repo up dateリポジトリ更新

I updated code about mishimasyk6. URL is following. https://github.com/iwatobipen/mishimasyk/tree/master/mishimasyk6_1 repo is https://github.com/iwatobipen/mishimasyk I added tooltip in the scatterplot. So, when user mouse over the point, tooltip will draw structure and mw, fr_sp3. D3js is powerful library for drawing charts. 勉強会でツールチップ実装できなかったって話したんで実装しました。 mishimasyl6_1のコードでは散布図を書いたあとマウスオーバーすると構造とかそれ以外のアノテーションを描画します。 d3.events.pageXでダイレクトにマウスの位置を検出してdivタグ要素にSVGを突っ込めば完了です。 ダイナミックな図ができて面白いと思います。 コードはこんな感じ もしレポジトリをDLして動かない場合はvar RDKit = rdk()のコメント部分を有効にすると動くと思います。 // var RDKit = rdk(); var paddingContinue reading “repo up dateリポジトリ更新”

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mishima.syk#6 etc.

Today I presented at mishima.syk#6 about rdkitjs. I wrote very simple script using rdkitjs and d3js. This script can make scatter plot about fraction of Csp3 and molwt and when user mouse over the circle, rdkitjs return molecule image. Like this. I uploaded the script to github. https://github.com/iwatobipen/mishimasyk/tree/master/mishimasyk6 I hope, participants enjoyed my presentation…. TheContinue reading “mishima.syk#6 etc.”

The result

I went to my old school the day before yesterday, I like my old school. An event about chemoinformatics was held here. I enjoyed presentation of all participants. My prediction result was …….(please don’t ask ;-)) All teams used two approaches SBDD or LBDD, and winner used LBDD approach. It’s worth to think about whichContinue reading “The result”

calculate 3d pharmacophore fingerprint in rdkit

I read document about RDKit for the first time in a while and found nice snippet. A 3D Pharmacophore finger print can be caluclated very easily. If dMat = None( default setting), fp means 2D Pharamcophore fingerprint, but now I passed dMat so the fingerprint has 3D information. Now 3D pharmacophore fingerprint in hand, itContinue reading “calculate 3d pharmacophore fingerprint in rdkit”

Is CyTOF new technology ?

In some projects, pharmacologists showed me FACS data set. It’s useful to analyse cell response. I have not measured FACS by myself (I’m chemist…), so I didn’t understand details. Ala F. Nassar et al. published exciting review ( for me ) in DDT. About ‘mass’ cytometry. The link is following. http://www.sciencedirect.com/science/article/pii/S1359644615002317 I searched CyTOF asContinue reading “Is CyTOF new technology ?”

Think about SAR analysis.

I lost a chance of participation in RDKIT-UGM because ticket was sold out. ;-( I’ll try next year…. SAR analysis is key for drug discovery. MMPA is one of major tool, I like the method. Because MMPA is easy to check effect of substituent in molecule. But sometime, it difficult to understand why the parameterContinue reading “Think about SAR analysis.”