Hi Maria,
This is one of many routines molecule undergoes when reading from a "Corina
Mol2", which is implemented in RDKit. Unfortunately there is no way to turn
it off, due to the (gu)estimation of formal charges.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2018-03-28 11:46 GMT+02:00 Maria Matveyeva <yurievnama...@gmail.com>:
> Hello all,
> When i read mol2 format from either mol2 file or block, it changes
> represenation of carboxylic group from tripos aromatic representaiton with
> -0.5 charges on oxygens to representaion with one single and one double
> bond (when same representation read from sdf/mol it retains "aromatic"
> form):
>
>
>
> from rdkit import Chem
>
> mol = Chem.MolFromMol2Block('@<TRIPOS>MOLECULE\n\n7 6
> 1\nSMALL\nUSER_CHARGES\n@<TRIPOS>ATOM\n1\tC1 83.1235 48.4843
> -1.9335\tC.3\t\t1\tnoname\t0.0000\n2\tC2 84.4055 49.1718
> -2.1563\tC.2\t\t1\tnoname\t0.0000\n3\tO1 85.5783 48.5739
> -1.8454\tO.co2\t1\tnoname -0.5000\n4\tO2 84.4327 50.3304
> -2.6301\tO.co2\t1\tnoname -0.5000\n5\tH1 82.7117 47.9177
> 0.7151\tH\t\t1\tnoname\t0.0000\n6\tH2 82.6153 48.8969
> -1.0496\tH\t\t1\tnoname\t0.0000\n7\tH3 82.4727 48.5910
> -2.8139\tH\t\t1\tnoname\t0.0000\n@<TRIPOS>BOND\n1\t1\t2\
> t1\n2\t2\t3\tar\n3\t2\t4\tar\n4\t1\t6\t1\n5\t1\t7\t1\n6\t5\t1\t1\n@
> <TRIPOS>SUBSTRUCTURE\n1\tnoname\t1\n')
>
> Chem.MolToSmiles(mol)
>
> 'CC(=O)[O-]'
>
> Thanks in advance,
> Maria
>
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