Rendering tool of cube file on jupyter-notebook #psikit #psi4 #memo

Visualize molecular orbital is one of the good way for understating molecular reactivity. Opensource quantum chemistry package ‘Psi4’ can generate cube file for MO rendering and psikit has function for rendering MO with pymol. Here is an example notebook.https://github.com/Mishima-syk/psikit/tree/master/examples/Rendering_Orbital_in_PyMol And recently I found new tool for cube file rendering named fortecubeview package. The license ofContinue reading “Rendering tool of cube file on jupyter-notebook #psikit #psi4 #memo”

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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”

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”

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”

Partial charge visualization with RDKit #RDKit #QuantumChemistry #psikit

Last post, I showed how to visualize each fingerprint contribution for predictive model results with RDKit. The function also can visualize atomic properties such as a partial charge of atoms. Dr. Thomas Evangelidis shared me an example of visualization of quantum chemistry based atom property. He showed an example of conformation effect to the QMContinue reading “Partial charge visualization with RDKit #RDKit #QuantumChemistry #psikit”

Added Notebook Example for psikit #psi4 #RDKit

Some days ago. I updated psikit, added new function, SAPT. The method can calculate inter-intra molecular interaction with psi4. Psikit can call the method very easily. And I added sample notebook in the repository. Following codes are very simple example of SATP for water dimer and FSAPT for phenol dimer. SAPT for water dimer. F-SAPTContinue reading “Added Notebook Example for psikit #psi4 #RDKit”

Coloring molecule with RESP charge on pymol #Pymol

To visualize 3D structure of molecule, PyMol is nice tool. What I would like to write on the post is how to visualize calculated RESP charge on pymol ;)One idea is embed calculated RESP charge to b_factor of molecule pdb. PDB file can make easily from rdkit mol object.A problem for me is how toContinue reading “Coloring molecule with RESP charge on pymol #Pymol”

Draw HOMO LUMO with psikit-2 #chemoinformatics

Yesterday I wrote a post about psikit function for HOMO LUMO drawing. And @fmkz__ gave me very suggestive comment. He performed QM calculation about tetrazole and disclosed the its distribution of negative charge. I had interested in his suggestion and I tried it. By using psikit, I calculated energy of acetic acid and 5-methyl-1H-tetrazole andContinue reading “Draw HOMO LUMO with psikit-2 #chemoinformatics”

Draw HOMO LUMO with psikit #RDKit #Psi4 #PyMol

Now I and @fmkz___ are developing a thin wrapper library for Psi4 and RDKit named psikit.Today I added new function for viewing molecular orbital HOMO and LUMO with pymol. Psi4 has the function which can output cube format file of MO named ‘cubeprop’. So I try to implement the function in to psikit.By using theContinue reading “Draw HOMO LUMO with psikit #RDKit #Psi4 #PyMol”