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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