Re: [Rdkit-discuss] identify anti-aromatic bonds

2015-08-27 Thread Greg Landrum
Hi Yingfeng, Non-aromatic is not a problem, but there's no easy way I can think of off the top of my head for identifying anti-aromatic systems without making C++ code changes. If you were willing to limit yourself to simple rings, you could write some python code to identify all the conjugated

Re: [Rdkit-discuss] Clustering 1M molecules

2015-08-27 Thread Jing Lu
Hi Greg, Thanks! It works! But, is that possible to fold the fingerprint to smaller size? np.zeros((100,2048)) still takes a lot of memory... Best, Jing On Wed, Aug 26, 2015 at 11:02 PM, Greg Landrum greg.land...@gmail.com wrote: On Thu, Aug 27, 2015 at 3:00 AM, Jing Lu

Re: [Rdkit-discuss] Clustering 1M molecules

2015-08-27 Thread Maciek Wójcikowski
Hi Jing, Most fingerprints are binary, thus can be stored as np.bool_, which compared to double should be 64 times more memory efficient. Best, Maciej Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-08-27 16:15 GMT+02:00 Jing Lu ajin...@gmail.com: Hi Greg,

Re: [Rdkit-discuss] identify anti-aromatic bonds

2015-08-27 Thread Yingfeng Wang
Could anyone please share your experience with identifying non-aromatic bonds using RDKit? I would greatly appreciate your help. Yingfeng On Mon, Aug 24, 2015 at 9:42 PM, Yingfeng Wang ywang...@gmail.com wrote: Sorry, my previous email has a typo. According to the following link,