Maybe you can try like this $CMD ='/usr/local/bin/python /home/monkey/Monkey0.01/selected.py -p '.$_POST['types'].' -s -1'.' -l'. $_POST['classlabel'].' -i '.$uploadfile_train.' -o '.$ig_anal_out.'2>&1'; echo `$CMD`;
lirong -----Original Message----- From: openbabel-discuss-requ...@lists.sourceforge.net [mailto:openbabel-discuss-requ...@lists.sourceforge.net] Sent: Thursday, September 09, 2010 11:11 AM To: openbabel-discuss@lists.sourceforge.net Subject: OpenBabel-discuss Digest, Vol 52, Issue 3 Send OpenBabel-discuss mailing list submissions to openbabel-discuss@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/openbabel-discuss or, via email, send a message with subject or body 'help' to openbabel-discuss-requ...@lists.sourceforge.net You can reach the person managing the list at openbabel-discuss-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of OpenBabel-discuss digest..." Today's Topics: 1. Problem of Calling OB with PHP (Jie Shen) 2. Re: Release candidates available for testing (Chris Morley) 3. Re: Release candidates available for testing (Douglas Houston) 4. Re: Release candidates available for testing (Craig A. James) 5. Re: protonation and structure normalization (david.lagorce) 6. inchi/inchikey and WriteString (Bradley Worley) ---------------------------------------------------------------------- Message: 1 Date: Tue, 7 Sep 2010 07:09:04 +0800 From: Jie Shen <jiees...@gmail.com> Subject: [Open Babel] Problem of Calling OB with PHP To: openbabel-discuss@lists.sourceforge.net Message-ID: <aanlktim8wcbnu=2lmn3vuuc4rerzuv0y559jxzqxz...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear all, I am now trying to built a web-based calculation server. It will work like this: Using PHP call the python script in linux. The script could run well in the terminal of linux, but the same commands can not run successfully under PHP calling (using "shell_exec") The error listed: Traceback (most recent call last): ?File "/home/monkey/Monkey0.01/selected.py", line 137, in ? main(sys.argv[1:]) ?File "/home/monkey/Monkey0.01/selected.py", line 74, in main ? import getopt, string, readsdf ?File "/home/monkey/Monkey0.01/readsdf.py", line 33, in ? import pybel as pb ?File "/home/monkey/program/OB-2.2.3/lib/python2.6/site-packages/pybel.py", line 16, in ? import openbabel as ob ?File "/home/monkey/program/OB-2.2.3/lib/python2.6/site-packages/openbabel.py", line 36, in ? _openbabel = swig_import_helper() ?File "/home/monkey/program/OB-2.2.3/lib/python2.6/site-packages/openbabel.py", line 35, in swig_import_helper ? return _mod UnboundLocalError: local variable '_mod' referenced before assignment The calling line in PHP is: (attached is the php file) $results=shell_exec('/usr/local/bin/python /home/monkey/Monkey0.01/selected.py -p '.$_POST['types'].' -s -1'.' -l '.$_POST['classlabel'].' -i '.$uploadfile_train.' -o '.$ig_anal_out.' 2>&1'); BTW, this command can run successfully in the terminal after translation. and we have exclude following reasons: 1. safe mode is already off 2. The shell command is right 3. there is no problem with "permission" issues. I am grateful if anyone can help me. Best regards, Sincerely, Jie Shen -------------- next part -------------- A non-text attachment was scrubbed... Name: upload_basic.php Type: application/octet-stream Size: 5231 bytes Desc: not available ------------------------------ Message: 2 Date: Wed, 08 Sep 2010 16:50:13 +0100 From: Chris Morley <c.mor...@gaseq.co.uk> Subject: Re: [Open Babel] Release candidates available for testing To: openbabel-discuss@lists.sourceforge.net Message-ID: <4c87b0b5.6060...@gaseq.co.