Package ffx.algorithms.optimize.manybody

Class EliminatedRotamers

java.lang.Object
ffx.algorithms.optimize.manybody.EliminatedRotamers
public class EliminatedRotamers extends Object

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    boolean[][][][]
    eliminatedPairs
    Eliminated rotamer pairs.
    boolean[][]
    eliminatedSingles
    Eliminated rotamers.
    boolean[][][][]
    onlyPrunedPairs
    Pruned rotamer pairs.
    boolean[][]
    onlyPrunedSingles
    Pruned rotamers.

  • Constructor Summary

    Constructors
    Constructor
    Description
    EliminatedRotamers(RotamerOptimization rO, DistanceMatrix dM, List<Residue> allResiduesList, int maxRotCheckDepth, double clashThreshold, double pairClashThreshold, double multiResClashThreshold, double nucleicPruningFactor, double nucleicPairsPruningFactor, double multiResPairClashAddn, boolean pruneClashes, boolean prunePairClashes, boolean print, Residue[] residues)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    check(int i, int ri)
    Check for eliminated rotamer; true if eliminated.
    boolean
    check(int i, int ri, int j, int rj)
    Check for eliminated rotamer pair; true if eliminated.
    boolean
    checkPrunedPairs(int i, int ri, int j, int rj)
    Check for pruned rotamer pair; true if eliminated.
    boolean
    checkPrunedSingles(int i, int ri)
    Check for pruned rotamer; true if eliminated.
    boolean
    checkToJ(int i, int ri, int j, int rj)
    Checks to see if any eliminations with j,rj have occurred; assumes i,ri self has already been checked.
    boolean
    checkToK(int i, int ri, int j, int rj, int k, int rk)
    Checks to see if any eliminations with k,rk have occurred; assumes i,ri,j,rj 2-Body has already been checked.
    boolean
    checkToL(int i, int ri, int j, int rj, int k, int rk, int l, int rl)
    Checks to see if any eliminations with l,rl have occurred; assumes i,ri,j,rj,k,rk 3-Body has already been checked.
    boolean
    eliminateRotamer(Residue[] residues, int i, int ri, boolean verbose)
    Safe method to eliminate a rotamer: will not eliminate if there are no alternate rotamers for residue i, or if i-ri is already eliminated.
    boolean
    eliminateRotamerPair(Residue[] residues, int i, int ri, int j, int rj, boolean verbose)
     
    int
    eliminateRotamerPairs(Residue[] residues, int i, int ri, boolean verbose)
     
    boolean
    pairsToSingleElimination(Residue[] residues, int i, int j)
    Method to check if pairs elimination for some residue pair has enabled a singles rotamer elimination by eliminating all ri-rj for some ri or some rj.
    void
    prePrunePairs(Residue[] residues)
    Pre-prunes any pairs that have a pair-energy of Double.NaN before pruning and eliminations happen.
    void
    prePruneSelves(Residue[] residues)
    Pre-prunes any selves that have a self-energy of Double.NaN before pruning and eliminations happen.
    void
    prunePairClashes(Residue[] residues)
    Prunes rotamer ri of residue i if all ri-j pair energies are worse than the best i-j pair by some threshold value; additionally prunes ri-rj pairs if they exceed the best i-j pair by a greater threshold value; additionally performs this in reverse (searches over j-i).
    void
    pruneSingleClashes(Residue[] residues)
    Uses calculated energies to prune rotamers based on a threshold distance from that residue's minimum energy rotamer (by default 20 kcal/mol).
    void
    setEnergyExpansion(EnergyExpansion eE)
     
    String
    toString()
     
    boolean
    validateDEE(Residue[] residues)
     

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Field Details

    • eliminatedSingles

      public boolean[][] eliminatedSingles
      Eliminated rotamers. [residue][rotamer]

    • eliminatedPairs

      public boolean[][][][] eliminatedPairs
      Eliminated rotamer pairs. [residue1][rotamer1][residue2][rotamer2]

    • onlyPrunedSingles

      public boolean[][] onlyPrunedSingles
      Pruned rotamers. Only for JUnit testing purposes.

    • onlyPrunedPairs

      public boolean[][][][] onlyPrunedPairs
      Pruned rotamer pairs. Only for JUnit testing purposes.

  • Constructor Details

    • EliminatedRotamers

      public EliminatedRotamers(RotamerOptimization rO, DistanceMatrix dM, List<Residue> allResiduesList, int maxRotCheckDepth, double clashThreshold, double pairClashThreshold, double multiResClashThreshold, double nucleicPruningFactor, double nucleicPairsPruningFactor, double multiResPairClashAddn, boolean pruneClashes, boolean prunePairClashes, boolean print, Residue[] residues)

  • Method Details

    • check

      public boolean check(int i, int ri)
      Check for eliminated rotamer; true if eliminated.
      Parameters:
      i - Residue i.
      ri - Rotamer ri.
      Returns:
      True if rotamer eliminated.

    • check

      public boolean check(int i, int ri, int j, int rj)
      Check for eliminated rotamer pair; true if eliminated.
      Parameters:
      i - Residue i.
      ri - Rotamer ri.
      j - Residue j.
      rj - Rotamer rj.
      Returns:
      True if eliminated pair.

