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feat: descriptor calculations using RDKit
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from rdkit import Chem | ||
from rdkit.Chem import Descriptors, QED, Lipinski, rdMolDescriptors, rdmolops | ||
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def checkRo5Violations(mol): | ||
"""Takes a molecules and checks whether the molecule violates | ||
the Lipinski's Rule of Five. | ||
Args : molecules rdkit.Chem.rdmol.Mol: rdkit_mol Objects | ||
Returns (int): A number of violations on Lipinski Rules. | ||
""" | ||
num_of_violations = 0 | ||
if Descriptors.MolLogP(mol) > 5: | ||
rule_break += 1 | ||
if Descriptors.MolWt(mol) > 500: | ||
rule_break += 1 | ||
if Lipinski.NumHAcceptors(mol) > 10: | ||
rule_break += 1 | ||
if Lipinski.NumHDonors(mol) > 5: | ||
rule_break += 1 | ||
return num_of_violations | ||
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def GetBasicDescriptors(smiles): | ||
"""Take an input SMILES and generates a selected set of molecular | ||
descriptors as a dictionary | ||
Args (str): SMILES string | ||
Returns (dict): a dictionary of calculated descriptors | ||
""" | ||
mol = Chem.MolFromSmiles(smiles) | ||
AtomC = rdMolDescriptors.CalcNumAtoms(mol) | ||
HeavyAtomsC = rdMolDescriptors.CalcNumHeavyAtoms(mol) | ||
MolWt = "%.2f" % Descriptors.MolWt(mol) | ||
ExactMolWt = "%.2f" % Descriptors.ExactMolWt(mol) | ||
ALogP = "%.2f" % QED.properties(mol).ALOGP | ||
NumRotatableBonds = rdMolDescriptors.CalcNumRotatableBonds(mol) | ||
PSA = "%.2f" % rdMolDescriptors.CalcTPSA(mol) | ||
HBA = Descriptors.NumHAcceptors(mol) | ||
HBD = Descriptors.NumHDonors(mol) | ||
Lipinski_HBA = Lipinski.NumHAcceptors(mol) | ||
Lipinski_HBD = Lipinski.NumHDonors(mol) | ||
Ro5Violations = checkRo5Violations(mol) | ||
AromaticRings = rdMolDescriptors.CalcNumAromaticRings(mol) | ||
QEDWeighted = "%.2f" % QED.qed(mol) | ||
FormalCharge = "%.2f" % rdmolops.GetFormalCharge(mol) | ||
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AllDescriptors = { | ||
"Atom count": AtomC, | ||
"Heavy atom count": HeavyAtomsC, | ||
"Molecular weight": MolWt, | ||
"Exact molecular weight": ExactMolWt, | ||
"ALogP": ALogP, | ||
"Rotatable bond count": NumRotatableBonds, | ||
"Topological polar surface area": PSA, | ||
"Hydrogen bond acceptors": HBA, | ||
"Hydrogen bond donors": HBD, | ||
"Hydrogen bond acceptors(Lipinski)": Lipinski_HBA, | ||
"Hydrogen bond donors(Lipinski)": Lipinski_HBD, | ||
"Lipinski's rule of five violations": Ro5Violations, | ||
"Aromatic rings count": AromaticRings, | ||
"QED drug likeliness": QEDWeighted, | ||
"Formal Charge": FormalCharge, | ||
} | ||
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return AllDescriptors |
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