Announcing a C++ Class Library for Molecular Modeling

Greg Couch %CGL gregc at
Fri Jul 15 20:57:01 EST 1994

Enclosed is the README file for the first release of our C++ class library
for building a molecule object class.  The library is available as a
compressed tar file via anonymous ftp from in pub/otf.tar.Z.
The support classes focus on atoms, bonds, and residues and are designed for
computational chemistry problems that need coordinate information.  In
addition, the library handles reading and writing of Brookhaven Protein
DataBank files and building and traversing molecular connectivity.  We will
be using this library to build molecular visualization tools in the coming
year and are interested in keeping the base classes flexible enough for other
applications.  We welcome any and all feedback.

	Greg Couch
	gregc at

Welcome to the alpha release of the UCSF Computer Graphics Laboratory's
Object Technology Framework (OTF) for molecular modeling and computational

This release just contains the molecule object toolkit.  The IFS (Item
File System), that you may have read about in the Proceedings of the NSF
Scientic Database Projects 1991-1993, will be part of a future release.

The source directory structure is:

	./bin/		source for applications (both developer and end user)
	./lib/		source for linkable libraries
	./doc/		source for documention

The installation tree is the familar:

	${OTFHOME}/bin/		installed programs
	${OTFHOME}/include/	installed include files for libraries
	${OTFHOME}/lib/		installed code libraries and data files for
	${OTFHOME}/man/		installed manual pages

All of the code is written in C++ and was developed using the GNU project's
gcc and libg++.  It was compiled locally with gcc version 2.5.8 and libg++
version 2.5.3.  The C++ is fairly generic, but there are dependencies on the
container classes provided by the libg++ library.  We plan to add support
for other container class libraries in a future release.  g++ 2.5.8 did not
work for us on the NeXT platform and we went back to version 2.5.4.

The Makefile's in the the source hierarchy support three different types
of installation, sysv.install, bsd.install, and osf1.install.  You should
be able to do a "make xxxx.install" in this directory and have everything
install correctly.

There is a mailing list, otf at for reporting bugs and for
general discussion of the OTF.  Send mail to otf-request at to
be put on the mailing list.  We are especially interested in hearing
about what functionality you think should be added.

	Greg Couch, gregc at
	March 1994

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