Package org.jmol.modelsetbio

Class AminoPolymer

java.lang.Object
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.AlphaPolymer
org.jmol.modelsetbio.AminoPolymer
All Implemented Interfaces:
Structure
public class AminoPolymer extends AlphaPolymer

  • Field Details

    • maxHbondAlphaDistance

      private static final float maxHbondAlphaDistance
      See Also:

    • maxHbondAlphaDistance2

      private static final float maxHbondAlphaDistance2
      See Also:

    • minimumHbondDistance2

      private static final float minimumHbondDistance2
      See Also:

    • structureList

      private Map<STR,float[]> structureList

  • Constructor Details

    • AminoPolymer

      AminoPolymer(Monomer[] monomers, int pt0)

  • Method Details

    • resetHydrogenPoints

      protected void resetHydrogenPoints()
      Overrides:
      resetHydrogenPoints in class BioPolymer

    • calcPhiPsiAngles

      protected boolean calcPhiPsiAngles()
      Overrides:
      calcPhiPsiAngles in class BioPolymer

    • calcPhiPsiAngles2

      private void calcPhiPsiAngles2(AminoMonomer residue1, AminoMonomer residue2)

    • calculateRamachandranHelixAngle

      protected float calculateRamachandranHelixAngle(int m, char qtype)
      Overrides:
      calculateRamachandranHelixAngle in class BioPolymer
      Returns:
      calculated value

    • 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)

    • calculateStructures

      public void calculateStructures(boolean alphaOnly)
      Description copied from class: AlphaPolymer
      Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.

      Levitt and Greer
      Automatic Identification of Secondary Structure in Globular Proteins
      J.Mol.Biol.(1977) 114, 181-293

      http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf

      Overrides:
      calculateStructures in class AlphaPolymer
      Parameters:
      alphaOnly - caught by AminoPolymer and discarded if desired

    • 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(Map<STR,float[]> structureList)
      Parameters:
      structureList - protein only -- helix, sheet, turn definitions