From owner-chemistry@ccl.net Fri Oct 23 03:33:00 2009 From: "Vincent Leroux vincent.leroux . loria.fr" To: CCL Subject: CCL: Multi SDF to many files in folder Message-Id: <-40516-091023032423-26224-gvYzmRPICXn7A6GVaHdnhA]|[server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Oct 2009 09:24:08 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux!^!loria.fr] Hi Chi, Be very careful with scripts that generates a lot a files named from content. Imagine what could happen if one of the molecules has the same name as the parent multi file... or worse, there are many molecules with '../' in their name... Once you are sure there is no such problem, you can try: mkdir childs cd childs awk ' (i==0) {f=$0; if (f=="") f=/dev/null; print $0 > f; i=1; next} (i==1) {print $0 >> f; if ($0=="$$$$") i=0} ' ../parent.sdf Regards, VL c p Mpamhanga chido.mpamhanga,+,gmail.com a écrit : > Sent to CCL by: "c p Mpamhanga" [chido.mpamhanga-*-gmail.com] > Hi all, > > Does anyone have a script to split an SDFfile into single sdfs named after each after each individual molecule as specified in first line of parent multi file? (I have written one but it seems not too robust) > > Cheers > > Chi > > e.g. below files names would be 241.sdf and 355.sdf > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 241 > OpenBabel10220916392D > > 20 20 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 > 0.0000 0.0000 0.0000 Cl 0 0 0 0 0 > 1 2 1 0 0 0 > 2 3 1 0 0 0 > 3 4 1 0 0 0 > 3 6 1 0 0 0 > 4 5 1 0 0 0 > 6 7 1 0 0 0 > 7 8 1 0 0 0 > 8 9 1 0 0 0 > 9 10 2 0 0 0 > 9 11 1 0 0 0 > 11 16 1 0 0 0 > 11 12 2 0 0 0 > 12 13 1 0 0 0 > 13 14 2 0 0 0 > 13 20 1 0 0 0 > 14 15 1 0 0 0 > 14 19 1 0 0 0 > 15 16 2 0 0 0 > 16 17 1 0 0 0 > 17 18 1 0 0 0 > M END > $$$$ > 355 > OpenBabel10220916392D > > 22 23 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 N 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 0.0000 0.0000 0.0000 C 0 0 0 0 0 > 1 2 1 0 0 0 > 2 3 1 0 0 0 > 3 4 1 0 0 0 > 3 6 1 0 0 0 > 4 5 1 0 0 0 > 6 7 1 0 0 0 > 7 8 1 0 0 0 > 8 9 1 0 0 0 > 9 10 2 0 0 0 > 9 11 1 0 0 0 > 11 16 1 0 0 0 > 11 12 1 0 0 0 > 11 17 1 0 0 0 > 12 13 1 0 0 0 > 13 14 1 0 0 0 > 14 15 1 0 0 0 > 15 16 1 0 0 0 > 17 22 1 0 0 0 > 17 18 1 0 0 0 > 18 19 1 0 0 0 > 19 20 1 0 0 0 > 20 21 1 0 0 0 > 21 22 1 0 0 0 > M END > > From owner-chemistry@ccl.net Fri Oct 23 09:28:01 2009 From: "Chido Mpamhanga chido.mpamhanga[#]gmail.com" To: CCL Subject: CCL: Multi SDF to many files in folder Message-Id: <-40517-091023065214-13326-WzPAl+q2ObipMAJqZsUfWA_-_server.ccl.net> X-Original-From: Chido Mpamhanga Content-Type: multipart/alternative; boundary=00151758ac46b04fb10476966b68 Date: Fri, 23 Oct 2009 09:58:50 +0100 MIME-Version: 1.0 Sent to CCL by: Chido Mpamhanga [chido.mpamhanga(-)gmail.com] --00151758ac46b04fb10476966b68 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you VL, for the awk sdf file splitter... On Fri, Oct 23, 2009 at 8:24 AM, Vincent Leroux vincent.leroux . loria.fr < owner-chemistry/a\ccl.net> wrote: > > Sent to CCL by: Vincent Leroux [vincent.leroux!^!loria.fr] > Hi Chi, > > Be very careful with scripts that generates a lot a files named from > content. Imagine what could happen if one of the molecules has the same n= ame > as the parent multi file... or worse, there are many molecules with '../'= in > their name... > > Once you are sure there is no such problem, you can try: > > mkdir childs > cd childs > awk ' > (i=3D=3D0) {f=3D$0; if (f=3D=3D"") f=3D/dev/null; print $0 > f; i=3D1; ne= xt} > (i=3D=3D1) {print $0 >> f; if ($0=3D=3D"$$$$") i=3D0} > ' ../parent.sdf > > Regards, > VL > > > > c p Mpamhanga chido.mpamhanga,+,gmail.com a =E9crit : > > Sent to CCL by: "c p Mpamhanga" [chido.mpamhanga-*-gmail.com] >> Hi all, >> >> Does anyone have a script to split an SDFfile into single sdfs named aft= er >> each after each individual molecule as specified in first line of parent >> multi file? (I have written one but it seems not too robust) >> >> Cheers >> >> Chi >> >> e.g. below files names would be 241.sdf and 355.sdf >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> 241 >> OpenBabel10220916392D >> >> 20 20 0 0 0 0 0 0 0 0999 V2000 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 Cl 0 0 0 0 0 >> 1 2 1 0 0 0 >> 2 3 1 0 0 0 >> 3 4 1 0 0 0 >> 3 6 1 0 0 0 >> 4 5 1 0 0 0 >> 6 7 1 0 0 0 >> 7 8 1 0 0 0 >> 8 9 1 0 0 0 >> 9 10 2 0 0 0 >> 9 11 1 0 0 0 >> 11 16 1 0 0 0 >> 11 12 2 0 0 0 >> 12 13 1 0 0 0 >> 13 14 2 0 0 0 >> 13 20 1 0 0 0 >> 14 15 1 0 0 0 >> 14 19 1 0 0 0 >> 15 16 2 0 0 0 >> 16 17 1 0 0 0 >> 17 18 1 0 0 0 >> M END >> $$$$ >> 355 >> OpenBabel10220916392D >> >> 22 23 0 0 0 0 0 0 0 0999 V2000 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 1 2 1 0 0 0 >> 2 3 1 0 0 0 >> 3 4 1 0 0 0 >> 3 6 1 0 0 0 >> 4 5 1 0 0 0 >> 6 7 1 0 0 0 >> 7 8 1 0 0 0 >> 8 9 1 0 0 0 >> 9 10 2 0 0 0 >> 9 11 1 0 0 0 >> 11 16 1 0 0 0 >> 11 12 1 0 0 0 >> 11 17 1 0 0 0 >> 12 13 1 0 0 0 >> 13 14 1 0 0 0 >> 14 15 1 0 0 0 >> 15 16 1 0 0 0 >> 17 22 1 0 0 0 >> 17 18 1 0 0 0 >> 18 19 1 0 0 0 >> 19 20 1 0 0 0 >> 20 21 1 0 0 0 >> 21 22 1 0 0 0 >> M END >> >> >> > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --00151758ac46b04fb10476966b68 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you VL,
for the awk sdf file splitter...



