Re: [Open Babel] SMILES, SMARTS, and PDB
I think this will work great. Thanks for the suggestion. -Original Message- From: Maciek Wójcikowski mac...@wojcikowski.pl Sent: 7/8/2013 12:06 PM To: Brett Hannigan godot_gil...@yahoo.com Cc: Brett T. Hannigan bret...@mail.med.upenn.edu; openbabel-discuss@lists.sourceforge.net openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] SMILES, SMARTS, and PDB I think you need custom code. For python, you could use pybel. There are three lines that do what you want (http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall). You only miss one or two lines to get the atoms by their indices. Although searching pdb files with it could be a demanding and time consuming task. It's really made for small molecules, i guess. I'd personally would loop through atoms check if they are HETATOMs and then check SMARTS pattern. Alternatively, you can filter them by name, if you can suspect what's your residues name could be (although it's the most error prone). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Brett Hannigan godot_gil...@yahoo.com Unfortunately, I don't think that's quite what I need. The obabel filter command will look at the given pdb and then output the entire pdb if it matches the given SMARTS query, right? What I would like to do is only get the atoms that match the SMARTS query. For example, let's say I have a pdb with a single phospho-serine residue. What I would like to do is get only the phosphate atoms from the pdb, and not get the rest of the residue atoms. Really what I am going for here is I'd like specify some groups that I find interesting, say a phosphate group, a phenyl group, etc. And then I have a database of protein + ligand pdbs. I'd like to loop through those pdbs and look for my groups that I am interested in. Rather than just identify the pdbs that have the sub-structure I am interested in (i.e. identify all pdbs with phosphates), I want to know which atoms in the pdb constitute the interesting sub-structure. That way I could then align all phosphate groups and look at the residues surrounding the phophates to see if I see common modes of binding etc. Phosphate would just be one example, you can imagine identifying many other interesting sub-structures. -Brett From: Maciek Wójcikowski mac...@wojcikowski.pl To: Brett T. Hannigan bret...@mail.med.upenn.edu Cc: openbabel-discuss@lists.sourceforge.net Sent: Saturday, July 6, 2013 6:21 AM Subject: Re: [Open Babel] SMILES, SMARTS, and PDB Hello, You can convert from PDB to PDB using filter option (http://openbabel.org/wiki/--filter_option) obabel input.pdb -O output.pdb --filter s='CN' If your database is really large, or you want to search multiple times, then I'd suggest using FastSearch for performance reasons. For further lecture: http://openbabel.org/wiki/FastSearch Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? -- ** Brett T. Hannigan 8011 Ardleigh St. Philadelphia, PA 19118 brett.hanni...@gmail.com ** -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss-- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
Unfortunately, I don't think that's quite what I need. The obabel filter command will look at the given pdb and then output the entire pdb if it matches the given SMARTS query, right? What I would like to do is only get the atoms that match the SMARTS query. For example, let's say I have a pdb with a single phospho-serine residue. What I would like to do is get only the phosphate atoms from the pdb, and not get the rest of the residue atoms. Really what I am going for here is I'd like specify some groups that I find interesting, say a phosphate group, a phenyl group, etc. And then I have a database of protein + ligand pdbs. I'd like to loop through those pdbs and look for my groups that I am interested in. Rather than just identify the pdbs that have the sub-structure I am interested in (i.e. identify all pdbs with phosphates), I want to know which atoms in the pdb constitute the interesting sub-structure. That way I could then align all phosphate groups and look at the residues surrounding the phophates to see if I see common modes of binding etc. Phosphate would just be one example, you can imagine identifying many other interesting sub-structures. -Brett From: Maciek Wójcikowski mac...@wojcikowski.pl To: Brett T. Hannigan bret...@mail.med.upenn.edu Cc: openbabel-discuss@lists.sourceforge.net Sent: Saturday, July 6, 2013 6:21 AM Subject: Re: [Open Babel] SMILES, SMARTS, and PDB Hello, You can convert from PDB to PDB using filter option (http://openbabel.org/wiki/--filter_option) obabel input.pdb -O output.pdb --filter s='CN' If your database is really large, or you want to search multiple times, then I'd suggest using FastSearch for performance reasons. For further lecture: http://openbabel.org/wiki/FastSearch Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? -- ** Brett T. Hannigan 8011 Ardleigh St. Philadelphia, PA 19118 brett.hanni...@gmail.com ** -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
