How to find certain source codes for a function

[LanceKnight]

Hello, I was wondering how rdkit calculate the rotatable bonds (what criteria it uses to classify a bond into a rotatable bond). So I was trying to read the Chem.Linpiski.NumRotatableBonds. However, I encountered several roadblocks:

1. I tried to search it in the C++ reference but I couldn't find the class Chem in the left panel where it says "Classes-Class List"
2. I then found Chem.Linpiski.NumRotatableBonds in the github repo. Then inside the rdkit/Chem folder in the repo, I found it uses Chem.rdMolDescriptors. However, I was not able to find a file or folder called rdMolDescriptors in the Chem folder in the github

Can someone teach how to, in general, look for source codes for certain things in rdkit? I'm more used to pytorch type of documentation where [source codes] is listed right next to the function in the documentation.

[greglandrum]

Hi @LanceKnight,

As you've discovered, it can be a bit complicated to find things like this due to the fact that most of the RDKit is implemented in C++ which is then wrapped to be used from Python. The names of things in the C++ code are usually not exactly the same as the names in Python.

Probably the easiest way to answer a question like "how is the number of rotatable bonds defined" is to search in the rdkit repo in github
for NumRotatableBonds:

Then look through the C++ results until you find something that looks like it might be the answer;

Click on that to go to the right file, and then you can find the actual function that implements the descriptor:

rdkit/Code/GraphMol/Descriptors/Lipinski.cpp

Line 108 in 4a69bc3

unsigned int calcNumRotatableBonds(const ROMol &mol,

The other piece of information you need in this case is that the default value of the strict argument is Strict.

[YunchaoLiu]

I see. Thank you so much for your detailed answer @greglandrum :)

[YunchaoLiu]

btw, if there is no rdMolDescriptor folder/file under Chem folder, how does this import realized? I guess it's also related to the C++ implementation? Sorry I really have little experience with C++ with python wrapping so I am not sure how that works

[bp-kelley]

Generally everything that starts with an “rd” is a shared library that python can import.