From Jeffrey.Gosper@brunel.ac.uk Wed Jul 23 05:12:59 1997 Received: from himiko.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id EAA17839; Wed, 23 Jul 1997 04:38:35 -0400 (EDT) Received: from castjjg.brunel.ac.uk (actually chem-pc-03.brunel.ac.uk) by himiko.brunel.ac.uk with SMTP-BRUNEL (PP); Wed, 23 Jul 1997 09:38:29 +0100 Date: Wed, 23 Jul 1997 09:35:08 PDT From: Jeffrey Gosper Subject: BABELWin on NT To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCL users, there has been a couple of problems using BABELWin under NT as well as the inclusion of spaces in filenames and directories names. Pat Walters has suggested and simple fix for the spaces problem by enclosing the filenames in double quotes. I am please to report that I have fixed these bugs and a new version of BABELWin (v1.03) for Win95/NT is now located on my ftp server (ftp.brunel.ac.uk in /pc/chem/babelwin.zip). I hope you all enjoy using BABELWin and please drop me a line if you download the program. Also free feel to report any bugs you find in the program. Cheers. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper, Dept. of Chemistry, BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187, facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's home page (molecular animations or Chem-4D): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From rgab@proteus.co.uk Wed Jul 23 09:12:55 1997 Received: from petersgate.proteus.co.uk for rgab@proteus.co.uk by www.ccl.net (8.8.3/950822.1) id IAA18782; Wed, 23 Jul 1997 08:54:35 -0400 (EDT) Received: from Icthus.proteus.co.uk (Icthus [193.115.24.114]) by petersgate.proteus.co.uk (8.6.12/8.6.6) with ESMTP id NAA18599; Wed, 23 Jul 1997 13:54:10 GMT Message-Id: <199707231354.NAA18599@petersgate.proteus.co.uk> From: Richard Bone Date: Wed, 23 Jul 1997 13:54:44 +0100 To: wdi@eros.ccc.uni-erlangen.de Subject: Re: CCL:SMILES databases - ERROR Cc: utz@pharmazie.uni-erlangen.de, CHEMISTRY@www.ccl.net References: <199707211209.MAA11059@petersgate.proteus.co.uk> Apologies: in sorting through my replies, I mis-attributed authorship. The message from Wolfgang Utz concerned a suggestion to use a structure- editor at http://schiele.organik.uni-erlangen.de Sorry again; there was no attempt by anyone to claim authorship for anything they hadn't done. Richard Bone ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Richard G. A. Bone, Ph.D. | | | Senior Computational Chemist | | | Proteus Molecular Design Ltd. | Tel: +44 (0)1625 500555 | | Lyme Green Business Park | Fax: +44 (0)1625 500666 | | Macclesfield, Cheshire | Email: rgab@proteus.co.uk | | United Kingdom SK11 0JL | Web: http://www.proteus.co.uk | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From MAILER-DAEMON@www.ccl.net Wed Jul 23 09:13:01 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA18754; Wed, 23 Jul 1997 08:46:14 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id OAA05700; Wed, 23 Jul 1997 14:46:33 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707231446.ZM5698@eros.ccc.uni-erlangen.de> Date: Wed, 23 Jul 1997 14:46:29 -0600 In-Reply-To: Richard Bone "CCL:SMILES databases - summary" (Jul 21, 12:08) References: <199707211209.MAA11059@petersgate.proteus.co.uk> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Richard Bone Subject: Re: CCL:SMILES databases - ERROR Cc: utz@pharmazie.uni-erlangen.de, CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 21, 12:08, Richard Bone wrote: > Subject: CCL:SMILES databases - summary > > Following up on my enquiry about SMILES databases last week, here is a brief > summary of the responses. > > They fell into 3 different categories (besides the inevitable "please send us > the answers ... "): > > 3) Examples of SMILES databases already 'out there'. > > a) 8,000 small organics. > Contact J. Eric Slone (eslone@patriot.net). > > b) Database of organic compounds (Possibly in SMILES, and probably used for > QSAR). > Contact Lowell Hall (hall@enc.edu); communicated by Tod Story, > (story@ksu.edu). > > c) First 4,000 (non metal-containing) entries of the NCI database. > > Supplied by Wolfgang Utz (utz@pharmazie.uni-erlangen.de). WHAT IS THIS? Wolfgang Utz DID NOT MAKE THESE COMPOUNDS AVAILABLE. He was not involved at all at any step. I (Wolf-D. Ihlenfeldt) did all the steps of the conversion myself, with my own software. Please refrain from claiming authorship for work you do not have participated in! > Available by FTP: > (ftp://schiele.organik.uni-erlangen.de/pub/nci/nci4000.smi.gz) > This is the server I administer. Wolfgang Utz does not even have an account here. