Using molconvert to convert smiles fields to SDF fields

Hi,





I read the relevant documentation and also tried to search the forum but I did not find any former post that was adequate.





I have a smiles file that begins like this:

Code:

#SMILES Log10IC50 OC(=O)CC1=CC=C(SSC2=CC=C(CC(O)=O)C=C2)C=C1 -2.95 NNP(=S)(NN)C1=CC=CC=C1 -4.00 OC1=CC=C(N=O)C(O)=C1N=O -3.82

I need an SDF that contains the Log10IC50 field associated with each molecule. Though molconvert seems not to recognise the Log10IC50 field and generates the wrong SDF as shown below:

Code:

-2.95   Marvin  09180811592D           22 23  0  0  0  0            999 V2000     0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0     0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0     0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

Any wise thoughts on that?





Thanks


Mico

Hi,





The documentation is here:


http://www.chemaxon.com/marvin/help/formats/smiles-doc.html#ioptions width="90%" cellspacing="0" cellpadding="3" border="0" align="center"> Quote:


f


{fFIELD1,fFIELD2,...} Import data fields from a multi-column file. The fields should be separated by tab character. The first column contains the SMILES/SMARTS strings, the second contains the data field called FIELD1, the third contains FIELD2, etc.


Example:





molconvert sdf "foo.smi{fname,fID}"


But on the other hand you are right, if the smiles file contains header information, it should be used automatically.





Andras

Hi,


If your header contains:


"#SMILES" followed by tab character and text field, then the text field is automatically used during the import process.


In your case the problem was that the text field was not separated by tab character (you used space character).


I have attached the a corrected smiles file.





Andras

Thanks for the help, the documentation did help, {fLog10IC50} solved the problem.


And tab did the trick! Is that documented somewhere?


Btw: why do we insist on tab, any other white space character should work as well, hm?





thx, i managed to convert my smiles with field to sdf with fields using molconver!





m

Quote:

And tab did the trick! Is that documented somewhere?

Only the following is written:

Quote:

The fields should be separated by tab character.

We may mention it at the beginning of the smiles documentation.

Quote:

Btw: why do we insist on tab, any other white space character should work as well, hm?

Actually we allow space in the field name/value. Which can be useful for text fields.


So you may call your field: "Log10 for IC50".





Andras