kull-centre / _2022_ml-ddg-blaabjerg Goto Github PK
View Code? Open in Web Editor NEWLicense: Other
_2022_ml-ddg-blaabjerg's People
Contributors
Stargazers
Watchers
_2022_ml-ddg-blaabjerg's Issues
The colab notebook uses the old version of the code
Dear Blaabjerg et al,
First of all, thanks for making the code available!
I am currently in the process of porting your model to a framework we're building for black box functions related to protein optimization, and I noticed something: the version on the interactive Colab notebook you use is the previous one instead of this one. Funnily, the previous one was easier to set-up for me (given that you don't use dssp in extract_environments.py).
I was wondering: is this by design? What was the main rationale for updating the code?
conda install - UnsatisfiableError
RaSP-log.txt
Hello,
Thank you for sharing this package - it looks really exciting and looking forward to testing it out a bit.
Unfortunately, when I try to install the dependencies with conda, I keep running into UnsatisfiableError problems - the main issue seems to be __glibc though I'm not sure - I've included the full output in the attached file.
Here's the command I'm using:
conda create -n rasp python=3.6 pyyaml=5.3.1 pandas=1.1.4 scipy=1.5.3 numpy=1.17.3 scikit-learn=0.24.0 mpl-scatter-density=0.7 pdbfixer=1.5 pytorch=1.2.0 cudatoolkit=10.0 biopython=1.72 openmm=7.3.1 matplotlib=3.1.1 seaborn=0.11.2 ptitprince=0.2.5 dssp=3.0.0 vaex=4.5.0 -c salilab -c omnia -c conda-forge -c anaconda -c defaults
And what seems to me to be the relevant output:
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.17=0
- feature:|@/linux-64::__glibc==2.17=0
- biopython=1.72 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- cudatoolkit=10.0 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
- dssp=3.0.0 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- matplotlib=3.1.1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- numpy=1.17.3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- pandas=1.1.4 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- pdbfixer=1.5 -> openmm[version='>=7.2.0'] -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
- ptitprince=0.2.5 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- python=3.6 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- pyyaml=5.3.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scikit-learn=0.24.0 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scipy=1.5.3 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.17
Do you have an environment.yml file available for the environment? I'm wondering if installing that way would make a difference at all. I'll also try installing with miniconda and/or mambaforge as well.
RHEL 7.9, anaconda3/2022.05 (conda 4.13.0)
How to use RaSP to calculate the stability of protein by inputting PDB file.
Hello! I am appreciated your job and want to use your software to calculate the stability of algal protein by the PDB file. Could you offer a process to help me? Thank you and best wishes.
colab notebook issue
Hi!
Thanks for sharing this method, I'm really looking forward to testing it.
I'm trying to use the colab notebook with default settings ie just pressing "rull all" (with a T4 GPU). The notebook crashes at "PRELIMINARY OPERATIONS: Retrieve parameters and RaSP files". Any help getting it working would be appreciated, thanks!
best wishes,
Nick
[BUG] Colab Notebook cannot retrieve RaSP files
Thanks for this great tool.
I succesfully ran the Colab notebook on 2024-01-08.
However, I've have been trying to re-run again since then but it the cell Retrieve RaSP files and parameters does not work. This is the error message:
---> Github data imported!
----> reduce installed
mv: cannot stat 'ds_models': No such file or directory
mv: cannot stat 'cavity_models': No such file or directory
mv: cannot move '/content/colab_additional/best_model_path.txt' to '/content/output/cavity_models/': Not a directory
mv: cannot move '/content/colab_additional/clean_pdb.py' to '/content/src/pdb_parser_scripts/': No such file or directory
mv: cannot move '/content/colab_additional/helpers.py' to '/content/src/': Not a directory
bash: line 41: cd: src/pdb_parser_scripts: No such file or directory
Cloning into 'reduce'...
mv: cannot move '/content/colab_additional/reduce' to '/content/src/pdb_parser_scripts/reduce/': No such file or directory
chmod: cannot access '/content/src/pdb_parser_scripts/reduce/reduce': No such file or directory
Is it perhaps related to Github sunsetting SVN support on Jan 8th 2024? https://github.blog/changelog/2024-01-08-subversion-has-been-sunset/
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.