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From r.ragno@mail.caspur.it Wed Jul 23 10:12:56 1997 Received: from mail.caspur.it for r.ragno@mail.caspur.it by www.ccl.net (8.8.3/950822.1) id JAA18875; Wed, 23 Jul 1997 09:14:15 -0400 (EDT) Received: from naxos.caspur.it (naxos.caspur.it [193.204.5.8]) by mail.caspur.it (8.8.6/8.8.6) with ESMTP id PAA22986; Wed, 23 Jul 1997 15:13:53 +0200 Received: from localhost (ragno@localhost) by naxos.caspur.it (8.8.6/8.8.6) with SMTP id PAA04532; Wed, 23 Jul 1997 15:13:22 +0200 (MET DST) Date: Wed, 23 Jul 1997 15:13:22 +0200 (MET DST) From: Antonello Mai and Gianluca Sbardella To: ANCHODD , Multiple recipients of OrgChem , chemistry@www.ccl.net, Multiple recipients of OrgList Subject: Electronic address of Dr. Donna L. Romero Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues, My apologies for eventual repetitions. I'm looking for the electronic address of Dr. Donna L. Romero (Upjohn Pharmaceutical Company), but I wasn't able to find it. Do you have any suggestions? Thank you a lot in advance, Gianluca Sbardella *************************************************************** * * * Dr. Antonello Mai, Ph.D. E-mail: r.ragno@caspur.it * * Dr. Gianluca Sbardella, Ph.D. * * * * Dip. Studi Farmaceutici * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * * * * "Il destino e' quel che e', non c'e' scampo piu' per me.." * * (Gene Wilder, "Frankenstein Junior") * * * * "Destiny, destiny, no escaping that for me..." * * (Gene Wilder, "Young Frankenstein") * * * *************************************************************** From MAILER-DAEMON@www.ccl.net Wed Jul 23 11:28:42 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA19550; Wed, 23 Jul 1997 11:02:41 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id RAA06562; Wed, 23 Jul 1997 17:02:52 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707231702.ZM6560@eros.ccc.uni-erlangen.de> Date: Wed, 23 Jul 1997 17:02:48 -0600 In-Reply-To: Richard Bone "CCL:SMILES databases - summary" (Jul 21, 12:08) References: <199707211209.MAA11059@petersgate.proteus.co.uk> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:SMILES databases - summary Cc: webmaster@clogp.pomona.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 21, 12:08, Richard Bone wrote: > Subject: CCL:SMILES databases - summary > In addition, I came across a web-site at Pomona College which contained a > number of files of compounds organised by molecular empirical formula, and > containing their SMILES strings. > > http://clogp.pomona.edu/medchem/chem/master/mf/ghindex.html > > It does not appear to be possible to download these 'in batch', but it is a > most \\formidable\\ source of data. Well, regularly structured websites can be easily milked: Hack, hack, hack... ---------------------------- #!tcl exec wget -r --no-parent http://clogp.pomona.edu/medchem/chem/master/mf/ set filelist [exec find clogp.pomona.edu/medchem/chem/master/mf/ \ -name *.html -print] foreach file $filelist { set fh [open $file] set data [read $fh] while {[regexp -nocase -indices "
smiles\[ \t\n\]+
(\[^\t\n\]*)\[ \t\n\]+
full name\[ \t\n\]*
(\[^\t\n\]*)\[ \t\n\]*" $data dummy sidx nidx]} { lassign $sidx sstart sstop if {$sstart>$sstop} break set smiles [string trim [crange $data $sstart $sstop]] lassign $nidx nstart nstop if {$nstart<$nstop} { set name [string trim [crange $data $nstart $nstop]] } else { set name "Unnamed" } puts "$smiles\t$name" set data [crange $data $nstart+5 end] } close $fh } exec rm -r clogp.pomona.edu ------------------------------------------------- You need tclx, wget and find on your machine to execute this. The program yields 30914 structures in an hour or so (limited by the speed of web access). Is this politically correct to execute? I don't know, the website is not very clear about this. To avoid problems, please do not ask me for the dataset. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From brian@bert.chem.wsu.edu Wed Jul 23 13:12:59 1997 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.8.3/950822.1) id MAA20196; Wed, 23 Jul 1997 12:59:05 -0400 (EDT) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.8.5/8.8.5) with SMTP id JAA05791 for ; Wed, 23 Jul 1997 09:59:04 -0700 (PDT) Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA16388; Wed, 23 Jul 1997 09:49:19 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9707231649.AA16388@bert.chem.wsu.edu> Subject: Software:Equation Editors (Summary) To: CHEMISTRY@www.ccl.net (Computational Chemistry List) Date: Wed, 23 Jul 1997 09:49:19 -0700 (PDT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Here is the summary of responses I got concerning equation editors for Mac using MS Word. Specifically, I was looking for something for equations as Endnote is for references and the most important feature I was looking for was global search and replace (i.e. replace all V(x) with U(t) through a