Re: [Rdkit-discuss] Chem.PandasTools

Hi Paul, You first have to read the MMP into a reaction object (Chem.ReactionFromSmarts). Greg On Friday, May 9, 2014, wrote: > Dear Gregori & Samo, > > thanks for your hints. > > I just tried running > > Draw.ReactionToImage("[*:1][H]>>[*:1]C") > > => > > AttributeError: 'str' object has no a

Re: [Rdkit-discuss] Chem.PandasTools

Hi Paul, The Draw modules also contains a "ReactionToImage" function; Your MMP can be read as a reaction. Hope this helps further! Grégori Date: Thu, 8 May 2014 16:31:32 +0200 > From: paul.czodrow...@merckgroup.com > Subject: [Rdkit-discuss] Chem.PandasTools > To: rdkit-discuss@lists.sourceforge

Re: [Rdkit-discuss] Problem reading a specific smiles with the cartridge

the DB was somehow corrupted, since I got subsequent warnings like "null argument to internal routine". Sorry to have bothered you with that! Grégori On 23 March 2014 10:30, Greg Landrum wrote: > > > On Saturday, March 22, 2014, Gerebtzoff, Gregori < > gregori.gerebtz...

Re: [Rdkit-discuss] Problem reading a specific smiles with the cartridge

just that one that's problematic? > > -greg > > > On Fri, Mar 21, 2014 at 6:30 PM, Gerebtzoff, Gregori < > gregori.gerebtz...@roche.com > > wrote: > >> Hi guys, >> >> I've been having problem reading this particular smiles string with the >>

[Rdkit-discuss] Problem reading a specific smiles with the cartridge

Hi guys, I've been having problem reading this particular smiles string with the PostgreSQL cartridge: C12CC(C1)C2 I don't know if I'm running the latest version of the cartridge though... Thanks for your help! Grégori >>> cursor.execute("select rdkit_version()") >>> cursor.fetchone() ['0.70.0

Re: [Rdkit-discuss] Possible rotatable bonds replacement

Hi, I would also go for the second option (i.e. replace the current SMART): I also see it as a bug fix. What you could do is to highlight in the release notes or somewhere else the call one would have to do to mimic the behavior of previous releases: Lipinski.RotatableBondSmarts = Chem.MolFromSmar

Re: [Rdkit-discuss] Counting amide groups in rotatable bond counts

Hi Toby, One additional note on what Greg wrote: you can define another smarts pattern for the identification of rotatable bonds: Lipinski.RotatableBondSmarts = Chem.MolFromSmarts("...") Some smarts from the literature: Daylight: [!$(*#*)&!D1&$(*(-[!#1])~[!#1])]-&!@[!$(*#*)&!D1&$(*(-[!#1])~[!#1])

Re: [Rdkit-discuss] Compound Neutralization

Hi Yingfeng, Let me remind you some chemistry basics: Chlorine atom has 17 electrons. In last orbit it has 7 electrons hence it requires 1 electron to complete octet. Hence it's valency is 1. Thus it's not a surprise that your smiles is generating an error. In order to check for get the charge st

[Rdkit-discuss] Transparency and enhanced molecular depiction

Hello RDKitters, I'm happy to advertise the improved molecular depiction which has just been pulled back in the main RDKit repository. I want to thank Paul Emsley for the preliminary work during the hackathon at the RDKit UGM, and Greg who helped me finalizing the changes, especially for other can

Re: [Rdkit-discuss] Size of drawn molecules

ved there. > The only problem I see after changing dotsPerAngstrom is that font size > stays the same so again you need to do the math and scale it on your own > (and set atomLabelFontSize accordingly). > > Regards, > Michal Nowotka > > > > > On Fri, Sep 6, 2013 at

[Rdkit-discuss] Size of drawn molecules

Hi guys, Is there an easy way to increase the maximal size of a molecule on the canvas? I realized that at some point increasing the canvas size won't increase the size of the molecule anymore. Looking at the code of MolDrawing.py the function scaleAndCenter seems to deal with that aspect, I trie

[Rdkit-discuss] RDKit cartridge speed issue

Hi RDKitters, I'm facing some performance issue using the RDKit cartridge; the database contains roughly 170k small molecules, I use the cartridge version 0.20.0 on PostgreSQL 8.4.7, and the tanimoto_threshold is set to 0.5 A simple similarity search takes at least 30 seconds to complete. The data

[Rdkit-discuss] Capturing warnings

Hi List, Is there a clean way to capture the warnings generated by RDKit, for instance "Warning: ring stereochemistry detected. The output SMILES is not canonical"? I tried several approaches (the warnings python module, by redirecting the stderr with os.devnull, or try/except) but none of them

Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)

> Hi - > > A RDKit-based implementation of the QED measure as described by > Richard Bickerton (Nature Chemistry, 2012, 4, 90-98) has been > implemented and made available for download from our website ( > www.silicos-it.com > Biscu-it). > > Regards, > - Hans > > Hi Hans, Thanks for the impl

Re: [Rdkit-discuss] Getting the list of descriptors

Hi Noel, You might try also the following: dir(Descriptors) The dir() function returns an alphabetized list of names. You can also have a look at the inspect module, especially the getdoc and getargspec functions; these will give you more information on each function. The inspect.isroutine or i