Subject: quatfit.c - program to fit molecules

From: [email-masked] (Jan Labanowski)
Date: Sat, 10 Oct 1992 00:30:05 -0400

Dear Netters,

Remember the fitest.f program by Dave Heisterberg ([email-masked])? The fitest.f
is a FORTRAN program which shows that the quaternion method of fitting two
sets of points is probably the fastest one available. There are several
approaches to the rigid fit of molecules (sorry for no authors and
citations --- I really do not have time to write a review), e.g.:
  1. Iterative methods
     a) points are connected with "springs" of zero length and force constant
        is equal to the statistical weight for a given atom pair, and the
        minimizer optimizes the stretch energy of the springs as a function
        of translation vector and Euler angles,
     b) Taylor expansions of rotation matrix after centers where superimposed,
        and iterative improvement of it.

  2. Methods based on linear algebra
     a) Principal component analysis of the X'Y product
     b) Quaternion method

Methods 1a, and 1b are O.K. but slow (iterative). Method 2a will perform
inversion if needed to get a better fit (i.e., can change chirality).
Method 2b is fast (one step) and will not inverse coordinates.

So now is the quatfit.c program, It uses quaternion method to fit molecules.
This method was developed before the Kearsley paper was published:
Kearley, S.K., J. Comput. Chem, 11, 1187-1192 (1990),  and is actually
slightly different. One day Dave may publish a paper on this, but he really
does not have time to do it now.

The program quatfit.c is placed in our archives on www.ccl.net in
/pub/chemistry/quatfit directory. The following files are there:
  quatfit.c      --- source of the program. Compile it with:
                        cc -o quatfit quatfit.c -lm
  quatfit.roff   --- (t|n|dit|pt)roff source of man page. To process it, use
                     your version of roff with -man. It is intended to be
                     installed on Unices with the Documenter's Workbench
                     option.
  quatfit.ps     --- a PostScript version of the man page.
  quatfit.txt    --- a pure text version of the man page.
  quatfit.ascii  --- a text version of man page as came from nroff (with
                     underlines and backspaces for printer or terminal
                     display
  readme         --- this file.
  rm.xyz         --- example of reference molecule
  fm.xyz         --- example of fitted molecule
  fmmod.xyz      --- example of the fit result
  stat.txt       --- example of fit statistics file
  pairs.tab      --- example of pairs and weights file

How to get it?

Via ftp:
ftp www.ccl.net  (or ftp 128.146.36.48)
Login: anonymous
Password: Your_email_address
ftp> ascii
ftp> cd /pub/chemistry/quatfit
ftp> mget *
ftp> quit

Via e-mail:
Send message:
   send ./quatfit/quatfit.c     from chemistry        
   send ./quatfit/quatfit.roff  from chemistry        
   send ./quatfit/quatfit.ps    from chemistry        
   send ./quatfit/quatfit.txt   from chemistry        
   send ./quatfit/quatfit.ascii from chemistry        
   send ./quatfit/readme        from chemistry        
   send ./quatfit/rm.xyz        from chemistry
   send ./quatfit/fm.xyz        from chemistry
   send ./quatfit/fmmod.xyz     from chemistry
   send ./quatfit/stat.txt      from chemistry
   send ./quatfit/pairs.tab     from chemistry
to [email-masked] or [email-masked] and the files will be
automatically sent to your mailbox.

Note, the program has a copyright notice, so if you want to sell it  (:-)},
you have to ask us first.

Jan Labanowski
Ohio Supercomputer Center
[email-masked]