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Chem4Word / Version3

Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word
https://www.chem4word.co.uk
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SMILES helper #4

Closed ruska612 closed 6 years ago

ruska612 commented 6 years ago

Hi, I want to convert structures to SMILES format and show in Word. The problem was when I imported sdf structures from the Import icon, the 2D structures could not be shown as SMILES at the same time when I clicked the Show As icon. It seemed the imported structures were deposited in the same object. Any advices would be helpful, thank you !

MikeWilliams-UK commented 6 years ago

From what you describe the structure imported did not contain and smiles data.

There are two ways to get smiles data which can be shown.

  1. Select the structure, then click on the "Edit Labels" button to add your own
  2. Edit the structure, change it (say add extra bond), save it. Then edit again to revert the first edit. During this process we calculate the InchiKey and see if the freely available PubChem database contains this InchiKey, if so it is fetched and will be available for you to display.
MikeWilliams-UK commented 6 years ago

Do you have any screen shots you can post?

MikeWilliams-UK commented 6 years ago

If you want to display the 2D structure and smiles at the same time you will need to use the navigator to insert a linked copy of the structure displaying one as 2D and the other as smiles. When the structure is edited both will be updated together.

ruska612 commented 6 years ago

image 1 These are the related screen shots, the sdf contains two structures, the 2D representations are fine. However, when I clicked Edit icon and clicked OK and then prepared to show both structures as SMILES formats, only one structure could be displayed normally.

MikeWilliams-UK commented 6 years ago

The software is operating correctly (as designed)

If you wish to display the textual label of both molecules

  1. Import the sdf twice.
  2. Edit the first one to remove cyclohexane
  3. Edit the second one to remove benzene
  4. Display both as individual names