Class BioModelSet


  • public class BioModelSet
    extends java.lang.Object
    • Field Summary

      Fields 
      Modifier and Type Field Description
      private BioExt ext  
      private ModelSet ms  
      private java.util.Map<java.lang.String,​javajs.util.BS>[] unitIdSets  
      private Viewer vwr  
    • Constructor Summary

      Constructors 
      Constructor Description
      BioModelSet()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      private boolean addUnit​(int tok, java.lang.String key, javajs.util.BS bsTemp, java.util.Map<java.lang.String,​javajs.util.BS> map)
      Repetitively AND unit components to get the final set of atoms
      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
      void calcSelectedMonomersCount()  
      void calculateAllPolymers​(Group[] groups, int groupCount, int baseGroupIndex, javajs.util.BS modelsExcluded)  
      java.lang.String calculateAllStructuresExcept​(javajs.util.BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)  
      java.lang.String calculateAllStuctures​(javajs.util.BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)  
      void calculateStraightnessAll()  
      int calculateStruts​(javajs.util.BS bs1, javajs.util.BS bs2)  
      private javajs.util.BS checkMap​(java.util.Map<java.lang.String,​javajs.util.BS> map, java.lang.String key, javajs.util.BS bsAtoms)
      Ensure that if two models have the same name or number, we appropriately OR their bitsets.
      private javajs.util.BS getAllBasePairBits​(java.lang.String specInfo)  
      java.lang.String getAllDefaultStructures​(javajs.util.BS bsAtoms, javajs.util.BS bsModified)  
      java.util.Map<java.lang.String,​java.lang.String> getAllHeteroList​(int modelIndex)  
      void getAllPolymerInfo​(javajs.util.BS bs, java.util.Map<java.lang.String,​javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>>> info)  
      void getAllPolymerPointsAndVectors​(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)  
      javajs.util.BS getAllSequenceBits​(java.lang.String specInfo, javajs.util.BS bsAtoms, javajs.util.BS bsResult)  
      private javajs.util.BS getAllUnitIds​(java.lang.String specInfo, javajs.util.BS bsSelected, javajs.util.BS bsResult)  
      boolean getAminoAcidValenceAndCharge​(java.lang.String s, java.lang.String atomName, int[] aaRet)  
      private javajs.util.BS getAnnotationBits​(java.lang.String name, int tok, java.lang.String specInfo)  
      javajs.util.BS getAtomBitsBS​(int tokType, javajs.util.BS bsInfo, javajs.util.BS bs)  
      javajs.util.BS getAtomBitsStr​(int tokType, java.lang.String specInfo, javajs.util.BS bs)  
      (package private) BioExt getBioExt()  
      int getBioPolymerCountInModel​(int modelIndex)  
      java.lang.String getFullProteinStructureState​(javajs.util.BS bsAtoms, int mode)  
      javajs.util.BS getGroupsWithinAll​(int nResidues, javajs.util.BS bs)  
      javajs.util.BS getIdentifierOrNull​(java.lang.String identifier)  
      private int getStructureLines​(javajs.util.BS bsAtoms, javajs.util.SB cmd, javajs.util.Lst<ProteinStructure> lstStr, STR type, boolean scriptMode, int mode)  
      private javajs.util.BS modelsOf​(javajs.util.BS bsAtoms, javajs.util.BS bsAtomsRet)
      general purpose; return models associated with specific atoms
      boolean mutate​(javajs.util.BS bs, java.lang.String group, java.lang.String[] sequence)  
      void recalculateAllPolymers​(javajs.util.BS bsModelsExcluded, Group[] groups)  
      void recalculatePoints​(int modelIndex)  
      BioModelSet set​(Viewer vwr, ModelSet ms)  
      void setAllConformation​(javajs.util.BS bsAtoms)  
      private void setAllDefaultStructure​(javajs.util.BS bsModels)  
      void setAllProteinType​(javajs.util.BS bs, STR type)  
      void setAllStructureList​(java.util.Map<STR,​float[]> structureList)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • unitIdSets

        private java.util.Map<java.lang.String,​javajs.util.BS>[] unitIdSets
    • Constructor Detail

      • BioModelSet

        public BioModelSet()
    • Method Detail

      • getBioExt

        BioExt getBioExt()
      • 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 java.lang.String calculateAllStructuresExcept​(javajs.util.BS alreadyDefined,
                                                             boolean asDSSP,
                                                             boolean doReport,
                                                             boolean dsspIgnoreHydrogen,
                                                             boolean setStructure,
                                                             boolean includeAlpha,
                                                             int version)
      • calculateAllStuctures

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

        public java.util.Map<java.lang.String,​java.lang.String> getAllHeteroList​(int modelIndex)
      • getAllPolymerInfo

        public void getAllPolymerInfo​(javajs.util.BS bs,
                                      java.util.Map<java.lang.String,​javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.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​(java.lang.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,
                                             java.lang.String specInfo,
                                             javajs.util.BS bs)
      • getBioPolymerCountInModel

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

        public java.lang.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​(java.lang.String identifier)
      • mutate

        public boolean mutate​(javajs.util.BS bs,
                              java.lang.String group,
                              java.lang.String[] sequence)
      • 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)
      • setAllStructureList

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

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

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

        private javajs.util.BS checkMap​(java.util.Map<java.lang.String,​javajs.util.BS> map,
                                        java.lang.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,
                                java.lang.String key,
                                javajs.util.BS bsTemp,
                                java.util.Map<java.lang.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​(java.lang.String name,
                                                 int tok,
                                                 java.lang.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​(java.lang.String s,
                                                    java.lang.String atomName,
                                                    int[] aaRet)