Class BioModelSet


  • public class BioModelSet
    extends Object
    • 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 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)
      • 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​(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)