On Fri, Oct 23, 2009 at 8:24 AM, Vincent Leroux vincent.le= roux . loria.fr <owner-chemistry/a\ccl.net> wrote:

Sent to CCL by: Vincent Leroux [vincent.leroux!^!loria.fr]
Hi Chi,

Be very careful with scripts that generates a lot a files named from conten= t. Imagine what could happen if one of the molecules has the same name as t= he parent multi file... or worse, there are many molecules with '../= 9; in their name...

Once you are sure there is no such problem, you can try:

mkdir childs
cd childs
awk '
(i=3D=3D0) {f=3D$0; if (f=3D=3D"") f=3D/dev/null; print $0 > f= ; i=3D1; next}
(i=3D=3D1) {print $0 >> f; if ($0=3D=3D"$$$$") i=3D0}
' ../parent.sdf

Regards,
VL



c p Mpamhanga chido.mpamhanga,+,gmail.com a =E9crit :

Sent to CCL by: "c p Mpamhanga" [chido.mpamhanga-*-gmail.com]
Hi all,

Does anyone have a script to split an SDFfile into single sdfs named after = each after each individual molecule as specified in first line of parent mu= lti file? (I have written one but it seems not too robust)

Cheers

Chi

e.g. below =A0files names would be 241.sdf and 355.sdf
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
241
=A0OpenBabel10220916392D

=A020 20 =A00 =A00 =A00 =A00 =A00 =A00 =A00 =A00999 V2000
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 N =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 N =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 O =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 O =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 N =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 Cl =A00 =A00 =A00 =A00 =A00
=A01 =A02 =A01 =A00 =A00 =A00
=A02 =A03 =A01 =A00 =A00 =A00
=A03 =A04 =A01 =A00 =A00 =A00
=A03 =A06 =A01 =A00 =A00 =A00
=A04 =A05 =A01 =A00 =A00 =A00
=A06 =A07 =A01 =A00 =A00 =A00
=A07 =A08 =A01 =A00 =A00 =A00
=A08 =A09 =A01 =A00 =A00 =A00
=A09 10 =A02 =A00 =A00 =A00
=A09 11 =A01 =A00 =A00 =A00
=A011 16 =A01 =A00 =A00 =A00
=A011 12 =A02 =A00 =A00 =A00
=A012 13 =A01 =A00 =A00 =A00
=A013 14 =A02 =A00 =A00 =A00
=A013 20 =A01 =A00 =A00 =A00
=A014 15 =A01 =A00 =A00 =A00
=A014 19 =A01 =A00 =A00 =A00
=A015 16 =A02 =A00 =A00 =A00
=A016 17 =A01 =A00 =A00 =A00
=A017 18 =A01 =A00 =A00 =A00
M =A0END
$$$$
355
=A0OpenBabel10220916392D

