SUMMARY - Software for combinatorial generation of structures

Dear CCL Readers,
      here you have a summary of my recent request for a software for
 combinatorial generation of structures.
      Some of the answers deal with virtual synthesis and are more
 sophisticated than I had in mind. The kind of structures I am
 planning to generate are related by a common heterocyclic skeleton
 containing different groups (N(CH3)2, NO2, CH3, OCH3, etc) connected
 to it. They are not related by a chemical reaction.
       The conversion of the AUTOBUILD program to work under Linux
 would be complicated by the fact that most of the changes would
 involve graphical routines and I wouldn't know how to convert the
 routines from Silicon Graphics to Linux.
       I have decided to generate my structures using SMILES and
 then converting them to XYZ.
       Once again I would like to say thanks for all the answers
 I have received. Sincerely yours,
                              Gustavo L.C. Moura
                          gustavo:at:mercury.chem.pitt.edu
 --------------------------------------------------------------------------------
 ORIGINAL MESSAGE
 Dear CCL Readers,
      I am looking for a program capable of generating structures of
 molecules in a combinatorial way. In other words, I want to be able to give a
 template and a series of fragments to the program and having the program to
 generate all the structures that can be obtained by connecting these
 fragments
 to the template. The program should be able to write the final structures
 in a
 format that can be converted to be read by the MOPAC program for optimization
 of geometry. I would like to be able to run such a program in a machine with
 Linux or, perhaps, Windows operating systems. Any suggestions are welcome,
 but
 I would prefer a free for academia program.
      I have already found in the INTERNET the AUTOBUILD program that is
 distributed by the INTERPROBE CHEMICAL SERVICES company
 (http://www.interprobe.co.uk/inter/interprobe.html).
 Unfortunately, the
 AUTOBUILD program works only on Silicon Graphics machines.
      Thank you very much in advance. Sincerely yours,
                                              Gustavo L.C. Moura
                                          gustavo:at:mercury.chem.pitt.edu
 ---------------------------------------------------------------------------------
 Konrad Koehler <konrad.koehler  \\at//  karobio.se>
 Dear Gustovao,
 One possible solution relying on perlmol (http://www.perlmol.org/) and SMARTS
 substructure notation
 (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html)
 to define
 reactant
 functional groups may be found on the following web site:
 http://www.perlmol.org/examples/
 I would be interested in reading a summary of your responses.  Best regards,
 Konrad
 ---------------------------------------------------------------------------------
 Armel Le Bail <alb  \\at//  cristal.org>
 See a list of programs in this paper;
 http://journals.iucr.org/b/issues/2002/04/00/bk0108/bk0108.pdf
 Though they may not completely fulfill your dreams...
 For inorganic compounds, see:
 http://journals.iucr.org/j/issues/2005/02/00/cg5019/cg5019.pdf
 and references inside.
 Best wishes,
 Armel Le Bail
 ----------------------------------------------------------------------------------
 Jeremy R. Greenwood <jgreenw  \\at//  speakeasy.net>
 Dear Gustavo,
 The forthcoming Schrodinger release later this year will include a new
 product,
 CombiGlide, which can do all of the above and more (with some intelligent
 machinery
 > from ligprep to cut down on knotting for example, handle pKa,
 stereochemistry
 tautomerism, etc.). Primary platform is Linux. GUI or command-line.
 Dicounted but not free for academic research, though it's free for teaching.
 Hope this helps,
 Jeremy
 -----------------------------------------------------------------------------------
 John Bushnell <bushnell  \\at//  chem.ucsb.edu>
 Hi,
    I took a quick look at the site below, and you can freely download
 the source code for Autobuild.  It gives all kinds of errors if I try:
 g77 autobuild.f
 on a Linux machine here, but it may be possible to clean up the code
 so that it will compile correctly, and/or play with compiler flags to
 make this work.
    So...if you've got somebody who is familiar with Fortran, you could
 probably get this to work.  But it will require some time and effort.
           - John
 ------------------------------------------------------------------------------------
 Tim Aitken <taitken  \\at//  accelrys.com>
 Dear Dr Moura,
 I read with interest your posting on CCL net regarding combinatorial tools
 for library enumeration. We offer several solutions for this purpose,
 using either reaction based or generic core (Markush) enumeration and have
 software that operates on Linux, Solaris and Windows. The Combichem
 Enumeration Components sound like they may be the right thing for you :
 http://www.accelrys.com/products/accord/accordproducts/combichem_enumeration.html
 Please contact me if you would like any further information, or discuss
 specific requirements. If our solutions do not meet your needs I may be
 able to point you in a more appropriate direction.
 Best regards,
 Tim
 -------------------------------------------------------------------------------------
 Gyorgy Pirok <pirok  \\at//  chemaxon.com>
 Dear Gustavo,
 I would like to draw your attention to a Java-based virtual synthesis
 program of ChemAxon called Reactor. It is fast (up to 500k reactions/hour),
 flexible (able to batch process reactions creating combichem libraries), and
 smart (evaluates reactions containing chemo-, regio- and stereoselectivity
 info). It supports a wide range of reaction an molecule formats, so I am
 sure that you can easily integrate it with MOPAC. It is also worth to
 mention, that all ChemAxon tools including Reactor is FREE for the academia
 and include API. Some useful links:
 Latest scientific poster about Reactor:
 http://www.chemaxon.com/conf/Making_Real_molecules_in_virtual_space.pdf
 Related user documentation:
 http://www.jchem.com/index.html?content=doc/user/Reactor.html
 You can download it from the www.chemaxon.com web site and require a FREE
 Academic license in an email.
 I hope, that you will have fun with it.
 Best regards,
 Gyvrgy