Open Babel 2.3 unable to filter batch SDF files on basis of logP and ROTATABLE_BOND

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Open Babel 2.3 unable to filter batch SDF files on basis of logP and ROTATABLE_BOND

baccilus
I am using batch files from ZINC and trying to apply Lipinksi filter on it with openbabel. I am using the official documentation. Although obabel is able to filter on the basis of MW, HBD and HBA, it seems to failing with logP and Rotatable bonds. If I include logP and Rotatable bond, it converts "0" molecules.
Here is an example code that I am using:

saurabh@saurabh-Inspiron-5521 ~ $ obabel NewcdpsPart2.sdf -O part2logP-Filter.sdf --filter "logP<=5"

or this:

obabel NewcdpsPart2.sdf -O part2logP-Filter.sdf --filter "ROTATABLE_BONDS<=10"

This works well:

obabel NewcdpsPart2.sdf -O part2Filter.sdf --filter "MW<=500 & HBA2<=10 & HBD<=5"

I am on Linux and have tried it on Ubuntu 14.04 and 16.04 with same results
Openbabel version 2.3.2

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Re: Open Babel 2.3 unable to filter batch SDF files on basis of logP and ROTATABLE_BOND

mirix
The descriptor "ROTATABLE_BONDS" is used as an example in the online documentation but not actually implemented in the code.

The easiest solution would be this:

https://sourceforge.net/p/openbabel/mailman/message/30659149/

Add the following item to /"OBABEL_INSTALLATION_DIRECTORY"/data/plugindefines.txt

SmartsDescriptor
rotors
[!$(*#*)&!D1]-!@[!$(*#*)&!D1]
Number of rotatable bonds\n


Then you can use the descriptor "rotors" for filtering and other purposed.


You may also want to try Filter-It:

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




--
Edelmiro Moman, PhD
Department of Molecular Medicine
Royal College of Surgeons in Ireland

POSTAL ADDRESS:

L5.08
Trinity Biomedical Sciences Institute - TBSI
Trinity College Dublin
152 - 160 Pearse St
Dublin 2
IRELAND

Phone: +353 (0)1 896 3527

On 5 August 2016 at 05:16, baccilus <[hidden email]> wrote:
I am using batch files from ZINC and trying to apply Lipinksi filter on it
with openbabel. I am using the official documentation. Although obabel is
able to filter on the basis of MW, HBD and HBA, it seems to failing with
logP and Rotatable bonds. If I include logP and Rotatable bond, it converts
"0" molecules.
Here is an example code that I am using:

saurabh@saurabh-Inspiron-5521 ~ $ obabel NewcdpsPart2.sdf -O
part2logP-Filter.sdf --filter "logP<=5"

or this:

obabel NewcdpsPart2.sdf -O part2logP-Filter.sdf --filter
"ROTATABLE_BONDS<=10"

This works well:

obabel NewcdpsPart2.sdf -O part2Filter.sdf --filter "MW<=500 & HBA2<=10 &
HBD<=5"

I am on Linux and have tried it on Ubuntu 14.04 and 16.04 with same results
Openbabel version 2.3.2





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Re: Open Babel 2.3 unable to filter batch SDF files on basis of logP and ROTATABLE_BOND

baccilus
Thank you so much. Silicos-it solved it for me. But I think it is really odd that they would include a function in the example of official documentation that doesn't actually exist.

On Fri, Aug 5, 2016 at 5:42 PM, mirix [via Open Babel] <[hidden email]> wrote:
The descriptor "ROTATABLE_BONDS" is used as an example in the online documentation but not actually implemented in the code.

The easiest solution would be this:

https://sourceforge.net/p/openbabel/mailman/message/30659149/

Add the following item to /"OBABEL_INSTALLATION_DIRECTORY"/data/plugindefines.txt

SmartsDescriptor
rotors
[!$(*#*)&!D1]-!@[!$(*#*)&!D1]
Number of rotatable bonds\n


Then you can use the descriptor "rotors" for filtering and other purposed.


You may also want to try Filter-It:

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




--
Edelmiro Moman, PhD
Department of Molecular Medicine
Royal College of Surgeons in Ireland

POSTAL ADDRESS:

L5.08
Trinity Biomedical Sciences Institute - TBSI
Trinity College Dublin
152 - 160 Pearse St
Dublin 2
IRELAND

Phone: +353 (0)1 896 3527

On 5 August 2016 at 05:16, baccilus <[hidden email]> wrote:
I am using batch files from ZINC and trying to apply Lipinksi filter on it
with openbabel. I am using the official documentation. Although obabel is
able to filter on the basis of MW, HBD and HBA, it seems to failing with
logP and Rotatable bonds. If I include logP and Rotatable bond, it converts
"0" molecules.
Here is an example code that I am using:

saurabh@saurabh-Inspiron-5521 ~ $ obabel NewcdpsPart2.sdf -O
part2logP-Filter.sdf --filter "logP<=5"

or this:

obabel NewcdpsPart2.sdf -O part2logP-Filter.sdf --filter
"ROTATABLE_BONDS<=10"

This works well:

obabel NewcdpsPart2.sdf -O part2Filter.sdf --filter "MW<=500 & HBA2<=10 &
HBD<=5"

I am on Linux and have tried it on Ubuntu 14.04 and 16.04 with same results
Openbabel version 2.3.2





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View this message in context: http://forums.openbabel.org/Open-Babel-2-3-unable-to-filter-batch-SDF-files-on-basis-of-logP-and-ROTATABLE-BOND-tp4659418.html
Sent from the General discussion mailing list archive at Nabble.com.

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Saurabh
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Re: Open Babel 2.3 unable to filter batch SDF files on basis of logP and ROTATABLE_BOND

Geoff Hutchison
> Thank you so much. Silicos-it solved it for me. But I think it is really
> odd that they would include a function in the example of official
> documentation that doesn't actually exist.

The example indicates that the SD file has a field called ROTATABLE_BOND. It’s an example of using a property embedded in a file to filter. Not all files have that particular field.

Best regards,
-Geoff
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