Package ffx.potential.cli

Class TopologyOptions

java.lang.Object
ffx.potential.cli.TopologyOptions
public class TopologyOptions extends Object
Represents command line options for scripts that utilize multiple physical topologies.
Since:
1.0
Author:
Michael J. Schnieders, Jacob M. Litman

  • Field Details

    • logger

      public static final Logger logger
      The logger for this class.

  • Constructor Details

    • TopologyOptions

      public TopologyOptions()

  • Method Details

    • getAlchemicalAtoms2

      public String getAlchemicalAtoms2()
      --ac2 or --alchemicalAtoms2 Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N].
      Returns:
      Returns alchemical atoms for the 2nd topology.

    • getAlchemicalResidues2

      public String getAlchemicalResidues2()
      --acRes2 or --alchemicalResidues2 Specify alchemical residues by chain and residue number [e.g. A4,B21].
      Returns:
      Returns alchemical residues for the 2nd topology.

    • getUnchargedAtoms2

      public String getUnchargedAtoms2()
      --uc2 or --unchargedAtoms2 Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].
      Returns:
      Returns atoms without electrostatics for the 2nd topology.

    • getTopologiesInParallel

      public int getTopologiesInParallel()
      --np or --nParallel sets the number of topologies to evaluate in parallel; currently 1, 2, or 4.
      Returns:
      Returns Number of topologies to evaluate in parallel.

    • getUnsharedA

      public String getUnsharedA()
      --uaA or --unsharedA sets atoms unique to the A dual-topology, as period-separated hyphenated ranges or singletons.
      Returns:
      Return atoms unique to the A dual-topology.

    • getUnsharedB

      public String getUnsharedB()
      --uaB or --unsharedB sets atoms unique to the A dual-topology, as period-separated hyphenated ranges or singletons.
      Returns:
      Return atoms unique to the B dual-topology.

    • getLambdaFunction

      public String getLambdaFunction()
      -sf or --switchingFunction

      Sets the switching function to be used by dual topologies.

      • TRIG produces the function sin^2(pi/2*lambda)*E1(lambda) + cos^2(pi/2*lambda)*E2(1-lambda)
      • MULT uses a 5th-order polynomial switching function with zero first and second derivatives at the end (same function as used for van der Waals switch)
      • A number uses the original function, of l^beta*E1(lambda) + (1-lambda)^beta*E2(1-lambda).

      All of these are generalizations of Udt = f(l)*E1(l) + f(1-l)*E2(1-lambda), where f(l) is a continuous switching function such that f(0) = 0, f(1) = 1, and 0 <= f(l) <= 1 for lambda 0-1. The trigonometric switch can be restated thusly, since cos^2(pi/2*lambda) is identical to sin^2(pi/2*(1-lambda)), f(1-l).

      Returns:
      Returns the lambda function.

    • getTopologiesInParallel

      public int getTopologiesInParallel(int nTopologies)
      The number of topologies to run in parallel.
      Parameters:
      nTopologies - The number of topologies.
      Returns:
      Number of topologies to run in parallel.

    • getThreadsPerTopology

      public int getThreadsPerTopology(int nTopologies)
      The number of threads per topology.
      Parameters:
      nTopologies - The number of topologies.
      Returns:
      Number of threads per topology.

    • getNumberOfTopologies

      public int getNumberOfTopologies(@Nullable List<String> topologyFilenames)
      Validate the number of topologies.
      Parameters:
      topologyFilenames - List of topology filenames.
      Returns:
      The number of topologies.

    • assemblePotential

      public Potential assemblePotential(MolecularAssembly[] assemblies, StringBuilder sb)
      Performs the bulk of the work of setting up a multi-topology system.

      The sb StringBuilder is often something like "Timing energy and gradients for". The method will append the exact type of Potential being assembled.

      Parameters:
      assemblies - Opened MolecularAssembly(s).
      sb - A StringBuilder describing what is to be done.
      Returns:
      a Potential object.

    • getSwitchingFunction

      public UnivariateSwitchingFunction getSwitchingFunction()
      Return the switching function between topology energies.
      Returns:
      the switching function.

    • getUniqueAtomsA

      public List<Integer> getUniqueAtomsA(MolecularAssembly topology)
      Collect unique atoms for the A dual-topology.
      Parameters:
      topology - A MolecularAssembly from dual-topology A.
      Returns:
      A List of Integers.

    • getTopology

      public Potential getTopology(MolecularAssembly[] topologies, UnivariateSwitchingFunction sf, List<Integer> uniqueA, List<Integer> uniqueB, int numParallel, StringBuilder sb)
      Configure a Dual-, Quad- or Oct- Topology.
      Parameters:
      topologies - The topologies.
      sf - The Potential switching function.
      uniqueA - The unique atoms of topology A.
      uniqueB - The unique atoms of topology B.
      numParallel - The number of energies to evaluate in parallel.
      sb - A StringBuilder for logging.
      Returns:
      The Potential for the Topology.

    • getUniqueAtoms

      public static List<Integer> getUniqueAtoms(MolecularAssembly assembly, String label, String unshared)
      Collect unique atoms for a dual-topology. List MUST be sorted at the end.
      Parameters:
      assembly - A MolecularAssembly from the dual topology.
      label - Either 'A' or 'B'.
      unshared - Atoms this dual topology isn't sharing.
      Returns:
      A sorted List of Integers.

    • getUniqueAtomsB

      public List<Integer> getUniqueAtomsB(MolecularAssembly topology)
      Collect unique atoms for the B dual-topology.
      Parameters:
      topology - A MolecularAssembly from dual-topology B.
      Returns:
      A List of Integers.

    • hasSoftcore

      public boolean hasSoftcore()
      If any softcore Atoms have been detected.
      Returns:
      Presence of softcore Atoms.

    • setSecondSystemAlchemistry

      public void setSecondSystemAlchemistry(MolecularAssembly topology)
      Set the alchemical atoms for this topology.
      Parameters:
      topology - a MolecularAssembly object.

    • setSecondSystemUnchargedAtoms

      public void setSecondSystemUnchargedAtoms(MolecularAssembly topology)
      Set uncharged atoms for this topology.
      Parameters:
      topology - a MolecularAssembly object.

    • setAlchemicalProperties

      public void setAlchemicalProperties(int numberOfTopologies)
      Relative free energies via the DualTopologyEnergy class require different default OST parameters than absolute free energies.
      Parameters:
      numberOfTopologies - The number of topologies.