=A022 23 =A00 =A00 =A00 =A00 =A00 =A00 =A00 =A00999 V2000
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 N =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 O =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 O =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A0 =A00.0000 =A0 =A00.0000 =A0 =A00.0000 C =A0 0 =A00 =A00 =A00 =A00
=A01 =A02 =A01 =A00 =A00 =A00
=A02 =A03 =A01 =A00 =A00 =A00
=A03 =A04 =A01 =A00 =A00 =A00
=A03 =A06 =A01 =A00 =A00 =A00
=A04 =A05 =A01 =A00 =A00 =A00
=A06 =A07 =A01 =A00 =A00 =A00
=A07 =A08 =A01 =A00 =A00 =A00
=A08 =A09 =A01 =A00 =A00 =A00
=A09 10 =A02 =A00 =A00 =A00
=A09 11 =A01 =A00 =A00 =A00
=A011 16 =A01 =A00 =A00 =A00
=A011 12 =A01 =A00 =A00 =A00
=A011 17 =A01 =A00 =A00 =A00
=A012 13 =A01 =A00 =A00 =A00
=A013 14 =A01 =A00 =A00 =A00
=A014 15 =A01 =A00 =A00 =A00
=A015 16 =A01 =A00 =A00 =A00
=A017 22 =A01 =A00 =A00 =A00
=A017 18 =A01 =A00 =A00 =A00
=A018 19 =A01 =A00 =A00 =A00
=A019 20 =A01 =A00 =A00 =A00
=A020 21 =A01 =A00 =A00 =A00
=A021 22 =A01 =A00 =A00 =A00
M =A0END





-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY/a\ccl.net or use:
=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST/a\ccl.net or use
=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtm= l