whole document. Hope this helps, -Brian --------------------------------------------------------------------- 1) Expressionist (from Waterloo MapleSoft ) shenkin@still3.chem.columbia.edu (Peter Shenkin) Hi. I've used Expressionist for many years, and it's very good. It's lots better than the equation formatter in MS/Word/5, but I've not tried the one in MS/Word/6. Pieter Stouten I have used (don't have much need for an equation editor at the moment) Expressionist extensively. It is not as seamlessly integrated with MSWord as EndNote (which I heavily use), but it is almost there. One can double-click Expressionist equations and that opens Expressionist. Closing the equation window pastes the updated equation back into Word. Expressionist is very easy to use and gives me enough control to produce equations that are good enough for me. Your mileage may vary, but I'd suggest you give Expressionist a try. --------------------------------------------------------------------- 2) Word Formula Entry Kieran F Lim (Lim Pak Kwan)" before Microsoft signed the deal with MathType to have an object based eqn. editor, Word (version 4) had a formula-entry capability eg something like CMD-OPTION-\ then FRAC to get a fraction .\frac(top,bottom) automatically set up in the old FORMALA GLOSSARY which came FREE with the Word program back in the good ol' days! R.G.Gilbert and S.C.Smith used this formula-entry capability to write EVERY equation in their book "Theory of Unimolecular Reactions ..." so it is a very powerful tool. have a look in your library to see what the final product looks like. (free plug for my friends here) this capability still exists in word 5 and 6, but is now omitted from the manual. and you don't get the FORMALA GLOSSARY any more. I use a mixture of Word's formula entry and a program called Expressionist which is another object based eqn. editor BUT it does the capability to convert all its objects INTO WORD MARKUP FORMULA ENTRIES. Expressionist is made by Prescience fax 1-(415) 882-0530] try Prescience.com as an e-mail or WWW site I do NOT know of any program which has the ability to back-convert word formula entries into an object based eqn for easy editting. personally, I prefer Expressionist, but I recommend you should get either the FULL version of MathType, not the toy version in Word or the Expressionist program or beg, borrow or steal a manual for Word 4 which sets out Word's formula entry capability. --------------------------------------------------------------------- 3) Mathtype (which appears to be the progenitor of the Eqn Ed.) Krzysztof Radacki Try MathType by Design Sicience Inc (http://www.mathtype.com/mathtype/). Guido Germano You can try "MathType", which is an enhanced version of "Equation Editor", but which hasn't all the features you want, or resort to "Scientific Word", a program which looks like a conventional WYSIWIG word processor, but saves the documents in LaTeX format; however, I don't know whether there exist a port for the Mac (I saw it only for Windows so far). Or convert yourself altogether to LaTeX, using for instance "TeXtures", which compiles your document while you write the source. --------------------------------------------------------------------- 4) TeX Editor for Macs Juan Carlos Paniagua I don't know such an equation editor for MSWord, but the TeX editor Scientific Word is, in principle, a good alternative: it has the tools for editing text and formulas in the same window (with e pseudo-wysiwyg look), distinguishes between both types of information, and imports documents produced with other editors via the MS-RTF format. The problem is that some important features, like the translation from RTF, don't work well due to bugs of the software, and the support service of the company that produces it (TCI) is inoperative. You can have a look at http://www.thomson.com/tcisoft/products/mac25.html or http://www.matstat.unit.no/~yngvesv/swp/swp.html victoria@acdlabs.com (Victoria Barclay) There *is* a version of TeX for the Mac; it's called OzTeX. It's shareware (I think) developed by an Australian fellow. clifford@lorentzian.com (Simon Clifford) After I used Word 5's equation editor to type the equations in my thesis I swore never again. Now by choice I use LaTeX. Since you already have experience with this it might be worth using LaTeX on the Mac? There is at least one very good shareware port, called OzTeX, which should be available on any info-mac mirror. --------------------------------------------------------------------- Since it seemed like a number of people were suggesting Expressionist, I sent a query to customer support. ptarr@maplesoft.com (Patti Tarr) Thanks for your interest in Maple software. Any questions