several general questions on OpenBabel usage

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several general questions on OpenBabel usage

Andrew Voronkov
Dear OpenBabel users,
I have several questions regarding OpenBabel usage.
1) Is it possible to compare two databases using obgrep, I mean if  I have not only SMARTS pattern, but for example
the datasets of ligands which I want to use against  other dataset?

2) obconformer generates conformers by Monte Carlo search, what is the difference with 3D obgen in the provided results?? It is just in methods, right?
But in obgen Monte Carlo conformational search is performed too, so obgen is like obconf, just the molecular mechanics minimization is also performed?
Is it possible to get a series of conformers using OpenBabel like in omega2 software?
And obminize also makes optimization of the conformation by moilecular mechanics right?

3) As I understand in GUI by conversion into 3D it is supposed that OpenBabel generates 3D structure like it is done in some conformation generators like Corina, Concord etc, or what does that 3D conversion mean?

Best regards,
Andrew

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Re: several general questions on OpenBabel usage

Geoffrey Hutchison
> 1) Is it possible to compare two databases using obgrep, I mean if  I have not only SMARTS pattern, but for example
> the datasets of ligands which I want to use against  other dataset?

It sounds like you want to perform some sort of "diff" between two databases? That's an interesting use, but it's not what obgrep does.

> 2) obconformer generates conformers by Monte Carlo search, what is the difference with 3D obgen in the provided results?? It is just in methods, right?
> But in obgen Monte Carlo conformational search is performed too, so obgen is like obconf, just the molecular mechanics minimization is also performed?

The "obconformer" program starts from an existing 3D structure, while obgen is designed to start from a SMILES or other "no-coordinate" format, generate rough 3D coordinates, and then yes perform some conformer searching and molecular mechanics optimization.

> And obminize also makes optimization of the conformation by moilecular mechanics right?

Yes.

> Is it possible to get a series of conformers using OpenBabel like in omega2 software?

That's not currently the aim of the programs, no.

> 3) As I understand in GUI by conversion into 3D it is supposed that OpenBabel generates 3D structure like it is done in some conformation generators like Corina, Concord etc, or what does that 3D conversion mean?

Yes, it generates an approximate 3D structure.

Hope that helps,
-Geoff
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Re: several general questions on OpenBabel usage

Craig James-2
In reply to this post by Andrew Voronkov
On 3/11/10 7:44 AM, Andrew Voronkov wrote:
> I have several questions regarding OpenBabel usage.
> 1) Is it possible to compare two databases using obgrep, I mean if  I have not only SMARTS pattern, but for example
> the datasets of ligands which I want to use against  other dataset?

Are these literally databases, or just data files?

A simple way to compare two databases is to generate the canonical SMILES of both, sort, and then compare.  If you're on Linux or a Macintosh, you can use sort(1) and diff(1) along with babel's canonical SMILES:

   babel file1.sdf -o smi -xc  | sort >file1.smi
   babel file2.sdf -o smi -xc | sort >file2.smi
   diff file1.smi file2.smi

For really huge databases, a more complex but faster approach would be to use a hash table of canonical SMILES.

Craig
   

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