Package ffx.algorithms.cli

Class ManyBodyOptions

java.lang.Object
ffx.algorithms.cli.ManyBodyOptions
public class ManyBodyOptions extends Object
Represents command line options for scripts that use a many-body expansion for global optimization.
Since:
1.0
Author:
Michael J. Schnieders, Mallory R. Tollefson

  • Constructor Details

    • ManyBodyOptions

      public ManyBodyOptions()

  • Method Details

    • initRotamerOptimization

      public void initRotamerOptimization(RotamerOptimization rotamerOptimization, MolecularAssembly activeAssembly)
      initRotamerOptimization.
      Parameters:
      rotamerOptimization - a RotamerOptimization object.
      activeAssembly - a MolecularAssembly object.

    • collectResidues

      public List<Residue> collectResidues(MolecularAssembly activeAssembly)
      Collect residues based on residue selection flags.
      Parameters:
      activeAssembly - a MolecularAssembly object.

    • getAlgorithm

      public RotamerOptimization.Algorithm getAlgorithm(int numResidues)
      Returns the user selected algorithm or one chosen based on number of residues.
      Returns:
      Returns the algorithm choice.

    • getUsingOriginalCoordinates

      public boolean getUsingOriginalCoordinates()

    • setOriginalCoordinates

      public void setOriginalCoordinates(boolean useOrig)

    • getApproximate

      public double getApproximate()

    • getRestartFile

      public File getRestartFile()
      Gets the restart file created during rotamer optimization.
      Returns:
      The restart file.

    • getRotamerLibrary

      public RotamerLibrary getRotamerLibrary(boolean reinit)

    • setAlgorithm

      public void setAlgorithm(int algorithm)

    • getLibrary

      public int getLibrary()
      Ponder and Richards (1) or Richardson (2) rotamer library.
      Returns:
      Returns the Rotamer library.

    • setLibrary

      public void setLibrary(int library)

    • getNaLibraryName

      public String getNaLibraryName()
      Nucleic acid library: currently only Richardson available.
      Returns:
      Returns a String for the nucleic acid library.

    • setNaLibraryName

      public void setNaLibraryName(String naLibraryName)

    • isDee

      public boolean isDee()
      Use dead-end elimination criteria instead of Goldstein criteria.
      Returns:
      Returns true if using DEE instead of Goldstein.

    • setDee

      public void setDee(boolean dee)

    • getChain

      public String getChain()
      Single character chain ID of the residues to optimize.
      Returns:
      Returns the Chain name.

    • setChain

      public void setChain(String chain)

    • getOnlyTitration

      public boolean getOnlyTitration()

    • setOnlyTitration

      public void setOnlyTitration(boolean onlyTitration)

    • getOnlyProtons

      public boolean getOnlyProtons()

    • setOnlyProtons

      public void setOnlyProtons(boolean onlyProtons)

    • getInterestedResidue

      public int getInterestedResidue()

    • setInterestedResidue

      public void setInterestedResidue(int interestedResidue)

    • getInclusionCutoff

      public double getInclusionCutoff()

    • setInclusionCutoff

      public void setInclusionCutoff(double inclusionCutoff)

    • getStart

      public int getStart()
      Starting residue to perform the optimization on (-1 exits). For box optimization, first box to optimize.
      Returns:
      Returns the starting index.

    • setStart

      public void setStart(int start)

    • getFinish

      public int getFinish()
      Final residue to perform the optimization on (-1 exits). For box optimization, final box to optimize.
      Returns:
      Returns the finish index.

    • setFinish

      public void setFinish(int finish)

    • getTwoBodyCutoff

      public double getTwoBodyCutoff()
      Cutoff distance for two-body interactions.
      Returns:
      Returns the 2-body cutoff.

    • setTwoBodyCutoff

      public void setTwoBodyCutoff(double twoBodyCutoff)

    • isThreeBody

      public boolean isThreeBody()
      -T or --threeBody Include 3-Body interactions in the elimination criteria.
      Returns:
      Returns true if 3-body interactions are being used.

    • setThreeBody

      public void setThreeBody(boolean threeBody)

    • getThreeBodyCutoff

      public double getThreeBodyCutoff()
      Cutoff distance for three-body interactions.
      Returns:
      Returns the 3-body cutoff.

    • setThreeBodyCutoff

      public void setThreeBodyCutoff(double threeBodyCutoff)

    • getPrune

      public int getPrune()
      Prune no clashes (0), only single clashes (1), or all clashes (2).
      Returns:
      Returns the pruning condition.

    • setPrune

      public void setPrune(int prune)

    • isRevert

      public boolean isRevert()
      Revert unfavorable changes.
      Returns:
      Returns true if unfavorable changes are reverted.

