New function of RDKit 2017.09 #RDKit

Recently I updated my rdkit env from 201703 to 201709 by using conda. New version of rdkit was implemented cool function named rdRGroupDeompositon. The function enable us to render RGroups as DataFrame. I tried to visualize cdk2.sdf dataset. Code that I wrote is bellow.(using jupyter notebook) Then visualize RGdecomp result. Result is following image. ;-)Continue reading “New function of RDKit 2017.09 #RDKit”

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molecule encoder/decoder in deepchem #rdkit #deepchem

Today I updated deepchem in my mac. It was easy to install new version of deepchem on Mac. That’s all. ;-) New version of deepchem is implemented MoleculeVAE. MoeculeVAE generates new molecules by using pre defined model. Deepchem can use pre defined model that was trained with Zinc Dataset. OK let’s run the code. IContinue reading “molecule encoder/decoder in deepchem #rdkit #deepchem”

tensorboard embeddings + RDKit #RDKit

Mainly I use Keras for deep learning. Because Keras is easy to use and easy to understand for me. Keras has callback function to call tensorboard. But It has difficulties in use tensorboard embeddings. You know, tensorboard embeddings is unique function to visualize future of word vectors. I want to use tensorboard embeddings for visualizationContinue reading “tensorboard embeddings + RDKit #RDKit”

Create MMPDB ( matched molecular pair )!

Matched molecular pair analysis is very common method to analyze SAR for medicinal chemists. There are lots of publications about it and applications in these area. I often use rdkit/Contrib/mmpa to make my own MMP dataset. The origin of the algorithm is described in following URL. https://www.ncbi.nlm.nih.gov/pubmed/20121045 Yesterday, good news announced by @RDKit_org. It isContinue reading “Create MMPDB ( matched molecular pair )!”

3d conformer fingerprint calculation using RDKit # RDKit

Recently, attractive article was published in ACS journal. The article describes how to calculate 3D structure based fingerprint and compare some finger prints that are well known in these area. New method called “E3FP” is algorithm to calculate 3D conformer fingerprint like Extended Connectivity Fingerprint(ECFP). E3FP encodes information only atoms that are connected but alsoContinue reading “3d conformer fingerprint calculation using RDKit # RDKit”

Platfrom-as-a-Service for Deep Learning.

Yesterday, I enjoyed mishima.syk #10. I uploaded my presentation and code to mishimasyk repo. I introduced briefly about a PaaS for DL named ‘Floyd’. I think the service is interesting because I can run DL on cloud with GPU! So, I describe very simple example to start DL with “FLOYD” ;-) At first, Make accountContinue reading “Platfrom-as-a-Service for Deep Learning.”

Installing TensorFlow on Mac OX X with GPU support

Yesterday, I tried to install tensorflow-gpu on my mac. My PC is MacBook Pro (Retina, 15-inch, Mid 2014). The PC has NVIDA GPU. OS is Seirra. Details are described in following URL. https://www.tensorflow.org/install/install_mac I installed tensorflow directly by using pip command. Almost done, but not finished yet. To finish the installation, I need to disableContinue reading “Installing TensorFlow on Mac OX X with GPU support”

Open drug discovery toolkit for python

Recently There are lots of python libraries for chemoinformatics and machine learning. One of my favorites is RDKit. ;-) These area is still active. And today I tried new library named “ODDT” open drug discovery toolkit. Reference URL is https://jcheminf.springeropen.com/articles/10.1186/s13321-015-0078-2. ODDT is well documented in http://oddt.readthedocs.io/en/latest/index.html?highlight=InteractionFingerprint. ⭐️ Oddt is implemented shape and electronic similarities!! IContinue reading “Open drug discovery toolkit for python”

Graph convolution classification with deepchem

I posted about graph convolution regression using deepchem. And today, I tried graph convolution classification using deepchem. Code is almost same as regression model. The only a difference point is use dc.models.MultitaskGraphClassifier instead of dc.models.MultitaskGraphRegressor. I got sample ( JAK3 inhibitor ) data from chembl and tried to make model. At first I used pandasContinue reading “Graph convolution classification with deepchem”

Graph convolution regression with deepchem

Somedays ago, I posted blog about deepchem. I am still playing with deepchem. Today I tried to use graph convolution regression model. Deepchem provided Graph convolution Regressor. Cool. I used solubility data provided from AstraZeneca. https://www.ebi.ac.uk/chembl/assay/inspect/CHEMBL3301364 My test code is following. Almost same as deepchem”s example code. CSVLoader method is very useful because it canContinue reading “Graph convolution regression with deepchem”

how to get molecular graph features

Belated I am interested in deepchem that is an open-source deep learning toolkit for drug discovery. Deep-chem supported many features for chemoinformatics. And one of interested feature is calculation of molecular graphs. It is more primitive than hashed finger print. I tried to caluclate it. Currently the toolkit supports only linux, so I installed deepchemContinue reading “how to get molecular graph features”

Compile LeapPython and Manipulate protein structure with Leap Motion.

I was interested in Kinect as input device, because Kinect can detect motion as input it feels feature. ;-) And some days ago, I got new input device “Leap Motion”. The Leap Motion controller is a small USB peripheral device which is designed to be placed on a physical desktop, facing upward. ( from wikiContinue reading “Compile LeapPython and Manipulate protein structure with Leap Motion.”

Target prediction using local ChEMBL

Yesterday, I posed about target prediction using ChEMBLDB web API. If I want to predict many molecules, it will need many time. So, I changed code to use local chembldb. I used sqlalchemy, because the library is powerful and flexible to use any RDB. Test code is following. The sample code needs a smiles stringsContinue reading “Target prediction using local ChEMBL”

Target prediction using ChEMBL

You know, there are some database that can publicly available database in chemo informatics area. ChEMBL DB is one of useful database. George Papadatos introduced useful tool for target prediction using ChEMBL. He provided chembl target prediction model via ftp server ! So, everyone can use the model. I used the model and tried toContinue reading “Target prediction using ChEMBL”

Python Sudoku solver ;-D

Recently, I am learning about linear optimization using python. From Wiki.. Sudoku is a logic-based, combinatorial number-placement puzzle. The objective is to fill 9 x 9 grid with digits so that each column, each row, and each of the 3 x 3 subgrids that compose the grid contains all of the digits from 1 toContinue reading “Python Sudoku solver ;-D”

High speed sorting algorithm ( sketch sort )

Somedays ago, I attended CBI about AI for drug discovery. A presenter introduced about sorting algorithm named “sketch sort”. Detail of the algorithm is described in following url. Click to access tabei10a.pdf The algorithm can k-search nearest neighbor in short time. The source code has been published in google corde archive. I tried to sortContinue reading “High speed sorting algorithm ( sketch sort )”

Draw molecule with atom index in RDKit

I found interesting topics in rdkit discuss. How to draw molecule with atom index. Greg developer of RDKit answered tips to do it. It can use molAtomMapNumber. https://sourceforge.net/p/rdkit/mailman/message/31663468/ I didn’t know that! I tried that in my PC. RDKit can draw molecule easily using IPythonConsole. Test in a kinase inhibitor Draw molecule. https://github.com/iwatobipen/chemo_info/blob/master/rdkit_notebook/drawmol_with%2Bidx.ipynb