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import warnings |
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import numpy as np |
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from loguru import logger |
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from sklearn.ensemble import RandomForestRegressor |
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from rdkit.Chem import Descriptors, rdMolDescriptors |
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import joblib |
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from transformation import TransformFunction |
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from rdkit import Chem, rdBase, DataStructs |
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from rdkit.Chem import AllChem |
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from typing import List |
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def fingerprints_from_mol(molecule, radius=3, size=2048, hashed=False): |
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""" |
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Create ECFP fingerprint of a molecule |
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""" |
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if hashed: |
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fp_bits = AllChem.GetHashedMorganFingerprint(molecule, radius, nBits=size) |
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else: |
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fp_bits = AllChem.GetMorganFingerprintAsBitVect(molecule, radius, nBits=size) |
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fp_np = np.zeros((1,)) |
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DataStructs.ConvertToNumpyArray(fp_bits, fp_np) |
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return fp_np.reshape(1, -1) |
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def fingerprints_from_smiles(smiles: List, size=2048): |
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""" Create ECFP fingerprints of smiles, with validity check """ |
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fps = [] |
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valid_mask = [] |
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for i, smile in enumerate(smiles): |
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mol = Chem.MolFromSmiles(smile) |
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valid_mask.append(int(mol is not None)) |
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fp = fingerprints_from_mol(mol, size=size) if mol else np.zeros((1, size)) |
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fps.append(fp) |
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fps = np.concatenate(fps, axis=0) if len(fps) > 0 else np.zeros((0, size)) |
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return fps, valid_mask |
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def getMolDescriptors(mol, missingVal=0): |
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""" calculate the full list of descriptors for a molecule """ |
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values, names = [], [] |
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for nm, fn in Descriptors._descList: |
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try: |
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val = fn(mol) |
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except: |
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val = missingVal |
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values.append(val) |
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names.append(nm) |
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custom_descriptors = {'hydrogen-bond donors': rdMolDescriptors.CalcNumLipinskiHBD, |
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'hydrogen-bond acceptors': rdMolDescriptors.CalcNumLipinskiHBA, |
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'rotatable bonds': rdMolDescriptors.CalcNumRotatableBonds,} |
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for nm, fn in custom_descriptors.items(): |
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try: |
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val = fn(mol) |
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except: |
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val = missingVal |
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values.append(val) |
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names.append(nm) |
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return values, names |
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def get_pep_dps_from_smi(smi): |
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try: |
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mol = Chem.MolFromSmiles(smi) |
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except: |
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print(f"convert smi {smi} to molecule failed!") |
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mol = None |
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dps, _ = getMolDescriptors(mol) |
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return np.array(dps) |
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def get_pep_dps(smi_list): |
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if len(smi_list) == 0: |
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return np.zeros((0, 211)) |
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return np.array([get_pep_dps_from_smi(smi) for smi in smi_list]) |
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"""def get_smi_from_helms(helm_seqs: list): |
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valid_idxes = [] |
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valid_smiles = [] |
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for idx, helm in enumerate(helm_seqs): |
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# Ignore helm which cannot converted into molecules |
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try: |
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smi = get_cycpep_smi_from_helm(helm) |
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if smi: |
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valid_idxes.append(idx) |
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valid_smiles.append(smi) |
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except Exception as e: |
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# logger.debug(f'Error: {e} in helm {helm}') |
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pass |
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return valid_smiles, valid_idxes""" |
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def check_smi_validity(smiles: list): |
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valid_smi, valid_idx = [], [] |
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for idx, smi in enumerate(smiles): |
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try: |
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mol = Chem.MolFromSmiles(smi) if smi else None |
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if mol: |
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valid_smi.append(smi) |
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valid_idx.append(idx) |
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except Exception as e: |
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pass |
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return valid_smi, valid_idx |
