python in astronomy

When I was junior high school age, I read a book written by Stephen Hawking. The book was very difficult for me so I could not understand well, but it was exciting. Now I often read journals about organic chemistry, medicinal chemistry. However Today I read another review letters about astronomy because some days ago

SDWriter in rdkit

I have a fever since yesterday… ;-( But not Flu. I hope I’ll get well soon…… By the way, I have a problem about molecular chirality handling in rdkit. I often use SDWriter for write molecules as SDF format. The function write molecule as V2000 format. I wander can rdkit write molecule as v3000? The

Structure generation from query molecule using rdkit

I’m thinking about making app for auto structure generator that generate compounds from query_mol and fragment list. Query mol is the molecule that will be changed and fragment list is the fragment molecule stocker. I tried to code simple test script. Following code is not smart I’ll refine ASAP. (It’s difficult to handle large dataset.)

Compound quality for drug discovery

I think there are some approaches to start drug discovery project. HTS, 2. Phenotypic screening, 3. FBDD, 4. Me too (Patent) etc. We have to improve succeed rate of screening. So, compound quality is key factor. Because good starting point is key for compound quality. Serge et. al. published good review in drug discovery today.

Several reaction steps handling in RDKit

I want to make molecule using several reaction steps. My situation was focused in substituted phenyl ring. Greg who is Developer of RDKit posted great blog post before. http://rdkit.blogspot.jp/2015/01/chemical-reaction-notes-i.html So, I read the post and try to make sample code. My strategy is run reaction and get products as smiles because products of RunReactants need

Create matched molecular series with RDKit.

New version of rdkit implemented new function about MMP named rdMMPA. The class has FragmentMol function that returns fragments for MMP. The function can set max number of Cut, and also can set cutting rules. That’s means rdkit provide flexibility to chemo-informatician. Now I’m trying to develop web app about mmpa and mmps. So, I