Erlwood Chemical File Writer SDF Compound Names

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1

Hi,

I am using the Erlwood Chemical File Writer to write my compounds as an sdf file. However, when I open the compounds in another program, the compound names are missing. I can’t seem to find an option anywhere to select which column to use for compound names. Is there a workaround?

Thanks

2

Is there a reason you’re not using the built-in SDF Writer node?

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It doesn’t keep the hydrogens as explicit. The second program I’m using requires all atoms including hydrogens to be explicit. I couldn’t find the option for this, but the chemical file writer node does keep these hydrogens.

I did find a workaround, but it might not work for all cases. My compound names were in another column, so I concatenated the two columns with the Column Aggregator node, then used the string to compound node from Erlwood. This gave me my compounds with explicit hydrogens and with a compound name.

But if there is an option in the SDF writer that keeps all atoms explicit that would be great.

4

That’s interesting. I’ve found that using a Hydrogen Adder node and a Generate 2D Coordinates node (or the 3D coordinates node) before the SDF Writer gives me SD files that contain hydrogens in the connection table along with their coordinates.

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