From chemistry-request@ccl.net Fri Jun 19 05:35:14 1992 Date: Fri, 19 Jun 92 4:07:26 EDT From: Dongchul Lim Subject: application of graph theory in chemistry To: chemistry@ccl.net (Computational Chemistry) Status: R Hi, I want to represent a chemical structure as graph, where the atoms are nodes and the bonds are edges. I think graph theory has been widely applied in structural searching, perception, etc. I want to know what is the good point to start and if there're any publicly available softwares that use graph theory. -dl From chemistry-request@ccl.net Fri Jun 19 11:28:26 1992 Date: Fri, 19 Jun 92 09:50:38 EDT From: states@ncbi.nlm.nih.GOV (David States) Subject: Re: application of graph theory in chemistry To: chemistry@ccl.net, lim@omega.chem.yale.EDU Status: R |> I want to represent a chemical structure as graph, where the atoms |> are nodes and the bonds are edges. I think graph theory has been |> widely applied in structural searching, perception, etc. |> I want to know what is the good point to start and if there're any |> publicly available softwares that use graph theory. |> -dl (lim@omega.chem.yale.edu) The CarbBank, complex carbohydrate structure group at the University of Georgia has done some interesting work using subgraph pattern matching to retrieve complex carbohydrate structures. You can reach them by E-mail at CarbBank @ UGA.Bitnet or they have deposited software, databases, and documentation with the National Library of Medicine. The latter can be retrieved by anonymous ftp from the host: ncbi.nlm.nih.gov in the subdirectory: repository/CarbBank/... David States National Center for Biotechnology Information / National Library of Medicine From chemistry-request@ccl.net Fri Jun 19 11:28:30 1992 Date: Fri, 19 Jun 92 09:48:45 -0400 From: roberto@medusa.boston.sgi.COM (Roberto Gomperts) Subject: Re: MOPAC 6 bug To: system@alchemy.chem.utoronto.CA, chemistry@ccl.net Status: R > This bug was already reported in QCPE Bulletin Vol. 12, No. 1, page 5, > and for those who didn't see it, the solution is (envelope please...) I had not seen this solution. It seems very similar to what George Fitzgerald was suggesting. I implemented a slightly different solution on SGI's version of Mopac. Since MULLIK.f is the offending routine I decided to tackle the problem there. I use a scratch area (that I have been using as a REAL scratch area for some multiprocessing sections of the code). So, in MULLIK.f I declare: common /sgi_scrch/ scr_sgi(3*morb2) (some where after the inclusion of SIZES) and then, almost at the end of the routine, starting at the call to DENSIT I use "scr_sgi" instead of C: CALL DENSIT(VECS,NORBS,NORBS,NCLOSE,NOPEN,FRACT,scr_sgi,2) LINEAR=(NORBS*(NORBS+1))/2 DO 100 I=1,LINEAR 100 scr_sgi(I)=scr_sgi(I)*STORE(I) SUMM=0.D0 DO 130 I=1,NORBS SUM=0 DO 110 J=1,I 110 SUM=SUM+scr_sgi(IFACT(I)+J) DO 120 J=I+1,NORBS 120 SUM=SUM+scr_sgi(IFACT(J)+I) SUMM=SUMM+SUM 130 scr_sgi(IFACT(I+1))=SUM CALL VECPRT(scr_sgi,NORBS) RETURN END Advantages of this approach: - No extra transfer of data (back and forth) to temporary arrays - If by any chance MULLIK is going to be called from other places of the program, no precautions have to be taken to protect C in /VECTOR/ Disadvantage: - Need extra space (In SGI's version if use this space anyway...) I will be passing these suggestions to Richard Counts at QCPE.. Roberto Gomperts roberto@sgi.com phone: (508) 562 4800 Fax: (508) 562 4755 From chemistry-request@ccl.net Fri Jun 19 18:24:47 1992 Date: Fri, 19 Jun 92 15:13:56 MDT From: hogue@sdisu1.den.mmc.COM (Pat Hogue) Subject: MNDO interactions To: chemistry@ccl.net Status: RO Dear netter: Is anyone out there familiar with "through space" techniques to study the approach of one molecule to another? I want to try this using oranic molecules "bonded" to inorganic molecules. Any advice or experience will be appreciated.