Package ffx.potential.utils

Class GetProteinFeatures

java.lang.Object
ffx.potential.utils.GetProteinFeatures
public class GetProteinFeatures extends Object

  • Constructor Details

    • GetProteinFeatures

      public GetProteinFeatures(MolecularAssembly molecularAssembly)

  • Method Details

    • saveFeatures

      public String[] saveFeatures(Residue residue, double surfaceArea, boolean includeAngles, boolean includeStructure, boolean includePPI)
      Make a string array of surface area and additional selected features (phi,psi,omega,and structure annotations)
      Parameters:
      residue - Residue
      surfaceArea - residue surface area
      includeAngles - select angles
      includeStructure - select structure annotation
      includePPI - select protein-interface annotation
      Returns:
      String array of features

    • getPhi

      public void getPhi(Residue currentRes)
      Get the phi angle of a residue
      Parameters:
      currentRes - current residue

    • getPsi

      public void getPsi(Residue currentRes)
      Get the psi angle of a residue
      Parameters:
      currentRes - current residue

    • getOmega

      public void getOmega(Residue currentRes)
      Get the omega angle of a residue
      Parameters:
      currentRes - current residue

    • getSecondaryStructure

      public String getSecondaryStructure()
      Get the secondary structure annotation from the ramachandran angle map
      Returns:
      string of secondary structure

    • getTotalSurfaceArea

      public double getTotalSurfaceArea()
      Get the total surface area for the protein
      Returns:
      The total surface area.

    • getConfidenceScore

      public double getConfidenceScore(Residue currentRes)
      Get the alphafold confidence score or b-factor from an X-ray model.
      Parameters:
      currentRes - current residue
      Returns:
      confidence/b-factor value

    • ddgunToNPChange

      public List<String> ddgunToNPChange(List<String> ddgun)
      Use the ddgun output file to get the amino acid changes
      Parameters:
      ddgun - List of lines from ddGun output file
      Returns:
      List of NP Changes

    • getDDGunValues

      public List<Double[]> getDDGunValues(List<String> ddgun)
      Get ddgun values from ddgun file
      Parameters:
      ddgun - List of lines from ddGun output file
      Returns:
      List of ddGun values (raw and abs value)

    • getPolarityAndAcidityChange

      public List<String[]> getPolarityAndAcidityChange(List<String> npChanges, boolean includePolarity, boolean includeAcidity)
      Get the polarity and acidity changes
      Parameters:
      npChanges - list of protein changes
      includePolarity - select polarity
      includeAcidity - select acidity
      Returns:
      list of polarity and acidity changes

    • getPPI

      public String getPPI(Residue residue)