public final class ModelLoader
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private int |
adapterModelCount |
private int |
adapterTrajectoryCount |
private boolean |
appendNew |
private int |
baseAtomIndex |
private int |
baseGroupIndex |
private int |
baseModelCount |
private int |
baseModelIndex |
private int |
baseTrajectoryCount |
private Chain[] |
chainOf |
private Chain |
currentChain |
private char |
currentChainID |
private java.lang.String |
currentGroup3 |
private char |
currentGroupInsertionCode |
private int |
currentGroupSequenceNumber |
private Model |
currentModel |
private int |
currentModelIndex |
private static int |
defaultGroupCount |
private boolean |
doAddHydrogens |
private boolean |
doMinimize |
private boolean |
doRemoveAddedHydrogens |
private java.lang.String |
fileHeader |
private int[] |
firstAtomIndexes |
private int[][] |
group3Counts |
private java.lang.String[] |
group3Lists |
private java.lang.String[] |
group3Of |
private int |
groupCount |
private Group[] |
groups |
private java.util.Map<java.lang.Object,Atom> |
htAtomMap |
private boolean |
is2D |
private boolean |
isPDB |
private boolean |
isTrajectory |
private JmolBioResolver |
jbr |
private java.lang.String |
jmolData |
private Group[] |
mergeGroups |
private ModelSet |
mergeModelSet |
private boolean |
merging |
private ModelSet |
modelSet |
private boolean |
noAutoBond |
private Group |
nullGroup |
private int[] |
seqcodes |
private boolean |
someModelsHaveUnitcells |
private int[] |
specialAtomIndexes |
private java.util.BitSet |
structuresDefinedInFile |
private Viewer |
viewer |
private java.util.List<Bond> |
vStereo |
Constructor and Description |
---|
ModelLoader(Viewer viewer,
java.lang.String name) |
ModelLoader(Viewer viewer,
java.lang.StringBuffer loadScript,
java.lang.Object atomSetCollection,
ModelSet mergeModelSet,
java.lang.String modelSetName,
java.util.BitSet bsNew) |
Modifier and Type | Method and Description |
---|---|
private void |
addAtom(boolean isPDB,
java.util.BitSet atomSymmetry,
int atomSite,
java.lang.Object atomUid,
short atomicAndIsotopeNumber,
java.lang.String atomName,
int formalCharge,
float partialCharge,
java.lang.Object[] ellipsoid,
int occupancy,
float bfactor,
float x,
float y,
float z,
boolean isHetero,
int atomSerial,
java.lang.String group3,
float vectorX,
float vectorY,
float vectorZ,
char alternateLocationID,
float radius) |
private void |
addGroup(Chain chain,
Group group) |
private void |
applyStereochemistry() |
private void |
bondAtoms(java.lang.Object atomUid1,
java.lang.Object atomUid2,
short order) |
private void |
checkNewGroup(JmolAdapter adapter,
char chainID,
java.lang.String group3,
int groupSequenceNumber,
char groupInsertionCode,
boolean addH) |
private void |
countGroup(int modelIndex,
java.lang.String code,
java.lang.String group3) |
private void |
createModelSet(JmolAdapter adapter,
java.lang.Object atomSetCollection,
java.util.BitSet bsNew) |
private void |
defineStructure(int modelIndex,
EnumStructure subType,
java.lang.String structureID,
int serialID,
int strandCount,
char startChainID,
int startSequenceNumber,
char startInsertionCode,
char endChainID,
int endSequenceNumber,
char endInsertionCode) |
void |
deleteAtoms(java.util.BitSet bsDeletedAtoms)
called from org.jmol.modelsetbio.resolver when adding hydrogens.
|
private void |
distinguishAndPropagateGroup(int groupIndex,
Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int maxAtomIndex) |
private void |
finalizeGroupBuild() |
private void |
finalizeModels(int baseModelCount)
Model numbers are considerably more complicated in Jmol 11.
|
private void |
finalizeShapes() |
private void |
findElementsPresent() |
private void |
freeze() |
int |
getAtomCount() |
private java.util.BitSet |
getBranch2dZ(int atomIndex,
int atomIndexNot,
java.util.BitSet bs0,
java.util.BitSet bsBranch,
javax.vecmath.Vector3f v,
javax.vecmath.Vector3f v0,
javax.vecmath.Vector3f v1) |
int |
getFirstAtomIndex(int iGroup) |
java.lang.String |
getGroup3(int iGroup) |
ModelSet |
getModelSet() |
private Chain |
getOrAllocateChain(Model model,
char chainID) |
private int |
getPdbCharge(java.lang.String group3,
java.lang.String name) |
private void |
initializeAtomBondModelCounts(int nAtoms) |
private void |
initializeBonding() |
private void |
initializeInfo(java.lang.String name,
java.util.Map<java.lang.String,java.lang.Object> info) |
private void |
initializeUnitCellAndSymmetry() |
private void |
iterateOverAllNewAtoms(JmolAdapter adapter,
java.lang.Object atomSetCollection) |
private void |
iterateOverAllNewBonds(JmolAdapter adapter,
java.lang.Object atomSetCollection) |
private void |
iterateOverAllNewModels(JmolAdapter adapter,
java.lang.Object atomSetCollection) |
private void |
iterateOverAllNewStructures(JmolAdapter adapter,
java.lang.Object atomSetCollection)
Pull in all spans of helix, etc.
