I am trying to use RDKit to process ChEMBL compounds. However, there is a subset of compounds that get thrown out of the 'fail' port.
Examples of such compounds (I am using molfile or smiles and get same result) are:
CCCCCCCCCCCC(=O)Oc1ccc(CC[n+]2c(C)cc(C)cc2C)cc1OC(=O)CCCCCCCCCCC.F[P-](F)(F)(F)(F)F
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<p>CN(C)c1ccc2C(=C3C=CC(=[N+](C)C)C=C3[Se]c2c1)c4ccsc4C(=O)O.F[P-](F)(F)(F)(F)F</p>
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<p>CCCCCCC\C=C/CCCCCCCCC(=O)Oc1ccc(CC[n+]2c(C)cc(C)cc2C)cc1OC(=O)CCCCCCCC\C=C/CCCCCCC.F[P-](F)(F)(F)(F)F</p>
<p> </p>
<p>Any advice on why RDKit doesn't like these would be welcomed.</p>
<p> </p>
<p>thanks</p>
<p> </p>
<p>Louisa</p>
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