Transportation in Uppsala and Surrounding Areas (2025 Update)

This article was first published on Uppsala University’s Zhihu platform (https://zhuanlan.zhihu.com/p/590668337). However, because Uppsala province changed its transport payment system, some content is no longer correct, so we updated it. Thanks to the original author Wadlo for their contribution.

–Last Update: 2025 DEC

Geographic Areas and Local Transport Operating Zones - What’s the Difference?

The beautiful city of Uppsala sits within Uppsala University campus. But “Uppsala” can mean either Uppsala Province (Uppsala län) or Uppsala Municipality (Uppsala Kommun) within Uppsala Province. Uppsala Province includes not only Uppsala city but also cities like Enköping, Östhammar, and Tierp.

Introduction

ChEMBL is a database beloved by chemistry professionals. ~~~~(Because it’s free)~~~~ However, if we want to collect information in bulk, searching individually through the web interface can be quite troublesome. So, is there a method to obtain molecular information in bulk and automatically?

Actually, besides the well-known ChEMBL website, ChEMBL thoughtfully provides a ChEMBL web service client that can be used with Python. By simply entering the desired keywords in Python code, we can search in bulk for the content we need and save it as a CSV file for subsequent processing. ~~~~(For example, cyber alchemy,aka Machine Learning)~~~~

Advanced Molecular Modelling Applied to Drug Discovery(3FK181)，Uppsala University Exam Preparation Notes- 2023

Note

This is an personal examination preparation note for the course Advanced Molecular Modelling Applied to Drug Discovery(3FK181)，Uppsala University.Converted atuomatically by Claude AI

Click hereto download the original hand-written notebook.

Chapter 1: Ligand-Protein Interaction

Key Points:

1. Describing the interaction of molecules

   • Determining if a molecule is a good target or not

2. Types of Interactions:

   • Electrostatics: Follow Coulomb’s Law

InDraw for web is a powerful online chemical structure drawing tool. It can convert chemical figures (in articles, for example) to SMILES so that we can edit the structures ourselves. Currently, it only supports Chinese. Let’s see how it works.

Step 1. Register

Background

It’s hard to remove the white background of molecular 2D figures created directly with RDKit. They don’t look good when placed in PowerPoint. This article provided a way to make TRANSPARENT ones.

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from rdkit import Chem
from rdkit import rdBase
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import rdFMCS
from rdkit import DataStructs
import io
from PIL import Image

def show_png(data):
    bio = io.BytesIO(data)
    img = Image.open(bio)
    return img
smi = "CCCCCC" #Take cyclohexane as an example
drawer = rdMolDraw2D.MolDraw2DCairo(300,300) #You can adjust the image size
drawer.drawOptions().clearBackground = False
drawer.drawOptions().addStereoAnnotation = False
drawer.DrawMolecule(Chem.MolFromSmiles(smi))
drawer.FinishDrawing()
mol = drawer.GetDrawingText()
show_png(mol)

Right click and save it, done! Cheers!🍺