Comments (5)
Hi,
Great 👍
The distogram is predicted in bins mapped from the pair representation. Therefore, the amino acid type doesn't matter as long as the ground truth coordinates (CB for protein) is provided for that loss.
Hope this helps.
Best,
Patrick
from umol.
Hi,
I would like to explain this in detail, but don't have time right now. I will provide a better answer in the first weeks of July.
Right now what I can say is that comment is probably wrong. What matters is that each 'ligand atom token' can be mapped to a CA and that the masks use only CA for the losses. Any amino acid selection will take care of this.
Hope this helps (somewhat).
Best,
Patrick
from umol.
Thanks for the quick answer!
You may disregard the second portion of the question, my issues were due to poor indexing on my part in one of the frame aligned point error losses. All looks good now and I am getting expected behavior during training.
For the distogram loss, it still looks to me like using any other amino acid than glycine would essentially remove the ligand from the distogram loss, as the distances considered are between CBs (except for glycine, that uses CAs, and would be compatible with setting the ligand heavy atoms to CAs).
Umol/src/net/model/tf/data_transforms.py
Lines 308 to 324 in f7cd2b4
Lines 1244 to 1273 in f7cd2b4
I think I should be fine for the most part, but would love to have detailed explanations regardless if you find the time.
Thanks again,
Alexander
from umol.
I will close this issue now, please email me if you have any further more detailed questions and I will try my best to answer.
I realize the code is not that neat, but I partly blame DeepMind for this and all their nested calls to all the different files.
Best,
Patrick
from umol.
I will close this issue now, please email me if you have any further more detailed questions and I will try my best to answer.
I've been able to get some results I'm pretty happy with so I should be all set, thanks! Will definitely shoot you an e-mail if I need to.
I realize the code is not that neat, but I partly blame DeepMind for this and all their nested calls to all the different files.
Yup, not the easiest piece of code to work with for sure...
Thanks again,
Alexander
from umol.
Related Issues (20)
- colab notebook error in prediction step HOT 7
- Docker to run it HOT 9
- Can ligand be inputted via sdf files instead of LIGAND_SMILES format? HOT 6
- Error during conda env creation HOT 1
- How to output more predicted poses HOT 2
- Some question about giant Protein HOT 1
- Environment failed to resolve HOT 2
- 'Config' object has no attribute 'define_bool_state' HOT 6
- Can Umol take 1 protein and 2 small molecules at the same time? HOT 1
- ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (1313,) + inhomogeneous part. HOT 1
- Error 'bash predict.sh' HOT 1
- conda enviroment problem HOT 8
- Predict ligand positions for large protein by multiple GPUs HOT 1
- FileNotFoundError
- Colab crashes due to error in Install dependencies step HOT 1
- RecursionError: maximum recursion depth exceeded HOT 1
- About the FAPE loss HOT 3
- About the num_ligand_atoms HOT 1
- Why are the following packages not available from the current channels?
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from umol.