[Open Babel] Segmentation fault in inchi conversion
Hi, I get a segmentation fault when running the following command: obabel -iinchi -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;" -osmi I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via homerbrew). I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1 and here it's working without problem. Is there anyone else having problems with this, or is it just me? Kind regards, Fredrik -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Segmentation fault in inchi conversion
Hi again, Some more information… The InChI "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-" gives the same problem. I have now updated the ubuntu box to also run ob 2.3.2 and it segfaults now as well, so it seems it has something to do with differences between 2.3.1 and 2.3.2. Kind regards, Fredrik 11 apr 2013 kl. 14:45 skrev Fredrik Wallner : > Hi, > > I get a segmentation fault when running the following command: > obabel -iinchi > -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;" > -osmi > > I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via > homerbrew). > I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1 and here > it's working without problem. Is there anyone else having problems with this, > or is it just me? > > Kind regards, > Fredrik > -- > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Confusion in similarity search
Hi, In a similarity search, obabel consider another molecule than the reference I'm giving. My library being test.smi: C1(=CC2=C(C(C(C2)(C#N)C#N)(CC(=O)C)C#N)C(=O)N)C(=O)NC(=O)S1 A C1(=Cc2c(oc3c(cc(cc3)Br)c2=O)C(=O)N)C(=O)NC(=O)S1B C1(=CC2=C(C(C(C2)(C#N)C#N)(C22=O)C#N)C(=O)N)C(=O)NC(=O)S1C after conversion in fs format: obabel test.smi -ofs The command: obabel test.fs -SA.smi -ofpt -at0.0 is giving: >C >A Tanimoto from C = 1 Possible superstructure of C >B Tanimoto from C = 0.278689 3 molecules converted A is _not_ the reference (first line). obabel is considering C instead. B as reference is ok: obabel test.fs -SB.smi -ofpt -at0.0 >B >C Tanimoto from B = 0.278689 >A Tanimoto from B = 0.278689 3 molecules converted C as reference is OK, and is producing the same result as if taking A as reference. Changing the order in test.smi (e.g. C, A, B), using C as reference returns A in the first line. Using A as reference is OK. I have 43 similar cases out of my 1579 compounds library. Any ideas apart from shuffling the smiles file? :) Regards, Pascal -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Confusion in similarity search
> Any ideas apart from shuffling the smiles file? :) At least, for this question, it's ok, I get round the problem to fetch all the values I need. Regards, Pascal -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Confusion in similarity search
On 11/04/2013 15:45, Pascal Muller wrote: > Hi, > > In a similarity search, obabel consider another molecule than the > reference I'm giving. > > My library being test.smi: > > C1(=CC2=C(C(C(C2)(C#N)C#N)(CC(=O)C)C#N)C(=O)N)C(=O)NC(=O)S1 A > C1(=Cc2c(oc3c(cc(cc3)Br)c2=O)C(=O)N)C(=O)NC(=O)S1B > C1(=CC2=C(C(C(C2)(C#N)C#N)(C22=O)C#N)C(=O)N)C(=O)NC(=O)S1C > > after conversion in fs format: > obabel test.smi -ofs > > The command: > obabel test.fs -SA.smi -ofpt -at0.0 > is giving: > >> C >> A Tanimoto from C = 1 > Possible superstructure of C >> B Tanimoto from C = 0.278689 > 3 molecules converted > > A is _not_ the reference (first line). obabel is considering C instead. > > > B as reference is ok: > obabel test.fs -SB.smi -ofpt -at0.0 >> B >> C Tanimoto from B = 0.278689 >> A Tanimoto from B = 0.278689 > 3 molecules converted > > C as reference is OK, and is producing the same result as if taking A > as reference. > > > Changing the order in test.smi (e.g. C, A, B), using C as reference > returns A in the first line. Using A as reference is OK. > > I have 43 similar cases out of my 1579 compounds library. > Any ideas apart from shuffling the smiles file? :) fs and fpt formats are not really intended to be used together. If you want to find the 10 most similar molecules to molecule A in a *large* dataset use obabel test.fs -osmi -s A.smi -at10 OR to show similarities from A to each molecule in a *small* dataset obabel A.smi test.smi -ofpt (The target molecule is the first molecule that is output.) You shouldn't need to use -at0.0 (even when its bugs are corrected, see next post). Chris -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Similarity search / Open Babel Warning in ParseSmiles
