Dear Noel and all, That's great! I wonder know whether we can use PubChem fingerprint in openbabel or pybel? There are about 1,000 substurcture SMARTS patterns available.
ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt Thank you very much Best regards, Jie Shen 2010/3/9 Noel O'Boyle <[email protected]> > (Please cc to openbabel-scripting) > > You're right that the MACCS fingerprint was not included in pybel in the > current release. Future releases will include all of the available > fingerprints automatically. In the meanwhile, we can hack it in as follows: > > import pybel > pybel.fps.append("MACCS") > pybel._fingerprinters = > pybel._getplugins(pybel.ob.OBFingerprint.FindFingerprint, pybel.fps) > mol = pybel.readstring("smi", "CCCC(=O)Cl") > print mol.calcfp("MACCS").bits > # [103, 107, 114, 115, 132, 134, 147, 154, 155, 160, 164] > > Alternatively, you can use the pybel.py included in cinfony, which has this > feature already. > > - Noel > > > 2010/3/9 David Lagorce <[email protected]> > >> Hello Noel, >> >> I am carrying out tests for similarity between various molecules and I >> read in the babel doc that fingerprints MACCS are not are not implemented in >> the pybel function calcfp (), but present in the openbabel command line way >> Is this true?? >> If so, have you intention to do it in the next versions, and/or can I do >> it with the 2.2.3 version?? >> >> Thanks >> >> regards >> >> >> David >> >> >> >> >> >> -- >> >> *David Lagorce* >> >> INSERM U973 – MT*i* Bioinformatics >> >> Université Paris Diderot >> >> Batiment Lamarck >> >> 35, rue Hélène Brion >> >> 75013 PARIS >> >> 01 57 27 83 89 >> >> [email protected] >> >> http://www.mti.univ-paris-diderot.fr >> >> >> Bonjour à tous, >> >> Merci de bien vouloir diffuser et afficher cette offre de formation. >> >> Cordialement, >> >> >> >> *Inès BELHADJ* >> >> Responsable formation >> >> Inserm Délégation Régionale PARIS 7 >> >> Tour les Mercuriales >> >> 40 rue Jean Jaurès >> >> 93176 Bagnolet cedex >> >> Tél. (33)1 43 62 27 07 >> >> Fax. (33)1 43 62 27 30 >> >> Email : [email protected] >> >> Site web : http://www.parisnord.idf.inserm.fr >> >> <http://www.inserm.fr> >> <http://www.inserm.fr> >> >> >> >> *Formation «Sécurité laser»** * >> >> >> >> *Objectifs :* >> >> À l'issue de cette formation, les stagiaires devront : >> >> >> >> - avoir des notions sur les caractéristiques d'émission d'un laser >> >> >> >> - connaître les effets des rayonnements laser sur l'oeil et la peau >> >> >> >> - connaître les procédures de contrôle du danger en particulier les >> mesures de prévention (étiquetage, signification des symboles, classes...) >> >> >> >> - être conscients de la nécessité d'une protection collective ou >> individuelle. >> >> >> >> *Public** :* >> >> Personne responsable d’appareils intégrant des lasers de classe 3A, 3B ou >> 4 (microscopes confocaux, cytométres, …). >> >> *Durée / Dates :** * >> >> *1 jour / 29 avril 2010* >> >> *Date limite d’inscription :** * *6 avril 2010* >> >> >> >> *Dossier d'inscription : **cliquez >> ici*<http://www.rh.inserm.fr/INSERM/IntraRH/RHActionsFormation.nsf/vAFSearch/EBA78C52AC5B2061C12576DB005E1537?OpenDocument&1&mode=imp> >> >> <http://www.rh.inserm.fr/INSERM/IntraRH/RHActionsFormation.nsf/vAFSearch/EBA78C52AC5B2061C12576DB005E1537?OpenDocument&1&mode=imp> >> ------------------------------ >> size=2 width=620 style='width:465.0pt' noshade color="#ff6600" align=left> >> >> >> >> >> *LAURENCE DOUMENC** >> Responsable formation continue >> *Délégation régionale Inserm Midi-Pyrénées / Limousin >> BP 3048 - CHU Purpan - 31024 Toulouse cedex 3 >> Téléphone : 05 62 74 83 58 >> Télécopie : 05 61 31 97 52 >> [email protected] >> >> >> >> >> >> Site : >> http://www.rh.inserm.fr/INSERM/IntraRH/RHActionsFormation.nsf/mvActionsFormation?OpenForm >> >> >> ------------------------------ >> >> >> >> -- >> >> >> >> > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > OpenBabel-scripting mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > >
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