Hi All, I am trying to remove hydrogens from a molecule using RemoveHs, but the function isn't behaving as I expect.
I am using it as part of some code that removes ring systems from a molecule and replaces them with a dummy atom, here are the SMILES for an example molecule and the 3 subsequent molecules as rings are removed 1 - O=C1NC(=O)N(C2CC3CCC2(CS(=O)(=O)N2CCC4(C5=CC=CC=C5CC4)CC2)C3(C)C)C1=O 2 - c1ccc2c(c1)CCC21CCN(SCC23C([*])([*])C(CC2)CC3N2C(=[*])NC(=[*])C2=[*])CC1 3 - [*]=C1NC(=[*])N(C2CC3CCC2([*])C3([*])[*])C1=[*] 4 - [*]C1([*])C2C[CH]C1([*])CC2 On each of these I have used RemoveHs, but for some reason, in molecule 4, one of the carbons of the norbornane system is defined explicitly as CH. Does anyone have any idea why this is, or know how I can remove the hydrogen? Perhaps the hydrogen is added when I use MolToSmiles? Many thanks, Sarah The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
