Python package for Ensemble learning #Chemoinformatics #Scikit learn

Ensemble learning is a technique for machine learning. I wrote post about blending learning before. URL is below. implemented the code by myself at that time. Ensemble learning sometime outperform than single model. So it is useful for try to use the method. Fortunately now we can use ensemble learning very easily by using aContinue reading “Python package for Ensemble learning #Chemoinformatics #Scikit learn”

Quantum Chemistry data of drug bank #QCportal #Quantum_Chemistry

I’m still learning QCArchive. I posted qcportal with reaction dataset. And today I tried to retrieve of drug bank from qcportal. QCportal provides not only calculated numeric data but also 3D mol view by using py3Dmol. OK let’s go to code. get_molecule method provides many data from qcportal web server. What kinds of data inContinue reading “Quantum Chemistry data of drug bank #QCportal #Quantum_Chemistry”

Open data source of Quantum chemistry! #qcportal #rdkit #cheminformatics #quantum_chemisry

In RDKit UGM 2019, I had interest about QCArchive. QCArchive is MolSSI quantum chemistry archive. It provides useful data and python packages. By using one package named qcportal, we can access huge data source of quantum chemistry. It is very useful because QC calculation is useful but it requires computational cost. QC data is usefulContinue reading “Open data source of Quantum chemistry! #qcportal #rdkit #cheminformatics #quantum_chemisry”

Small molecule MD with openMM #MD #Openforcefield

I updated openforcefield from ver 0.5 to ver 0.6. ForceField of SMIRNOFF is also updated. I tried to use new version of OpenFF.At first, I calculated partial charge with semi empirical method ‘AM1-BCC’. Ambertools is used for the calculation, it is easy. Just finished, check the result. Nitrogen has the most negative charge and neighborContinue reading “Small molecule MD with openMM #MD #Openforcefield”

Calculate free solvent accessible surface area #RDKit #Chemoinformatics

Recent version of rdkit has method to calculate FreeSASA.I never used the function so I used it. So I tried to use it. I calculated freeSASA with very simple molecules Phenol and hydroxy pyridine. To calculate FreeSASA, prepare raddii is needed. Now ready, let’s calculate FreeSASA. At first I expected that FreeSASA of pyridine isContinue reading “Calculate free solvent accessible surface area #RDKit #Chemoinformatics”