|
private void |
mergeGroups() |
private void |
set2dZ(int iatom1,
int iatom2) |
private static void |
setAtom2dZ(Atom atomRef,
Atom atom2,
javax.vecmath.Vector3f v,
javax.vecmath.Vector3f v0,
javax.vecmath.Vector3f v1) |
private void |
setAtomProperties() |
private static void |
setBranch2dZ(Atom atom,
java.util.BitSet bs,
java.util.BitSet bsToTest,
javax.vecmath.Vector3f v,
javax.vecmath.Vector3f v0,
javax.vecmath.Vector3f v1) |
private void |
setDefaultRendering(int maxAtoms) |
private boolean |
setModelNameNumberProperties(int modelIndex,
int trajectoryBaseIndex,
java.lang.String modelName,
int modelNumber,
java.util.Properties modelProperties,
java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo,
java.lang.String jmolData) |
void |
undeleteAtom(int iAtom)
called from org.jmol.modelsetbio.resolver when adding hydrogens.
|
private Viewer viewer
private ModelSet modelSet
private ModelSet mergeModelSet
private boolean merging
private java.lang.String jmolData
private java.lang.String[] group3Lists
private int[][] group3Counts
private final int[] specialAtomIndexes
private boolean someModelsHaveUnitcells
private boolean isTrajectory
private boolean doMinimize
private boolean doAddHydrogens
private boolean doRemoveAddedHydrogens
private java.lang.String fileHeader
private JmolBioResolver jbr
private boolean isPDB
private Group[] groups
private int groupCount
private final java.util.Map<java.lang.Object,Atom> htAtomMap
private static final int defaultGroupCount
private Chain[] chainOf
private java.lang.String[] group3Of
private int[] seqcodes
private int[] firstAtomIndexes
private int currentModelIndex
private Model currentModel
private char currentChainID
private Chain currentChain
private int currentGroupSequenceNumber
private char currentGroupInsertionCode
private java.lang.String currentGroup3
private Group nullGroup
private int baseModelIndex
private int baseModelCount
private int baseAtomIndex
private int baseGroupIndex
private int baseTrajectoryCount
private boolean appendNew
private int adapterModelCount
private int adapterTrajectoryCount
private boolean noAutoBond
private boolean is2D
private Group[] mergeGroups
private java.util.List<Bond> vStereo
private java.util.BitSet structuresDefinedInFile
public ModelLoader(Viewer viewer, java.lang.String name)
private void initializeInfo(java.lang.String name, java.util.Map<java.lang.String,java.lang.Object> info)
public java.lang.String getGroup3(int iGroup)
public int getFirstAtomIndex(int iGroup)
public ModelSet getModelSet()
public int getAtomCount()
private void createModelSet(JmolAdapter adapter, java.lang.Object atomSetCollection, java.util.BitSet bsNew)
private void setDefaultRendering(int maxAtoms)
private void setAtomProperties()
private void initializeAtomBondModelCounts(int nAtoms)
private void mergeGroups()
private void iterateOverAllNewModels(JmolAdapter adapter, java.lang.Object atomSetCollection)
private boolean setModelNameNumberProperties(int modelIndex, int trajectoryBaseIndex, java.lang.String modelName, int modelNumber, java.util.Properties modelProperties, java.util.Map<java.lang.String,java.lang.Object> modelAuxiliaryInfo, java.lang.String jmolData)
private void finalizeModels(int baseModelCount)
baseModelCount
- private void iterateOverAllNewAtoms(JmolAdapter adapter, java.lang.Object atomSetCollection)
private int getPdbCharge(java.lang.String group3, java.lang.String name)
private void addAtom(boolean isPDB, java.util.BitSet atomSymmetry, int atomSite, java.lang.Object atomUid, short atomicAndIsotopeNumber, java.lang.String atomName, int formalCharge, float partialCharge, java.lang.Object[] ellipsoid, int occupancy, float bfactor, float x, float y, float z, boolean isHetero, int atomSerial, java.lang.String group3, float vectorX, float vectorY, float vectorZ, char alternateLocationID, float radius)
private void checkNewGroup(JmolAdapter adapter, char chainID, java.lang.String group3, int groupSequenceNumber, char groupInsertionCode, boolean addH)
private void iterateOverAllNewBonds(JmolAdapter adapter, java.lang.Object atomSetCollection)
private void bondAtoms(java.lang.Object atomUid1, java.lang.Object atomUid2, short order)
private void iterateOverAllNewStructures(JmolAdapter adapter, java.lang.Object atomSetCollection)
adapter
- atomSetCollection
- private void defineStructure(int modelIndex, EnumStructure subType, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSequenceNumber, char startInsertionCode, char endChainID, int endSequenceNumber, char endInsertionCode)
private void initializeUnitCellAndSymmetry()
private void initializeBonding()
private void finalizeGroupBuild()
private void distinguishAndPropagateGroup(int groupIndex, Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int maxAtomIndex)
private void countGroup(int modelIndex, java.lang.String code, java.lang.String group3)
private void freeze()
private void findElementsPresent()
private void applyStereochemistry()
private void set2dZ(int iatom1, int iatom2)
private java.util.BitSet getBranch2dZ(int atomIndex, int atomIndexNot, java.util.BitSet bs0, java.util.BitSet bsBranch, javax.vecmath.Vector3f v, javax.vecmath.Vector3f v0, javax.vecmath.Vector3f v1)
atomIndex
- atomIndexNot
- bs0
- bsBranch
- v
- v0
- v1
- private static void setBranch2dZ(Atom atom, java.util.BitSet bs, java.util.BitSet bsToTest, javax.vecmath.Vector3f v, javax.vecmath.Vector3f v0, javax.vecmath.Vector3f v1)
private static void setAtom2dZ(Atom atomRef, Atom atom2, javax.vecmath.Vector3f v, javax.vecmath.Vector3f v0, javax.vecmath.Vector3f v1)
private void finalizeShapes()
public void undeleteAtom(int iAtom)
iAtom
- public void deleteAtoms(java.util.BitSet bsDeletedAtoms)
bsDeletedAtoms
-