How to stop MolFragment cutting aliphatic rings???

Hi All,

Can anyone please tell me how to run MolFragment without letting it fragment aliphatic rings?

Kind regards,

Sean

Currently there is not option in MolFragment which prevent the cleavage of aliphatic rings but we can add this if you need.

However, Fragmenter (command line: fragment) never allows the cleavage of rings. Possibly you can use that, I can help in the configuration if you send an example.

May I ask why you would like to avoid opening aliphatic rings? What do you use molfargment for?

Gyuri wrote:

May I ask why you would like to avoid opening aliphatic rings? What do you use molfargment for?

Dear Gyuri, We wish to 'mol'fragment some steriodal structures through their long-chain substituents that carry functional groups, but without cutting the steriodal four-ring core.

Nora wrote:

Currently there is not option in MolFragment which prevent the cleavage of aliphatic rings but we can add this if you need. However, Fragmenter (command line: fragment) never allows the cleavage of rings. Possibly you can use that, I can help in the configuration if you send an example.

Dear Nora, We wish to use molfragment rather than fragmenter because we want to avoid cutting through functional groups like amides and esters on the long-chain steriod substituents (see message above). Can you please add the option to avoid cutting any rings (aromatic or aliphatic) to molfragment?

We discuss what we can do and will get back to you in a couple of days.

Gyuri wrote:

We discuss what we can do and will get back to you in a couple of days.

Thanks, much appreciated!

We will introduce an option for that probably in version 5.4.1.

Gyuri wrote:

We will introduce an option for that probably in version 5.4.1.

Thanks! When do you think this will be out?

Probably early next year, but I cannot tell it more precisely at the moment.

Hi,

I know this question was asked back in 2009, but I could not find a clear answer.

Is it possible to tell 'molfragment' not to break aliphatic rings?

Thanks in advance,

Miquel

Hi Miquel,

Yes, this functionality is available from JChem 5.4.1, but it is accessible only via Java/.NET API. For more see the API documentation.

Zsolt