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TREEKIN(1) User Commands TREEKIN(1) NAME treekin - manual page for treekin 0.5.1 SYNOPSIS treekin [OPTIONS]... [FILES]... DESCRIPTION treekin 0.5.1 Compute biopolymer macrostate dynamics treekin computes a reduced dynamics of biopolymer folding by means of numeric integration of a Markov process that generally operates at the level of macrostates, i.e. basins of attraction of the underlying en- ergy landscape. treekin expects a .bar file via stdin, and optionally a rates file in the current working directory. Both the .bar file and the rates file (default name is rates.out) can be obtained from barriers. In case of -m I option (default) the program needs just the rate file provided as standard input. -h, --help Print help and exit -V, --version Print version and exit -a, --absorb=state Make a state absorbing -m, --method=STRING Select method to build transition matrix: A ==> Arrhenius-like kinetics I ==> use input as a rate matrix (possible values="A", "I" default=`I') --num-err=STRING Specify how to treat issues with numerical errors in probabil- ity: I ==> Ignore H ==> Halt the program R ==> Rescale the prob- ability (possible values="I", "H", "R" default=`H') --t0=time Start time (default=`0.1') --t8=time Stop time (default=`1E12') -T, --Temp=DOUBLE Temperature in Celsius (default=`37.0') -n, --nstates=INT Read only first <int> states (assume quasi-stationary distribu- tion (derivation of others is = 0)) --p0=STRING Set initial population of state <int> to <double> Can be given multiple times (NOTE: sum of <double> must equal 1) (example: "--p0 2=1.0" - state 2 has initial population 100 percent) --tinc=DOUBLE Time scaling factor (for log time-scale) (default=`1.02') --degeneracy Consider degeneracy in transition rates (default=off) --exponent Use matrix-expontent routines, rather than diagonalization (de- fault=off) --dumpU Dump transition matrix U to file mx.txt (and to binary mx.bin - not fixed yet) (default=off) --mathematicamatrix Dump transition matrix U to Mathematica-readable file mxMat.txt (default=off) -b, --bin Assume binary rates input (default=off) -B, --bar=STRING Read barriers input from file instead of standard input. Re- quired in case "-m I" (rates kinetics) AND "-a" (absorbing state) is given -t, --fpt=STRING Compute first passage times (FPT). Arguments: all => compute all FPT (slow) <num> - compute FPT to state <num> from all states -r, --recoverE Recover from pre-ccomputes eigenvalues and eigenvectors (de- fault=off) -e, --dumpE Dump eigenvalues and eigenvectors to a binary recovery file and continue with iteration (default=off) -x, --dumpX Dump eigenvalues to ASCII file and exit (do not iterate) (de- fault=off) --info Show settings (default=off) -f, --ratesfile=STRING Read transition rates from file instead of standard input. -v, --verbose Verbose output (default=off) -q, --quiet Be silent (do not print out the output) (default=off) --fptfile=STRING Filename of FPT file (provided -t option given) --visualize=STRING Filename where to print a visualization of rate graph (without file subscript, two files will be generated: .dot and .eps with text and visual representation of graph) --just-shorten Do not diagonalize and iterate, just shorten input (meaningfull only with -n X option or -fpt option or --visualize option) (de- fault=off) --max-decrease=INT Maximal decrease in dimension in one step (default=`1000000') --feps=DOUBLE Machine precision used by LAPACK routines (and matrix aritmetic) -- if set to negative number, the lapack suggested value is used (2*DLAMCH("S") ) (default=`1E-15') --useplusI Use old treekin computation where we add identity matrix to transition matrix. Sometimes less precise (maybe sometimes also more precise), in normal case it should not affect results at all. (default=off) --minimal-rate=DOUBLE Rescale all rates to be higher than the minimal rate using for- mula "rate -> rate^(ln(desired_minimal_rate)/ln(mini- mal_rate))", where desired_minimal_rate is from input, mini- mal_rate is the lowest from all rates in rate matrix. --hard-rescale=DOUBLE Rescale all rates by a hard exponent (usually 0.0<HR<1.0). For- mula: "rate -> rate^(hard-rescale)". Overrides --minimal-rate argument. --equil-file=STRING Write equilibrium distribution into a file. --times=DOUBLE Multiply rates with a constant number. --warnings Turn all the warnings about underflow on. (default=off) -c, --mlapack-precision=INT Number of bits for the eigenvalue method of the mlapack library. A value > 64 is recommended, otherwise the standard lapack method would be faster. --mlapack-method=STRING The mlapack precision method. "LD", "QD", "DD", "DOUBLE", "GMP", "MPFR", "FLOAT128". You have to set mlapack-precision if "GMP", "MPFR" is selected! "LD" is the standard long double with 80 bit. REFERENCES M.T. Wolfinger, W.A. Svrcek-Seiler, Ch. Flamm, I.L. Hofacker, P.F. Stadler "Efficient computation of RNA folding dynamics" J.Phys.A: Math.Gen. 37: 4731-4741 (2004) I.L. Hofacker, Ch. Flamm, Ch. Heine, M.T. Wolfinger, G. Scheuermann, P.F. Stadler "BarMap: RNA folding on dynamic energy landscapes" RNA: 2010 16: 1308-1316 (2010) EXAMPLES Typically, computation of a reduced dynamics based on the analysis of folding landscapes requires two steps: Elucidation of the landscape (topology) and - based on that - calculation of the reduced dynamics. The first step involves computing the relevant properties of an energy landscape by barriers (see barriers(1) for details). The resulting .bar-file contains information on local minima, basins, saddle points as well as thermodynamic properties of the energy landscape. Addition- ally, the --rates option in the below example triggers barriers to gen- erate another output file (rates.out) containing the transition rates between all pairs of macrostates (ie. basins of attraction), calculated by summing over the corresponding microscopic rates. $ barriers --saddle --bsize --rates < foo.sub > foo.bar In a second step, treekin is called with options to calculate the macrostate dynamics on the previously generated landscape by means of applying microscopic transition rates (option -m I): $ treekin --p0 2=1 < rates.out In this example, the simulation starts with 100% of the initial popula- tion in macrostate 2, i.e. the second lowest minimum in the barrier tree (option --p0 2=1). The transition matrix is computed from a set of microscopic rates, read from a rates file (as computed by barriers). Generally, calculation of the macrostate dynamics by means of micro- scopic rates (option -m I) is consiberably more accurate than the sim- plified Arrhenius-like dynamics (option -m A). Looking at the default output produced by treekin, there are two sec- tions: Overall status information on the computation (marked by hash signs at the beginning of the line) are printed at the top. Below, the actual data is printed for each time step in (n+1) space-separated columns, where n is the number of investigated (macro)states. The first column lists the current time, whereas all remaining columns correspond to the population probabilities of individual (macro)states. AUTHOR Michael T. Wolfinger, Marcel Kucharik, Ivo Hofacker, Christoph Flamm, Andreas Svrcek-Sailer, Peter Stadler. SEE ALSO barriers(1) treekin 0.5.1 June 2019 TREEKIN(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | EXAMPLES | AUTHOR | SEE ALSO
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