From owner-chemistry@ccl.net Tue Feb 15 07:02:01 2011 From: "Wolf Ihlenfeldt wdi^-^xemistry.com" To: CCL Subject: CCL: distance matrix Message-Id: <-43948-110215065043-9199-/RtqatJBymwQ3dQICeI8qA]-[server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=000e0cd4d35ccdcfe1049c50c5a8 Date: Tue, 15 Feb 2011 12:50:36 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi{}xemistry.com] --000e0cd4d35ccdcfe1049c50c5a8 Content-Type: text/plain; charset=UTF-8 It the use of the original MACSS keys is not a condition, and you are satisfied with using an alternative screen bit implementation, here is a solution in the form of a tidy Cactvs script (www.xemistry/com/academic, free for academic uses): ---snip--- prop setparam E_SCREEN extended 2 set idx 0 molfile hloop "the_file.sdf" eh { set bits($idx) [ens get $eh E_SCREEN] incr idx } loop i 0 $idx { loop j 0 $idx { set simval [expr [prop compare E_SCREEN $bits($i) $bits($j) tanimoto]/100.0] if {$j==$idx-1} { puts [format "%.2f" $simval] } else { puts -nonewline [format "%.2f " $simval] } } } ---snip--- The results will be very similar to using MACSS keys. On Tue, Feb 15, 2011 at 3:16 AM, amit dong dongamit123~!~gmail.com < owner-chemistry^ccl.net> wrote: > > Hello group, > > I need to calculate a tanimoto coefficient matrix from the MACCS > fingerprints of a set of compounds. Is there any tool that can do it? > Any help will be much appreciated. > > Thanks > AD > > > -- Wolf-D. Ihlenfeldt, Xemistry GmbH www.xemistry.com --000e0cd4d35ccdcfe1049c50c5a8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
It the use of the original MACSS keys is not a condition, and you are s= atisfied with using an alternative screen bit implementation, here is a sol= ution in the form of a tidy Cactvs script (www.xemistry/com/academic, free = for academic uses):

---snip---
prop setparam E_SCREEN extended 2
set idx 0
molfile= hloop "the_file.sdf" eh {=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = set bits($idx) [ens get $eh E_SCREEN]
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 incr idx
}
loop i 0 $idx {
=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 loop j 0 $idx {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 set simval [expr [prop compare E_SCREEN $bits($i) $bits($j)= tanimoto]/100.0]
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 if {$j=3D=3D$idx-1} {
=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 puts [format "%.2f= " $simval]
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 } else {
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 puts -nonew= line [format "%.2f " $simval]
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }
=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 }
}
---snip---

The results w= ill be very similar to using MACSS keys.



On Tue, Feb 15, 2011 at 3:16 AM, amit dong dongamit123~!~gmail.com <owner-chemistry^ccl.net> wrote:

Hello group,

I need to calculate a tanimoto coefficient matrix f= rom the MACCS fingerprints of a set of compounds. Is there any tool that ca= n do it?
Any help will be much appreciated.

