Class ProteinStructure

    • Field Detail

      • type

        STR type
      • subtype

        STR subtype
      • structureID

        java.lang.String structureID
      • strucNo

        int strucNo
      • serialID

        int serialID
      • strandCount

        int strandCount
      • nRes

        public int nRes
      • monomerIndexFirst

        protected int monomerIndexFirst
      • monomerIndexLast

        int monomerIndexLast
      • axisA

        protected javajs.util.P3 axisA
      • axisB

        protected javajs.util.P3 axisB
      • axisUnitVector

        protected javajs.util.V3 axisUnitVector
      • vectorProjection

        protected javajs.util.V3 vectorProjection
      • globalStrucNo

        private static int globalStrucNo
      • segments

        private javajs.util.P3[] segments
      • resMap

        private java.util.Map<Monomer,​java.lang.Integer> resMap
    • Constructor Detail

      • ProteinStructure

        public ProteinStructure()
    • Method Detail

      • setupPS

        protected void setupPS​(AlphaPolymer apolymer,
                               STR type,
                               int monomerIndex,
                               int monomerCount)
        Parameters:
        apolymer -
        type -
        monomerIndex -
        monomerCount -
      • addMonomer

        void addMonomer​(int index)
        Note that this method does not check to see that there are no overlapping protein structures.
        Parameters:
        index -
      • removeMonomer

        void removeMonomer​(int index)
        should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
        Parameters:
        index -
      • calcAxis

        public void calcAxis()
      • isWithin

        public boolean isWithin​(int monomerIndex)
      • getIndex

        public int getIndex​(Monomer monomer)
      • getSegments

        public javajs.util.P3[] getSegments()
        Returns:
        points for rocket segment rendering
      • getStructureMidPoint

        javajs.util.P3 getStructureMidPoint​(int index)
      • calcSegments

        private void calcSegments()
      • getAxisStartPoint

        public javajs.util.P3 getAxisStartPoint()
      • getAxisEndPoint

        public javajs.util.P3 getAxisEndPoint()
      • resetAxes

        void resetAxes()
      • setAtomBits

        public void setAtomBits​(javajs.util.BS bs)
        Specified by:
        setAtomBits in interface Structure
      • setAtomBitsAndClear

        public void setAtomBitsAndClear​(javajs.util.BS bs,
                                        javajs.util.BS bsOut)
        Specified by:
        setAtomBitsAndClear in interface Structure
      • findMonomer

        public Monomer findMonomer​(javajs.util.BS bsAtoms,
                                   boolean isFirst)