Draw scaffold tree as network with molecular image #RDKit #Cytoscape

I posted new function about scaffold tree which is implemented in rdkit 2020 03 before. In previous my post, I showed example to draw scaffold tree with networkx. It could draw the scaffold tree as a network but molecular structures are not shown on the node. For chemist, structure image is important so I triedContinue reading “Draw scaffold tree as network with molecular image #RDKit #Cytoscape”

Visualize missing data with ipython notebook #visualization

Combination of Pandas and jupyter notebook is useful for data analysis. In the case of handling real world data, there many data set which has missing value. So fist step of data analysis is checking these missing data. Pandas_profiling is the one of useful package to do it. It’s able to make rich report withContinue reading “Visualize missing data with ipython notebook #visualization”

Test new method of rdkit:2020

Now beta version of rdkit is available from anaconda! So I would like to try it. However I would like to test without contaminating current my environment. So I tried new version of rdkit with Docker. Fortunately rdkit can be installed via conda, so I made Dockerfie based on miniconda3. Following dockerfile used continuumio/miniconda3. ByContinue reading “Test new method of rdkit:2020”

Use ORBKIT for rendering MO #orbkit #rdkit #psikit #quantum_chemistry

As you know, there many packages for quantum chemistry not only commercial software but also free tools. And each soft has own output format. So user need to understand how to use it. But it is very time consuming step I think. ORBIKIT is a modular python toolbox for cross-platform post processing of quantum chemicalContinue reading “Use ORBKIT for rendering MO #orbkit #rdkit #psikit #quantum_chemistry”

New molecular fingerprint for chemoinformatics #map4 #RDKit #memo #chemoinformatics

Molecular fingerprint(FP) is a very important for chemoinformatics because it is used for building many predictive models not only ADMET but also biological activities. As you know, ECFP (Morgan Fingerprint) is one of golden standard FP of chemoinformatics. Because it shows stable performance against any problems. After ECFP is reported, many new fingerprint algorithm isContinue reading “New molecular fingerprint for chemoinformatics #map4 #RDKit #memo #chemoinformatics”

Benchmarking platform for generative models. #RDKit #Chemoinformatics #DeepLearning #guacamol

Yesterday I posted benchmarking platform named ‘moses’ and found it worked for test data. And then I could get comment from @Mufei Li, developer of DGL that how about to try guacamol. I checked guacamol before but didn’t try it. So I installed guacamol and used it. From original repo, GuacaMol is an open source PythonContinue reading “Benchmarking platform for generative models. #RDKit #Chemoinformatics #DeepLearning #guacamol”

Benchmarking platform for generative models. #RDKit #Chemoinformatics #DeepLearning #moses

There are lots of publications about molecular generators. Each publication implements novel algorithms so we need tool for comparing these models that which is better for us. I often use PCA, tSNE for chemical space visualization and calculate some scores such as QED, SA/SC Score and molecular properties. However I need the unified metrics. SoContinue reading “Benchmarking platform for generative models. #RDKit #Chemoinformatics #DeepLearning #moses”

Rendering molecular orbital on Jupyter notebook #psikit #py3dmol #rdkit #memo

@fmkz___ and I( @iwatobipen ) are developing psikit which is a thin wrapper of psi4 and rdkit. I hope the package integrates quantum chemistry (Psi4) and chemoinformatics (RDKit). By using psikit, user can make molecular orbital data very convinienlry. Rendering MO is useful for understanding molecular electrostatic shape and nature, but sometime it is difficultContinue reading “Rendering molecular orbital on Jupyter notebook #psikit #py3dmol #rdkit #memo”

Make input file for geomeTRIC #openbabel #psi4 #geomeTRIC

geomeTRIC is code for molecular structures geometry optimization. TRIC means translation-rotation-internal coordinate (TRIC) system. As described in their publication, geomeTRIC can optimize molecular geometry rapidly and few iteration numbers. It seems useful for Quantum Chemistry. And geomeTRIC supports many QC engines Q-Chem, TeraChem, Psi4 andMolpro. I like psi4 so I tried to use geomeTRIC withContinue reading “Make input file for geomeTRIC #openbabel #psi4 #geomeTRIC”

Example usage of psi4-openmm-interface #Psi4 #OpenMM #RDKit

Molecular dynamics and Quantum Chemistry are important tools for CADD. I have interested in these topics and OpenMM and Psi4 are nice tool to handing MD and QM. Today I tried to use psi4-openmm-interface which allows passing of molecular systems between each program. I reviewed test script and found that the package pass the moleculeContinue reading “Example usage of psi4-openmm-interface #Psi4 #OpenMM #RDKit”

New chapter in my life #memo #diary

As I tweeted before, I left the company where I worked for almost 17 years last month and will work for a new company. My background was organic chemistry and I worked as a Medicinal Chemist because I like organic synthesis and the skill seems useful for medicinal chemist. Recently I have an interest notContinue reading “New chapter in my life #memo #diary”