Class BioModelSet

java.lang.Object
org.jmol.modelsetbio.BioModelSet

public class BioModelSet extends Object
  • Field Details

  • Constructor Details

    • BioModelSet

      public BioModelSet()
  • Method Details

    • getBioExt

      BioExt getBioExt()
    • set

      public BioModelSet set(Viewer vwr, ModelSet ms)
    • calcAllRasmolHydrogenBonds

      public void calcAllRasmolHydrogenBonds(javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, javajs.util.BS bsHBonds, int dsspVersion)
      only for base models, not trajectories
      Parameters:
      bsA -
      bsB -
      vHBonds - will be null for autobonding
      nucleicOnly -
      nMax -
      dsspIgnoreHydrogens -
      bsHBonds -
      dsspVersion - 1 or 2
    • calcSelectedMonomersCount

      public void calcSelectedMonomersCount()
    • calculateAllPolymers

      public void calculateAllPolymers(Group[] groups, int groupCount, int baseGroupIndex, javajs.util.BS modelsExcluded)
    • calculateAllStructuresExcept

      public String calculateAllStructuresExcept(javajs.util.BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)
    • calculateAllStuctures

      public String calculateAllStuctures(javajs.util.BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)
    • calculateStraightnessAll

      public void calculateStraightnessAll()
    • calculateStruts

      public int calculateStruts(javajs.util.BS bs1, javajs.util.BS bs2)
    • getAllDefaultStructures

      public String getAllDefaultStructures(javajs.util.BS bsAtoms, javajs.util.BS bsModified)
    • getAllHeteroList

      public Map<String,String> getAllHeteroList(int modelIndex)
    • getAllPolymerInfo

      public void getAllPolymerInfo(javajs.util.BS bs, Map<String,javajs.util.Lst<Map<String,Object>>> info)
    • getAllPolymerPointsAndVectors

      public void getAllPolymerPointsAndVectors(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
    • getAllSequenceBits

      public javajs.util.BS getAllSequenceBits(String specInfo, javajs.util.BS bsAtoms, javajs.util.BS bsResult)
    • getAtomBitsBS

      public javajs.util.BS getAtomBitsBS(int tokType, javajs.util.BS bsInfo, javajs.util.BS bs)
    • getAtomBitsStr

      public javajs.util.BS getAtomBitsStr(int tokType, String specInfo, javajs.util.BS bs)
    • getBioPolymerCountInModel

      public int getBioPolymerCountInModel(int modelIndex)
      Parameters:
      modelIndex -
      Returns:
      number of polymers
    • getFullProteinStructureState

      public String getFullProteinStructureState(javajs.util.BS bsAtoms, int mode)
    • getGroupsWithinAll

      public javajs.util.BS getGroupsWithinAll(int nResidues, javajs.util.BS bs)
    • getIdentifierOrNull

      public javajs.util.BS getIdentifierOrNull(String identifier)
    • mutate

      public boolean mutate(javajs.util.BS bs, String group, String[] sequence, String alphaType, float[] phipsi)
    • recalculateAllPolymers

      public void recalculateAllPolymers(javajs.util.BS bsModelsExcluded, Group[] groups)
    • recalculatePoints

      public void recalculatePoints(int modelIndex)
    • setAllConformation

      public void setAllConformation(javajs.util.BS bsAtoms)
    • setAllProteinType

      public void setAllProteinType(javajs.util.BS bs, STR type)
      called from state STRUCTURE command
      Parameters:
      bs -
      type -
    • setAllStructureList

      public void setAllStructureList(Map<STR,float[]> structureList)
    • getAllBasePairBits

      private javajs.util.BS getAllBasePairBits(String specInfo)
    • getAllUnitIds

      private javajs.util.BS getAllUnitIds(String specInfo, javajs.util.BS bsSelected, javajs.util.BS bsResult)
    • checkMap

      private javajs.util.BS checkMap(Map<String,javajs.util.BS> map, String key, javajs.util.BS bsAtoms)
      Ensure that if two models have the same name or number, we appropriately OR their bitsets.
      Parameters:
      map -
      key -
      bsAtoms -
      Returns:
      current BS
    • addUnit

      private boolean addUnit(int tok, String key, javajs.util.BS bsTemp, Map<String,javajs.util.BS> map)
      Repetitively AND unit components to get the final set of atoms
      Parameters:
      tok -
      key -
      bsTemp -
      map -
      Returns:
      true if there are still atoms to consider
    • getAnnotationBits

      private javajs.util.BS getAnnotationBits(String name, int tok, String specInfo)
    • getStructureLines

      private int getStructureLines(javajs.util.BS bsAtoms, javajs.util.SB cmd, javajs.util.Lst<ProteinStructure> lstStr, STR type, boolean scriptMode, int mode)
    • modelsOf

      private javajs.util.BS modelsOf(javajs.util.BS bsAtoms, javajs.util.BS bsAtomsRet)
      general purpose; return models associated with specific atoms
      Parameters:
      bsAtoms -
      bsAtomsRet - all atoms associated with these models.
      Returns:
      bitset of base models
    • setAllDefaultStructure

      private void setAllDefaultStructure(javajs.util.BS bsModels)
    • getAminoAcidValenceAndCharge

      public boolean getAminoAcidValenceAndCharge(String s, String atomName, int[] aaRet)