openmolecules.org Forum: Cheminformatics

Home » DataWarrior » Cheminformatics » fragments

Show: Today's Messages :: Polls :: Message Navigator

Re: fragments [message #528 is a reply to message #521]

Sun, 14 April 2019 22:10

thomas
Messages: 741
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

Report message to a moderator

[Message index]

		fragments By: pc419714@ohio.edu on Thu, 11 April 2019 19:34
		Re: fragments By: thomas on Sun, 14 April 2019 22:10
		Re: fragments By: pc419714@ohio.edu on Mon, 15 April 2019 22:10
		Re: fragments By: thomas on Tue, 16 April 2019 16:19
		Re: fragments By: pc419714@ohio.edu on Tue, 16 April 2019 22:56
		Re: fragments By: Max marine on Sun, 29 December 2019 09:21

Previous Topic:	Molecular Flexibility Descriptor
Next Topic:	Molecular Flexibility Descriptor

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Mon Jan 05 05:59:58 CET 2026

Total time taken to generate the page: 0.80874 seconds