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs Conferences: http://server.ccl.net/chemistry/anno= uncements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 http= ://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--00151758ac46b04fb10476966b68-- From owner-chemistry@ccl.net Fri Oct 23 11:20:00 2009 From: "Jamel MESLAMANI meslamani-.-ulp.u-strasbg.fr" To: CCL Subject: CCL: Multi SDF to many files in folder Message-Id: <-40518-091023111319-17944-h65nYlogQQrtNsJG9qauQg a server.ccl.net> X-Original-From: Jamel MESLAMANI Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Oct 2009 16:15:29 +0200 MIME-Version: 1.0 Sent to CCL by: Jamel MESLAMANI [meslamani ~~ ulp.u-strasbg.fr] Hi Chi, If you are not used to make scripts, I recommend you to use the mayachemtools ( http://www.mayachemtools.org ) or the SDF_toolkit ( http://cactus.nci.nih.gov/SDF_toolkit ) , both are collections of perl scripts related to file manipulation and even descriptors calculations and more... You can use one of their script to split your SD file. (look at splitsdfile.pl or something similar...) Hope this will help. > > c p Mpamhanga chido.mpamhanga,+,gmail.com a écrit : >> Sent to CCL by: "c p Mpamhanga" [chido.mpamhanga-*-gmail.com] >> Hi all, >> >> Does anyone have a script to split an SDFfile into single sdfs named >> after each after each individual molecule as specified in first line >> of parent multi file? (I have written one but it seems not too robust) >> >> Cheers >> >> Chi >> >> e.g. below files names would be 241.sdf and 355.sdf >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> 241 >> OpenBabel10220916392D >> >> 20 20 0 0 0 0 0 0 0 0999 V2000 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 Cl 0 0 0 0 0 >> 1 2 1 0 0 0 >> 2 3 1 0 0 0 >> 3 4 1 0 0 0 >> 3 6 1 0 0 0 >> 4 5 1 0 0 0 >> 6 7 1 0 0 0 >> 7 8 1 0 0 0 >> 8 9 1 0 0 0 >> 9 10 2 0 0 0 >> 9 11 1 0 0 0 >> 11 16 1 0 0 0 >> 11 12 2 0 0 0 >> 12 13 1 0 0 0 >> 13 14 2 0 0 0 >> 13 20 1 0 0 0 >> 14 15 1 0 0 0 >> 14 19 1 0 0 0 >> 15 16 2 0 0 0 >> 16 17 1 0 0 0 >> 17 18 1 0 0 0 >> M END >> $$$$ >> 355 >> OpenBabel10220916392D >> >> 22 23 0 0 0 0 0 0 0 0999 V2000 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 N 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 O 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 0.0000 0.0000 0.0000 C 0 0 0 0 0 >> 1 2 1 0 0 0 >> 2 3 1 0 0 0 >> 3 4 1 0 0 0 >> 3 6 1 0 0 0 >> 4 5 1 0 0 0 >> 6 7 1 0 0 0 >> 7 8 1 0 0 0 >> 8 9 1 0 0 0 >> 9 10 2 0 0 0 >> 9 11 1 0 0 0 >> 11 16 1 0 0 0 >> 11 12 1 0 0 0 >> 11 17 1 0 0 0 >> 12 13 1 0 0 0 >> 13 14 1 0 0 0 >> 14 15 1 0 0 0 >> 15 16 1 0 0 0 >> 17 22 1 0 0 0 >> 17 18 1 0 0 0 >> 18 19 1 0 0 0 >> 19 20 1 0 0 0 >> 20 21 1 0 0 0 >> 21 22 1 0 0 0 >> M END >> >> From owner-chemistry@ccl.net Fri Oct 23 12:20:01 2009 From: "Andreas Klamt klamt%%cosmologic.de" To: CCL Subject: CCL:G: solvation energy in mopac/Comment about COSMO-RS/COSMOtherm Message-Id: <-40519-091023032344-26117-GVnBMAaeX5cP/cdZ/wZOSw+*+server.ccl.net> X-Original-From: Andreas Klamt Date: Fri, 23 Oct 2009 09:23:23 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt+*+cosmologic.de] References: <40513-091021164200-28792-kC3jADUAzy4UQ8MwUVg/HA:+:server.ccl.net> In-Reply-To: <40513-091021164200-28792-kC3jADUAzy4UQ8MwUVg/HA:+:server.ccl.net> Content-Type: text/plain; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable X-Spam-Status: No, score=-2.6 required=5.8 tests=BAYES_00 autolearn=ham version=3.1.9 X-Spam-Checker-Version: SpamAssassin 3.1.9 (2007-02-13) on server.ccl.net Dear David, I am somewhat surprised about your offense. Here is my response: 1) Please note that COSMO-RS is a scientifically well published method.=20 There are at least 4 remakes of COSMO-RS, which are based on my publicati= ons - the COSMO-SAC remake by Lin and Sandler (available for free in a=20 simple form from a Virginia-Tech website) - the COSMO-RS(Ol) remake by Gensemann and Gmehling, available withn = the DDBST software (as far as I know at a low price) - the re-implementation by Banerjee et al., which to my best=20 knowledge is not distributed as software - the re-implementation in the ADF program, which is commercial Anyway, this proofs that I have sufficiently well published the COSMO-RS = method that it can be reproduced. Admittedly, in our COSMOtherm=20 implementation of COSMO-RS we have a few parameters being not completely = disclosed. 2) In my CCL entry on solvation energy in MOPAC I have only spoken about = the COSMO-RS method. You will not find the product name COSMOtherm in=20 there. As developer of COSMO in MOPAC I have given the reasons why COSMO = in MOPAC has not been developed up to the level of quantitative=20 prediction of dG_solv. Is there anything wrong with the fact, that I -=20 who should know these things best - am giving this explanation in CCL? 3) From your comment I understand that you suspect that people working=20 commercially in Computational Chemistry cannot be considered as serious=20 scientist. I am afraid that this is the opinion of a part of our=20 community, but it is quite specific for it. I guess nobody would suspect = that the researchers in automotive industries, or in pharmaceutical=20 companies are not doing good research. Yes, if you like you can decide=20 to use only those drugs which have been developed at universities. But=20 very few people do so. The difference is that these people mostly patent = their breakthroughs. I did not patent COSMO-RS. So I am asking the=20 question: What is wrong with the fact that I decided to earn my income=20 (and meanwhile that of about 6 additional scientists, 2 programmers, and = one secretary) based on my scientific invention? Does this make me a=20 less honest or less serious scientist? If the CCL should decide to become a forum exclusive for academic=20 computational chemists, and exclusively about public domain software,=20 then I will stay out of it. I did not have this impression yet. By the=20 way, then all the discussion about bugs and problems with Gaussian=20 should also stay out there. Gaussain may be a little bit cheaper, but it = is commercial. Maybe the entry price for academics is lower, but I am=20 not sure whether you are the person to decide which price is acceptable=20 for academic licenses of comp. chem. software. The entry price for=20 COSMOtherm is 3000 EURO for a permanent academic group license (I am not = sure where you take the $12 K). This price is for a permanent academic=20 group license, including training, maintenance and updates for one year, = and including a graphcal user interface. If you consider this as too=20 high, you may use a public domain remake of COSMO-RS, or other solvation = methods. That is your decision. I also encourage