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The MONSSTER package is used to setup and run MONSSTER
simulations. Methods are also provided to extract
output data and simulated lattice chains from completed
simulation runs.
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new([sequence]); |
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creates a new MONSSTER object. A Sequence object may be given as argument
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setDirectory(directory) |
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set working directory
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$status = complete([requiretrajectory]) |
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determines files from a MONSSTER simulation run are complete. If the argument is set to a non-zero value it requires the trajectory file to be present in addition to the final chain and output file.
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setParameter(parameters) |
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sets MONSSTER simulation parameters that are expected as hash-type key=>value pair arguments.
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setPositionalRestraints(list) |
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sets the positional restraint list
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setDistanceRestraints(force,list) |
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sets the distance restraint list and force
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setup(input) |
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sets up all necessary files to run MONSSTER. An input SICHO lattice chain is required as argument.
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energy(input) |
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sets up and runs mener to get MONSSTER energies An input SICHO lattice chain is required as argument.
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run(input) |
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sets up and runs a MONSSTER simulation An input SICHO lattice chain is required as argument.
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initChain() |
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returns the input chain from a MONSSTER run as SICHO object
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finalChain() |
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returns the final chain from a MONSSTER run as SICHO object
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trajFrame(timestep,cycle) |
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reads a MONSSTER trajectory file and returns the frame corresponding to the time step and cycle arguments
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finalEnergy() |
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returns the final energy from the MONSSTER output
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nSteps() |
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returns the number of time steps from the MONSSTER output
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nCycle() |
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returns the number of cycles at each time step from the MONSSTER output
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$step = stepInfo(index) |
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returns a data structure with MONSSTER output for a given time step
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$cycle = cycleInfo(index) |
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returns a data structure with MONSSTER output for a given cycle
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writeInput(file) |
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writes a MONSSTER input parameter file from previously set parameters.
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writePosRestraints(file) |
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writes a MONSSTER restraint file from a previously set positional restraint list
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sequence |
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Sequence object used to generate input for MONSSTER
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workdir |
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Working directory for running MONSSTER
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par -> { random, ncycle, icycle, tsteps,
resmin, resmax, temp, softcore,
central, stiff, pair, kdcore,
hbond, short, burial,
multibody, threebody,
rgyr, krgyr, rho, krho } |
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MONSSTER simulation parameters
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posrest[] -> { from, to, force } |
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list of positional restraints
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distrest[] -> { from, to } |
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list of distance restraints
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distrestforce |
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restraint force for distance restraints
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output -> { final -> { short, long, total, central },
list[] -> { cycle[] -> { r2, s2, ener, ecent },
step, temp } } |
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simulation data extracted from MONSSTER output
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