For me, 2.3.0 gives: noboyle@boole:~/tools/openbabel/openbabel-2.3.0-install/bin$ ./obabel -:"Clc1c(/C=C/C(=O)NNC(=O)Cn2nc(cc2C)C)c(F)ccc1" -ofpt -xf FP4 > 19 bits set 00000000 00000000 00000000 00000000 00000000 00000000 00007843 40060000 00000000 00000000 00980c00 00000100 00000000 00800000 00000000 00000011 1 molecule converted
noboyle@boole:~/tools/openbabel/openbabel-2.3.0-install/bin$ ./obabel -:"Clc1c(/C=C/C(=O)NNC(=O)Cn2nc(cc2C)C)c(F)ccc1" -ofpt -xf FP4 -xs > Primary_carbon Alkene Carboxylic_acid_derivative Vinylogous_ester Arylchloride Arylfluoride Hetero_N_basic_no_H Hetero_N_nonbasic Heteroaromatic Aromatic Heterocyclic Conjugated_double_bond Cis_double_bond Trans_double_bond C_ONS_bond 1,3-Tautomerizable 1,5-Tautomerizable Rotatable_bond Michael_acceptor 1 molecule converted Current SVN gives the same. It has likely changed since 2.2.3 for the reason you mentioned - we added stereo support to the SMARTS. - Noel On 17 July 2011 15:11, Andrew Dalke <[email protected]> wrote: > Hi, > > I'm doing regressions for my chemfp package. > > I have OpenBabel 2.2.3, 2.3.0 and today's "2.3.90" compiled from SVN, each > compiled against various versions of Python. What's below is with Python 2.6. > > It looks like there's a change to the FP4 fingerprints, but I can't figure > out why. > > Here's the reproducible > > > ---> Version 2.2.3 and 2.3.0 <--- > > bash-3.2$ /Users/dalke/envs/py26-ob230/bin/python2.6 > Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) > [GCC 4.2.1 (Apple Inc. build 5646)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import openbabel >>>> openbabel.OBReleaseVersion() > '2.3.0' >>>> >>>> import pybel >>>> reader = pybel.readfile("sdf","tests/pubchem.sdf") >>>> mol=reader.next() >>>> mol.write("smi") > 'Clc1c(/C=C/C(=O)NNC(=O)Cn2nc(cc2C)C)c(F)ccc1\t9425004\n' >>>> mol.calcfp("FP4").bits > [1, 5, 88, 137, 171, 172, 180, 181, 184, 274, 275, 287, 295, 300, 301, 302, > 303] > > ---> Version 2.3.90 (built today from SVN) <--- > > bash-3.2$ /Users/dalke/envs/py26-ob23svn1/bin/python2.6 > Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) > [GCC 4.2.1 (Apple Inc. build 5646)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import openbabel >>>> openbabel.OBReleaseVersion() > '2.3.90' >>>> import pybel >>>> reader = pybel.readfile("sdf","tests/pubchem.sdf") >>>> mol = reader.next() >>>> mol.write("smi") > 'Clc1c(/C=C/C(=O)NNC(=O)Cn2nc(cc2C)C)c(F)ccc1\t9425004\n' >>>> mol.calcfp("FP4").bits > [1, 5, 88, 137, 171, 172, 180, 181, 184, 274, 275, 287, 289, 290, 295, 300, > 301, 302, 303] > > > > You can see that the subversion build has two new bits; 289 and 290. > > The SMARTS_InteLigand.txt file is unchanged between the two releases. Indeed, > there's been no SVN change for many years. > > The canonical SMILES are identical, so it's unlikely to be an aromaticity > perception issue. > > > I believe pybel's bit start counting from 1 since if I extract the SMARTS > definitions from the SMARTS file I see that the first one (which I've labeled > '1') is: > > 1 Primary_carbon: [CX4H3][#6] > > This means that 289 and 290 deal with the "D" pattern and deal with '/' and > '\' bonds. > > 288 Conjugated_tripple_bond: *#*[*]=,#,:[*] > 289 Cis_double_bond: */[D2]=[D2]\* > 290 Trans_double_bond: */[D2]=[D2]/* > 291 Mixed_anhydrides: > [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))] > > Has the SMARTS pattern matcher for either of those changed? (I'm betting > stereo.) > > > Andrew > [email protected] > > Here's the original structure file > > =================================== > 9425004 > -OEChem-01150805002D > > 40 41 0 0 0 0 0 0 0999 V2000 > 2.0000 -3.0580 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 > 5.4641 -3.0580 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 > 7.1962 0.9420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 3.7321 -0.0580 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 7.1962 2.9420 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 7.3007 3.9365 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 5.4641 0.9420 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 5.4641 -0.0580 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 8.1097 2.5353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.3301 2.4420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 8.7788 3.2784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 8.2788 4.1444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 8.3176 1.5571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.3301 1.4420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 8.6856 5.0580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.7321 -3.0580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.7321 -2.0580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.5981 -0.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.8660 -3.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.5981 -3.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.5981 -1.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.8660 -4.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.5981 -4.5580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.7321 -5.0580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 6.1181 3.0246 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.7195 2.3343 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 9.3954 3.2136 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 7.7112 1.4282 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 8.4465 0.9507 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 8.9241 1.6860 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 8.1192 5.3102 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 8.9377 5.6244 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 9.2520 4.8058 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 4.9272 1.2520 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 6.0010 -0.3680 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 3.1951 -1.7480 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 -1.8680 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 2.3291 -4.8680 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1350 -4.8680 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 3.7321 -5.6780 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1 19 1 0 0 0 0 > 2 20 1 0 0 0 0 > 3 14 2 0 0 0 0 > 4 18 2 0 0 0 0 > 5 6 1 0 0 0 0 > 5 9 1 0 0 0 0 > 5 10 1 0 0 0 0 > 6 12 2 0 0 0 0 > 7 8 1 0 0 0 0 > 7 14 1 0 0 0 0 > 7 34 1 0 0 0 0 > 8 18 1 0 0 0 0 > 8 35 1 0 0 0 0 > 9 11 2 0 0 0 0 > 9 13 1 0 0 0 0 > 10 14 1 0 0 0 0 > 10 25 1 0 0 0 0 > 10 26 1 0 0 0 0 > 11 12 1 0 0 0 0 > 11 27 1 0 0 0 0 > 12 15 1 0 0 0 0 > 13 28 1 0 0 0 0 > 13 29 1 0 0 0 0 > 13 30 1 0 0 0 0 > 15 31 1 0 0 0 0 > 15 32 1 0 0 0 0 > 15 33 1 0 0 0 0 > 16 17 1 0 0 0 0 > 16 19 1 0 0 0 0 > 16 20 2 0 0 0 0 > 17 21 2 0 0 0 0 > 17 36 1 0 0 0 0 > 18 21 1 0 0 0 0 > 19 22 2 0 0 0 0 > 20 23 1 0 0 0 0 > 21 37 1 0 0 0 0 > 22 24 1 0 0 0 0 > 22 38 1 0 0 0 0 > 23 24 2 0 0 0 0 > 23 39 1 0 0 0 0 > 24 40 1 0 0 0 0 > M END >> <PUBCHEM_COMPOUND_CID> > 9425004 > > $$$$ > =================================== > ------------------------------------------------------------------------------ > AppSumo Presents a FREE Video for the SourceForge Community by Eric > Ries, the creator of the Lean Startup Methodology on "Lean Startup > Secrets Revealed." This video shows you how to validate your ideas, > optimize your ideas and identify your business strategy. > http://p.sf.net/sfu/appsumosfdev2dev > _______________________________________________ > OpenBabel-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