the organizer of the CCL (Jan) and the community to=20 comment on this debate. If the organizer or the majority of the CCLers=20 should share the opinion of David, I will stay out of CCL in future. Best regards Andreas David A. Mannock dmannock^ualberta.ca schrieb: > > Sent to CCL by: "David A. Mannock" [dmannock++ualberta.ca] > > Andreas, we have talked before about Cosmo-RS.. You need to disclose=20 > your financial interests in this software when answering messages and=20 > where possible suggest alternative free DFT software where similar=20 > solutions are available. Many of your answers in this forum seem=20 > contain scientific solutions relative to your own product which if I=20 > recall was $12K for a small group licence. I think I said to you at=20 > the time that even 1/10th of the price for a single person user=20 > licence was excessive for academic use. While I have to be realistic=20 > about science and the modern business world, personally I understood=20 > that this forum was for help of a scientific nature. Maybe the=20 > moderators of this forum would care to comment on this policy. David > > At 12:18 AM 21/10/2009, you wrote: > >> Sent to CCL by: Andreas Klamt [klamt#%#cosmologic.de] >> Dear Daniel, >> >> as author of COSMO in MOPAC I like to emphazise that the COSMO in=20 >> MOPAC is not parameterized for the quantitative calculation of=20 >> dG_solv. It is definitely good for getting the calculations closer to = >> solvation than just a gasphase calculation, but for two reasons I=20 >> recommend higher levels for optimal calculation of dG_solv: >> 1) The electrostatics of semi-empirical methods is usually not very=20 >> accurate (because this mostly is not in the target properties of the=20 >> parameterizations). At least in AM1, PM3, and PM5 (we did not test=20 >> PM6) dipole moments of some functional groups can be off by one Debye = >> (e.g. nitro groups) and if the dipole moment is of that much the=20 >> solvation energy will be very bad. This is the reason why I left the=20 >> semi-empirical level for quantitative solvation calculations a few=20 >> years after developing COSMO in MOPAC. And most likely this is also=20 >> why the Minnesota group developed parameterized charge models based=20 >> on semi-empirical methods in order to improve the SMx models. Since=20 >> HF is generally overestimating polarities, this is also not extremely = >> reliable. The good message is that DFT is very reliable in that=20 >> regard, and this quite independent of the special functional. From my = >> perspective DFT is currently the method of choice, although for=20 >> getting the solvations energies much better than 0.3 kcal/mol one=20 >> will need even more accurate methods than DFT. By the way, a=20 >> semi-emirical geometry furnished with a single point DFT calculation=20 >> can be a very good choice for calculating solvation energies. >> 2) The second reason is that a dielectric continuum solvation model=20 >> alone cannot give the complete solvation free energies. One needs in=20 >> addition "non-electrostatic contributions". While in the SMx and PCM=20 >> models these have been parameterized with many additional, solute and = >> solvent specific parameters and descriptors, I have never implemented = >> such non-electrostatic terms in MOPAC, at least not quantitatively.=20 >> MOPAC/COSMO thus does not have these terms. Instead, I have attacked=20 >> this question with the much more rigorous COSMO-RS approach, which=20 >> combines COSMO with a statistical thermodynamics of interacting=20 >> surfaces (using the COSMO polarization charges for the quantification = >> of the interactions) and thus describes solutes and solvents on the=20 >> same quantum-chemical footing, gives enthalpies and entropies,=20 >> temperature dependencies, and allows for the treatment of mixtures.=20 >> But due to the earlier finding of 1) I have only developed COSMO-RS=20 >> quantitatively on the DFT level. Based on a comparison on ~ 2500=20 >> dG_solv predictions (see "On the Performance of Continuum Solvation=20 >> Methods. A Comment on "Universal Approaches to Solvation Modeling"",=20 >> Acc. Chem. Res., 2009, 42 (4), pp 489--492) and on the outcome of the = >> recent SAMPL blindtest ( publications in preparation) I dare to say=20 >> that COSMO-RS currently is the most accurate method for the=20 >> prediction of dG_solv. >> >> Andreas >> >> >> >> Daniel Glossman-Mitnik dglossman%a%gmail.com schrieb: >>> Dear netters: >>> >>> How should one calculate the solvation energy of a given molecule=20 >>> using MOPAC 2009? >>> It is enough with doing one calculation in gas phase and another in=20 >>> solvent and then >>> substracting both heats of formation? >>> Any example input related to these questions will be appreciated. >>> >>> Best regards, >>> >>> Daniel >>> >>> *********************************************************************= ****************************************=20 >>> >>> Dr. Daniel Glossman-Mitnik: >>> Centro de Investigaci=F3n en Materiales Avanzados, SC >>> Grupo NANOCOSMOS - Nanotecnolog=EDa Computacional, Simulaci=F3n y=20 >>> Modelado Molecular >>> Miguel de Cervantes 120 - Complejo Industrial Chihuahua - Chihuahua, = >>> Chih 31109, Mexico >>> Phone: +52 614 4391151 Secretary/FAX: +52 614 4394852 Lab: +52 614=20 >>> 4394805 >>> E-mail: daniel.glossman[A]cimav.edu.mx=20 >>> dglossman[A]gmail.com=20 >>> >>> WWW: http://www.cimav.edu.mx/cv/daniel.glossman >>> http://blogs.cimav.edu.mx/daniel.glossman >>> *********************************************************************= ****************************************=20 >>> >> >> >> --=20 >> PD. Dr. Andreas Klamt >> CEO / Gesch=E4ftsf=FChrer >> COSMOlogic GmbH & Co. KG >> Burscheider Strasse 515 >> D-51381 Leverkusen, Germany >> >> phone +49-2171-731681 >> fax +49-2171-731689 >> e-mail klamt*_*cosmologic.de >> web www.cosmologic.de >> >> HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt >> Komplementaer: COSMOlogic Verwaltungs GmbH >> HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt >> >> >> >> -http://www.ccl.net/chemistry/sub_unsub.shtmlConferences:=20 >> http://server.ccl.net/chemistry/announcements/conferences/> >> > > > > -=3Dhis is automatically added to each message by the mailing script =3D= - > To recover the email address of the author of the message, please chang= ehttp://www.ccl.net/chemistry/sub_unsub.shtm= lConferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/> > > --=20 PD. Dr. Andreas Klamt CEO / Gesch=E4ftsf=FChrer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt:+:cosmologic.de web www.cosmologic.de HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Fri Oct 23 13:32:00 2009 From: "Jim Kress ccl_nospam : kressworks.com" To: