Lose of Sulfur and Phosphorus mol2 types using standardize

Good afternoon,

 

Using standardize (JChem 5.4), i've noticed that this line:

18 S2         -5.8503    6.3842   -8.6714 S.o2      1 <0>         1.4223

Becomes this line:

18    S2    -5.8503     6.3842    -8.6714    S    1    noname    0.0000

"S" alone isn't part of the possible mol2 types http://tripos.com/data/support/mol2.pdf (page 53) and therefore, it can cause compatibility problems with other programs (well, it's the case for me).

I've tried to find the action in the standardisation responsible for this behavior but as it stands, even if you apply zero actions, it perform this transformation. (More on the how at the bottom of this post).

 

I've got the same problem for phosphorus:

This line:

7 P1         -3.0620    1.7566    2.6980 P.3       1 <0>         1.0438

Becomes this line:

7    P1    -3.0620     1.7566     2.6980    P    1    noname    0.0000

Same thing here, P alone isn't a possible output. http://tripos.com/data/support/mol2.pdf (page 53)

 

I've got two questions:

Is it intended?

Is there a method I can use to avoid this behavior?

Here are the used command lines:

For S:

standardize_path/standardize ZINC00031727.mol2 -c Empty_Standardizer.xml -o ZINC00031727_standardized.mol2 -f mol2

For P:

standardize_path/standardize ZINC01885530.mol2 -c Empty_Standardizer.xml -o ZINC01885530_standardized.mol2 -f mol2

Please find attach the input/output files, and the xml used by Standardize.

Thank you for the report.

We take a look at and check what the problem is.

I'm a bit overloaded right know so I apologize for the late answer.

Is there anything new on this?

Thank you for the time you take to solve this problem.

Thank you again for the report. The problem lies in the atom typing function of mol2 export format: not all SYBYL atom types are recognized corectly. Improvement in this area is not scheduled currently.

Regards,

Gabor

I moved the topic to "Structure representation: molecule handling and file formats" forum, because it's not related to Standardizer.

Zsolt