you may have can be directed to me at ptarr@maplesoft.com or by calling 1-800-267-6583 ext. 227. There are no compatiblity issues using Expressionist 3.2 with Word 5.1a for Mac. You should have no problems running Expressionist in this environment. me> me> Can I do global search and replace with me> Expressionist? For example, if I have me> a paper full of equations and I me> want to change all the V(r) to U(r) me> through the whole document, can I do me> this? A global search and replace won't work. When you paste an expression into Word, it is considered a graphic rather than text so is not included when Word searches through the document. Unfortunately, there isn't really a way around this. The only alternative to manually make each change. Please let me know if I can be of further assistance. Sincerely, Patti Tarr Waterloo Maple Inc. 1-800-267-6583 ext. 227 ptarr@maplesoft.com ---------------------------------------------------------------------------- Finally, I asked them if it were possible to keep a "library" of equations which could be "Publish/Subscribed" into a word document such that the word document would automatically update if you changed the Expressionist "library". They indicated that this was partially possible in that you could make a library of equations, but that each time you put an equation into Word, it became an independent entity and double-clicking would bring up a new Expressionist document not the original "library". -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | || Biochem/Biophysics | brian@bert.chem.wsu.edu | || \\ WSU || Washington St. Univ| brian_beck@wsu.edu | |\ - *|| 639 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA, USA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From bernhold@tarkovsky.npac.syr.edu Wed Jul 23 18:13:02 1997 Received: from postoffice.npac.syr.edu for bernhold@tarkovsky.npac.syr.edu by www.ccl.net (8.8.3/950822.1) id SAA22606; Wed, 23 Jul 1997 18:10:35 -0400 (EDT) Received: from tarkovsky.npac.syr.edu (tarkovsky-007.npac.syr.edu [128.230.7.175]) by postoffice.npac.syr.edu (8.7.5/8.7.1) with ESMTP id SAA21548; Wed, 23 Jul 1997 18:08:14 -0400 (EDT) Received: from localhost (bernhold@localhost) by tarkovsky.npac.syr.edu (8.8.5/8.7.1) with SMTP id SAA26888; Wed, 23 Jul 1997 18:08:13 -0400 (EDT) Message-Id: <199707232208.SAA26888@tarkovsky.npac.syr.edu> X-Authentication-Warning: tarkovsky.npac.syr.edu: bernhold@localhost didn't use HELO protocol To: "Ping Du" cc: chemistry@www.ccl.net Subject: Re: CCL: CCL:Object-oriented means for computational chemist In-reply-to: <19970722083948.138bb7cb.in@S2> Date: Wed, 23 Jul 1997 18:08:13 -0400 From: "David E. Bernholdt" On Tue, 22 Jul 1997 07:45:08 +0000 "Ping Du" wrote: > Inheritance is pobably the most important feature of > OO design if you would like your program to be extensible and > reusable. I don't entirely agree. Having done OO _design_ and implemented those designs in "non-OO" languages, I believe that the other principles of OO design (abstraction, encapsulation, modularity) are probably more important and more powerful. I have not encountered a case where I felt at a serious disadvantage because the languages I was using did not support inheritance. But in any case, I must stress the importance of design. Looking back, I think that a thorough design phase probably allowed us to find the right abstractions so that inheritance was really not an issue, and we could do what inheritance was required "manually". It also may be a property of the problem to some extent (in our case a broad spectrum of electronic structure methods). -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From ccl@www.ccl.net Wed Jul 23 20:13:04 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id TAA23059; Wed, 23 Jul 1997 19:55:39 -0400 (EDT) Received: from auric.chem.csiro.au for Dave.Winkler@molsci.csiro.au by bedrock.ccl.net (8.8.6/950822.1) id TAA17524; Wed, 23 Jul 1997 19:55:34 -0400 (EDT) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA18471 (5.67b/IDA-1.5 for chemistry@ccl.net); Thu, 24 Jul 1997 09:52:18 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Jul 1997 09:54:30 +1000 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Pi stacking energies Hi, Netters, Can anyone give me an estimate of the contribution to ligand binding energy which may result from an optimum pi-stacking interaction in the active site? I have a tyrosine forming the base of a site and good ligands contain aromatic rings which lie ~3.5 A above the aromatic ring of tyrosine. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Division of Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC, http://www.csiro.au Clayton 3169, Australia http://www.molsci.csiro.au