Class AminoPolymer

    • Field Detail

      • maxHbondAlphaDistance

        private static final float maxHbondAlphaDistance
        See Also:
        Constant Field Values
      • maxHbondAlphaDistance2

        private static final float maxHbondAlphaDistance2
        See Also:
        Constant Field Values
      • minimumHbondDistance2

        private static final float minimumHbondDistance2
        See Also:
        Constant Field Values
      • structureList

        private java.util.Map<STR,​float[]> structureList
    • Constructor Detail

      • AminoPolymer

        AminoPolymer​(Monomer[] monomers,
                     int pt0)
    • Method Detail

      • calcRasmolHydrogenBonds

        public void calcRasmolHydrogenBonds​(BioPolymer polymer,
                                            javajs.util.BS bsA,
                                            javajs.util.BS bsB,
                                            javajs.util.Lst<Bond> vHBonds,
                                            int nMaxPerResidue,
                                            int[][][] min,
                                            boolean checkDistances,
                                            boolean dsspIgnoreHydrogens)
        Overrides:
        calcRasmolHydrogenBonds in class BioPolymer
      • checkRasmolHydrogenBond

        private void checkRasmolHydrogenBond​(AminoMonomer source,
                                             BioPolymer polymer,
                                             int indexDonor,
                                             javajs.util.P3 hydrogenPoint,
                                             javajs.util.BS bsB,
                                             javajs.util.Lst<Bond> vHBonds,
                                             int[][] min,
                                             boolean checkDistances)
      • calcHbondEnergy

        private int calcHbondEnergy​(javajs.util.P3 nitrogenPoint,
                                    javajs.util.P3 hydrogenPoint,
                                    AminoMonomer target,
                                    boolean checkDistances)
        based on RasMol 2.7.2.1.1 model checkDistances: When we are seriously looking for H bonds, we want to also check that distCN > distCH and that the OH distance is less than 3 Angstroms. Otherwise that's just too strange a hydrogen bond. (We get hydrogen bonds from i to i+2, for example) This check is skipped for an actual DSSP calc., where we want the original definition and are not actually creating hydrogen bonds H .......... O | | | | N C
        Parameters:
        nitrogenPoint -
        hydrogenPoint -
        target -
        checkDistances -
        Returns:
        energy in cal/mol or 0 (none)
      • addResidueHydrogenBond

        private void addResidueHydrogenBond​(Atom nitrogen,
                                            Atom oxygen,
                                            int indexAminoGroup,
                                            int indexCarbonylGroup,
                                            float energy,
                                            javajs.util.Lst<Bond> vHBonds)
      • isTurn

        private boolean isTurn​(float psi,
                               float phi)
        Parameters:
        psi - N-C-CA-N torsion for NEXT group
        phi - C-CA-N-C torsion for THIS group
        Returns:
        whether this corresponds to a helix
      • isSheet

        private boolean isSheet​(float psi,
                                float phi)
      • isHelix

        private boolean isHelix​(float psi,
                                float phi)
      • checkPhiPsi

        private static boolean checkPhiPsi​(float[] list,
                                           float psi,
                                           float phi)
      • setStructureList

        public void setStructureList​(java.util.Map<STR,​float[]> structureList)
        Parameters:
        structureList - protein only -- helix, sheet, turn definitions