yes Geoff, this does help *a lot* - especially considering the call from
the command line.
One more question and a suggestion please.
Q: The weighted rotor conformer gives only one conformer (lowest energy)?
What happens when you specify the num of conformers to say 50 ?
S: Also a suggestion obabel --help totally ignores the fact that there is
this wealth of functionality available.
-
Jean-Paul Ebejer
Early Stage Researcher
On 9 December 2011 17:12, Geoffrey Hutchison <ge...@geoffhutchison.net>wrote:
> > Specifically, I was wondering if there is an example of how to use
> OBConformerSearch from Python (and is there a way how to use this directly
> from the command line?).
>
> Sorry the documentation isn't online -- we should definitely fix that.
> It's easy to use from the command-line:
>
> obabel -L conformer
> One of the ops
> conformer Conformer Searching (not displayed in GUI)
> Typical usage: obabel infile.xxx -O outfile.yy --conformer --nconf
> options: description
> --log output a log of the energies (default = no log)
> --nconf # number of conformers to generate
> forcefield based methods for finding stable conformers:
> --systematic systematically generate all conformers
> --random randomly generate conformers
> --weighted weighted rotor search for lowest energy conformer
> --ff # select a forcefield (default = MMFF94)
> genetic algorithm based methods (default):
> --children # number of children to generate for each parent (default
> = 5)
> --mutability # mutation frequency (default = 5)
> --converge # number of identical generations before convergence is
> reached
> --score # scoring function [rmsd|energy] (default = rmsd)
>
> For example:
> # generate 50 conformers, scoring with MMFF94 energies, but default
> children, etc.
> obabel EtOT5D.cml -O EtOT5D0.xyz --conformer --nconf 50 --score energy
>
> As far as Python, I haven't tried, but the code is "wrapped" so it should
> be available. If you want some example code, I can probably whip something
> up based on the C++ (e.g., src/ops/conformer.cpp).
>
> > Also, do the conformers undergo some form of energy minimization in this
> GA approach?
>
> As of yet, no. That could be done new scoring function (e.g., minenergy)
> which determines the energy after some minimization. It's a good idea.
>
> > Also, I can see I can generate a fixed number of conformers (e.g. 50)
> using Weighted Rotor Score, what is a decent parameter for geomSteps in
> > WeightedRotorSearch (unsigned int conformers, unsigned int geomSteps) ?
> Why do the other structure methods have a default for 2500 and this one
> has not?
> > Is this an oversight?
>
> I usually use a few hundred geomSteps, maybe 250 or 500. IMHO, the point
> isn't to produce a fully converged structure, but to quickly minimize
> steric collisions generated from a particular rotamer. Once I have some
> low-energy conformers, I'll minimize the low-energy set to find more
> converged energies and geometries.
>
> Hope that helps,
> -Geoff
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