ANNOUNCE: TOPS:- Protein Topology Cartoon Generator

Tom Flores t-flores at nimr.mrc.ac.uk
Tue Apr 26 10:56:05 EST 1994

The TOPS package has been placed on the ftp server at 
ftp.biochem.ucl.ac.uk in pub/TOPS. The readme file is
appended to this message.


Program and Editor for Generating Protein Topology Cartoons

The disk (or directory if obtained via ftp) contains several files.

1) README      - This file
2) Licence.h   - Authentication file (Not included in ftp versions, see 
                 appendix 3)
3) tops.tar.gz - Archived and compressed unix file for TOPS (see appendix 1)
4) tops.zip    - Archived and compressed dos file for TOPS (see appendix 2)
5) academic.ps - Academic licence agreement (no charge for academic use)
6) industry.ps - Industrial licence agreemnet (there is a small charge for
                 industrial copies)

TOPS is made of two parts: Tops, the main ansi C program and Xtops, an X
windows topology cartoon editor. Tops should compile with any ansi standard
C compiler. However, Xtops will only work on machines running X windows. The
source for Tops is supplied shrouded for which I make no apology. There is 
also an authentication file which is required when compiling the program. This
authentication will not protect against the avid hacker - but this is not the
aim. People who correctly licence versions of TOPS will receive notices of
updates and bug fixes. This is particularly useful as Xtops is very much a
beta release (if not alpha!). It is written to fit into an old version of my
interface system which is being actively developed to include many other useful
tools involving both sequence and structure analysis. I will also inform 
licenced users of these tools as they become available. 

The package is by no means perfect (its one thing getting a program to work on
a small set of proteins as opposed to every possible protein). I welcome any
comments or suggestions on useful new features or peculiar existing features
(bugs). The documentation is only a draft version and will be updated when I
release the next version of TOPS. (The documentation is written in postscript,
if necessary I can supply some other format).

Compiling Tops on a unix machine.

1) Copy tops_tar.gz into directory where you wish to install TOPS as 
2) Decompress tops.tar.gz using gzip (ie. "gzip -d tops.tar.gz")
3) Untar tops.tar (ie. "tar -vfox tops.tar")
4) Copy the licence.h file into the TOPS/src directory as Licence.h (Note.
   that the capital 'L' is important as unix is case sensitive).
5) Edit Makefile to correct values for your system (this is a very
   simple makefile and should be easy to alter - alternatively compile
   and link all of the source files at the command line (eg. "gcc -o Tops
   *.c -lm"), include your favourite optimisation flags - fastmath etc.
6) Executable can be run from the bin directory (eg. "TOPS/bin/Tops")

Using Xtops on a unix machine.

1) Xtops requires tcl/tk these are available free via anonymous ftp from
   sprite.berkeley.edu in the tcl/code directory. Compilation and installation
   of this toolkit is a very simple matter (one of simplest if not the simplest
   I have found).
2) Once installed make sure that "wish" is in your path.
3) The Xtops script can be run from the exe directory (eg. "TOPS/exe/Xtops")

Compiling Tops on a DOS machine.

1) Copy tops.zip into directory where you wish to install Tops
2) Decompress tops.zip using pkunzip (ie. "pkunzip tops.zip)
3) Copy the licence.h file into this directory
4) Compile using any ansi standard C compiler (eg. "tcc -eTops *.c"), include
   your favourite optimisation flags.

Known features:
1) Text and line positions are not saved in the TOPS file and will also be lost
   after optimisation. Add text when you wish to print the cartoon. This will
   be fixed in the next version.
2) Some people have had trouble printing colour (B+W works). This will also
   be fixed in the next version when I work out what is wrong.

Last comment:
Read the documentation!

Appendix 1: TOPS for unix

Contents of tops_tar.gz:

README        bin/          exe/          industry.ps   ps/
academic.ps   def/          ico/          prc/          src/




Topol.xbm     bomb.bm       exclaim       plus.bm       text.bm
Unknown.xbm   draw.bm       noentry       point.bm

Browse.tcl         OKBox.tcl          callHelpOn.tcl     symbolicName.tcl
Execute.tcl        TempFile.tcl       saveDefaults.tcl   tclIndex
Help.tcl           Utils.tcl          setDefaults.tcl


Files.c        Manipulate.c   Postgen.c      Print.c        Tops.h
Makefile       Optimise.c     Postgen.h      Tops.c         Utils.c

Appendix 2: TOPS for DOS

Contents of tops.zip:

Searching ZIP: TOPS.ZIP

 Length  Method   Size  Ratio   Date    Time    CRC-32  Attr  Name
 ------  ------   ----- -----   ----    ----   -------- ----  ----
  27407  DeflatX   3458  88%  04-03-94  12:03  3894dea1 --w-  TOPS.C
  14339  DeflatX   3063  79%  04-03-94  12:08  e066a7f2 --w-  FILES.C
  16542  DeflatX   3717  78%  04-03-94  11:58  a0825d91 --w-  UTILS.C
  21196  DeflatX   5428  75%  04-03-94  12:00  d2b34976 --w-  MANIPULA.C
   5705  DeflatX   1527  74%  04-03-94  12:01  88885e62 --w-  POSTGEN.C
   7672  DeflatX   1807  77%  04-03-94  12:01  4153e9a8 --w-  PRINT.C
  12960  DeflatX   3784  71%  04-03-94  12:02  eae577ab --w-  OPTIMISE.C
   4714  DeflatX   1112  77%  04-03-94  12:03  dddcb9f7 --w-  TOPS.H
    925  DeflatX    252  73%  04-03-94  12:03  ab1180a9 --w-  POSTGEN.H
 210740  DeflatX  52421  76%  27-01-94  16:24  396d901a --w-  TOPS.PS
 ------          ------  ---                                  -------
 322200           76569  77%                                       10

Appendix 3: Obtaining a licence.h file to compile TOPS

As mentioned earlier TOPS has a rudimentary licence protection scheme. To
obtain the licenced header file (Licence.h) you need to complete the 
appropriate licence form and return it to me:

	Dr T. P. Flores
	Mathematical Biology
	The National Institute for Medical Research
	The Ridgeway
	Mill Hill
	NW7 1AA. UK.

Once I receive this form I will send the header file by email, so don't
forget to include your email address. If you have any queries you may
email me at t-flores at nimr.mrc.ac.uk

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