CCL Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6!! Message-Id: <-40520-091023133028-32507-Tb3yxJhXmiDvgMcwwE9yPw .. server.ccl.net> X-Original-From: "Jim Kress" Date: Fri, 23 Oct 2009 13:30:24 -0400 Sent to CCL by: "Jim Kress" [ccl_nospam~~kressworks.com] > Before getting too exited please note that the DFT methods used in the > validation do not describe London dispersion ... this may introduce Not totally correct. See: http://www.pnas.org/content/101/9/2673.abstract for more information. Jim Kress ccl_nospam---kressworks.com > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com---ccl.net > [mailto:owner- > chemistry+ccl_nospam==kressworks.com---ccl.net] On Behalf Of Kalju Kahn > kalju^chem.ucsb.edu > Sent: Sunday, October 18, 2009 12:13 AM > To: Kress, Jim > Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 > using PM6!! > > > Sent to CCL by: "Kalju Kahn" [kalju^chem.ucsb.edu] > > Fabio, > > Before getting too exited please note that the DFT methods used in the > validation do not describe London dispersion ... this may introduce > significant errors for larger flexible molecules where pi-stacking is > possible ... like the oximes in this study. > > Kalju > > > Sent to CCL by: "Fabio P. Costa" [fabioparanho=gmail.com] I'd like > > to performed a conformational analysis in order to investigate a > > chemical reaction when I've found this interesting paper: > > Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6 and RM1 Methods! > > > > http://jbcs.sbq.org.br/online/fpapers/09036SR.pdf > > Supplementary Material: > > :http://jbcs.sbq.org.br/online/fpapers/09036SI.pdf > > > > It shows that new semi-empirical methods are able to correctly > > reproduce DFT ones. It is really sound nice, I mean to able to > > obtain good results with a semi-empirical approach. What do you think about it? > > > > > > Best regards. > > > > Fabio Costa> > > > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 > > > > -= 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> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Fri Oct 23 15:49:01 2009 From: "Mihaly Mezei Mihaly.Mezei,+,mssm.edu" To: CCL Subject: CCL: Commercial/Scientific software Message-Id: <-40521-091023145552-3040-++WUUbFq+TBCYyXTIq1BFg-$-server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Fri, 23 Oct 2009 14:05:52 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei _ mssm.edu] Greetings, Andreas Klimt invited the community to comment on the issues raised by Daniel Glossman-Mitnik. Here is my take on the problem. I think most of us agree that certain things should not be made object of commerce. The debate is, where should we draw the line. In case of science, there are even more than one lines: (1) Would a scientist be able to judge the result of an experiment when there is financial interest involved? (2) Would the community accept a scientific product that is not fully specified (e.g., source code is not distributed, or in case of COSMO - to quote Andreas' letter - "we have a few parameters being not completely disclosed")? (3) Is it ok to sell life-saving drugs to those who can afford it? So, it is not a question of suspecting "that the researchers in automotive industries, or in pharmaceutical companies are not doing good research" but of questioning the evaluation of their result. Also, I am afraid that commercializing science is a Faustian bargain - the initial gain is offset by the lessening of public (i.e., governmental) support to science, resulting in a stronger push for commercialization, with the concomitant rise of conflict of interest problems, both in the publishing and in the fund distributing process. So I think the above justifies a certain amount of wariness that some of us feel about commercial software, notwithstanding our taking advantage of them. I think that at the minimum, Daniel's complaint about not disclosing commercial interest should be taken to heart. As for the pricing, I think that 3000 Euro is indeed unaffordable to the majority of prospective academic users, Best regards, Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Fri Oct 23 16:24:00 2009 From: "Marcel Swart marcel.swart[*]icrea.es" To: CCL Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6!! Message-Id: <-40522-091023162035-23423-rXia8BH+rVdq9qlwJXAGtQ*|*server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 23 Oct 2009 22:13:33 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart a icrea.es] DFT methods DO have problems with dispersion energy; see for instance our paper in J. Mol. Model. 2007, 13, 1245-1257 how this can be handled however: http://dx.doi.org/10.1007/s00894-007-0239-y Furthermore, the most popular solution is to use Grimme's dispersion correction (J. Comput. Chem. 2006, 27, 1787-1799), as also used in the SSB-D functional (J. Chem. Phys. 2009, 131, 094103; http://dx.doi.org/10.1063/1.3213193). Your example of X3lYP is actually a bad example (I'm sorry Jim): "The X3LYP extended density functional accurately describes H-bonding =20 but fails completely for stacking" by Cerny, Hobza, http://dx.doi.org/10.1039/b502769c Quoting "Jim Kress ccl_nospam : kressworks.com" : > > Sent to CCL by: "Jim Kress" [ccl_nospam~~kressworks.com] >> Before getting too exited please note that the DFT methods used in the >> validation do not describe London dispersion ... this may introduce > > Not totally correct. See: > > http://www.pnas.org/content/101/9/2673.abstract > > for more information. > > Jim Kress > ccl_nospam.:.kressworks.com > > >> -----Original Message----- >> From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com.:.ccl.net >> [mailto:owner- >> chemistry+ccl_nospam=3D=3Dkressworks.com.:.ccl.net] On Behalf Of Kalju Ka= hn >> kalju^chem.ucsb.edu >> Sent: Sunday, October 18, 2009 12:13 AM >> To: Kress, Jim >> Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 >> using PM6!! >> >> >> Sent to CCL by: "Kalju Kahn" [kalju^chem.ucsb.edu] >> >> Fabio, >> >> Before getting too exited please note that the DFT methods used in the >> validation do not describe London dispersion ... this may introduce >> significant errors for larger flexible molecules where pi-stacking is >> possible ... like the oximes in this study. >> >> Kalju >> >> > Sent to CCL by: "Fabio P. Costa" [fabioparanho=3Dgmail.com] I'd like >> > to performed a conformational analysis in order to investigate a >> > chemical reaction when I've found this interesting paper: >> > Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6 =20 >> and RM1 Methods! >> > >> > http://jbcs.sbq.org.br/online/fpapers/09036SR.pdf >> > Supplementary Material: >> > :http://jbcs.sbq.org.br/online/fpapers/09036SI.pdf >> > >> > It shows that new semi-empirical methods are able to correctly >> > reproduce DFT ones. It is really sound nice, I mean to able to >> > obtain good results with a semi-empirical approach. What do you =20 >> think about it? >> > >> > >> > Best regards. >> > >> > Fabio Costa> >> > >> > >> >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Dr. Kalju Kahn >> Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 >> >> >> >> -=3D This is automatically added to each message by the mailing script >> =3D- 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> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart%icrea.es marcel.swart%udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Fri Oct 23 17:24:00 2009 From: "David A. Mannock dmannock^-^ualberta.ca" To: CCL Subject: CCL: solvation energy in mopac/Comment about COSMO-RS/COSMOtherm Message-Id: <-40523-091023155413-10636-u/JqU7wOnvd/VKuOXwe3Bw.:.server.ccl.net> X-Original-From: "David A. Mannock" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 23 Oct 2009 13:54:07 -0600 Mime-Version: 1.0 Sent to CCL by: "David A. Mannock" [dmannock---ualberta.ca] Andreas, It was not my intention to offend or pour scorn on science or scientists in industry. There is a thin dividing line between telling someone how to solve a problem with software "X" and advertising software which has those features that is available from your company. I know that I see occasional update notices and bug fixes here which I am sure are useful for the subscribers to this forum. I do not think that the forum should be for academic users only, simply that users with commercial interests should disclose those interests when discussing their own product. Your listing of Cosmo resources in your message to me is useful and I'm sure that others will agree with me on this point. I do understand in this scientific age that it is sometimes necessary for science and commerce to join hands, my concern is that the forum will be used by too many people in this situation as a means of advertising their product. My understanding is that this was not the purpose of the forum, hence my comments. A simple disclosure by all commercial subscribers to this list would clarify the context of messages from those users. This was the purpose of the message, nothing more. David From owner-chemistry@ccl.net Fri Oct 23 18:09:00 2009 From: "Gustavo L.C. Moura gustavo.-*-.mercury.chem.pitt.edu" To: CCL Subject: CCL:G: GTO Integral Routine Message-Id: <-40524-091023180722-23568-4U1kbD78ZuM8xZRKNsQFRA-*-server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Fri, 23 Oct 2009 18:07:19 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo(_)mercury.chem.pitt.edu] Dear CCL Readers, I am looking for the Fortran 90 source codes of routines that calculate molecular integrals over Gaussian type orbitals (GTOs). I need to be able to efficiently calculate the integrals with s, p, d and f GTOs. I would appreciate receiving information on where I could find available such routines. Thank you very much in advance. Sincerely yours, Dr. Gustavo L.C. Moura From owner-chemistry@ccl.net Fri Oct 23 18:43:00 2009 From: "N. Sukumar nagams^_^rpi.edu" To: CCL Subject: CCL: Commercial/Scientific software Message-Id: <-40525-091023173520-7312-nY/7JPEJzCAAHbzs+fNqtA- -server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Fri, 23 Oct 2009 17:35:08 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams[#]rpi.edu] On Fri, 23 Oct 2009 14:05:52 EDT "Mihaly Mezei Mihaly.Mezei,+,mssm.edu" wrote: > ... Would a scientist be able to judge the result of an experiment when there is financial interest involved? There are always financial interests involved, for academic researchers in the form of research grants, prizes, tenure. No faculty appointment is made in the US these days without a history or a strong likelihood of "attracting funding" to the appointing institute. > ... Would the community accept a scientific product that is not fully specified e.g., source code is not distributed ... Alas, the answer seems to be yes. > ... commercializing science is a Faustian bargain ... I'm afraid that boat has sailed - science has already been commercialized, and not just by commercial software developers struggling to make a living from their intellectual property. Since before the birth of chemistry as a modern science, chemists have been striving to commercialize the products of their discoveries and intellectual property. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ From owner-chemistry@ccl.net Fri Oct 23 19:19:00 2009 From: "Geoffrey Hutchison geoffh#,#pitt.edu" To: CCL Subject: CCL: ANNOUNCE: Avogadro 1.0 Release Message-Id: <-40526-091023180245-21660-GdSaKIKxV14bemziIfyCTA-,-server.ccl.net> X-Original-From: Geoffrey Hutchison Content-type: multipart/alternative; boundary=Apple-Mail-1-1002763751 Date: Fri, 23 Oct 2009 18:02:34 -0400 MIME-version: 1.0 (Apple Message framework v1076) Sent to CCL by: Geoffrey Hutchison [geoffh*pitt.edu] --Apple-Mail-1-1002763751 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes I am very proud to announce the availability of Avogadro 1.0. Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Mac OSX, Windows and Linux. The source code source is available under the GNU GPLv2. What does Avogadro do? * We've tried to make the best, most intuitive "builder," including common fragments, downloading directly from PDB or PubChem, and peptide sequences. * Innovative "auto-optimize" tool which allows you to continue to build and modify, during molecular mechanics optimization. * Interfaces to many common computational packages. * Designed to help both educational users and advanced research. * Plugins that allow Avogadro to be extended and customized. * Well defined public API, library and Python bindings for development. * Embedded Python interpreter. * Translations available in 12+ languages. Download: https://sourceforge.net/projects/avogadro/files/latest What's New? See the Release Notes: http://avogadro.openmolecules.net/wiki/Avogadro_1.0.0 For more information: http://avogadro.openmolecules.net/wiki/ This is a community project and we couldn't have made this release without you. Many thanks to all the contributors to Avogadro including those of you who submitted feedback, bug reports, and code. Particular thanks go to all the translators. Thanks, Geoff Hutchison The Avogadro Project http://avogadro.openmolecules.net/ P.S. We consider this as a milestone, but really "the end of the beginning." We'd like to make this a real community project. Please give us your feedback and your suggestions to make Avogadro the best possible molecular editor. --Apple-Mail-1-1002763751 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii I am very proud to announce the = availability of Avogadro 1.0.

