Comments (4)
@jadolfbr I feel the problem as well. We wrap the execution in a separate script that deletes the intermediate files as well.
from proteinmpnn.
I think this is a good point from other point of view, since splited scripts could be used in other task. For instance, the parse_multiple_chains.py
could be used to process PDB file in a more understandable way.
But I'm just a user of this instead of the developer of this project, my point may go wrong direction.
from proteinmpnn.
The initial idea was to process inputs and save them into dictionaries in case they need to be run multiple times with different models, or with different settings. Moreover, one can easily check if parsing was done correctly for the inputs by looking at jsonl files. There is a more streamlined way to use the code too, e.g.
path_to_PDB="../inputs/PDB_complexes/pdbs/3HTN.pdb"
output_dir="../outputs/example_3_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
chains_to_design="A B"
python ../protein_mpnn_run.py \
--pdb_path $path_to_PDB \
--pdb_path_chains "$chains_to_design" \
--out_folder $output_dir \
--num_seq_per_target 2 \
--sampling_temp "0.1" \
--seed 37 \
--batch_size 1
from proteinmpnn.
from proteinmpnn.
Related Issues (20)
- Questions about model weights
- .Fa Output reorganization question
- Sampling temperature for flexible chains
- what pdbx package does parse_cif_noX.py expect? HOT 1
- Global_score
- No use of GPU?
- jsonl file to pdb
- --omit_AA "CM" parameter?
- How to confirm the global polar amino acid bias value? What is the meaning of 1.39?
- whether to redesign low confidence aas
- Design complexes with unknown chains (proposed fix included)
- Amino acid sequence has too many "K/E" HOT 2
- How do I use a PSSM with proteinMPNN?
- Need of assistance and advising
- Model is adding an amino acid to the original sequence HOT 5
- Creates hydrophobic surface patches wit many Ala side chains HOT 2
- Training time HOT 1
- What is the difference between --conditional_probs_only_backbone and --unconditional_probs_only HOT 1
- Empty parsed_pdbs.jsonl file from parse_multiple_chains.py helper script? HOT 1
- RuntimeError: Class values must be smaller than num_classes. | protein_mpnn_utils.py & mask_size issue?
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π 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. πππ
-
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 β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from proteinmpnn.