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 08/09/2010 13:17, Douglas Houston wrote: > Hi, > > According to this page: > > http://baoilleach.webfactional.com/site_media/ob-docs/Features/Fingerprints. html#fingerprints > > I can use the -s option with the name of a file, e.g.: > > babel mymols.sdf -sSubstructure.sdf mymols_filtered.sdf > > will write out all the compounds in mymols.sdf that contain the group > in Substructure.sdf. However, what I'd like is the opposite, i.e. to > write out everything that doesn't match. I tried using -v instead of > -s but this didn't work. I think the following will do what you want babel mymols.sdf -s ~Substructure.sdf mymols_filtered.sdf > > It would also be nice if I could use a file that contained more than > one entry, i.e. the file Substructure.sdf could define multiple > fragments that I don't want in my molecules, rather than having to > run Babel on each one separately. It would have to be decided whether the combination was AND or OR. What you want is NOT(frag1 OR frag2 OR...) In the related --filter option there is an implicit AND between tests, but I think for both the -s filter and its inverse the OR behaviour is more intuitive. > > Would this be doable before the final release? It may be, but I am about to go on holiday, so don't hold your breath. Thanks for this suggestion. Other suggestions for useful features are very welcome. You could look at the Sieve program, http://www.silicos.be/sieve.html which is an industrial-strength filtering program, now using OpenBabel. Chris ------------------------------ Message: 3 Date: Wed, 08 Sep 2010 17:32:19 +0100 From: Douglas Houston <dhous...@staffmail.ed.ac.uk> Subject: Re: [Open Babel] Release candidates available for testing To: openbabel-discuss@lists.sourceforge.net Message-ID: <20100908173219.u5lu3lmb4o4os...@www.staffmail.ed.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Thanks Chris, The line you gave seemed to do the trick - after I escaped out the tilde. Is the usage of the tilde to reverse the sense of the filter documented? I would have thought the -v option would be logical. Sieve seems to do what I want - almost. It looks like it filters using SMARTS - but all my undesirable groups are in SDF format. How do I convert to SMARTS? OpenBabel doesn't seem to do it (although it can filter using them, strangely). I realise I could potentially use SMILES as input but this doesn't work in some cases, e.g. 'C1=CC=CC=C1' is a benzene ring in SMILES format but according to the following link will not match benzene if it's used as a SMARTS string. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html cheers, Doug Quoting Chris Morley <c.mor...@gaseq.co.uk>: > On 08/09/2010 13:17, Douglas Houston wrote: >> Hi, >> >> According to this page: >> >> http://baoilleach.webfactional.com/site_media/ob-docs/Features/Fingerprints. html#fingerprints >> >> I can use the -s option with the name of a file, e.g.: >> >> babel mymols.sdf -sSubstructure.sdf mymols_filtered.sdf >> >> will write out all the compounds in mymols.sdf that contain the group >> in Substructure.sdf. However, what I'd like is the opposite, i.e. to >> write out everything that doesn't match. I tried using -v instead of >> -s but this didn't work. > > I think the following will do what you want > babel mymols.sdf -s ~Substructure.sdf mymols_filtered.sdf >> >> It would also be nice if I could use a file that contained more than >> one entry, i.e. the file Substructure.sdf could define multiple >> fragments that I don't want in my molecules, rather than having to >> run Babel on each one separately. > > It would have to be decided whether the combination was AND or OR. > What you want is NOT(frag1 OR frag2 OR...) > In the related --filter option there is an implicit AND between tests, > but I think for both the -s filter and its inverse the OR behaviour is > more intuitive. >> >> Would this be doable before the final release? > > It may be, but I am about to go on holiday, so don't hold your breath. > > Thanks for this suggestion. Other suggestions for useful features are > very welcome. > > You could look at the Sieve program, http://www.silicos.be/sieve.html > which is an industrial-strength filtering program, now using OpenBabel. > > Chris > > ---------------------------------------------------------------------------- -- > This SF.net Dev2Dev email is sponsored by: > > Show off your parallel programming skills. > Enter the Intel(R) Threading Challenge 2010. > http://p.sf.net/sfu/intel-thread-sfd > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > _____________________________________________________ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------ Message: 4 Date: Wed, 08 Sep 2010 10:05:42 -0700 From: "Craig A. James" <cja...