Class BioModelSet


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

      • unitIdSets

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

      • BioModelSet

        public BioModelSet()
    • Method Detail

      • getBioExt

        BioExt getBioExt()
      • calcAllRasmolHydrogenBonds

        public void calcAllRasmolHydrogenBonds​(BS bsA,
                                               BS bsB,
                                               javajs.util.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 java.lang.String calculateAllStructuresExcept​(BS alreadyDefined,
                                                             boolean asDSSP,
                                                             boolean doReport,
                                                             boolean dsspIgnoreHydrogen,
                                                             boolean setStructure,
                                                             boolean includeAlpha,
                                                             int version)
      • calculateAllStuctures

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

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

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

        public BS getAllSequenceBits​(java.lang.String specInfo,
                                     BS bsAtoms,
                                     BS bsResult)
      • getAtomBitsBS

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

        public BS getAtomBitsStr​(int tokType,
                                 java.lang.String specInfo,
                                 BS bs)
      • getBioPolymerCountInModel

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

        public java.lang.String getFullProteinStructureState​(BS bsAtoms,
                                                             int mode)
      • getGroupsWithinAll

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

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

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

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

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

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

        private BS checkMap​(java.util.Map<java.lang.String,​BS> map,
                            java.lang.String key,
                            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,
                                BS bsTemp,
                                java.util.Map<java.lang.String,​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 BS getAnnotationBits​(java.lang.String name,
                                     int tok,
                                     java.lang.String specInfo)
      • getStructureLines

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

        private BS modelsOf​(BS bsAtoms,
                            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​(BS bsModels)
      • getAminoAcidValenceAndCharge

        public boolean getAminoAcidValenceAndCharge​(java.lang.String s,
                                                    java.lang.String atomName,
                                                    int[] aaRet)