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fragments [message #521] Thu, 11 April 2019 19:34 Go to next message
pc419714@ohio.edu is currently offline  pc419714@ohio.edu
Messages: 20
Registered: February 2019
Junior Member
Thomas,

How does data warrior define a fragment? Why do you use fragments? My guess would be because of metabolism. Does a fragment correspond with a functional group?

Thanks,

Patrick
Re: fragments [message #528 is a reply to message #521] Sun, 14 April 2019 22:10 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 247
Registered: June 2014
Senior Member
Hi Patrick,

in DataWarrior the word fragment usually refers to a substructure fragment, which in contrast to a normal molecule is incomplete such open valences are not considered to be filled with hydrogen atoms. Fragments may also contains atom and bond query features.

In some cases, however, 'fragment' also refers to a molecule, e.g. the functionality 'Add largest fragment', which identifies all non-connected parts of a molecule (e.g. in salts) and just copies that one with the highest number of non-hydrogens atoms into a new column. This column then contains 'molecules', where all free atoms valences are implicitly considered to be filled with hydrogen atoms.

Finally it is a matter of the context. I assume this does not fully answer your question. What was the context in your case?


Thomas
Re: fragments [message #531 is a reply to message #528] Mon, 15 April 2019 22:10 Go to previous messageGo to next message
pc419714@ohio.edu is currently offline  pc419714@ohio.edu
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Registered: February 2019
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I was just wondering how fragments were defined for purposes of calculating the drug score. Thanks!
Re: fragments [message #534 is a reply to message #531] Tue, 16 April 2019 16:19 Go to previous messageGo to next message
thomas is currently offline  thomas
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Registered: June 2014
Senior Member
The drug score does not use fragments. It is a mathematical equation combining other properties.
The druglikeness, however, uses >5000 substructures. Everyone has an associated druglikeness contribution value, some positiv, some negativ, which were derived from the frequency these fragments occur in commercial drugs or organic chemicals. I attach a text file, which when opened from DataWarrior shows the chemical structures and the contributions of these fragments.
Re: fragments [message #535 is a reply to message #534] Tue, 16 April 2019 22:56 Go to previous message
pc419714@ohio.edu is currently offline  pc419714@ohio.edu
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Registered: February 2019
Junior Member
This is great! Thanks! One idea my boss had was to modify the code so that it calculated the drug score each generation and picked the best ones. I might try to modify the source code to try this but the way it is set up, if you select compounds with a high drug score to begin with, it generates compounds with high drug scores. We ended up doing 2 evolutions.

This is very helpful knowing more details about the fragments.
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