I'm resending this mail in as Plain Text hopefully so the sourceforge doesn't turn it into an attached HTML message:
I found there are a few molecules that have undergone a crazy transformation from 2D to 3D with RDKit in my batch conversion due to having a long carbon chain. Here is one example molecules on eMolecules.com: http://www.emolecules.com/cgi-bin/more?vid=600149 I've attached the input (2D) and output (3D) SDFs. Here are other examples that result in the same "messy" 3D structures: http://www.emolecules.com/cgi-bin/more?vid=479405 http://www.emolecules.com/cgi-bin/more?vid=445711 Has anyone seen this type of problem before? Is there a way to fix the "messy" conversion? Or a way to detect when this long carbon chain is present and tell RDKit to not convert/output these molecules? -Marshall
