Thank you all!
maria
2018-03-28 12:29 GMT+02:00 Chris Earnshaw <cgearns...@gmail.com>:
> Hi Maria
>
> I would say that the behaviour of RDKit with your MOL2 file is right.
> SMILES notation doesn't have a way to represent the delocalised form of a
> carboxylate anion, so the O=C[O-] form is the correct SMILES for this
> structure. RDKit does a good job in recognising that it's the anion based
> on the fractional charges in the MOL2 file (openBabel would give the
> neutral carboxylic acid as output).
>
> Using aromatic atoms/bonds to represent delocalisation generally is not
> possible in SMILES. It's also not strictly correct to use aromatic bonds
> (type 4) in an SD or MOL file either unless the structure is a query - the
> representation of a 'real' molecule in this file format should also be in
> the charge-separated rather than delocalised form.
>
> Sorry that this isn't particularly helpful for your case, but it is
> correct behaviour.
>
> Best regards,
> Chris
>
> On 28 March 2018 at 10:53, Maria Matveyeva <yurievnama...@gmail.com>
> wrote:
>
>> Sorry, i forgot to ask a question: how can i retain the initial form?
>> Maria
>>
>> 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\n
>>> 2\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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