molecule | Go library for parsing protobufs | Serialization library

I am a complete novice in programming and am currently taking an introductory level class at my local university, I am currently stuck on a question and the prof provides no help whatsoever.

I am taking 3 inputs from an input file molecules.txt (the first two are element names, the third is the number of the surrounding atoms) and printing them into an output file called geometricalshapes.txt

When I run my program nothing gets printed into the output file

Here is the code I have so far that does not work:

The objective of this program is to return the atomic mass from a given formula (as a String), using a CSV file that contains elements and their atomic masses.

My code for this particular problem is this:

I am trying to use RDKit to enumerate large libraries of compounds and output the result as a single column of SMILES strings in a CSV file. I was able to use the following code successfully:

I am in the process of implementing the backend for a business idea in moleculer microservice framework. It works quite well for now using the NATS transporter.

In the near future the number of messages will stay quite low (compared to this example in moleculer documentation) and scaling won't be an issue for now. Therefor In-Memory communication should not be an issue and I would like to remove the whole transporter overhead.

My motivation to use a microservice framework is loose coupling for a clean separation of responsibilities and the option to scale in the future with low effort.

Are there any major disadvantages in using the monolithic architecture for early stage projects or should I directly implement it as a "One service - one/multiple node(s)"-solution? The official documentation describes multiple architectures.

Any practical experience is highly appreciated!

I have a set of 3d coordinates of a molecule and a vector passing through its center of mass. I want to rotate the molecule coordinates and the vector to make the vector align with z-axis.
I used a script in the link below to calculate the rotation matrix from the vector to z-axis, then apply the same rotation matrix to the other 3d coordinates: Calculate rotation matrix to align two vectors in 3D space?
But this method makes my molecule "flat" (in magentas the molecule before rotation and in yellow after rotation): Front view of molecule and Side view of molecule

Does anyone know why this method doesn't work? Is it mathematically correct? Thank you!

I'm trying to create a simple chemistry simulator with atoms (circles) and bonds between them. The problem I'm having is that when atoms 'bond' using a pin joint, the circles rotate independently of the joint. I've tried using more than one pin joint, but the molecules end up oscillating, sometimes wildly, as they stretch and correct themselves. I would appreciate any ideas.

I am using Protegè to model a human drug domain: molecules, medicines, producers, related codes, etc.

Would there be some easier form of GUI in which I could draw classes, object and data properties graphically as nodes, edges and labels?

I'd like to plot imshow heatmap but the final image looks very small and disproportional. My data represent a distance measured between atoms (cca 10 atoms of one molecule to cca 30 atoms of other molecule) - the result is array of arrays. I prepared similar output for illustration, however my original dataset is bigger:

I set up my DataFrame like so: