other MMTK-like languages/extensions/classes

Andrew Dalke dalke@ks.uiuc.edu
Wed, 9 Jul 97 17:49:29 -0500


I want to point out some of the other work being done in developing
a language framework for molecular modeling being done be some
other places.

1) Someone here pointed out something called the Molecular Operating
Environment (MOE) from the Chemical Computing Group, Inc. in Montreal,
Canada (http://www.chemcomp.com/).  They developed their own language
called SVL for doing work in chemical structures (see http://www.chemcomp.com/feature/svl.htm).

I was thinking MMTK could get some ideas of what kind of functions
could be useful.  There aren't many code examples, so there isn't
much we can get out of it, but it is (IMHO) always nice to know
what other people are working on.

The code that is present is okay, but Python with the Numeric
extensions looks better, and without Python's versatility (no
classes, no associative arrays, no ...).


2) Two Tcl-based extensions for molecular modeling that could be useful
are:
 the Tcl extensions I wrote for VMD (http://www.ks.uiuc.edu/Research/vmd/
 the Tcl extensions from MSI for Cerius2 at
     http://www.msi.com/support/sdk/index.html

I personally like VMD's better than Cerius2's because of how I
implemented atom selections as objects (so you can pass a list
of atoms easily to a routine) whereas they stuck with the standard
Tcl way of passing around very large strings of labels, but YMV.


3) As one last one, that I don't have a URL for, is the Python-based
work done at UCSF for Chimera, their next generation structure
viewer/analysis program.  Perhaps one of them subscribes to this
list and can pass a pointer along?  I've seen a demo of it and it
looked powerful.


Also, there was a recent post to the computational chemistry mailing
list with some other relevant information.  I see Konrad contributed
information to it, but others here might not read CCL:

From:    Walter Koppensteiner <walter@came.sbg.ac.at>
Date:    Wed Jul  9,  4:26pm +0200
To:      CCL <chemistry@infomeister.osc.edu>

here is a summary of class libraries and other object oriented
approaches to biopolymer representation.

Molecular Mechanics Toolkit: 
    Phyton
    http://starship.skyport.net/crew/hinsen/mmtk.html
    program library for molecular modelling applications
    
Bioperl Project:
    Perl
    http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html
    handling of biosequence and alignment data
    current modules: Bio::PreSeq and Bio::UnivAln
    
bioWidgets Consortium:
    java
    http://fruitfly.berkeley.edu/biowidgets/
    graphical displays of genome data
     
NAMD/VMD:
    C++
    http://www.ks.uiuc.edu/Research/vmd/
    Molecular Dynamics and visulatization of biomolecules
    
Open Molecule Foundation (OMF)
    Java
    http://www.ch.ic.ac.uk/omf/
    several java class libraries and related stuff
    
PDBlib:
    C++
    http://www.sdsc.edu/pb/pdblib/pdblib.html
    class library is designed for representing macromolecular structure
    
JaMBW: Java Molecular Biology Workbench
    Java
    http://www.embl-heidelberg.de/JaMBW/
    
Birkbeck Bioinformatics Class Library
    C++
    http://www.cryst.bbk.ac.uk/classlib/
    object-oriented software library for use by the bioinformatics and
    molecular modelling communities
    
SCL (Sequence Class Library):
    C++
    http://Molbiol.grumed.fu-berlin.de/scl/
    C++ class library for sequence analysis in molecular biology
    
OTF (Object Technology Framework):
    C++
    http://www.cgl.ucsf.edu/home/otf/
    C++ classes for biochemical application developers
    
Democritos:
    C++
    http://gserv1.dl.ac.uk/CBMT/democ/HOME.html
    C++ classes for bioinformatics and computational chemistry

molbio++:
    C++
    ftp://golgi.harvard.edu/pub/robinson
    ftp://ftp.ebi.ac.uk/pub/software/unix
    C++ library for molecular biosequence analysis


						Andrew Dalke
						dalke@ks.uiuc.edu
P.S.
  Outgoing mail at dalke@ks.uiuc.edu seems to be broken so my
apologizes if you see this email twice.