    • setRevert

      public void setRevert(boolean revert)

    • getEnergyRestart

      public String getEnergyRestart()
      Energy restart file from a previous run (requires that all parameters are the same).
      Returns:
      Returns the energy restart file to use.

    • setEnergyRestart

      public void setEnergyRestart(String energyRestart)

    • isNoOriginal

      public boolean isNoOriginal()
      Do not include starting coordinates as their own rotamer.
      Returns:
      Returns true if original side-chain coordinates should not be used as a rotamer.

    • setNoOriginal

      public void setNoOriginal(boolean noOriginal)

    • isDecompose

      public boolean isDecompose()
      -E or --decompose Print energy decomposition for the input structure (no optimization).
      Returns:
      Returns true if the input structure should undergo an energy decomposition.

    • setDecompose

      public void setDecompose(boolean decompose)

    • getListResidues

      public String getListResidues()
      Choose a list of individual residues to optimize (eg. A11,A24,B40).
      Returns:
      Returns the list of selected residues.

    • setListResidues

      public void setListResidues(String listResidues)

    • getMonteCarlo

      public int getMonteCarlo()
      Follow elimination criteria with 'n' Monte Carlo steps, or enumerate all remaining conformations, whichever is smaller.
      Returns:
      Returns the number of Monte Carlo optimization steps to apply.

    • setMonteCarlo

      public void setMonteCarlo(int monteCarlo)

    • isSaveOutput

      public boolean isSaveOutput()
      Save eliminated singles and eliminated pairs to a text file (global and box optimization).
      Returns:
      Returns true to Save eliminated rotamers to a file.

    • setSaveOutput

      public void setSaveOutput(boolean saveOutput)

    • getWindow

      public int getWindow()
      Size of the sliding window with respect to adjacent residues (default = 7).
      Returns:
      Returns the sliding window size.

    • setWindow

      public void setWindow(int window)

    • getIncrement

      public int getIncrement()
      Sliding window increment (default = 3).
      Returns:
      Returns the sliding window increment.

    • setIncrement

      public void setIncrement(int increment)

    • getCutoff

      public double getCutoff()
      The sliding window and box cutoff radius (Angstroms).
      Returns:
      Returns the sliding window cutoff radius.

    • setCutoff

      public void setCutoff(double cutoff)

    • getClashThreshold

      public double getClashThreshold()
      The threshold for pruning clashes. If two self-energies on the same residue have an energy difference greater than 25 kcal/mol, the high energy rotamers get pruned.
      Returns:
      Returns the clash threshold for self energies.

    • setClashThreshold

      public void setClashThreshold(double clashThreshold)

    • getPairClashThreshold

      public double getPairClashThreshold()
      The threshold for pruning clashes. If two pair-energies on the same residues have an energy difference greater than 25 kcal/mol, the high energy rotamers get pruned.
      Returns:
      Returns the clash threshold for pair energies.

    • setPairClashThreshold

      public void setPairClashThreshold(double pairClashThreshold)

    • getNumBoxes

      public String getNumBoxes()
      The number of boxes along X, Y, and Z (default: '3,3,3').
      Returns:
      Returns the number of boxes.

    • setNumBoxes

      public void setNumBoxes(String numBoxes)

    • getBoxBorderSize

      public double getBoxBorderSize()
      Extent of overlap between optimization boxes (default: 0.0 A).
      Returns:
      Returns the overlap between optimization boxes.

    • setBoxBorderSize

      public void setBoxBorderSize(double boxBorderSize)

    • getApproxBoxLength

      public double getApproxBoxLength()
      Approximate side lengths of boxes to be constructed (over-rides numXYZBoxes). Box sizes are rounded up to make a whole number of boxes along each axis (default of 0 disables this function).
      Returns:
      Returns the approximate box length.

    • setApproxBoxLength

      public void setApproxBoxLength(double approxBoxLength)

    • getBoxInclusionCriterion

      public int getBoxInclusionCriterion()
      Criterion to use for adding residues to boxes. (1) uses C alpha only (N1/9 for nucleic acids) (2) uses any atom. (3) uses any rotamer.
      Returns:
      Returns the Box inclusion criteria.

    • setBoxInclusionCriterion

      public void setBoxInclusionCriterion(int boxInclusionCriterion)

    • setTitrationPH

      public void setTitrationPH(double pH)

    • getTitrationPH

      public double getTitrationPH()

    • setPHRestraint

      public void setPHRestraint(double pHRestraint)

    • getPHRestraint

      public double getPHRestraint()

    • isTitrating

      public boolean isTitrating()

    • getTitration

      public boolean getTitration()

    • selectInclusionResidues

      public String selectInclusionResidues(List<Residue> residueList, int mutatingResidue, boolean onlyTitration, boolean onlyProtons, double inclusionCutoff)