@emolecules.com> Subject: Re: [Open Babel] Release candidates available for testing To: openbabel-discuss@lists.sourceforge.net Message-ID: <4c87c266.6050...@emolecules.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/8/10 9:32 AM, Douglas Houston wrote: > I realise I could potentially use SMILES as input but this doesn't > work in some cases, e.g. 'C1=CC=CC=C1' is a benzene ring in SMILES > format but according to the following link will not match benzene if > it's used as a SMARTS string. > > http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html If you canonicalize a SMILES (babel ... -o can), it usually works correctly as a SMARTS. That's one of the features of the canonical algorithm. In the case you cite, it would convert to "c1ccccc1", which is the SMARTS that you want. Craig ------------------------------ Message: 5 Date: Thu, 9 Sep 2010 02:44:39 -0700 (PDT) From: "david.lagorce" <david.lago...@univ-paris-diderot.fr> Subject: Re: [Open Babel] protonation and structure normalization To: openbabel-discuss@lists.sourceforge.net Message-ID: <1284025479853-2532557.p...@n4.nabble.com> Content-Type: text/plain; charset=us-ascii > openbabel command line, it would seem that the results are different > from those obtained with the AddHydrogens() method embedded in the pybel > library, with the correctforpH option. >Well yes, if you're comparing AddHydrogens() with and without correctForPH, then the results are >different. But I can assure you that Pybel calls the same calls as the command-line when you supply >the same options. > Does pybel use also the /data/phmodel.txt file? > Yes. ok, thanks a lot > It is documented that it is possible to convert [N+]([O-])=O to N(=O)=O, > but it doesn't work for the other representations of the nitro groups, > like [N](-OH)=O. >I have never seen a nitro group represented with an explicit H. Can you give us a real example? Or a >list of the "other representations of nitro groups" that you expect? I am also agree with you, a nitro with an explicit H, by definition is not a cleary possible, but you can sometimes find it in some databases....Thus, how to correclty re-write it....with babel? In the same way, a nitro group as N(=O)=O loaded in pybel is converted internaly in background to N(OH)OH.... N(=O)=O is possible, so pybel will found 2 H-Bond Donors (lipinski definition) but in fact there is no one... > To this end, which file (containing the SMARTS patterns) is employed in > the pybel method? >CorrectDativeBonds does not use SMARTS patterns. Instead, it looks for atom pairs with neighboring "+" and "-" formal charges and it increases the bond order to remove the formal charges. >Hope that helps, >-Geoff Thanks a lot for your help... David -- View this message in context: http://open-babel.957263.n4.nabble.com/protonation-and-structure-normalizati on-tp2528314p2532557.html Sent from the openbabel-discuss mailing list archive at Nabble.com. ------------------------------ Message: 6 Date: Wed, 8 Sep 2010 13:48:36 -0500 From: Bradley Worley <bradley.wor...@huskers.unl.edu> Subject: [Open Babel] inchi/inchikey and WriteString To: <openbabel-discuss@lists.sourceforge.net> Message-ID: <1283971716.6354.2.ca...@bionmr-16.unl.edu> Content-Type: text/plain hi all, i have a segment of C++ code that loads a "mol" file and tries to write two strings: an inchi string and an inchikey string. the inchi conversion works, but the inchikey WriteString() command that immediately follows gives the inchi string, not the inchikey. (yes, i'm using SetOptions("K",conv.OUTOPTIONS)). am i missing something? thanks, ~ brad worley. ------------------------------ ---------------------------------------------------------------------------- -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss End of OpenBabel-discuss Digest, Vol 52, Issue 3 ************************************************ ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
