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evaluate_confs.py
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import pickle, random
from argparse import ArgumentParser
from multiprocessing import Pool
import numpy as np
import pandas as pd
from rdkit import Chem
from rdkit.Chem import AllChem
from tqdm import tqdm
parser = ArgumentParser()
parser.add_argument('--confs', type=str, required=True, help='Path to pickle file with generated conformers')
parser.add_argument('--test_csv', type=str, default='./data/DRUGS/test_smiles_corrected.csv', help='Path to csv file with list of smiles')
parser.add_argument('--true_mols', type=str, default='./data/DRUGS/test_mols.pkl', help='Path to pickle file with ground truth conformers')
parser.add_argument('--n_workers', type=int, default=1, help='Numer of parallel workers')
parser.add_argument('--limit_mols', type=int, default=0, help='Limit number of molecules, 0 to evaluate them all')
parser.add_argument('--dataset', type=str, default="drugs", help='Dataset: drugs, qm9 and xl')
parser.add_argument('--filter_mols', type=str, default=None, help='If set, is path to list of smiles to test')
parser.add_argument('--only_alignmol', action='store_true', default=False, help='If set instead of GetBestRMSD, it uses AlignMol (for large molecules)')
args = parser.parse_args()
"""
Evaluates the RMSD of some generated conformers w.r.t. the given set of ground truth
Part of the code taken from GeoMol https://github.com/PattanaikL/GeoMol
"""
with open(args.confs, 'rb') as f:
model_preds = pickle.load(f)
test_data = pd.read_csv(args.test_csv) # this should include the corrected smiles
with open(args.true_mols, 'rb') as f:
true_mols = pickle.load(f)
threshold = threshold_ranges = np.arange(0, 2.5, .125)
def calc_performance_stats(rmsd_array):
coverage_recall = np.mean(rmsd_array.min(axis=1, keepdims=True) < threshold, axis=0)
amr_recall = rmsd_array.min(axis=1).mean()
coverage_precision = np.mean(rmsd_array.min(axis=0, keepdims=True) < np.expand_dims(threshold, 1), axis=1)
amr_precision = rmsd_array.min(axis=0).mean()
return coverage_recall, amr_recall, coverage_precision, amr_precision
def clean_confs(smi, confs):
good_ids = []
smi = Chem.MolToSmiles(Chem.MolFromSmiles(smi, sanitize=False), isomericSmiles=False)
for i, c in enumerate(confs):
conf_smi = Chem.MolToSmiles(Chem.RemoveHs(c, sanitize=False), isomericSmiles=False)
if conf_smi == smi:
good_ids.append(i)
return [confs[i] for i in good_ids]
rdkit_smiles = test_data.smiles.values
corrected_smiles = test_data.corrected_smiles.values
if args.limit_mols:
rdkit_smiles = rdkit_smiles[:args.limit_mols]
corrected_smiles = corrected_smiles[:args.limit_mols]
num_failures = 0
results = {}
jobs = []
filter_mols = None
if args.filter_mols:
with open(args.filter_mols, 'rb') as f:
filter_mols = pickle.load(f)
for smi, corrected_smi in tqdm(zip(rdkit_smiles, corrected_smiles)):
if filter_mols is not None and corrected_smi not in filter_mols:
continue
if args.dataset == 'xl':
smi = corrected_smi
if corrected_smi not in model_preds:
print('model failure', corrected_smi)
num_failures += 1
continue
true_mols[smi] = true_confs = clean_confs(corrected_smi, true_mols[smi])
if len(true_confs) == 0:
print(f'poor ground truth conformers: {corrected_smi}')
continue
n_true = len(true_confs)
n_model = len(model_preds[corrected_smi])
results[(smi, corrected_smi)] = {
'n_true': n_true,
'n_model': n_model,
'rmsd': np.nan * np.ones((n_true, n_model))
}
for i_true in range(n_true):
jobs.append((smi, corrected_smi, i_true))
def worker_fn(job):
smi, correct_smi, i_true = job
true_confs = true_mols[smi]
model_confs = model_preds[correct_smi]
tc = true_confs[i_true]
rmsds = []
for mc in model_confs:
try:
if args.only_alignmol:
rmsd = AllChem.AlignMol(Chem.RemoveHs(tc), Chem.RemoveHs(mc))
else:
rmsd = AllChem.GetBestRMS(Chem.RemoveHs(tc), Chem.RemoveHs(mc))
rmsds.append(rmsd)
except:
print('Additional failure', smi, correct_smi)
rmsds = [np.nan] * len(model_confs)
break
return smi, correct_smi, i_true, rmsds
def populate_results(res):
smi, correct_smi, i_true, rmsds = res
results[(smi, correct_smi)]['rmsd'][i_true] = rmsds
random.shuffle(jobs)
if args.n_workers > 1:
p = Pool(args.n_workers)
map_fn = p.imap_unordered
p.__enter__()
else:
map_fn = map
for res in tqdm(map_fn(worker_fn, jobs), total=len(jobs)):
populate_results(res)
if args.n_workers > 1:
p.__exit__(None, None, None)
stats = []
for res in results.values():
stats_ = calc_performance_stats(res['rmsd'])
cr, mr, cp, mp = stats_
stats.append(stats_)
coverage_recall, amr_recall, coverage_precision, amr_precision = zip(*stats)
for i, thresh in enumerate(threshold_ranges):
print('threshold', thresh)
coverage_recall_vals = [stat[i] for stat in coverage_recall] + [0] * num_failures
coverage_precision_vals = [stat[i] for stat in coverage_precision] + [0] * num_failures
print(f'Recall Coverage: Mean = {np.mean(coverage_recall_vals) * 100:.2f}, Median = {np.median(coverage_recall_vals) * 100:.2f}')
print(f'Recall AMR: Mean = {np.nanmean(amr_recall):.4f}, Median = {np.nanmedian(amr_recall):.4f}')
print(f'Precision Coverage: Mean = {np.mean(coverage_precision_vals) * 100:.2f}, Median = {np.median(coverage_precision_vals) * 100:.2f}')
print(f'Precision AMR: Mean = {np.nanmean(amr_precision):.4f}, Median = {np.nanmedian(amr_precision):.4f}')
print(len(results), 'conformer sets compared', num_failures, 'model failures', np.isnan(amr_recall).sum(),
'additional failures')