Package org.jmol.modelsetbio

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)