Call psi4 from web app! #Psi4 #QuantumChemistry

Psi4 is a python package for quantum chemistry. I like it. Native psi4 has some difficulties for preparing input file. So psikit is useful I think. And I think webmo is useful package for calling psi4. I’ve always been interested webmo. So I tried to use it today.Basic function of webmo is provided free licence.Continue reading “Call psi4 from web app! #Psi4 #QuantumChemistry”

Advertisement

A new function of rdkit201909 #RDKit #Chemoinformatics

Last week, I got cool information that new version of rdkit is available by installing conda! You can check new feature in ReleaseNotes in original repo,https://github.com/rdkit/rdkit/blob/master/ReleaseNotes.md I installed RDKit201909 now and am reading document now. MolHash function originally developed from nextmove software is implemented in the version.[RDKit Document]https://www.rdkit.org/docs/source/rdkit.Chem.rdMolHash.html[Nextmove software]https://nextmovesoftware.github.io/molhash/commandline.html#usage MolHash can generates some hashes ofContinue reading “A new function of rdkit201909 #RDKit #Chemoinformatics”

Virtual screening with quantum computing! #Quantum_computing #chemoinformatics #memorandum

Quantum computing is one of the hot area in these days. Now google reported exciting article to nature. Quantum computing reach is also very useful for drug discovery. Some days ago I found interesting article published by researcher in 1QBit, Univ. Drive, Accenture Labs and Biogen. URL is below.A Quantum-Inspired Method for Three-Dimensional Ligand-Based VirtualContinue reading “Virtual screening with quantum computing! #Quantum_computing #chemoinformatics #memorandum”

Electrostatic Potential Surface(ESP) calculation with GCNN #RDKit #chemoinformatics

ESP is a key feature in Drug Discovery. There are many publications discussing ESP in Drug Design. However getting accurate ESP is time-consuming because it needs high level QM calculations. To reduce the calculation cost of QM, predict quantum nature by using Deep learning is researched. And some days ago, I found interesting article publishedContinue reading “Electrostatic Potential Surface(ESP) calculation with GCNN #RDKit #chemoinformatics”

Old but new molecular generator #RDKit #mishima.syk

In this February, we had opportunity to learn how to use molecular generator in Mishima.syk #13. We used REINVENT for generator. It works on pytorch ver0.3, but raise error when the code run on new version of pytorch. Deep learning framework is rapidly upgraded. It is difficult to maintenance OSS code I think. I demonstratedContinue reading “Old but new molecular generator #RDKit #mishima.syk”

Integration of RDKit and Neo4j #RDKit #Neo4j #GraphDB #Chemoinformatics

One of the most powerful storms of the year named ‘Hagibis’ is coming now. All weekend schedules are cancelled. I’m staying at my home and writing code… BTW, In the RDKit UGM 2019, neo4j-rdkit integration project was introduced. The project is one of the topic in Google summer of code. You can find the projectContinue reading “Integration of RDKit and Neo4j #RDKit #Neo4j #GraphDB #Chemoinformatics”

Particle Swarm Optimization for molecular design #RDKit #Chemoinformatics

I participated RDKit UGM last week. It was worth to go I think. And in the meeting I got useful information for de novo molecular design. You can find the slide deck following URL. https://github.com/rdkit/UGM_2019/blob/master/Presentations/Montanari_Winter_Utilizing_in_silico_models.pdf They used Particle Swarm Optimization(PSO) for de novo molecular design. PSO is very simple method for parameter optimization. Details areContinue reading “Particle Swarm Optimization for molecular design #RDKit #Chemoinformatics”

Make RGroup decompose table with old ver. RDKit #RDKit #Chemoinformatics

ObjectiveRecent version of RDKit has rdRGroupDecomposition module for R Group decomposition. You know, it is very useful module for SAR analysis. However this function is not implemented in old version of rdkit (i.e. rdkit for 32 bit windows). I would like to implement similar module for 32bit windows system. My approach with codeSo, I triedContinue reading “Make RGroup decompose table with old ver. RDKit #RDKit #Chemoinformatics”