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.
Tom
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
tops.tar.gz
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:
TOPS:
README bin/ exe/ industry.ps ps/
academic.ps def/ ico/ prc/ src/
TOPS/bin:
Tops@
TOPS/def:
TOPS/exe:
Xtops*
TOPS/ico:
Topol.xbm bomb.bm exclaim plus.bm text.bm
Unknown.xbm draw.bm noentry point.bm
TOPS/prc:
Browse.tcl OKBox.tcl callHelpOn.tcl symbolicName.tcl
Execute.tcl TempFile.tcl saveDefaults.tcl tclIndex
Help.tcl Utils.tcl setDefaults.tcl
TOPS/ps:
tops.ps
TOPS/src:
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
London
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
