Update README.md
Browse files
README.md
CHANGED
@@ -49,7 +49,7 @@ running the model in zero-shot is that it doesn't require any further training.
|
|
49 |
### **Example 1: Generating nitrilases (EC 3.5.5.1)**
|
50 |
|
51 |
The script below will be used for the generation of any BRENDA class in a zero-shot fashion,
|
52 |
-
here we showcase the generation of novel
|
53 |
|
54 |
To run this script, you should download ZymCTRL to a local folder in your workstation.
|
55 |
Then replace the placeholders in the script with your actual folder path.
|
@@ -62,8 +62,8 @@ it will store the sequence's computed perplexity value. Perplexity is a measure
|
|
62 |
in that generation, with lower values being better. The sequences are ordered by perplexity before writing them out,
|
63 |
so those that finish in *_0.fasta and *_1.fasta will be the best ones per batch.
|
64 |
|
65 |
-
**Given that generation runs so fast, we recommend generating hundreds or thousands and then only picking the best 5
|
66 |
-
With the script below, that would mean picking only those that finish in '_0.fasta'
|
67 |
|
68 |
```
|
69 |
import torch
|
|
|
49 |
### **Example 1: Generating nitrilases (EC 3.5.5.1)**
|
50 |
|
51 |
The script below will be used for the generation of any BRENDA class in a zero-shot fashion,
|
52 |
+
here we showcase the generation of novel nitrilases.
|
53 |
|
54 |
To run this script, you should download ZymCTRL to a local folder in your workstation.
|
55 |
Then replace the placeholders in the script with your actual folder path.
|
|
|
62 |
in that generation, with lower values being better. The sequences are ordered by perplexity before writing them out,
|
63 |
so those that finish in *_0.fasta and *_1.fasta will be the best ones per batch.
|
64 |
|
65 |
+
**Given that generation runs so fast, we recommend generating hundreds or thousands and then only picking the best 5% or less.
|
66 |
+
With the script below, that would mean picking only those that finish in '_0.fasta'. Good perplexity values for this model so be below 1.75-1.5.**
|
67 |
|
68 |
```
|
69 |
import torch
|