cxcalc MajorMS/major tautomer extraneous output

 

Hello,

Everything works normally when I do thousands of molecules using:

echo "C[C@]1(OC(=CC1=O)C([O-])=O)c1ccccc1 ID01" | molconvert sdf | cxcalc -S majorms -H 7.4 | molconvert smiles:-nTMAJORMS

But when I add the -M switch to get the major tautomer, I occasially get extraneous output that breaks the molcovert step.

Here is one molecule that does it:

echo "C[C@]1(OC(=CC1=O)C([O-])=O)c1ccccc1 ID01" | molconvert sdf | cxcalc -S majorms -H 7.4 -M

Output

"""

C[C@]1([O+]=C([CH-]C1=O)C([O-])=O)C1=CC=CC=C1
C[C@]1([O+]=C(C=C1[O-])C([O-])=O)C1=CC=CC=C1
C[C@]1(O[C+](C=C1[O-])C([O-])=O)C1=CC=CC=C1
C[C@]1(OC([CH+]C1=O)=C([O-])[O-])C1=CC=CC=C1
C[C@]1(OC(=C[C+]1[O-])C([O-])=O)C1=CC=CC=C1
C[C@]1(OC(=CC1=O)[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1([O+]=C([CH-]C1=O)[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1([O+]=C(C=C1[O-])[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1(OC(=C[C+]1[O-])[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1(OC(=CC1=O)C([O-])=O)C1=CC=CC=C1
C[C@]1([O+]=C([CH-]C1=O)C([O-])=O)C1=CC=CC=C1
C[C@]1([O+]=C(C=C1[O-])C([O-])=O)C1=CC=CC=C1
C[C@]1(O[C+](C=C1[O-])C([O-])=O)C1=CC=CC=C1
C[C@]1(OC([CH+]C1=O)=C([O-])[O-])C1=CC=CC=C1
C[C@]1(OC(=C[C+]1[O-])C([O-])=O)C1=CC=CC=C1
C[C@]1(OC(=CC1=O)[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1([O+]=C([CH-]C1=O)[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1([O+]=C(C=C1[O-])[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1(OC(=C[C+]1[O-])[C+]([O-])[O-])C1=CC=CC=C1
C[C@]1(OC(=CC1=O)C([O-])=O)C1=CC=CC=C1
ID01
  Marvin  06071216242D          

 16 17  0  0  1  0            999 V2000
    0.6320   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
...

"""

Am I doing something wrong?

Thanks,

Michael

Hi Michael,

 

We could not reproduce this issue with version 5.9.4.

Which cxcalc version are you using ?

 

BR,

Viktoria

vpalfi wrote:

Hi Michael,   We could not reproduce this issue with version 5.9.4. Which cxcalc version are you using ?   BR, Viktoria

 

Running version 5.3.1.

Thanks,

Michael

I recommend updating to the latest version of Marvin or JChem (version 5.10.0), as the mentioned problem did not come up in version 5.9.0 or above.

Moreover, the accuracy of calculations has been improved and several bugs have been fixed since version 5.3.1.

You can download the latest version of Marvin or JChem form here: http://www.chemaxon.com/download/ />
Best regards,
Viktoria

 

Thanks Viktoria,

I finally got a chance to install the new version. It does work much better, but the calculations take over 10 times longer than before. It will now take around a week to process my, admittedly humoungous, workload on 16 cores. 

Michael

Hi,

 

The slowest step is the major tautomer calculation in yor comand line description above.

I'm a little supprised  why you are faced with a significant slow down. Because the speed of the major tautomer calculation was improved recently. It is about 100 times faster than in the earlier versions. 

We check what may be the problem and inform you soon.

Thanks.

Jozsi

 

If the tautomer calculation is the rate limiting step, then that would explain the slowdown as it was frequently erroring out in the older version.

 

Thanks again,

Michael

Hi,

 If the tautomer calculation is the rate limiting 

step, then that would explain the slowdown as it was frequently erroring

 out in the older version.

Could you show one more example for this situation?

 

Thanks.

Jozsi