Class BioModelSet

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

public class BioModelSet extends Object
  • Constructor Details

    • BioModelSet

      public BioModelSet()
  • Method Details

    • set

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

      public void calcAllRasmolHydrogenBonds(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, 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, BS modelsExcluded)
    • calculateAllStructuresExcept

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

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

      public void calculateStraightnessAll()
    • calculateStruts

      public int calculateStruts(BS bs1, BS bs2)
    • getAllDefaultStructures

      public String getAllDefaultStructures(BS bsAtoms, BS bsModified)
    • getAllHeteroList

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

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

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

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

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

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

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

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

      public BS getGroupsWithinAll(int nResidues, BS bs)
    • getIdentifierOrNull

      public BS getIdentifierOrNull(String identifier)
    • mutate

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

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

      public void recalculatePoints(int modelIndex)
    • setAllConformation

      public void setAllConformation(BS bsAtoms)
    • setAllProteinType

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

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

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