On 10/04/2013 16:55, Pascal Muller wrote: > Dear all, > > I would like to find similar molecules within library and compute > Tanimoto coefficient. > > I'm right by assuming that, using -at0.0, I should retrieve all molecules? > > obabel library.fs -Smol.smi -ofpt -at0.0 > (version 2.3.2) > > But I get only 1098 compounds out of a total of 1579, along with 262 > warning messages like: > > Open Babel Warning in ParseSmiles > Invalid SMILES string: 1 unmatched ring bonds. > > or: > Open Babel Warning in ParseRingBond > Number not parsed correctly as a ring bond > > If I use the library.smi file instead of .fs, I get only 19 molecules > (-at0.0), and no error message. > > If I convert the library smiles file into sdf, and depending on the > compound in -Smol.smi, sometimes all molecules are converted, as I > expect with -at0.0, sometimes only a few are converted, sometimes only > one with e.g. this output: > > ZINC00089110 183 bits set > 00410030 01248d00 a0084102 40100e04 40050001 00200809 > 1480 102c1402 03484900 821a4081 40350020 40011a80 > 540a8518 202d 0420 0104 24484000 02000b00 > 400920c0 02000101 000a0500 38040694 40808c00 0448829e > 00200010 20203620 44404010 88040150 008000e2 c11e0003 > ac824010 c3010680 > 1 molecule converted > > > I'm trying to get a sample smi file to send as example, but until now > I'm not able to reproduce every case I have written above. > > Did you already encounter such behavior, or is there a known bug I'm > not aware of? Your problem with missing molecules when using fastsearch with -at0.0 seems to be caused by two bugs: 1) comparing Tanimoto coeffs with > rather than >= and 2) for files which do not have a new line at the end, the conversion stopped because of an eof when the last molecule was read. In fastsearch, unusually, the molecules are read non-sequentially. I'll commit the changes soon. Thanks for finding these bugs. Incidentally, the -S option is deprecated; use -s instead, which can take either SMARTS or a file name containing molecule(s), and is more versatile. Chris -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] What's New and Cooking in Open Babel?
I presented a short talk at the recent ACS meeting describing what's new and under development in Open Babel. You can check it out at: http://baoilleach.blogspot.com/2013/04/talk-on-open-babel-at-new-orleans-acs.html Regards, Noel -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] What's New and Cooking in Open Babel?
Nice! Craig On Thu, Apr 11, 2013 at 1:39 PM, Noel O'Boyle wrote: > I presented a short talk at the recent ACS meeting describing what's > new and under development in Open Babel. You can check it out at: > > http://baoilleach.blogspot.com/2013/04/talk-on-open-babel-at-new-orleans-acs.html > > Regards, >Noel > > > -- > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] forcefield setting
Good afternoon, I installed Openbabel on my Windows 7 laptop. I could minimize a molecule by obabel input.sdf -O output.sdf --minimize but when I tried to use a different forcefield by obabel input.sdf -O output.sdf --minimize -ff MMFF94 or "-ff Ghemical" or "-ff MMFF94s" it complains that it 'Cannot read input format "" for file "MMFF94". What am I missing? Probably I need to correctly set the environment variables LD_LIBRARY_PATH , BABEL_DATADIR , BABEL_LIBDIR ? What should I set them to be? Thank you. Ling -- View this message in context: http://forums.openbabel.org/forcefield-setting-tp4656179.html Sent from the General discussion mailing list archive at Nabble.com. -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] forcefield setting
I just found my answer for the forcefield setting in an earlier post. I should use "--ff" instead of "-ff". But still, if there is a proper way to set up the environment variables, I would be interested to know. LIng -- View this message in context: http://forums.openbabel.org/forcefield-setting-tp4656179p4656180.html Sent from the General discussion mailing list archive at Nabble.com. -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
