Snakefile_site_screen

import os
import json
import pandas as pd
import ase.io

# get target filenames and import paths for software.

df = pd.read_csv('data/input.smi', delimiter = '\t', names = ['hmdb_id', 'smiles'])
ids = df['hmdb_id'].tolist()
targets = []
for theID in ids:
    for thecharge in os.listdir('results/' + theID):
        targets.append('results/' + theID + '/' + thecharge + '/site_screen/0.in')

with open('paths.json', 'r') as f:
    paths = json.load(f)

# Snakemake rules

rule all:
     input: targets

rule starting_structure:
     input: "results/{hmdb_id}/{adduct}/model.smi"
     output: "results/{hmdb_id}/{adduct}/site_screen/0.in"
     shell: 
     	    """
	    mkdir -p results/{wildcards.hmdb_id}/{wildcards.adduct}/site_screen
	    src/make_models.py {input} results/{wildcards.hmdb_id}/{wildcards.adduct}/site_screen/
	    """