Avogadro is a free, open source, cross-platform = molecular editor designed for flexible use in computational chemistry, = molecular modeling, bioinformatics, materials science, and related = areas. Packages are available for Mac OSX, Windows and Linux. The source = code source is available under the GNU GPLv2.

What does = Avogadro do?
* We've tried to make the = best, most intuitive "builder," including common fragments, downloading = directly from PDB or PubChem, and peptide sequences.
* Innovative "auto-optimize" tool which allows you to = continue to build and modify, during molecular mechanics = optimization.
* Interfaces to many common = computational packages.
* = Designed to help both educational users and advanced = research.
* Plugins that allow = Avogadro to be extended and customized.
* Well defined public API, library and Python bindings = for development.
* = Embedded Python interpreter.
* = Translations available in 12+ languages.


What's = New? See the Release Notes: http://avog= adro.openmolecules.net/wiki/Avogadro_1.0.0


This is a community project and we couldn't have made = this release without you. Many thanks to all the contributors to = Avogadro including those of you who submitted feedback, bug reports, and = code. Particular thanks go to all the translators.

Thanks,
Geoff = Hutchison
The Avogadro = Project

P.S. We consider this as a milestone, but really "the = end of the beginning." We'd like to make this a real community project. = Please give us your feedback and your suggestions to make Avogadro the = best possible molecular editor.

= = --Apple-Mail-1-1002763751-- From owner-chemistry@ccl.net Fri Oct 23 22:42:01 2009 From: "Jan Labanowski janl^^speakeasy.net" To: CCL Subject: CCL: CCL and ads and discussing commercial software Message-Id: <-40527-091023223554-9413-50i9TPnimS6dO33TYRjcxg+/-server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 23 Oct 2009 22:35:42 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl||speakeasy.net] Dear CCL, Hear... Hear... Your moderator is speaking {:-)}. For obvious reasons I try to follow Eugene Onegin: who "had the happy knack= to touch upon any topic lightly in informal conversations, but kept silent dur= ing serious discussions, where he made people smile with a flash of his unexpec= ted jibes" (sorry for a travesty of translation from memory...). The rules of CCL were established LOOOONG time ago. They are a compromise. = You can find them here: http://server.ccl.net/chemistry/aboutccl/rules/index.shtml Please note that we have both academic and corporate researchers on the lis= t. We also have people in government and "non-for-profit" labs though at this mom= ent, I do not know if they are more academic or more corporate. Moreover, I am not= even sure if academic and corporate is not the same thing... But bitter humor as= ide, in many corporate environments they cannot use "free software". There are of course understandable legal, maintenance, business, security, etc., etc.. r= easons for this. For example, the corporate legal department has to have someone t= o sue if the software does some harm. And they cannot sue when the license says: = "use at your own risk". Moreover, there is a productivity issue -- management do= es not like when the researchers are debugging academic software for free or try to figure out how to work "this thing" since there is no manual. Managers pref= er that corporate researchers crank "valuable and competitive results" so they= can present how good they are at making their subordinates "productive", when t= he reports are passed to the higher level of incompetence where the real decis= ions are being made. For these reasons managers prefer when the corporate resear= chers fill out a short "Bug report" form rather than "find a way around it". Not = only this... To install and use the "free software" someone needs to make a "decision" and take lashes if the thing does not work. No covering the behi= nds with the glossy promotional literature that lists the "benefits for the com= pany". Last, but not least, much of the commercial software IS SIMPLY GOOD and competitive to whatever is "latest and greatest" from academia. How it beca= me commercial will be touched in the next few lines. So... please... Be more practical about the commercial software. People use= it and will use it and there is nothing that we/them/us can do about in the fr= ee market system. Our corporate scientists need to get the information about commercial software and advice on how to use it. Yes... We may agree or di= sagree what Jennifer Washburn (oh well, if you do not know the name, you just Goog= le) told as in Atlantic Monthly many years ago. But she is "onto something". I personally do not agree with the fact that Academic Institutions own the Intellectual Property Rights to the discoveries produced with Tax Payer mon= ies. It created several restrains on the scientific freedom, created completely inefficient and useless academic bureaucracies, and changed the way we do s= cience for ever. IMHO, a complete failure both for our economies and our universit= ies. But we cannot change it much by bitching on CCL. The guys that could change= it are your Senators and/or Congressmen. Though, if you think about it, they "= do not give a damn" what you think -- it is not you who paid for their TV ads. Jan Labanowski CCL Manager P.S. I hope, I avoided another flame war on CCL rather than started it.