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
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
quer
