Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-10 Thread Brett T. Hannigan
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

Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-10 Thread Brett Hannigan
. -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

Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-08 Thread Maciek Wójcikowski
*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

Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-08 Thread Maciek Wójcikowski
@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

Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-08 Thread Wang, LiRong
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

Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-06 Thread Maciek Wójcikowski
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

Re: [Open Babel] SMILES, SMARTS, and PDB

2013-07-06 Thread Chris Morley
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

[Open Babel] SMILES, SMARTS, and PDB

2013-07-05 Thread Brett T. Hannigan
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