Atom[] atoms) |
void |
finalizeHydrogens() |
java.lang.Object |
fixPropertyValue(BS bsAtoms,
java.lang.Object data,
boolean toHydrogens) |
boolean |
getAminoAcidValenceAndCharge(java.lang.String g3,
java.lang.String atomName,
int[] aaRet) |
int[] |
getArgbs(int tok) |
Model |
getBioModel(int modelIndex,
int trajectoryBaseIndex,
java.lang.String jmolData,
java.util.Properties modelProperties,
java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo) |
short |
getGroupID(java.lang.String g3) |
void |
initializeHydrogenAddition() |
boolean |
isHetero(java.lang.String g3) |
boolean |
isKnownPDBGroup(java.lang.String g3) |
void |
iterateOverAllNewStructures(JmolAdapter adapter,
java.lang.Object atomSetCollection) |
byte |
lookupSpecialAtomID(java.lang.String name) |
void |
setGroupLists(int ipt) |
void |
setHaveHsAlready(boolean b) |
JmolBioResolver |
setLoader(ModelLoader modelLoader) |
Resolver |
setViewer(Viewer vwr) |
Group distinguishAndPropagateGroup(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int maxAtomIndex, int modelIndex, int[] specialAtomIndexes, Atom[] atoms)
void initializeHydrogenAddition()
void finalizeHydrogens()
void setHaveHsAlready(boolean b)
void addImplicitHydrogenAtoms(JmolAdapter adapter, int i, int nH)
JmolBioResolver setLoader(ModelLoader modelLoader)
java.lang.Object fixPropertyValue(BS bsAtoms, java.lang.Object data, boolean toHydrogens)
Model getBioModel(int modelIndex, int trajectoryBaseIndex, java.lang.String jmolData, java.util.Properties modelProperties, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo)
void iterateOverAllNewStructures(JmolAdapter adapter, java.lang.Object atomSetCollection)
void setGroupLists(int ipt)
boolean isKnownPDBGroup(java.lang.String g3)
boolean isHetero(java.lang.String g3)
boolean getAminoAcidValenceAndCharge(java.lang.String g3, java.lang.String atomName, int[] aaRet)
byte lookupSpecialAtomID(java.lang.String name)
int[] getArgbs(int tok)
short getGroupID(java.lang.String g3)