So yesterday I spent at least 3 hours to deal with Python package development in Conda environment. So I wrote this post as a self-reminder, since the steps are somewhat long. And also for those of you who is facing the same problem as I do. Why do I need to use pip when I can use Conda to install Open Babel If you’re an experienced Python package developer you should have known the following trick:...
There are many ways to improve structure-based virtual screening, from something as simple as screening the ligand based on the physico-chemical properties (MW, number of H-donor, number of aromatic rings, pKa, etc.), using consensus docking, or even post-analysis using FEP-based method. One of the simplest and yet fruitful approach to enhance the virtual screening workflow is using interaction fingerprinting. It has been known for long time that certain interaction from certain residue holds more significance than others....
Prerequisite Basic command prompt Basic Python (variable type, collection, loop, decision, and functions) Python virtual environment (conda/mamba) Jupyter notebook/lab Create new environment So first as always, start with creating new environment (preferably mamba). If you have never used mamba before and have some experience with conda then great, you can simply change every conda command with mamba and vice versa. Create new environment for this series using this command:...
What is a Domain-Specific Language? It is more common than you think. Few of us – computational chemists – have heard the term Domain-Specific Language (DSL for short), even though this is somewhat ubiquitous in our workflow, especially when dealing with molecule visualisation. Don’t you believe me? Check out the command you type on VMD, PyMOL, YASARA, or Chimera. YASARA command: LoadPDB 1crn, download=yes AutoPosOriObj 1, x = 1, y = 10, z = 0, alpha = 0, beta = 0, gamma = 0 ColorRes cys, green ShowRes cys BallStickRes cys AutoRotateObj 1, Y = 1 wait 180 AutoRotateObj 1, Y = 0 ZoomRes Cys 16, step = 50 wait 100 ZoomRes all VMD Tcl/Tk command:...