    • checkPrunedPairs

      public boolean checkPrunedPairs(int i, int ri, int j, int rj)
      Check for pruned rotamer pair; true if eliminated. Only used during testing.
      Parameters:
      i - Residue i.
      ri - Rotamer ri.
      j - Residue j.
      rj - Rotamer rj.
      Returns:
      a boolean.

    • checkPrunedSingles

      public boolean checkPrunedSingles(int i, int ri)
      Check for pruned rotamer; true if eliminated. Only used during testing.
      Parameters:
      i - The residue.
      ri - The rotamer.
      Returns:
      a boolean.

    • checkToJ

      public boolean checkToJ(int i, int ri, int j, int rj)
      Checks to see if any eliminations with j,rj have occurred; assumes i,ri self has already been checked. Checks j,rj self and i,ri,j,rj 2-Body. The intent is to be part of a loop over i,ri,j,rj, and check for eliminations at the j,rj point.
      Parameters:
      i - Residue i
      ri - Rotamer ri
      j - Residue j
      rj - Rotamer rj
      Returns:
      j eliminated with i

    • checkToK

      public boolean checkToK(int i, int ri, int j, int rj, int k, int rk)
      Checks to see if any eliminations with k,rk have occurred; assumes i,ri,j,rj 2-Body has already been checked. Checks the k,rk self, all pairs with k,rk, and the i,ri,j,rj,k,rk 3-Body. The intent is to be part of a loop over i,ri,j,rj,k,rk, and check for eliminations at the k,rk point.
      Parameters:
      i - Residue i
      ri - Rotamer ri
      j - Residue j
      rj - Rotamer rj
      k - Residue k
      rk - Rotamer rk
      Returns:
      k eliminated with i,j

    • checkToL

      public boolean checkToL(int i, int ri, int j, int rj, int k, int rk, int l, int rl)
      Checks to see if any eliminations with l,rl have occurred; assumes i,ri,j,rj,k,rk 3-Body has already been checked. Checks the l,rl self, all pairs with l,rl, all triples with l,rl, and the 4-Body. The intent is to be part of a loop over i,ri,j,rj,k,rk,l,rl, and check for eliminations at the l,rl point.
      Parameters:
      i - Residue i
      ri - Rotamer ri
      j - Residue j
      rj - Rotamer rj
      k - Residue k
      rk - Rotamer rk
      l - Residue l
      rl - Rotamer rl
      Returns:
      l eliminated with i,j,k

    • eliminateRotamer

      public boolean eliminateRotamer(Residue[] residues, int i, int ri, boolean verbose)
      Safe method to eliminate a rotamer: will not eliminate if there are no alternate rotamers for residue i, or if i-ri is already eliminated.
      Parameters:
      residues - Residues under consideration.
      i - A residue index based on the current residue list.
      ri - A rotamer to attempt elimination of.
      verbose - Request verbose logging.
      Returns:
      If the rotamer was eliminated.

    • eliminateRotamerPair

      public boolean eliminateRotamerPair(Residue[] residues, int i, int ri, int j, int rj, boolean verbose)

    • eliminateRotamerPairs

      public int eliminateRotamerPairs(Residue[] residues, int i, int ri, boolean verbose)

    • pairsToSingleElimination

      public boolean pairsToSingleElimination(Residue[] residues, int i, int j)
      Method to check if pairs elimination for some residue pair has enabled a singles rotamer elimination by eliminating all ri-rj for some ri or some rj.
      Parameters:
      residues - Residues under consideration.
      i - A residue index.
      j - A residue index j!=i
      Returns:
      If any singletons were eliminated.

    • prePrunePairs

      public void prePrunePairs(Residue[] residues)
      Pre-prunes any pairs that have a pair-energy of Double.NaN before pruning and eliminations happen.
      Parameters:
      residues - Array of all residues.

    • prePruneSelves

      public void prePruneSelves(Residue[] residues)
      Pre-prunes any selves that have a self-energy of Double.NaN before pruning and eliminations happen.
      Parameters:
      residues - Array of all residues.

    • prunePairClashes

      public void prunePairClashes(Residue[] residues)
      Prunes rotamer ri of residue i if all ri-j pair energies are worse than the best i-j pair by some threshold value; additionally prunes ri-rj pairs if they exceed the best i-j pair by a greater threshold value; additionally performs this in reverse (searches over j-i).
      Parameters:
      residues - Residues whose rotamers are to be pruned.

    • pruneSingleClashes

      public void pruneSingleClashes(Residue[] residues)
      Uses calculated energies to prune rotamers based on a threshold distance from that residue's minimum energy rotamer (by default 20 kcal/mol). The threshold can be modulated by presence of nucleic acids or MultiResidues, which require more generous pruning criteria.
      Parameters:
      residues - Residues to prune rotamers over.

    • setEnergyExpansion

      public void setEnergyExpansion(EnergyExpansion eE)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • validateDEE

      public boolean validateDEE(Residue[] residues)