Import of Multi-Column SMILES Files

Hi!





I like to convert a multi-column SMILES file with "molconvert" into an sdf-file. The README tells to use the "f" option ({fFIELD1,fFIELD2,...} ) to get the data of every column. But there's no description about the separators of the columns. I tested withespaces, tabs, commas and nearly everything imagineable. But if "f" reads a column, then only the first one. If I want to access more than one FIELD, I get "test2.smi{fField1: not found" as error message.





Could anyone please give me a hint how to use the the multi-column import option correctly?!





Thanks a lot!


Sebastian Moll

We are already checking it.

Hi!





I think you were doing the right thing just the documentation was missing an important point (sorry):


The data fields must be separated by tab characters from the SMILES string and from each other. Spaces are not used as separators so a data field can contain spaces.

Code:

scripts/molconvert sdf "2.smi{fName,fnum1,fnum2}"

would import 3 fields the Name, num1, and num2 fields.


(See documentation: http://www.chemaxon.com/marvin/doc/user/smiles-doc.html#ioptions )


But the Name, num1 and num2 fields must be separated by tab character.


I will make this important note at the documantation.





All the best


Andras

Hi!





Thank you very much for your help! But I don't know what I'm doing wrong... My Smiles-Files looks as follows:





[CH3][C]=1[C]([CH]=[CH][C]([CH]1)=[O])=[O] MolName1 1234


[NH2][c]1[cH][cH][c]2[c]([cH]1)[C]([c]1[c]([C]2=[O])[cH][cH][cH][cH]1)=[O] MolName2 12345





Allright, SmileTabField1TabField2Newline.


When running the script on this constellation, I get the Error:





$ /cygdrive/c/Programme/ChemAxon/MarvinBeans/bin/molconvert.bat sdf "test2.smi{fField1,fField2}"


test2.smi{fField1: not found





Don't know what "he" doesn't like... :o(


Do you?





Thank you for your help!


Sebastian

Ooops, the Message-Editor devoured the tabs between Smiles-String, Field1 and Field2.





Sebastian

Hi,





I guess you are using cygwin.


In this case your shell probably differs from mine. So you may try this (change " -> '):


molconvert.bat sdf 'test2.smi{fField1,fField2}'





If this still not working, please let me know which shell you are using.





Andras

Hi Andreas!





Your hint concerning "Cygwin" was very good! It didn't work by change of " to ', in fact! But when I used the DOS-command line instead of Cygwin, everything worked well and I got all columns! Super!





Don't know, what's the problem with Cygwin. Apparently some Shell-depending crux... Or something with the control characters...





Thank you very much!


Sebastian

We have tested it under cygwin, but under cygwin the unix commands should be run and not the .bat files. This may also cause problem.


Anyway, you have succeeded, great!





Andras

Jeah, it works well under cygwin even when using the .bat files, as long as I don't use the mutli-column option. This option is the single one not working I found 'till now. Everything else does well!





Thank you for the fast help!


Sebastian

If you need Unix like shell scripts for Marvin, which also work in cygwin, you can find them in "marvinbeans-VERSION.zip". It is the platform independent version of Marvin Beans (without installer).

Allright, now it works under cygwin!





Thank you very much!

Dear All,





I have a chemical file with extention .sdf, and I tried to open this file using excel but all the contents are similer to numbers, how can I convert this file to SMILES using WinXP, Please help me as soon as possible.





Thanks a lot!

I can suggest Standardizer or MolConverter to convert structures between various file types.


Other useful links:


Standardizer User Guide


Molecule file conversion with MolConverter