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 forwar
> 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 y
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
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 represe
On Mon, Mar 19, 2012 at 2:58 AM, Fredrik Wallner 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 molecu
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
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
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
--
> *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
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
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
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
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