I think you need custom code. For python, you could use pybel. There are three lines that do what you want ( http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall). You only miss one or two lines to get the atoms by their indices. Although searching pdb files with it could be a demanding and time consuming task. It's really made for small molecules, i guess. I'd personally would loop through atoms check if they are HETATOMs and then check SMARTS pattern. Alternatively, you can filter them by name, if you can suspect what's your residues name could be (although it's the most error prone). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Brett Hannigan godot_gil...@yahoo.com Unfortunately, I don't think that's quite what I need. The obabel filter command will look at the given pdb and then output the entire pdb if it matches the given SMARTS query, right? What I would like to do is only get the atoms that match the SMARTS query. For example, let's say I have a pdb with a single phospho-serine residue. What I would like to do is get only the phosphate atoms from the pdb, and not get the rest of the residue atoms. Really what I am going for here is I'd like specify some groups that I find interesting, say a phosphate group, a phenyl group, etc. And then I have a database of protein + ligand pdbs. I'd like to loop through those pdbs and look for my groups that I am interested in. Rather than just identify the pdbs that have the sub-structure I am interested in (i.e. identify all pdbs with phosphates), I want to know which atoms in the pdb constitute the interesting sub-structure. That way I could then align all phosphate groups and look at the residues surrounding the phophates to see if I see common modes of binding etc. Phosphate would just be one example, you can imagine identifying many other interesting sub-structures. -Brett -- *From:* Maciek Wójcikowski mac...@wojcikowski.pl *To:* Brett T. Hannigan bret...@mail.med.upenn.edu *Cc:* openbabel-discuss@lists.sourceforge.net *Sent:* Saturday, July 6, 2013 6:21 AM *Subject:* Re: [Open Babel] SMILES, SMARTS, and PDB Hello, You can convert from PDB to PDB using filter option ( http://openbabel.org/wiki/--filter_option) obabel input.pdb -O output.pdb --filter s='CN' If your database is really large, or you want to search multiple times, then I'd suggest using FastSearch for performance reasons. For further lecture: http://openbabel.org/wiki/FastSearch Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? -- ** Brett T. Hannigan 8011 Ardleigh St. Philadelphia, PA 19118 brett.hanni...@gmail.com ** -- This SF.net http://sf.net/ email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
You could also look into ProDy, if you use PDB files. http://www.csb.pitt.edu/prody/reference/atomic/flags.html#term-hetero Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Maciek Wójcikowski mac...@wojcikowski.pl I think you need custom code. For python, you could use pybel. There are three lines that do what you want ( http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall). You only miss one or two lines to get the atoms by their indices. Although searching pdb files with it could be a demanding and time consuming task. It's really made for small molecules, i guess. I'd personally would loop through atoms check if they are HETATOMs and then check SMARTS pattern. Alternatively, you can filter them by name, if you can suspect what's your residues name could be (although it's the most error prone). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Brett Hannigan godot_gil...@yahoo.com Unfortunately, I don't think that's quite what I need. The obabel filter command will look at the given pdb and then output the entire pdb if it matches the given SMARTS query, right? What I would like to do is only get the atoms that match the SMARTS query. For example, let's say I have a pdb with a single phospho-serine residue. What I would like to do is get only the phosphate atoms from the pdb, and not get the rest of the residue atoms. Really what I am going for here is I'd like specify some groups that I find interesting, say a phosphate group, a phenyl group, etc. And then I have a database of protein + ligand pdbs. I'd like to loop through those pdbs and look for my groups that I am interested in. Rather than just identify the pdbs that have the sub-structure I am interested in (i.e. identify all pdbs with phosphates), I want to know which atoms in the pdb constitute the interesting sub-structure. That way I could then align all phosphate groups and look at the residues surrounding the phophates to see if I see common modes of binding etc. Phosphate would just be one example, you can imagine identifying many other interesting sub-structures. -Brett -- *From:* Maciek Wójcikowski mac...@wojcikowski.pl *To:* Brett T. Hannigan bret...@mail.med.upenn.edu *Cc:* openbabel-discuss@lists.sourceforge.net *Sent:* Saturday, July 6, 2013 6:21 AM *Subject:* Re: [Open Babel] SMILES, SMARTS, and PDB Hello, You can convert from PDB to PDB using filter option ( http://openbabel.org/wiki/--filter_option) obabel input.pdb -O output.pdb --filter s='CN' If your database is really large, or you want to search multiple times, then I'd suggest using FastSearch for performance reasons. For further lecture: http://openbabel.org/wiki/FastSearch Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? -- ** Brett T. Hannigan 8011 Ardleigh St. Philadelphia, PA 19118 brett.hanni...@gmail.com ** -- This SF.net http://sf.net/ email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
On 05/07/2013 17:54, Brett T. Hannigan wrote: I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? I would suggest that you can browser the ligand-expo service provided by PDB and download the smiles or 3D structures of small molecules http://ligand-expo.rcsb.org/ld-download.html Lirong Wang, PhD School of Pharmacy University of Pittsburgh -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
Hello, You can convert from PDB to PDB using filter option ( http://openbabel.org/wiki/--filter_option) obabel input.pdb -O output.pdb --filter s='CN' If your database is really large, or you want to search multiple times, then I'd suggest using FastSearch for performance reasons. For further lecture: http://openbabel.org/wiki/FastSearch Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? -- ** Brett T. Hannigan 8011 Ardleigh St. Philadelphia, PA 19118 brett.hanni...@gmail.com ** -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
