From owner-chemistry@ccl.net Thu Oct 15 00:27:01 2015 From: "Andrey Voronkov av%a%digitalbiopharm.com" To: CCL Subject: CCL: Software, scripts and approaches for the similarity analysis Message-Id: <-51816-151014152617-28877-omq1S9lBvWE7CUbkuSiEKA:_:server.ccl.net> X-Original-From: "Andrey Voronkov" Date: Wed, 14 Oct 2015 15:26:16 -0400 Sent to CCL by: "Andrey Voronkov" [av]=[digitalbiopharm.com] Dear CCL users, can you please recommend papers/Software on compounds similarity evaluations? It would be nice to find a script, which can analyze compounds in a dataset and rank them by their mutual similarity (give different scoring on combined basis). Best regards, Andrey From owner-chemistry@ccl.net Thu Oct 15 04:47:01 2015 From: "Michel Petitjean petitjean.chiral**gmail.com" To: CCL Subject: CCL: Software, scripts and approaches for the similarity analysis Message-Id: <-51817-151015043834-32421-0dWxELVoqZVLxReCs7AhTQ-.-server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=UTF-8 Date: Thu, 15 Oct 2015 10:38:27 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral##gmail.com] Dear Andrey, CSR computes the number of atoms of the maximal 3D motif common to two molecules. It needs the 3D cartesian coordinates of each molecule, not necessarily in a common set of axis (CSR will compute it). No need of the pairwise correspondence (CSR will compute it within the maximal common 3D motif, together with the RMSD). The dissimilarity coefficient is D12=n1+n2-2*n12, where n1 is the number of atoms of molecule 1, n2 is the number of atoms of molecule 2, n12 is the number of atoms of the common 3D motif, computed by CSR. A dissimilarity index is I12=D12/(n1+n2). I12 takes values in [0..1]. CSR is downloadable for free at: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html It is callable by script. Hope it helps. Best regards, Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral[]gmail.com (preferred), michel.petitjean[]univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2015-10-14 21:26 GMT+02:00 Andrey Voronkov av%a%digitalbiopharm.com : > > Sent to CCL by: "Andrey Voronkov" [av]=[digitalbiopharm.com] > Dear CCL users, can you please recommend papers/Software on compounds similarity evaluations? It would be nice to find a script, which can analyze compounds in a dataset and rank them by their mutual similarity (give different scoring on combined basis). > > > Best regards, > Andrey > From owner-chemistry@ccl.net Thu Oct 15 06:39:00 2015 From: "Andras P. Borosy borosy .. bluewin.ch" To: CCL Subject: CCL: Software, scripts and approaches for the similarity analysis Message-Id: <-51818-151015063754-11337-g2Rn+p48ILQb8jVRdekmoQ\a/server.ccl.net> X-Original-From: "Andras P. Borosy" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 15 Oct 2015 12:37:47 +0200 MIME-Version: 1.0 Sent to CCL by: "Andras P. Borosy" [borosy * bluewin.ch] Dear Andrey, Some articles to start with: Willett, P. Similarity methods in chemoinformatics. Ann. Rev. Inform. Sci. Technol. 2009 , 43, 3 − 71. R.D. Brown, Y.C. Martin, Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection, J. Chem. Inf. Comput. Sci. 36 (1996) 572–584. G.M. Downs, P. Willet, Similarity searching and clustering of chemical-structure databases using molecular property data, J. Chem. Inf. Sci. 34 (1994) 1094–1102. Riniker, S.; Landrum, G. A. Open-source platform to benchmark fingerprints for ligand-based virtual screening. J. Cheminform. 2013, 5,26. I would try KNIME-CDK Beisken et al., KNIME-CDK: Workflow-driven cheminformatics, BMC Bioinformatics 2013, 14:257 Thiel K, Wiswedel B: KNIME: The Konstanz Information Miner. In Studies in Classification, Data Analysis, and Knowledge Organization (GfKL 2007). Heidelberg-Berlin: Springer-Verlag; 2007 Best wishes, András P. Borosy On 14.10.2015 21:26, Andrey Voronkov av%a%digitalbiopharm.com wrote: > Sent to CCL by: "Andrey Voronkov" [av]=[digitalbiopharm.com] > Dear CCL users, can you please recommend papers/Software on compounds similarity evaluations? It > would be nice to find a script, which can analyze compounds in a dataset and rank them by their > mutual similarity (give different scoring on combined basis). > > > Best regards, > Andrey> > > From owner-chemistry@ccl.net Thu Oct 15 07:13:00 2015 From: "Rajarshi Guha rajarshi.guha|gmail.com" To: CCL Subject: CCL: Software, scripts and approaches for the similarity analysis Message-Id: <-51819-151015065156-16510-G90lny6ybQ2kk5R0sZPlsw]^[server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=001a11490778bae7600522227661 Date: Thu, 15 Oct 2015 06:51:39 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha^_^gmail.com] --001a11490778bae7600522227661 Content-Type: text/plain; charset=UTF-8 if you consider fingerprint based similarities the framework described in http://www.jcheminf.com/content/5/1/26 maybe a usefu starting point On Wed, Oct 14, 2015 at 3:26 PM, Andrey Voronkov av%a%digitalbiopharm.com < owner-chemistry###ccl.net> wrote: > > Sent to CCL by: "Andrey Voronkov" [av]=[digitalbiopharm.com] > Dear CCL users, can you please recommend papers/Software on compounds > similarity evaluations? It > would be nice to find a script, which can analyze compounds in a dataset > and rank them by their > mutual similarity (give different scoring on combined basis). > > > Best regards, > Andrey> > > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science --001a11490778bae7600522227661 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
if you consider fingerprint based similarities the framewo= rk described in=C2=A0htt= p://www.jcheminf.com/content/5/1/26 maybe a usefu starting point
<= div class=3D"gmail_extra">
On Wed, Oct 14, 20= 15 at 3:26 PM, Andrey Voronkov av%a%= digitalbiopharm.com <owner-chemistry###ccl.net> wrot= e:

