From owner-chemistry@ccl.net Wed Mar 14 08:20:01 2007 From: "Richard Casey rcasey:+:rmcbiosciences.com" To: CCL Subject: CCL: Renaming Stereomers in SDF file Message-Id: <-33790-070313184023-9727-Wh7ZtUHGMS9GJyBZ/PxeOw---server.ccl.net> X-Original-From: "Richard Casey" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 13 Mar 2007 16:10:18 -0600 MIME-Version: 1.0 Sent to CCL by: "Richard Casey" [rcasey!^!rmcbiosciences.com] Latha, If I understand what you are trying to do, you might want to use awk or sed (http://www.vectorsite.net/tsawk.html; http://www.grymoire.com/Unix/Sed.html) rather than vi. The form of the regular expressions for making substitutions would depend on the exact nature of the strings you're renaming. Regards, Richard RMC Biosciences ----- Original Message ----- > From: "Prema latha Mallipeddi plmallip~!~mail.uh.edu" To: "Casey, Richard " Sent: Tuesday, March 13, 2007 2:10 PM Subject: CCL: Renaming Stereomers in SDF file > > Sent to CCL by: "Prema latha Mallipeddi" [plmallip++mail.uh.edu] > Can anyone help me find a "Vi command" or an "Text editing idea"; i need > to rename duplicate names repeating in an SDF file with chemical > compounds. I would have used cerius2 or catalyst, but these platforms > aren't accepting SD files with morethan 4000 compounds and some of my SD > files have more than 20000 compounds (Splitting the SDfile doesn't serve > my purpose) > > > Thanks & regards, > Latha.> > > > From owner-chemistry@ccl.net Wed Mar 14 08:54:01 2007 From: "Gustavo Seabra gustavo.seabra _ gmail.com" To: CCL Subject: CCL: Renaming Stereomers in SDF file Message-Id: <-33791-070314070601-15171-4Tp7HZ5ilwgcBnFeeMA/3g*o*server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 14 Mar 2007 06:36:28 -0400 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra{=}gmail.com] Prema latha Mallipeddi plmallip~!~mail.uh.edu wrote: > Sent to CCL by: "Prema latha Mallipeddi" [plmallip++mail.uh.edu] > Can anyone help me find a "Vi command" or an "Text editing idea"; i need to rename duplicate names repeating in an SDF file with chemical compounds. I would have used cerius2 or catalyst, but these platforms aren't accepting SD files with morethan 4000 compounds and some of my SD files have more than 20000 compounds (Splitting the SDfile doesn't serve my purpose) > > > Thanks & regards, > Latha. > Sounds like a work for Sed or Awk. Try 'man sed', or 'man awk' for details. Gustavo. From owner-chemistry@ccl.net Wed Mar 14 10:00:01 2007 From: "Vincent Xianlong Wang xloongw- -yahoo.com" To: CCL Subject: CCL: Renaming Stereomers in SDF file Message-Id: <-33792-070314095723-7400-Go2tmmv4z0ex0XKpXuupvA#%#server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 14 Mar 2007 06:56:54 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw|a|yahoo.com] Hi Latha, Not sure what exactly you want to do, but the following command may be helpful to you. perl -pi -e 's/old_name/new_name/g' filename. Best regards, Xianlong --- "Prema latha Mallipeddi plmallip~!~mail.uh.edu" wrote: > > Sent to CCL by: "Prema latha Mallipeddi" > [plmallip++mail.uh.edu] > Can anyone help me find a "Vi command" or an "Text > editing idea"; i need to rename duplicate names > repeating in an SDF file with chemical compounds. I > would have used cerius2 or catalyst, but these > platforms aren't accepting SD files with morethan > 4000 compounds and some of my SD files have more > than 20000 compounds (Splitting the SDfile doesn't > serve my purpose) > > > Thanks & regards, > Latha. > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the () > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST() ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/ From owner-chemistry@ccl.net Wed Mar 14 10:59:01 2007 From: "Van Dam, HJJ \(Huub\) h.j.j.vandam_-_dl.ac.uk" To: CCL Subject: CCL: sutton-chen potential DLPOLY Message-Id: <-33793-070314105723-698-ydYI9r1F1OvkpDM+uEj6Qg-,-server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 14 Mar 2007 14:14:38 -0000 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam=-=dl.ac.uk] Hi Sabri, Below is the answer to your query as given to me by Bill Smith who is heading the DL_POLY programme at Daresbury Laboratory. I hope this answers your question sufficiently. Best wishes, Huub ========================================================== Huub van Dam (h.j.j.vandam]-[dl.ac.uk, +44-1925-603933) ========================================================== -----Original Message----- > From: Smith, W (Bill) It is quite