Class BioModel


  • public final class BioModel
    extends Model
    • Field Detail

      • bioPolymerCount

        int bioPolymerCount
      • isMutated

        boolean isMutated
      • defaultStructure

        java.lang.String defaultStructure
    • Constructor Detail

      • BioModel

        BioModel​(ModelSet modelSet,
                 int modelIndex,
                 int trajectoryBaseIndex,
                 java.lang.String jmolData,
                 java.util.Properties properties,
                 java.util.Map<java.lang.String,​java.lang.Object> auxiliaryInfo)
    • Method Detail

      • addBioPolymer

        int addBioPolymer​(BioPolymer polymer)
      • addSecondaryStructure

        void addSecondaryStructure​(STR type,
                                   java.lang.String structureID,
                                   int serialID,
                                   int strandCount,
                                   int startChainID,
                                   int startSeqcode,
                                   int endChainID,
                                   int endSeqcode,
                                   int istart,
                                   int iend,
                                   javajs.util.BS bsAssigned)
      • addStructureByBS

        void addStructureByBS​(int count,
                              int dsspType,
                              STR type,
                              javajs.util.BS bs)
      • calculateDssx

        private java.lang.String calculateDssx​(javajs.util.Lst<Bond> vHBonds,
                                               boolean doReport,
                                               boolean dsspIgnoreHydrogen,
                                               boolean setStructure,
                                               int version)
      • calculateStructures

        java.lang.String calculateStructures​(boolean asDSSP,
                                             boolean doReport,
                                             boolean dsspIgnoreHydrogen,
                                             boolean setStructure,
                                             boolean includeAlpha,
                                             int version)
      • clearBioPolymers

        void clearBioPolymers()
      • fixIndices

        public void fixIndices​(int modelIndex,
                               int nAtomsDeleted,
                               javajs.util.BS bsDeleted)
        Overrides:
        fixIndices in class Model
      • freeze

        public boolean freeze()
        Overrides:
        freeze in class Model
      • getBioBranches

        public javajs.util.Lst<javajs.util.BS> getBioBranches​(javajs.util.Lst<javajs.util.BS> biobranches)
      • getBioPolymerCount

        public int getBioPolymerCount()
      • getCachedAnnotationMap

        java.lang.Object getCachedAnnotationMap​(java.lang.String key,
                                                java.lang.Object ann)
      • getConformation

        public boolean getConformation​(int conformationIndex0,
                                       boolean doSet,
                                       javajs.util.BS bsAtoms,
                                       javajs.util.BS bsRet)
        Parameters:
        conformationIndex0 -
        doSet -
        bsAtoms -
        bsRet -
        Returns:
        true;
      • getDefaultLargePDBRendering

        public void getDefaultLargePDBRendering​(javajs.util.SB sb,
                                                int maxAtoms)
      • getFullPDBHeader

        public java.lang.String getFullPDBHeader()
      • getPdbData

        public void getPdbData​(java.lang.String type,
                               char ctype,
                               boolean isDraw,
                               javajs.util.BS bsSelected,
                               javajs.util.OC out,
                               LabelToken[] tokens,
                               javajs.util.SB pdbCONECT,
                               javajs.util.BS bsWritten)
      • getRasmolHydrogenBonds

        void getRasmolHydrogenBonds​(javajs.util.BS bsA,
                                    javajs.util.BS bsB,
                                    javajs.util.Lst<Bond> vHBonds,
                                    boolean nucleicOnly,
                                    int nMax,
                                    boolean dsspIgnoreHydrogens,
                                    javajs.util.BS bsHBonds,
                                    int version)
      • getUnitID

        public java.lang.String getUnitID​(Atom atom,
                                          int flags)
        Get a unitID. Note that we MUST go through the | after InsCode, because if we do not do that we cannot match residues only using string matching.
        Parameters:
        atom -
        flags -
        Returns:
        a unitID
      • recalculateLeadMidpointsAndWingVectors

        void recalculateLeadMidpointsAndWingVectors()
      • resetRasmolBonds

        public void resetRasmolBonds​(javajs.util.BS bs,
                                     int dsspVersion)
        from Trajectory.setAtomPositions base models only; not trajectories
        Parameters:
        bs -
        dsspVersion -
      • getAtomicDSSRData

        public void getAtomicDSSRData​(float[] dssrData,
                                      java.lang.String dataType)