tutorials on small molecule energy minimization and substructure searching

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tutorials on small molecule energy minimization and substructure searching

Benji Horning
Hi everyone,

I'm a new user to openbabel, and my initials goals are to do energy minimization of small molecules and substructure searching within sdf files. I've been trying to find good info or documentation for these uses, but I'm having trouble finding what I'm looking for. Any help would be most appreciated.

Thanks!
Benjamin Horning

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Re: tutorials on small molecule energy minimization and substructure searching

Fredrik Wallner
Hi,
For the second one, look at http://openbabel.org/docs/current/Fingerprints/fingerprints.html#id1 Even though the docs use babel in that case, obabel is the preferred command and could be easily switched in. So obabel mymols.sdf -sN#Cc1ccccc1C#N -O results.smi should give the desired result.
For energy minimization, look at obabel -L minimize

Kind regards,
Fredrik

29 aug. 2016 kl. 18:33 skrev Benji Horning <[hidden email]>:

Hi everyone,

I'm a new user to openbabel, and my initials goals are to do energy minimization of small molecules and substructure searching within sdf files. I've been trying to find good info or documentation for these uses, but I'm having trouble finding what I'm looking for. Any help would be most appreciated.

Thanks!
Benjamin Horning
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Re: tutorials on small molecule energy minimization and substructure searching

mirix
In addition to Fredrik advise, you may also want to take a look at:

http://openbabel.org/wiki/Obminimize

As for fingerprints, I have found Filter-It to be more efficient than OB:

http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/software.html


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On 30 August 2016 at 14:37, Fredrik Wallner <[hidden email]> wrote:
Hi,
For the second one, look at http://openbabel.org/docs/current/Fingerprints/fingerprints.html#id1 Even though the docs use babel in that case, obabel is the preferred command and could be easily switched in. So obabel mymols.sdf -sN#Cc1ccccc1C#N -O results.smi should give the desired result.
For energy minimization, look at obabel -L minimize

Kind regards,
Fredrik

29 aug. 2016 kl. 18:33 skrev Benji Horning <[hidden email]>:

Hi everyone,

I'm a new user to openbabel, and my initials goals are to do energy minimization of small molecules and substructure searching within sdf files. I've been trying to find good info or documentation for these uses, but I'm having trouble finding what I'm looking for. Any help would be most appreciated.

Thanks!
Benjamin Horning
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