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