How to assign a column as the name of a compound in an sdf export?

[Andrew Orry]

Q. How to assign a column as the name of a compound in an sdf export?

A.

Assigning a column as the compound name in an SDF export ensures each molecule has a clear, consistent identifier, making it easier to track, analyze, and interpret results. It also helps maintain compatibility with downstream tools that rely on the name field for labeling and reference. In the SDF format, this name appears on the first line of each molecule entry and is commonly used by software to display or identify the compound.

To do this in ICM:

In GUI: Right click on the 'mol' column and choose "Set Compounds Names From"

On the command line:

set name Xdict.mol <S_names>

[Ruben]

That was a good recipe. In simple terms, keep in mind the following

1) the molecular name in a chemical table is stored as a column NAME_ with a fixed name <tablename>.NAME_

2) When you assign a column as a molecular name via GUI, a new column with the internal name NAME_ will be created.

3) the   write <table> mol    command will store the name of the molecule as the first row of a section corresponding to each molecule in a table. E.g.  

$$$$

Idoxuridine

  MOLSOFT 04182523062D

 17 18  0  0  1  0  0  0  0  0999 V2000
    1.1325    1.2377    0.0000 I   0  0  0
    4.0924    0.4760    0.0000 O   0  0  0

4) When you read this file two columns will be created in ICM: a .mol column and a .NAME_ column.

Ruben