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Standardizer (remove explicit H) doesnt work in IJChem
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Tobias

Joined: 26 Jan 2005
Posts: 580

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Link to postPosted: Fri Feb 27, 2009 2:15 amPost subject: Standardizer (remove explicit H) doesnt work in IJChem Reply with quote

Hi,

I downloaded some files from PubChem,

created a DB with Standardizer in Instant JCHem

and imported that field. I enabled all fields in the

remove H section.

The explicit Hs are still shown, I tested it with the

external Standardizer and that works fine.

This is version 2.4.1 (general ZIP install with latest update)


Tobias
Oleg

Joined: 04 Mar 2007
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Link to postPosted: Sat Feb 28, 2009 5:12 amPost subject: Reply with quote

try to change to "display as standardized" in molecule widget in your database form or view.
Tim
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Joined: 05 Oct 2004
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Link to postPosted: Sat Feb 28, 2009 6:11 amPost subject: Reply with quote

Yes, that is correct. Standardization is primarily for query purposes.
It determines how the queries are run, and as such is often not of direct relevance for display purposes.
For this reason the version of the structure that is displayed by default is the unstandardized form, but you can change this by setting the "display as standardized" dispaly setting for molecules.

See here for a related topic:
http://www.chemaxon.com/forum/viewpost13687.html

Tim
Tobias

Joined: 26 Jan 2005
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Link to postPosted: Mon Mar 02, 2009 3:37 amPost subject: Reply with quote

Hello Oleg and Tim,


thanks for your help, yes that resolves the issue.

Tim, now I know I fell into that trap twice....

I have two other problems I can not

1) get rid of the "Absolute" label with the widget property

2) show R/S labels even in case of stereochemistry.

Tobias
Tim
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Link to postPosted: Tue Mar 03, 2009 5:45 pmPost subject: Reply with quote

We will add the option to show/hide the R/S labels.

I'm not sure whether the "Absolute" label can be hidden, and need to investigate.
Also, I'm not sure its desirable to hide this as it contains important information about the stereo chemistry (the MDL chiral flag).

Tim
Tim
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Link to postPosted: Thu Mar 12, 2009 6:53 pmPost subject: Reply with quote

An option for showing/hiding R/S lablels is now present in the IJC 2.4.3 update.

Tim
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