santuchal / molecule_descriptors_and_fingerprint Goto Github PK

python fingerprint_and_descriptor.py --input_file data/smiles_input.csv --output_file data/smile.csv --remove_salt --method descriptors

You can run this application in three way:

1. Only Descriptor

2. Only Fingerprint

3. Descriptor and Fingerprint combined

4. When you are need only the descriptor file you need run as :

python fingerprint_and_descriptor.py --input_file data/smiles_input.csv --output_file data/smile.csv --remove_salt --method descriptor

It'll produce your _descriptor.csv with the necessary header and value.

2. When you are needed for fingerprint you need to run :

python fingerprint_and_descriptor.py --input_file data/smiles_input.csv --output_file data/smile.csv --remove_salt --method fingerprint --fp_type Morgan --n_bits 1024

In fingerprint types there are 5 different types of fingerprint added:

Default fingerprint type is Morgan and default n_bits is 2048

As an output it'll produce _fingerprint.csv

3. When you need both descriptor and fingerprint together, you need to run :

python fingerprint_and_descriptor.py --input_file data/smiles_input.csv --output_file data/smile.csv

It'll give you output as _descriptor_and_fingerprint.csv

There is also another parameter added to removing salts from the smiles. If you want to remove salts from molecule you need to add --remove_salt as a parameter in your cli. By default the remove_salt parameter is off.