possible that A LJ potential will give a good account of the structure of silver as it has a hexagonal close packed structure, which is what the LJ potential also favours. However the LJ potential is a simple pair potential, while the Sutton-Chen potential is a many body potential, which will have properties not shared by LJ. The most important of these is the elastic behaviour and the response to stress. If you want to give a faithful decription of metal properties, you should always prefer a many body potential. The UFF potential should only be considered as an alternative if it has many body terms. Also a lot of smart people have spent a lot of time deriving potentials for metals of the Finnis-Sinclair (e.g. Sutton-Chen) and similar embedded-atom kinds, which is something in their favour! The specification of the Sutton Chen potential in the DL_POLY FIELD file is fully described in the user manual. There's no point in repeating it here. Life is too short! -----Original Message----- > From: owner-chemistry]-[ccl.net [mailto:owner-chemistry]-[ccl.net] Sent: 13 March 2007 19:00 To: Vandam, Huub Subject: CCL: sutton-chen potential DLPOLY Sent to CCL by: "sabri alkis" [alkis|ufl.edu] Hi everyone, I am trying to explain the Ag-Ag interactions with DLPOLY program. I found a L-J potential from literature. It gives good agreement with the experimental findings. Do I have to use sutton-chen potential or is it OK to explain metal-metal interactions with the L-J potential? How do we describe the Sutton-chen potential in a FIELD file? Is it by default? Do we have to explain all the metal-metal interactions with Sutton-Chen? What is the advantage of this potential? Is it also OK to explain the metal-metal interactions with UFF potential? Does anybody have an idea? Best wishes and thanks.. From owner-chemistry@ccl.net Wed Mar 14 12:25:00 2007 From: "graham.mullier(!)syngenta.com" To: CCL Subject: CCL: Renaming Stereomers in SDF file Message-Id: <-33794-070314121633-29167-pGiIiKfwzWb63gvSFJXC3Q+*+server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 14 Mar 2007 15:16:04 -0000 MIME-Version: 1.0 Sent to CCL by: [graham.mullier%%syngenta.com] It's an awk or perl problem, if I've understood you right (particularly as you mention files of 20k or so entries) if you don't care what the names of things are but just want uniqueness then simply replace the name field for all the entries with a simple integer if you want to retain the (duplicated) portion of the name but then force uniqueness, add a suffix, so A A B B ... become A1 A2 B1 B2 ... etc but writing the code is your job, I think, especially as my examples above are imperfectly defined. For example, if "A2" already exists elsewhere in the file, the suffix suggestion will create a duplicate. Why not start by writing some code that looks for and reports duplicated names in an SD file, then modify it into something that fixes the problem? Graham -----Original Message----- --- "Prema latha Mallipeddi plmallip~!~mail.uh.edu" wrote: > > Sent to CCL by: "Prema latha Mallipeddi" > [plmallip++mail.uh.edu] > Can anyone help me find a "Vi command" or an "Text > editing idea"; i need to rename duplicate names > repeating in an SDF file with chemical compounds. I > would have used cerius2 or catalyst, but these > platforms aren't accepting SD files with morethan > 4000 compounds and some of my SD files have more > than 20000 compounds (Splitting the SDfile doesn't > serve my purpose) > > > Thanks & regards, > Latha. From owner-chemistry@ccl.net Wed Mar 14 22:09:00 2007 From: "Manish Sud msud^-^san.rr.com" To: CCL Subject: CCL: New release of MayaChemTools package... Message-Id: <-33795-070314220632-12505-sPFEEi2AzN259x+gsXAKzg^server.ccl.net> X-Original-From: "Manish Sud" Date: Wed, 14 Mar 2007 22:06:29 -0400 Sent to CCL by: "Manish Sud" [msud,+,san.rr.com] A new release of MayaChemTools, a growing collection of Perl scripts to support computational discovery needs, is available as free software; you can redistribute it and/or modify it under the terms of the GNU LGPL. New scripts: o InfoPDBFiles.pl o ExtractFromPDBFiles.pl o ModifyPDBFiles.pl o InfoSequenceFiles.pl o ExtractFromSequenceFiles.pl o AnalyzeSequenceFilesData.pl o InfoNucleicAcids.pl And miscellaneous changes to existing scripts. For further details about the scripts and to download the package, please visit www.MayaChemTools.org. Happy scripting. And your comments and suggestions are welcome. Manish Sud msud*san.rr.com