On 05/07/2013 17:54, Brett T. Hannigan wrote: I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? If you just want to visualize this and the substructures can represented by SMILES, put them in a file, and try obabel *.pdb -O out.svg -s substructs.smi green Only those molecules containing at least one substructure are displayed and the matched atoms are displayed colored green. If additional colors are specified in the command, each substructure can have its own color. For more details obabel -L ops s To do more you will need to use OBSmartsPattern in C++, python, etc. http://openbabel.org/api/2.3/classOpenBabel_1_1OBSmartsPattern.shtml Chris -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] SMILES, SMARTS, and PDB
I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain substructures, and if they do identify which atoms are part of that substructure. So it's easy enough to read the pdb file in, convert it to SMILES representation, and then do a SMARTS query to look for my substructures. However, if the SMARTS query reports that the substructure is present in the molecule, I'm not sure how to identify the atoms in the pdb file which make up the match. Any ideas? -- ** Brett T. Hannigan 8011 Ardleigh St. Philadelphia, PA 19118 brett.hanni...@gmail.com ** -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES SMARTS
On Mon, Mar 19, 2012 at 2:58 AM, Fredrik Wallner fred...@wallner.nu wrote: No, Geoff is right. Taken from the Daylight manual at http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html All SMILES expressions are also valid SMARTS expressions, but the semantics changes because SMILES describes molecules whereas SMARTS describes patterns. The molecule represented by a SMILES string is usually, but not always, matched by the same string when used as a SMARTS On the other hand, openbabel doesn't seem to handle multi component SMARTS, possibly due to the fact that the dot requires some special handling. So if you strip salts or something similar to only search for the largest fragment of your input molecule it should work fine. No, it's not because it requires special handling. It's just a plain old bug. There was a serious design flaw in the original code that caused a core dump with dot-disconnected SMARTS, and fixing it would have required a major rewrite. Nobody has had the time to do the rewrite, so we just put code into the SMARTS matcher that blocks dot-disconnected SMARTS. Craig -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES SMARTS
I think it's the other way around while SMARTS are SMILES one can treat them as such but since SMARTS are more specific and contain information more detailed, one cannot treat SMILES (canonical or not) as SMARTS. Pybel/openbabel seems to agree with me as i get this error message with SMILES but not with SMARTS: *** Open Babel Error in SMARTSError SMARTS Error: [Cl-].CCCN(CCC)C1CC1c1cc(F)ccc1O 2012/3/18 Geoff Hutchison ge...@geoffhutchison.net I am currently trying to generate SMARTS Patterns from an 'mol' or 'sdf' file using pybel. So far I haven't been able to succeed. Is it possible to convert Canonical-SMILES (which is possible) into SMARTS? Or can I use Canonical-SMILES with the pybel.smarts() module? I look forward to your answer. A SMILES string (canonical or not) is a SMARTS. What seems to be your specific problem or error? Best regards, -Geoff -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES SMARTS
No, Geoff is right. Taken from the Daylight manual at http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html All SMILES expressions are also valid SMARTS expressions, but the semantics changes because SMILES describes molecules whereas SMARTS describes patterns. The molecule represented by a SMILES string is usually, but not always, matched by the same string when used as a SMARTS On the other hand, openbabel doesn't seem to handle multi component SMARTS, possibly due to the fact that the dot requires some special handling. So if you strip salts or something similar to only search for the largest fragment of your input molecule it should work fine. Kind regards, Fredrik. 19 mar 2012 kl. 10:29 skrev Patrik Mika: I think it's the other way around while SMARTS are SMILES one can treat them as such but since SMARTS are more specific and contain information more detailed, one cannot treat SMILES (canonical or not) as SMARTS. Pybel/openbabel seems to agree with me as i get this error message with SMILES but not with SMARTS: *** Open Babel Error in SMARTSError SMARTS Error: [Cl-].CCCN(CCC)C1CC1c1cc(F)ccc1O 2012/3/18 Geoff Hutchison ge...@geoffhutchison.net I am currently trying to generate SMARTS Patterns from an 'mol' or 'sdf' file using pybel. So far I haven't been able to succeed. Is it possible to convert Canonical-SMILES (which is possible) into SMARTS? Or can I use Canonical-SMILES with the pybel.smarts() module? I look forward to your answer. A SMILES string (canonical or not) is a SMARTS. What seems to be your specific problem or error? Best regards, -Geoff -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] SMILES SMARTS
Hello everybody, I am currently trying to generate SMARTS Patterns from an 'mol' or 'sdf' file using pybel. So far I haven't been able to succeed. Is it possible to convert Canonical-SMILES (which is possible) into SMARTS? Or can I use Canonical-SMILES with the pybel.smarts() module? I look forward to your answer. best wishes, Patrik Mika -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES SMARTS
I am currently trying to generate SMARTS Patterns from an 'mol' or 'sdf' file using pybel. So far I haven't been able to succeed. Is it possible to convert Canonical-SMILES (which is possible) into SMARTS? Or can I use Canonical-SMILES with the pybel.smarts() module? I look forward to your answer. A SMILES string (canonical or not) is a SMARTS. What seems to be your specific problem or error? Best regards, -Geoff -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
