org.jmol.modelset
public final class ModelLoader extends ModelSet
Field Summary | |
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static int | ATOM_GROWTH_INCREMENT |
int | adapterModelCount |
int | adapterTrajectoryCount |
boolean | appendNew |
int | baseAtomIndex |
int | baseBondIndex |
int | baseModelCount |
int | baseModelIndex |
int | baseTrajectoryCount |
Chain[] | chainOf |
Chain | currentChain |
char | currentChainID |
String | currentGroup3 |
char | currentGroupInsertionCode |
int | currentGroupSequenceNumber |
Model | currentModel |
int | currentModelIndex |
static int | defaultGroupCount |
String | fileHeader |
int[] | firstAtomIndexes |
int[][] | group3Counts |
String[] | group3Lists |
String[] | group3Of |
static Hashtable | htAtom |
Hashtable | htAtomMap |
boolean | isMultiFile |
boolean | isTrajectory |
String | jmolData |
ModelLoader | mergeModelSet |
boolean | merging |
Group | nullGroup |
int[] | seqcodes |
boolean | someModelsHaveUnitcells |
int[] | specialAtomIndexes |
Constructor Summary | |
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ModelLoader(Viewer viewer, String name) | |
ModelLoader(Viewer viewer, JmolAdapter adapter, Object clientFile, ModelLoader mergeModelSet, String modelSetName) |
Method Summary | |
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void | addAtom(int modelIndex, BitSet atomSymmetry, int atomSite, Object atomUid, short atomicAndIsotopeNumber, String atomName, int size, int formalCharge, float partialCharge, Object[] ellipsoid, int occupancy, float bfactor, float x, float y, float z, boolean isHetero, int atomSerial, char chainID, String group3, int groupSequenceNumber, char groupInsertionCode, float vectorX, float vectorY, float vectorZ, char alternateLocationID, Object clientAtomReference, float radius) |
void | addGroup(Chain chain, Group group) |
void | bondAtoms(Object atomUid1, Object atomUid2, short order) |
void | checkNewGroup(int atomIndex, int modelIndex, char chainID, String group3, int groupSequenceNumber, char groupInsertionCode) |
void | countGroup(int modelIndex, String code, String group3) |
protected void | defineStructure(int modelIndex, String structureType, char startChainID, int startSequenceNumber, char startInsertionCode, char endChainID, int endSequenceNumber, char endInsertionCode) |
void | distinguishAndPropagateGroup(int groupIndex, Chain chain, String group3, int seqcode, int firstAtomIndex, int maxAtomIndex) |
void | finalizeGroupBuild() |
void | finalizeModels(int baseModelCount)
Model numbers are considerably more complicated in Jmol 11.
int modelNumber
The adapter gives us a modelNumber, but that is not necessarily
what the user accesses. |
void | finalizeShapes() |
void | findElementsPresent() |
void | freeze() |
Chain | getOrAllocateChain(Model model, char chainID) |
void | growAtomArrays(int byHowMuch) |
void | initializeAtomBondModelCounts() |
void | initializeBonding() |
void | initializeBuild(int atomCountEstimate) |
void | initializeGroupBuild()
also from calculateStructures
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void | initializeInfo(String name, int nAtoms, Properties properties, Hashtable info) |
void | initializeMerge() |
void | initializeModelSet(JmolAdapter adapter, Object clientFile) |
void | initializeUnitCellAndSymmetry() |
void | iterateOverAllNewAtoms(JmolAdapter adapter, Object clientFile) |
void | iterateOverAllNewBonds(JmolAdapter adapter, Object clientFile) |
void | iterateOverAllNewModels(JmolAdapter adapter, Object clientFile) |
void | iterateOverAllNewStructures(JmolAdapter adapter, Object clientFile)
Pull in all spans of helix, etc. in the file(s)
We do turn first, because sometimes a group is defined
twice, and this way it gets marked as helix or sheet
if it is both one of those and turn.
|
static byte | lookupSpecialAtomID(String atomName) |
void | mergeModelArrays() |
protected void | releaseModelSet() |
void | setAtomNamesAndNumbers() |
boolean | setModelNameNumberProperties(int modelIndex, int trajectoryBaseIndex, String modelName, int modelNumber, Properties modelProperties, Hashtable modelAuxiliaryInfo, boolean isPDB, String jmolData) |
Parameters: baseModelCount
Parameters: adapter clientFile