generate name by cxcalc problem

Hi

I tried to generate name from JChem by cxcalc, script:

cxcalc -S -t "iupac" -o names.sdf name test.sdf

the file name.sdf has been copied to the "bin" directory before run the script from command line (total commander).

the file name.sdf (attached) contains:

          11191122492D



 12 13  0  0  0  0  0  0  0  0999 V2000

    4.8708   -7.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

    5.6958   -7.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    4.6183   -6.3409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    6.6256   -5.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    6.3701   -5.0663    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

    5.5405   -5.0655    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

    5.2833   -5.8542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    5.9539   -6.3426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    7.1499   -6.2566    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0

    7.9349   -6.0028    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0

    6.9773   -7.0633    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0

    7.5542   -6.9667    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0

  2  8  1  0  0  0  0

  7  3  1  0  0  0  0

  3  1  1  0  0  0  0

  4  5  2  0  0  0  0

  6  7  1  0  0  0  0

  8  4  1  0  0  0  0

  7  8  2  0  0  0  0

  1  2  1  0  0  0  0

  9 10  1  0  0  0  0

  9 11  1  0  0  0  0

  5  6  1  0  0  0  0

  9 12  1  0  0  0  0

  4  9  1  0  0  0  0

M  END

.........................

$$$$

This command produces empty test.sdf file only.

is it mistake somewhere?

I have 14 days licence file, but when I'm running the script, it program do not asks me about licence.

thanks!

Igor

Dear Igor,

Your command is right; however the definition of files are confusing.

cxcalc -S -t "iupac" -o names.sdf name test.sdf

means that you have an input file: test.sdf and your output file will be names.sdf.

Try the following command to generate names for the molecules in your attached file:

cxcalc -S -t "iupac" -o name-output.sdf name name.sdf

Best regards,

Viktoria

cxcalc -S -t "iupac" -o names.sdf name test.sdf

Diar Viktoria,

Thank you very much for your replication!

 
I have one more question: is it possible to generate the name not from the matrix of a molecule (like in the SDF-file), but from the SMILE?

 
For example, can I convert the file with string:
CC (C) (C) NCC1 = CC = CC = C1 DR-014 78987270
to the file with next string:
N-benzyl-2-methylpropan-2-amine DR-014 78987270

 
Thanks in advance!

Hi Igor,

You can add SMILES containig string as input to generate name directly from SMILES.

In this case, the SMILES "part" of the string is recognized and will be converted to name.

$ cxcalc name "CC(C)(C)NCC1=CC=CC=C1 anything"
id      Preferred IUPAC Name
1       benzyl(tert-butyl)amine

You can use smiles file type as input as well.

$ cxcalc name d:/work/forum/smiles_names.smiles
id      Preferred IUPAC Name
1       4-{[5-(piperidin-3-yl)-1H-pyrazol-4-yl]carbonyl}morpholine
2       2-(2-methoxy-5-methylphenyl)-1-(piperidin-1-yl)ethan-1-one
3       3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one

Best regards,

Viktoria