Thanks
AD





--
Wolf-D. Ihlenfel= dt, Xemistry GmbH
= www.xemistry.com

--000e0cd4d35ccdcfe1049c50c5a8-- From owner-chemistry@ccl.net Tue Feb 15 08:04:01 2011 From: "Haya Kornweitz hayak _ ariel.ac.il" To: CCL Subject: CCL: Workshop first week of July Message-Id: <-43949-110215074817-19868-zx73J/9iNTKeB127QqyPhA#,#server.ccl.net> X-Original-From: "Haya Kornweitz" Date: Tue, 15 Feb 2011 07:48:13 -0500 Sent to CCL by: "Haya Kornweitz" [hayak::ariel.ac.il] Did someone save the message about the workshop in France in the first week of July? I am interested but I can't find the message. From owner-chemistry@ccl.net Tue Feb 15 08:38:00 2011 From: "Jan Labanowski janl-.-speakeasy.net" To: CCL Subject: CCL: Workshop first week of July Message-Id: <-43950-110215082620-1961-zKXA+06zsVD+dFD7YGaHdg~!~server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 15 Feb 2011 08:26:14 EST MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl%speakeasy.net] Dear Haya, Check: http://www.ccl.net/cgi-bin/ccl/message-new?2011+02+01+005 http://www.ccl.net/chemistry/resources/messages/2011/01/31.009- dir/index.html http://www.ccl.net/cca/info/conferencelist/mess0015788.shtml http://www.ccl.net/cgi-bin/ccl/message-new?2011+02+09+003 http://www.ccl.net/cgi-bin/ccl/message-new?2011+02+08+012 I have an appeal to CCL subscribers and their patrons. PUT THE CONFERENCES/WORKSHOPS on the CCL Conference Page. Please... Do it for your own good. http://www.ccl.net/chemistry/announcements/conferences/index.shtml It does not have to be your own workshop/conference. This service is free (but support is always welcome) and will bust publicity for the workshop and bring participants. Why people do not use this page that much, is quite puzzling to me (unless most workshops are fully funded by some grant and the organizers are actually happy if nobody shows up...). Note, the info about this page is under all of your plain text CCL messages that your receive. Jan From owner-chemistry@ccl.net Tue Feb 15 12:46:00 2011 From: "P.D.Jarowski]![surrey.ac.uk" To: CCL Subject: CCL: Desktop computing Message-Id: <-43951-110215124445-31811-3Gv7iPWagFOS4xQ0m0WzHQ!A!server.ccl.net> X-Original-From: Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_7573C7C772F1CB48A79EA49CDD41DD3DF39C2AB4BBEXMB01CMSsurr_" Date: Tue, 15 Feb 2011 17:44:36 +0000 MIME-Version: 1.0 Sent to CCL by: [P.D.Jarowski]^[surrey.ac.uk] --_000_7573C7C772F1CB48A79EA49CDD41DD3DF39C2AB4BBEXMB01CMSsurr_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGkgYWxsLA0KDQpJIGFtIGludGVyZXN0ZWQgaW4gYnV5aW5nIGEgZGVza3RvcCBwYyB0byBydW4g cmVkaGF0IG9uIGFzIGEgZGVkaWNhdGVkIGNvbXB1dGF0aW9uYWwgY2hlbWlzdHJ5IG1hY2hpbmUg Zm9yIG15IG9mZmljZS4gSSB3aWxsIGJlIHJ1bm5pbmcgdmIyMDAwLCBtb2xwcm8wOSBhbmQgZ2Ft ZXNzLiBJIHdvdWxkIGxvdmUgdG8gaGVhciB5b3VyIHN1Z2dlc3Rpb25zIGZvciBzcGVjcyB0aGF0 IEkgd2lsbCBuZWVkIHRvIHBlcmZvcm0gZmFpcmx5IHJvYnVzdCBhYiBpbml0aW8gY2FsY3VsYXRp b25zLiBJIHdhbnQgdG8gc3BlbmQgYWJvdXQgMTAwMCBVU0QsIHRoYXRzIHRoZSBjYXRjaCEhISBB bnkgaGVscCB3b3VsZCBiZSBncmVhdGx5IGFwcHJlY2lhdGVkLg0KDQpCZXN0LA0KDQpQZXRlcg0K DQoqKipTZW50IHZpYSBSb2FkU3luY8KuIGZvciBBbmRyb2lk4oSiDQo= --_000_7573C7C772F1CB48A79EA49CDD41DD3DF39C2AB4BBEXMB01CMSsurr_ Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 PHNwYW4gc3R5bGU9ImZvbnQtc2l6ZToxMS4wcHQ7IGZvbnQtZmFtaWx5OiZxdW90O0NhbGlicmkm cXVvdDssJnF1b3Q7c2Fucy1zZXJpZiZxdW90OyI+SGkgYWxsLDxicj48YnI+SSBhbSBpbnRlcmVz dGVkIGluIGJ1eWluZyBhIGRlc2t0b3AgcGMgdG8gcnVuIHJlZGhhdCBvbiBhcyBhIGRlZGljYXRl ZCBjb21wdXRhdGlvbmFsIGNoZW1pc3RyeSBtYWNoaW5lIGZvciBteSBvZmZpY2UuIEkgd2lsbCBi ZSBydW5uaW5nIHZiMjAwMCwgbW9scHJvMDkgYW5kIGdhbWVzcy4gSSB3b3VsZCBsb3ZlIHRvIGhl YXIgeW91ciBzdWdnZXN0aW9ucyBmb3Igc3BlY3MgdGhhdCBJIHdpbGwgbmVlZCB0byBwZXJmb3Jt IGZhaXJseSByb2J1c3QgYWIgaW5pdGlvIGNhbGN1bGF0aW9ucy4gSSB3YW50IHRvIHNwZW5kIGFi