microspeciesdistribution and majormicrospecies

Hello everyone,

I have two little questions regarding microspeciesdistribution and majormicrospecies calculations with the cxcalc plugins. I searched the forum but didn't find something that helps me.

Both questions are about output file formats:

For example

cxcalc -i mol2 test.mol2 -o testdist.sdf msdistr --pH "7" -f sdf

works well but if I try to get mol2 output with

cxcalc -i mol2 test.mol2 -o testdist.mol2 msdistr --pH "7" -f mol2

the mol2 file is written but no distribution information is included. Maybe it is lost during conversion from sdf to mol2 but in general the mol2 format would be able to contain such information in the comment section. Is there a possibility to get the distribution in the mol2 file ?

The other question is:

Is it possible to get sdf or mol2 output of microspeciesdistribution or majormicrospecies calculation with explicit hydrogen atoms ? In the examples above only the heavy atoms are written and the protonation is coded in formal charges.

Thanks for your help

Tim ten Brink

 

ttenbrink wrote:

Maybe it is lost during conversion from sdf to mol2 but in general the mol2 format would be able to contain such information in the comment section. Is there a possibility to get the distribution in the mol2 file ?

Unfortunately our mol2 format export does not support comments yet.

See: http://www.chemaxon.com/marvin/help/formats/mol2-doc.html

ttenbrink wrote:

Is it possible to get sdf or mol2 output of microspeciesdistribution or majormicrospecies calculation with explicit hydrogen atoms ? In the examples above only the heavy atoms are written and the protonation is coded in formal charges.

Yes, it is possible, use the ":H" molecule format export option.

See: http://www.chemaxon.com/marvin/help/formats/basic-export-opts.html

Examples (SMILES and sdf):

$ cxcalc majorms -H 7.4 "CC(N)C(O)=O" -f smiles:H
[H]C([H])([H])C([H])(C([O-])=O)[N+]([H])([H])[H]


$ cxcalc majorms -H 7.4 "CC(N)C(O)=O" -f sdf:H

Marvin 11260911172D

13 12 0 0 0 0 999 V2000
0.8250 1.4289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2375 0.7145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0625 0.7145 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
0.8250 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2375 -0.7145 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.5395 1.8414 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4125 2.1434 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1105 1.0164 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6500 1.4289 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0625 -0.1105 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8875 0.7145 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.0625 1.5395 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
4 5 1 0 0 0 0
4 6 2 0 0 0 0
1 7 1 0 0 0 0
1 8 1 0 0 0 0
1 9 1 0 0 0 0
2 10 1 0 0 0 0
3 11 1 0 0 0 0
3 12 1 0 0 0 0
3 13 1 0 0 0 0
M CHG 2 3 1 5 -1
M END
> <_MOLCOUNT>
1

$$$$

Apologies for not responding any sooner.

Zsolt