I think this will work great. Thanks for the suggestion.
-Original Message-
From: "Maciek Wójcikowski"
Sent: 7/8/2013 12:06 PM
To: "Brett Hannigan"
Cc: "Brett T. Hannigan" ;
"openbabel-discuss@lists.sourceforge.net"
Subject: Re: [Open Bab
nteresting sub-structures.
-Brett
From: Maciek Wójcikowski
To: Brett T. Hannigan
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 PD
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, conve
imagine identifying many other interesting sub-structures.
>>
>> -Brett
>>
>> --
>> *From:* Maciek Wójcikowski
>> *To:* Brett T. Hannigan
>> *Cc:* openbabel-discuss@lists.sourceforge.net
>> *Sent:* Saturday, July 6, 2013 6
--
> *From:* Maciek Wójcikowski
> *To:* Brett T. Hannigan
> *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 P
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
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