b3V0IDEwMDAgVVNELCB0aGF0cyB0aGUgY2F0Y2ghISEgQW55IGhlbHAgd291bGQgYmUgZ3JlYXRs eSBhcHByZWNpYXRlZC48YnI+PGJyPkJlc3QsPGJyPjxicj5QZXRlcjxicj48YnI+KioqU2VudCB2 aWEgUm9hZFN5bmPCriBmb3IgQW5kcm9pZOKEojwvc3Bhbj4NCg== --_000_7573C7C772F1CB48A79EA49CDD41DD3DF39C2AB4BBEXMB01CMSsurr_-- From owner-chemistry@ccl.net Tue Feb 15 22:13:00 2011 From: "Gabriel Merino gmerino . quijote.ugto.mx" To: CCL Subject: CCL: XXXVII Congress of Theoretical Chemists of Latin Expression (Quitel 20 Message-Id: <-43952-110215215005-26875-oHIyc6HhGLZaiQ9YcCPTqQ||server.ccl.net> X-Original-From: "Gabriel Merino" Date: Tue, 15 Feb 2011 21:50:01 -0500 Sent to CCL by: "Gabriel Merino" [gmerino.:.quijote.ugto.mx] The XXXVII Congress of Theoretical Chemists of Latin Expression (Quitel 2011) will be held in Riviera Maya, Mexico, from December 4th-9th, 2011. Following its long tradition, during this event, the state of the art of several branches of Theoretical Chemistry will be explored through plenary and invited lectures delivered by experts. It will also provide the opportunity to other members of our community, researchers and students, to present and discuss their work through oral communications and poster sessions Contributions in all areas of methods development and applications in theoretical chemistry are welcome. The venue will be Hotel Barcel Maya Palace Deluxe, which is located in one of the most beautiful beaches in the Mayan Riviera, in the famous Mexican Caribbean. We are certain that the academic program and the attractive location will make Quitel 2011 in Mexico an unforgettable occasion. Presently confirmed invited speakers include: * Alfredo Alexander-Katz (Massachusetts Institute of Technology - USA) * Alan Aspuru-Guzik (Harvard University USA) * Gustavo Aucar (Universidad Nacional del Nordeste, Argentina) * Roberto Car (Princeton University, USA) * Carlos Cardenas (Universidad de Chile, Chile) * Clemence Corminboeuf (cole Polytechnique Fdrale de Lausanne, Swizerland) * Roberto Dovesi (Universit degli Studi di Torino, Italy) * Helio Duarte (Universidade Federal de Minas Gerais, Brazil) * Jorge Garza (Universidad Autonoma Metropolitana-Iztapalapa, Mexico) * Paul Geerlings (Free University of Brussels, Belgium) * Francesc Illas (Universitat de Barcelona, Spain) * Vincent Ortiz (Auburn University, USA) * Patricia Perez (Universidad Andres Bello, Chile) * Mario Piris (Euskal Herriko Unibertsitatea, Spain) * Claude Pouchan (Universit de Pau et des Pays de l'Adour, France) * Maria Joao Ramos (Universidade do Porto, Portugal) * Albeiro Restrepo (Universidad de Antioquia, Colombia) * Andres Reyes (Universidad Nacional de Colombia, Colombia) * Adrian Roitberg (University of Florida, USA) * Angel Rubio (Euskal Herriko Unibertsitatea, Spain) * Nino Russo (University of Calabria, Italy) * Miquel Sola (Universitat de Girona, Spain) * Gustavo Scuseria (Rice University, USA) * William Tiznado (Univeridad Andres Bello, Chile) Further information and registration is available at: http://mty.cimav.edu.mx/quitel2011/index.html e-mail: quitel.2011**gmail.com On behalf of the Quitel Organizing Commitee, Gabriel Merino From owner-chemistry@ccl.net Tue Feb 15 22:52:00 2011 From: "Eli Lam elizabeth.shlam{=}gmail.com" To: CCL Subject: CCL:G: Absolute zero in orbital energies Message-Id: <-43953-110215225123-7803-0QggVih4A0A3ONbozeSTCg*_*server.ccl.net> X-Original-From: "Eli Lam" Date: Tue, 15 Feb 2011 22:51:21 -0500 Sent to CCL by: "Eli Lam" [elizabeth.shlam(~)gmail.com] Hi, I would like to ask about the physical meaning of the absolute zero in orbital energies calculated by gaussian03. I know the orbital energy is of relative meaning, but could I compare the orbital energies of different molecules simply by viewing their energies calculated from gaussian03? Thank you very much! Eli