Sent to CCL by: "Andrey=C2=A0 Voronkov" [av]=3D[digitalbiopharm.= com]
Dear CCL users, can you please recommend papers/Software on compounds simil= arity evaluations? It
would be nice to find a script, which can analyze compounds in a dataset an= d rank them by their
mutual similarity (give different scoring on combined basis).


Best regards,
Andrey



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY###ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST###ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

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

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/





--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Transla= tional Science
--001a11490778bae7600522227661-- From owner-chemistry@ccl.net Thu Oct 15 07:49:00 2015 From: "Wolf Ihlenfeldt wdi/a\xemistry.com" To: CCL Subject: CCL: Software, scripts and approaches for the similarity analysis Message-Id: <-51820-151015071814-4150-kQGwCfVIfGi4kzMk8bvzvg[#]server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 15 Oct 2015 13:18:07 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi|a|xemistry.com] On Wed, Oct 14, 2015 at 9:26 PM, Andrey Voronkov av%a%digitalbiopharm.com wrote: > > Sent to CCL by: "Andrey Voronkov" [av]=[digitalbiopharm.com] > Dear CCL users, can you please recommend papers/Software on compounds similarity evaluations? It > would be nice to find a script, which can analyze compounds in a dataset and rank them by their > mutual similarity (give different scoring on combined basis). > > > Best regards, > Andrey Here are rudimentary scripts to do this (i.e computing a lower triangular matrix of the similarities of the structures in a dataset, integer similarity values 0..100) with the Cactvs Cheminformatics toolkit (free academic version at www.xemistry/com/academic): a) Python: d=Molfile('myfile.sdf').hread(target='#new',attributes={'readscope':'dataset','limit':100}) simmat=[] for i in range(0,d.size): simrow=[] for j in range(0,i+1): if (i==j): simrow.append(100) else: simrow.append(Prop.Compare('E_SCREEN',d.index(i).E_SCREEN,d.index(j).E_SCREEN,'tanimoto')) simmat.append(simrow) print(simmat) b) Tcl: set d [molfile read "myfile.sdf" #new [dict create readscope dataset limit 100]] set simmat {} loop i 0 [dataset get $d size] { set simrow {} loop j 0 $i+1 { if ($i==$j) { lappend simrow 100 } else { lappend simrow [prop compare E_SCREEN [ens get [dataset index $d $i] E_SCREEN] \ [ens get [dataset index $d $j] E_SCREEN] tanimoto] } } lappend simmat $simrow } puts $simmat> > -- Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi!=!xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh – Geschäftsführer/Managing Director: Dr. W. D. Ihlenfeldt Address: Hainholzweg 11, D-61462 Königstein, Germany HR Königstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 From owner-chemistry@ccl.net Thu Oct 15 08:24:00 2015 From: "Dmitry Ovsyannikov amidius.1992(_)gmail.com" To: CCL Subject: CCL: MCSCF frequencies in excited state Message-Id: <-51821-151015075912-32256-03vWDEP3oVG6dpfmK0KUsA]![server.ccl.net> X-Original-From: "Dmitry Ovsyannikov" Date: Thu, 15 Oct 2015 07:59:11 -0400 Sent to CCL by: "Dmitry Ovsyannikov" [amidius.1992 * gmail.com] Dear all! I stucked with the problem in nwchem: when I start the calculations using energy task: start no2s1 charge 0 geometry N -0.00885 -0.16558 0.00000 O 0.00210 -0.72622 -1.08078 C -0.00054 1.30903 0.00000 O 0.00210 -0.72622 1.08078 H -0.49927 1.64573 -0.89278 H 1.03014 1.63298 0.00000 H -0.49927 1.64573 0.89278 end basis * library 6-311G* end mcscf maxiter 100 multiplicity 1 symmetry 2 active 6 actelec 6 end task mcscf energy it's OK. But when I start same calculations with task mcscf freq I recieve the message: ------------------------------------------------------------------------ singlet symmetry state not found in CAS 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 0: ------------------------------------------------------------------------ singlet symmetry state not found in CAS 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 0: ------------------------------------------------------------------------ ------------------------------------------------------------------------ There is an error related to the specified geometry singlet symmetry state not found in CAS 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 0: ------------------------------------------------------------------------ ------------------------------------------------------------------------ There is an error related to the specified geometry ------------------------------------------------------ Please, tell me what is wrong! Thanks! Ovsyannikov Dmitry.