Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Hi Nils, I don't think this is really a bug, it's more of a matter of default parameters that aren't appropriate for the molecules being considered. The RDKit fingerprint hashes subgraphs (branched and unbranched) within a particular range of sizes, as measured by the number of bonds in the

Re: [Rdkit-discuss] format.py in Pandas 0.20.1 Has Moved

Hi Steve, Thanks for pointing this out. Brian fixed this on master a while ago ( https://github.com/rdkit/rdkit/pull/1410) and we will have the fix in the 2017.03.2 patch release (coming, hopefully, next week). Here's a quick demo that it actually works: In [2]: pandas.__version__ Out[2]:

[Rdkit-discuss] format.py in Pandas 0.20.1 Has Moved

This may have already been addressed in the next release, but I wanted to be sure. It appears that Pandas was refactored in the 0.20.1 release in a way that breaks PandasTools: Python 3.6.1 |Continuum Analytics, Inc.| (default, May 11 2017, 13:25:24) [MSC v.1900 64 bit (AMD64)] on win32 Type

Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

That's *much* too easy. Thanks! -greg On Thu, Jun 1, 2017 at 6:09 PM, George Papadatos wrote: > Example: https://www.surechembl.org/chemical/SCHEMBL1895 > > George. > > Sent from my giPhone > > On 1 Jun 2017, at 17:05, Greg Landrum wrote: > > Hi

Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Hi Greg, I have an SDFile at hand (see attached). Lookup of SureChEMBL-structures is possible via https://www.surechembl.org/chemical/SCHEMBL16257312 (although we can argue whether that page is convenient...). Thanks for your help, Nils On Thu, Jun 1, 2017 at 6:05 PM, Greg Landrum

Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Example: https://www.surechembl.org/chemical/SCHEMBL1895 George. Sent from my giPhone > On 1 Jun 2017, at 17:05, Greg Landrum wrote: > > Hi Nils, > > Can you please send me the SMILES for those structures (or point me to an > easy way to lookup a SCHEMBL id)? > > I

Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Hi Nils, Can you please send me the SMILES for those structures (or point me to an easy way to lookup a SCHEMBL id)? I will take a look at these, but I don't currently have a convenient copy of SCHEMBL. -greg On Thu, Jun 1, 2017 at 4:28 PM, Nils Weskamp wrote: >

Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Hi Bruce, setting fpSize to 4096 or 8192 leads to fingerprints with a few 0s (although still a very high bit density). The same is true when I reduce the maximum path length. I do not see the same kind of behaviour with a different path-oriented fingerprint implementation (ChemAxon), which made

Re: [Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Hi, Did you try setting the length of the fingerprint (fpSize) to a higher value than the default 2048 to see if you can get one with 0's? Cheers, Bruce > > Message: 2 > Date: Thu, 1 Jun 2017 16:28:40 +0200 > From: Nils Weskamp > To: Rdkit-discuss@lists.sourceforge.net

[Rdkit-discuss] RDKit-fingerprints set all bits for complex molecules?

Dear RDKitters, I just calculated RDKit "Daylight-like" fingerprints for a number of public compound databases and found quite a number of examples where the resulting fingerprints have *all* bits set to 1. This happens in both KNIME 3.2.1 (1024/1/7) and also via the command line (2048/1/7/4) for

Re: [Rdkit-discuss] Using RDKit in PyCharm and Anaconda on Windows

Thanks, everyone, for the ideas and suggestions. The easiest thing we have come up with so far, in case this helps anyone else, is to find the shortcut to PyCharm in your Windows Start Menu folder, create a copy of it called something like "PyCharm - your_env" and edit the target so that

Re: [Rdkit-discuss] Using RDKit in PyCharm and Anaconda on Windows

I definitely have it working on Linux, too, but it might have been that I also only tried it with PyCharm 2017.1.3 first. Before that, I did what Greg suggested, starting pycharm from the activated environment. Unfortunately I have no experience with Windows in this regard, too. On Thu, Jun 1,

Re: [Rdkit-discuss] Using RDKit in PyCharm and Anaconda on Windows

I had some issues to run rdkit from Python console in PyCharm (4.5.5) on Linux. After recent installation of PyCharm 2017.1.3 it started to work. Maybe updating PyCharm will help on Win as well. Pavel. On 05/30/2017 10:10 PM, West, Richard wrote: We're having trouble getting RDKit to work