CYCLIZE revisions/changes list
v1.4
8 July, 2000
  • Added the btilt, broll, btwist harmonic force constant parameters to the CHAINPARMS structure (see src/cyclize_lib.h).
  • Added the params_calc_b() function to calculate the harmonic force constants from the temperature and flexibilities.
  • Added 'float Temp', a global to cyclize_lib.c, to store the temperature of the simulation.

  • v1.3
    7 July, 2000
  • Added the btilt, broll, btwist harmonic force constant parameters to the CHAINPARMS structure (see src/cyclize_lib.h).
  • Added the params_calc_b() function to calculate the harmonic force constants from the temperature and flexibilities.
  • Added 'float Temp', a global to cyclize_lib.c, to store the temperature of the simulation.
  • Rewrote the toplevel Makefiles, seperating the gcc, pgcc, sgi makefiles.
  • Rewrote the src/Makefile to link using the Fortran compiler.
  • Replaced the routine gauss_box_muller with a free version
  • Moved the ranu() function from random.c to math_routines.c, this required deleting random.c and random.h, and removing references to both files in various places.

  • v1.2
    5 July, 2000
  • Data fitting can be accomplished using EITHER the numerical recipies routines, or the odrpack routines (Weighted Orthogonal Distrance Regression, the default). The odrpack routines can be redistributed for free, whereas the NR routines require purchase of a license.
  • Use all chains in the radial distribution function that have an end-to-end distance less than the radial cutoff. This costs nothing in CPU time, and gives much better statistics in a poorly sampled region of the radial distribution function. Thus, you can still specify a 'nrad_stats' value less than the total number of whole chains, to speed up the calculation.

  • v1.1
    27 June, 2000
  • Use the CYCLIZE_HOME env. var. in show_results.pl to find the cyclize_params file. This is much better than expecting the file to always reside in /usr/local/lib/cyclize ...
  • Fixed the embarrasing Y2K bug in generate_chains.c and analyze_chains.c ... yes, I forgot to add 1900 to the year. Only affected the *.header files... doesn't change any results.
  • Changed all the perl #! lines to read "#! /usr/bin/perl" rather than "#! /usr/local/bin/perl" since perl is more likely to be installed under /usr/bin these days.

  • v1.0
    12 February, 2000
  • Converted cyclize_lib.pl to use 2 environment variables: CYCLIZE_HOME (mandatory) and CYCLIZE_NICE (optional) to set the installation root directory and 'niceness' level of the calculations, respectively.
  • Updates to the Makefile, uses more standardized 'sh' commands. Should work with most decent UNIces.

  • v1.0b
    23 April, 1999
  • Updates to the Makefile, is run from primary directory now.

  • v0.4
    14 November, 1998
  • Wrote the "Cyclize" perl subroutine, removing the need to make the "system" calls. Ahh, this is good.
  • Cleaned up the code a bit... stupid unused vars, etc... stopped a "-Wall" compile from complaining too much... made sure the SGI "cc" compiler can handle the code, in addition to 'gcc"...
  • Many updates to the manual.
  • New analysis files, "distfreq_halfchain.xm" and "dist_freq_wholechain.xm" are created. They contain informaiton on the distribution frequency of half and whole chain end-to-end distances, see the manual for a better description :)
  • The global distribution arrays (Rdist, Adist, Tdist) were converted to "double" from "unsigned long int" to protect from overflow errors.
  • The numerical recipies "machar" routine was added to "math_routines.c" so we can report on any potential problems with machine precision, etc. This hasn't been implimented, but the routine exists!
  • Fixed the cpu_time calculation, it was "forgetting" 1/10th of the CPU time!
  • The analyze_chains routine takes nrad_stats in whole_chains, instead of half_chains
  • The &find_positions subroutine has been added to work with &read_sequence for people who prefer to read the actual chain sequence in from a text file. &find_positions looks for and returns the base pair positions where a particular sequence is found. See the "program" section of the manual for a better description.
  • Ttracts are recognized by fill_Atract_params. The parameters used for the Ttracts are automatically generated from the parameters used in the Atracts.

  • v0.3
    3 November, 1998
  • Rise per helix axis "dz" was added to the parameter hash input.
  • $nkeepers variable was added to allow for limiting the number of cyclized chains that are stored in the "cyclized_chains.dat" file. This keeps this file from becoming huge.
  • A final "pseudo" basepair is calculated at the end of the chain. This makes more intuitive sense (?) in that the end-to-end distance should TRULY be zero and the Phi angle between the first BP and this pseudo BP should be zero.

  • v0.2
    13 September, 1998
  • The addition of the ability to specify "independent calculations" was added to give more reproducible results by reducing the "importance" of rare cyclizing half-chains.
  • This manual was written.

  • v0.1
    2 July, 1998
  • The original Fortran routines were converted to C and a simple PERL front end was written to allow for simple construction of new chain parameters.

  • Jon Lapham
    Yale University
    Department of Chemistry - Crothers Lab