Commit 1929c57e authored by hgarrereyn's avatar hgarrereyn
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update readme

parent 1e9600fe
......@@ -5,24 +5,25 @@
Utility script to generate fingerprints for a set of smiles strings. By precomputing the fingerprints for all the fragments in our dataset, we can speed up training.
To use, pass in the `fragments.h5` file created by the `process_pdbbind.py` script and specify the fingerprint type and output path.
To use, pass in the `moad.h5` file and specify the fingerprint type and output path.
Supported fingerprints:
- `rdk`: RDKFingerprint (2048 bits)
- `rdk10`: RDKFingerprint (path size 10) (2048 bits)
- `morgan`: Mogan fingerprint (r=2) (2048 bits)
- `gobbi2d`: Gobbi 2d pharmophocore fingerprint (folded to 2048 bits)
Usage:
```
usage: make_fingerprints.py [-h] -f FRAGMENTS -fp {rdk,morgan,gobbi2d}
usage: make_fingerprints.py [-h] -f FRAGMENTS -fp {rdk,rdk10,morgan,gobbi2d}
[-o OUTPUT]
optional arguments:
-h, --help show this help message and exit
-f FRAGMENTS, --fragments FRAGMENTS
Path to fragemnts.h5 containing "frag_smiles" array
-fp {rdk,morgan,gobbi2d}, --fingerprint {rdk,morgan,gobbi2d}
-fp {rdk,rdk10,morgan,gobbi2d}, --fingerprint {rdk,rdk10,morgan,gobbi2d}
Which fingerprint type to generate
-o OUTPUT, --output OUTPUT
Output file path (.h5)
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