Class ModelLoader

Method Details

• initializeInfo

  private void initializeInfo(String name, Map<String,Object> info)

• newTrajectory

  private Trajectory newTrajectory(ModelSet ms, javajs.util.Lst<javajs.util.P3[]> steps)

• getGroup3

  public String getGroup3(int iGroup)

• getFirstAtomIndex

  public int getFirstAtomIndex(int iGroup)

• getAtomCount

  public int getAtomCount()

• createModelSet

  private void createModelSet(JmolAdapter adapter, Object asc, javajs.util.BS bs2D)

• mergeTrajAndVib

  private void mergeTrajAndVib(ModelSet oldSet, ModelSet newSet)

• setDefaultRendering

  private void setDefaultRendering(int maxAtoms)

• setAtomProperties

  private void setAtomProperties()

• initializeAtomBondModelCounts

  private void initializeAtomBondModelCounts(int nAtoms)

• mergeGroups

  private void mergeGroups()

• iterateOverAllNewModels

  private void iterateOverAllNewModels(JmolAdapter adapter, Object asc)

• setModelNameNumberProperties

  private void setModelNameNumberProperties(int modelIndex, int trajectoryBaseIndex, String modelName, int modelNumber, Properties modelProperties, Map<String,Object> modelAuxiliaryInfo, String jmolData)

• finalizeModels

  private 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. If a single files is loaded this is: a) single file context: 1) the sequential number of the model in the file , or 2) if a PDB file and "MODEL" record is present, that model number b) multifile context: always 1000000 * (fileIndex + 1) + (modelIndexInFile + 1) int fileIndex The 0-based reference to the file containing this model. Used when doing "_modelnumber3.2" in a multifile context int modelFileNumber An integer coding both the file and the model: file * 1000000 + modelInFile (1-based) Used all over the place. Note that if there is only one file, then modelFileNumber < 1000000. String modelNumberDotted A number the user can use "1.3" String modelNumberForAtomLabel Either the dotted number or the PDB MODEL number, if there is only one file

  Parameters:

  baseModelCount -

• iterateOverAllNewAtoms

  private void iterateOverAllNewAtoms(JmolAdapter adapter, Object asc, boolean haveBonds)

• getAtomSiteBase

  private int getAtomSiteBase(javajs.util.BS mbs)

• addJmolDataProperties

  private void addJmolDataProperties(Model m, Map<String,float[]> jmolDataProperties)

• getPdbCharge

  private int getPdbCharge(String group3, String name)

  Adjust known N and O atom formal charges. Note that this does not take care of ligands.

  Parameters:

  group3 -

  name -

  Returns:

  0, 1, or -1

• addAtom

  private Atom addAtom(boolean isPDB, javajs.util.BS atomSymmetry, int atomSite, int atomicAndIsotopeNumber, String atomName, int formalCharge, float partialCharge, javajs.util.Lst<Object> tensors, float occupancy, float bfactor, javajs.util.P3 xyz, boolean isHetero, int atomSerial, int atomSeqID, String group3, javajs.util.V3 vib, char alternateLocationID, float radius, float bondRadius)

• checkNewGroup

  private void checkNewGroup(JmolAdapter adapter, int chainID, String group3, int groupSequenceNumber, char groupInsertionCode, boolean addH, boolean isLegacyHAddition)

• getOrAllocateChain

  private Chain getOrAllocateChain(Model model, int chainID)

• iterateOverAllNewBonds

  private void iterateOverAllNewBonds(JmolAdapterBondIterator iterBond)

• bondAtoms

  private Bond bondAtoms(Object atomUid1, Object atomUid2, short order)

• initializeUnitCellAndSymmetry

  private void initializeUnitCellAndSymmetry()

• initializeBonding

  private void initializeBonding()

• finalizeGroupBuild

  private void finalizeGroupBuild()

• distinguishAndPropagateGroup

  private void distinguishAndPropagateGroup(int groupIndex, Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)

• addGroup

  private void addGroup(Chain chain, Group group)

• countGroup

  private void countGroup(int modelIndex, String code, String group3)

• freeze

  private void freeze()

• findElementsPresent

  private void findElementsPresent()

• applyStereochemistry

  private void applyStereochemistry()

• set2DLengths

  private void set2DLengths(int iatom1, int iatom2)

• set2dZ

  private void set2dZ(int iatom1, int iatom2, javajs.util.V3 v)

• getBranch2dZ

  private javajs.util.BS getBranch2dZ(int atomIndex, int atomIndexNot, javajs.util.BS bs0, javajs.util.BS bsBranch, javajs.util.V3 v, javajs.util.V3 v0, javajs.util.V3 v1, int dir)

  Parameters:

  atomIndex -

  atomIndexNot -

  bs0 -

  bsBranch -

  v -

  v0 -

  v1 -

  dir -

  Returns:

  atom bitset

• setBranch2dZ

  private static void setBranch2dZ(Atom atom, javajs.util.BS bs, javajs.util.BS bsToTest, javajs.util.V3 v, javajs.util.V3 v0, javajs.util.V3 v1, int dir)

• setAtom2dZ

  private static void setAtom2dZ(Atom atomRef, Atom atom2, javajs.util.V3 v, javajs.util.V3 v0, javajs.util.V3 v1, int dir)

  set the z based on a cos relationship to the y axis. Specifically, theta = acos(v.dot.v0) z = 0.8 * sin(4 theta) so: theta 4 theta y 0 0 x pi/2 2 pi -y pi 4 pi -x pi/2 2 pi y -1/4 -pi/4 x +1/4 pi/4 -y -1/4 3pi/4 -x +1/4 -pi/4

  Parameters:

  atomRef -

  atom2 -

  v -

  v0 -

  v1 -

  dir -

• finalizeShapes

  private void finalizeShapes()

• undeleteAtom

  public void undeleteAtom(int iAtom)

  called from org.jmol.modelsetbio.resolver when adding hydrogens.

  Parameters:

  iAtom -

• createAtomDataSet

  public static String createAtomDataSet(Viewer vwr, ModelSet modelSet, int tokType, Object asc, javajs.util.BS bsSelected)