public final class ModelLoader extends Object
Constructor and Description |
---|
ModelLoader(Viewer viewer,
String modelSetName,
javajs.util.SB loadScript,
Object atomSetCollection,
ModelSet mergeModelSet,
BS bsNew) |
Modifier and Type | Method and Description |
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private void |
addAtom(boolean isPDB,
BS atomSymmetry,
int atomSite,
Object atomUid,
int atomicAndIsotopeNumber,
String atomName,
int formalCharge,
float partialCharge,
javajs.util.List<Object> tensors,
int occupancy,
float bfactor,
javajs.util.P3 xyz,
boolean isHetero,
int atomSerial,
String group3,
javajs.util.V3 vib,
char alternateLocationID,
float radius) |
private void |
addGroup(Chain chain,
Group group) |
private void |
applyStereochemistry() |
private Bond |
bondAtoms(Object atomUid1,
Object atomUid2,
short order) |
private void |
checkNewGroup(JmolAdapter adapter,
int chainID,
String group3,
int groupSequenceNumber,
char groupInsertionCode,
boolean addH,
boolean isLegacyHAddition) |
private void |
countGroup(int modelIndex,
String code,
String group3) |
static void |
createAtomDataSet(Viewer viewer,
ModelSet modelSet,
int tokType,
Object atomSetCollection,
BS bsSelected) |
private void |
createModelSet(JmolAdapter adapter,
Object atomSetCollection,
BS bsNew) |
void |
deleteAtoms(BS bsDeletedAtoms)
called from org.jmol.modelsetbio.resolver when adding hydrogens.
|
private void |
distinguishAndPropagateGroup(int groupIndex,
Chain chain,
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 BS |
getBranch2dZ(int atomIndex,
int atomIndexNot,
BS bs0,
BS bsBranch,
javajs.util.V3 v,
javajs.util.V3 v0,
javajs.util.V3 v1) |
int |
getFirstAtomIndex(int iGroup) |
String |
getGroup3(int iGroup) |
private Chain |
getOrAllocateChain(Model model,
int chainID) |
private int |
getPdbCharge(String group3,
String name)
Adjust known N and O atom formal charges.
|
private void |
initializeAtomBondModelCounts(int nAtoms) |
private void |
initializeBonding() |
private void |
initializeInfo(String name,
Map<String,Object> info) |
private void |
initializeUnitCellAndSymmetry() |
private void |
iterateOverAllNewAtoms(JmolAdapter adapter,
Object atomSetCollection) |
private void |
iterateOverAllNewBonds(JmolAdapter adapter,
Object atomSetCollection) |
private void |
iterateOverAllNewModels(JmolAdapter adapter,
Object atomSetCollection) |
private void |
mergeGroups() |
private void |
set2dZ(int iatom1,
int iatom2) |
private static void |
setAtom2dZ(Atom atomRef,
Atom atom2,
javajs.util.V3 v,
javajs.util.V3 v0,
javajs.util.V3 v1) |
private void |
setAtomProperties() |
private static void |
setBranch2dZ(Atom atom,
BS bs,
BS bsToTest,
javajs.util.V3 v,
javajs.util.V3 v0,
javajs.util.V3 v1) |
private void |
setDefaultRendering(int maxAtoms) |
private boolean |
setModelNameNumberProperties(int modelIndex,
int trajectoryBaseIndex,
String modelName,
int modelNumber,
Properties modelProperties,
Map<String,Object> modelAuxiliaryInfo,
String jmolData) |
void |
undeleteAtom(int iAtom)
called from org.jmol.modelsetbio.resolver when adding hydrogens.
|
private Viewer viewer
public ModelSet modelSet
private ModelSet mergeModelSet
private boolean merging
private boolean appendNew
private String jmolData
private String[] group3Lists
private int[][] group3Counts
private final int[] specialAtomIndexes
private boolean someModelsHaveUnitcells
private boolean someModelsAreModulated
private boolean is2D
private boolean isPDB
public boolean isTrajectory
private boolean isPyMOLsession
private boolean doMinimize
private boolean doAddHydrogens
private boolean doRemoveAddedHydrogens
private String fileHeader
private JmolBioResolver jbr
private Group[] groups
private int groupCount
private static final int defaultGroupCount
private Chain[] chainOf
private String[] group3Of
private int[] seqcodes
private int[] firstAtomIndexes
private int currentModelIndex
private Model currentModel
private int currentChainID
private boolean isNewChain
private Chain currentChain
private int currentGroupSequenceNumber
private char currentGroupInsertionCode
private String currentGroup3
private Group nullGroup
public int baseModelIndex
private int baseModelCount
public int baseAtomIndex
private int baseGroupIndex
private int baseTrajectoryCount
private int adapterModelCount
private int adapterTrajectoryCount
private boolean noAutoBond
private boolean modulationOn
private Group[] mergeGroups
private int iChain
private javajs.util.List<Bond> vStereo
public BS structuresDefinedInFile
public String getGroup3(int iGroup)
public int getFirstAtomIndex(int iGroup)
public int getAtomCount()
private void createModelSet(JmolAdapter adapter, Object atomSetCollection, BS bsNew)
private void setDefaultRendering(int maxAtoms)
private void setAtomProperties()
private void initializeAtomBondModelCounts(int nAtoms)
private void mergeGroups()
private void iterateOverAllNewModels(JmolAdapter adapter, Object atomSetCollection)
private boolean setModelNameNumberProperties(int modelIndex, int trajectoryBaseIndex, String modelName, int modelNumber, Properties modelProperties, Map<String,Object> modelAuxiliaryInfo, String jmolData)
private void finalizeModels(int baseModelCount)
baseModelCount
- private void iterateOverAllNewAtoms(JmolAdapter adapter, Object atomSetCollection)
private int getPdbCharge(String group3, String name)
group3
- name
- private void addAtom(boolean isPDB, BS atomSymmetry, int atomSite, Object atomUid, int atomicAndIsotopeNumber, String atomName, int formalCharge, float partialCharge, javajs.util.List<Object> tensors, int occupancy, float bfactor, javajs.util.P3 xyz, boolean isHetero, int atomSerial, String group3, javajs.util.V3 vib, char alternateLocationID, float radius)
private void checkNewGroup(JmolAdapter adapter, int chainID, String group3, int groupSequenceNumber, char groupInsertionCode, boolean addH, boolean isLegacyHAddition)
private void iterateOverAllNewBonds(JmolAdapter adapter, Object atomSetCollection)
private void initializeUnitCellAndSymmetry()
private void initializeBonding()
private void finalizeGroupBuild()
private void distinguishAndPropagateGroup(int groupIndex, Chain chain, String group3, int seqcode, int firstAtomIndex, int maxAtomIndex)
private void freeze()
private void findElementsPresent()
private void applyStereochemistry()
private void set2dZ(int iatom1, int iatom2)
private BS getBranch2dZ(int atomIndex, int atomIndexNot, BS bs0, BS bsBranch, javajs.util.V3 v, javajs.util.V3 v0, javajs.util.V3 v1)
atomIndex
- atomIndexNot
- bs0
- bsBranch
- v
- v0
- v1
- private static void setBranch2dZ(Atom atom, BS bs, BS bsToTest, javajs.util.V3 v, javajs.util.V3 v0, javajs.util.V3 v1)
private static void setAtom2dZ(Atom atomRef, Atom atom2, javajs.util.V3 v, javajs.util.V3 v0, javajs.util.V3 v1)
private void finalizeShapes()
public void undeleteAtom(int iAtom)
iAtom
- public void deleteAtoms(BS bsDeletedAtoms)
bsDeletedAtoms
-