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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Relation ship between dihedral deg and atomic charge #psi4 #RDKit #psikit

Recently psikit repository got PR about RESP charge calculation. Thanks for PR. And I have question about the relation ship between compound conformation and partial charge. Fortunately, psikit already has an example for torsion scan thank @fmkz___ for sharing useful code. The example code is here. Following code is same as example code linked above.Continue reading “Relation ship between dihedral deg and atomic charge #psi4 #RDKit #psikit”

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”

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”

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”

Calculate solvent effect in Psi4 #psi4 #quantumchemistry

Recently I use not only chemoinformatics tools but also quantum chemistry tool, my favorite is Psi4. Psi4 has many options and plug-ins for quantum calculation. Most setting of calculation is vacuum, but it actually true. So considering the solvent around the molecules is important. Can psi4 perform calculation with solvent effect? Yes! PCMSolver is pluginContinue reading “Calculate solvent effect in Psi4 #psi4 #quantumchemistry”

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”

Comparison of rdChemReactions and EditableMol #RDKit #chemoinformatics

In this year I moved from MedChem team to CompChem team. And now I need to learn SBDD. Today I struggled mol object that has 3D information. I would like to replace hydrogen which attached aromatic carbon to some atoms. I thought it is easy if I use rdChemReactions method. But I found that itContinue reading “Comparison of rdChemReactions and EditableMol #RDKit #chemoinformatics”

Visualize Molecular Orbital with pymol and psikit #RDKit #psi4 #psikit #pymol

I posted how to visualize MO with VMD, the data was generated from psikit. I used VMD because psi4 provides visualize function for cubefile and I could not find the same method on pymol. Pymol is familier for me than VMD. So I would like to do same thing on pymol. And today I couldContinue reading “Visualize Molecular Orbital with pymol and psikit #RDKit #psi4 #psikit #pymol”

Visualize HOMO LUMO with psi4 #RDKit #psi4 #psikit

Now thin wrapper of psi4 named psikit can generate cube file which has frontier orbital information. After calling getMOview, I would like to check the orbital shape. Psi4 provides vmd_cube.py script which generates cool view on VMD. To run the script on python3, it is needed to change line 332 from ‘for k,v in options.iteritems():’Continue reading “Visualize HOMO LUMO with psi4 #RDKit #psi4 #psikit”

Calculate atomic charges with psikit #RDKit #psi4

Recently I implemented new function in psikit for atomic charge calculation. Now user can get mulliken charges, RESP charges and Lowdin charges very easily. There is quick example below. At first import libraries. I used methanol and imidazole for demo. And psikit can generate 3D structure from SMILES and optimize the conformer with RDKit. ThenContinue reading “Calculate atomic charges with psikit #RDKit #psi4”

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”

New functionality of psikit #Chemoinformatics #RDKit #Psi4

Happy new year! ‘Akemashite Omedetou Gozaimasu’ in Japanese! I and @kzfm_ -san are developing a library which uses a rdkit & psi4 named psikit. You can find brief introduction the concept following URL.http://blog.kzfmix.com/entry/1536978824 Today I added new function that can calculate RESP charge of give molecule. RESP charge means ‘Restraints for Deriving Atomic Charges’. DetailsContinue reading “New functionality of psikit #Chemoinformatics #RDKit #Psi4”

Draw similarity network #RDKit #Cyjupyter

Recently Kei Ono who is developer of cytoscape developed cyjupyter. https://pypi.org/project/cyjupyter/0.2.0/ It seems attractive for me because the library can draw network diagram on jupyter notebook. There are many network structured data in chemoinformatics. For example molecule, molecular similarity map and MMP etc… I used the library to draw similarity map of molecules today. IContinue reading “Draw similarity network #RDKit #Cyjupyter”

Calculate HOMO and LUMO with Psi4 reviced #RDKit #Psi4

Yesterday, I got comments from reader. Regarding the comment, to calculate HOMO LUMO with psi4 correct way is below. Next, calculate HOMO-LUMO of benzene with the function and psi4. After the calculation, I could access HOMO-LUMO, the code is below. Check log file That’s all. I am happy because I can get many response throughContinue reading “Calculate HOMO and LUMO with Psi4 reviced #RDKit #Psi4”

Calculate HOMO and LUMO with Psi4 #RDKit #Psi4

You know Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. It is very easy to use and has an optional Python interface. It is useful for us I think. Because Psi4 can use in python, it means we can integrate manyContinue reading “Calculate HOMO and LUMO with Psi4 #RDKit #Psi4”

Quantum chemistry calculation with RDKit.

I enjoyed JCUP VII. All presentations were very impressive for me and I interested in psi4 that is open source tool for quantum chemistry. http://www.psicode.org/ Fortunately, I could install psi4 using conda command. It supports only python2.x. If user want to install psi4, just type “conda install -c psi4 psi4 “. That’s all ! ReadyContinue reading “Quantum chemistry calculation with RDKit.”