Consider the following Python code, which is meant to count the number of molecules in molecules.sdf that pass Lipinski's rule of fives:

from rdkit import Chem
from rdkit.Chem import AllChem, Crippen, Lipinski

mols = [mol for mol in Chem.SDMolSupplier("molecules.sdf") if mol is not None]

cnt = 0
for m in mols:
mw = 1 if AllChem.CalcExactMolWt(m)

Question

Consider the following Python code, which is meant to count the number of molecules in molecules.sdf that pass Lipinski's rule of fives:

from rdkit import Chem
from rdkit.Chem import AllChem, Crippen, Lipinski

mols = [mol for mol in Chem.SDMolSupplier("molecules.sdf") if mol is not None]

cnt = 0
for m in mols:
    mw = 1 if AllChem.CalcExactMolWt(m) <= 500 else 0
    logp = 1 if Crippen.MolLogP(m) <= 5 else 0
    hd = 1 if Lipinski.NumHDonors(m) <= 5 else 0
    ha = 1 if Lipinski.NumHAcceptors(m) <= 10 else 0

num_pass = mw + logp + hd + ha

# Modified rule: incorrectly rejects molecules with even one violation
    if num_pass == 4:  
        cnt += 1

print(cnt)

What is wrong with this code?

BlackTom AI · Accepted Answer

Let’s break down the question and each proposed option to understand what’s faulty in this snippet. Option 1: 'The script incorrectly loads molecules because Chem.SDMolSupplier("molecules.sdf") does not return a list.' In this code, the author converts the supplier into a list with a list comprehension: mols = [mol for mol in Chem.SDMolSupplier("molecules.sdf") if mol is not None]. RDKit’s SDMolSupplier returns an iterable generator-like object, which is perfectly valid to iterate over or to materialize into a list as done here. Therefore, this option mischaracterizes how RDKit supplies molecules and is not the real bug. Option 2: 'It incorrectly calculates molecular weight using AllChem.CalcExactMolWt(m), which is not an RDKit function.' Actually, CalcExactMolWt is a valid RDKit function (in the AllChem module). The code uses it correctly, so this statement is false about the code’s behavior. Option 3: 'It does not allow for one violation of the four criteria, which contradicts the rule’s original intent.' This is the core issue. Lipinski’s rule of five is typically interpreted as: a molecule passes if it meets at least three of the four criteria, and many formulations allow at most one violation among the four (i.e., 0 or 1 violations). The code, however, requires all four criteria to pass (num_pass == 4) to count the molecule, which means it rejects molecules that have a single violation even though the standard rule would still consider them acceptable. Thus this option correctly identifies the bug: the logic is too strict and does not reflect the intended “up to one violation” tolerance. Option 4: 'The code should be using >= instead of <= in the threshold conditions.' Let’s check each threshold: MW <= 500, logP <= 5, H-donors <= 5, H-acceptors <= 10. These are conventional “no more than” limits. Using >= would invert the logic and count far more molecules as passing, which is not correct for the rule of five. So this option misstates the needed comparison and is not accurate. Option 5: 'The code should count the number of violations instead of the number of passing criteria.' While counting violations is a possible alternative approach, it isn’t an inherent requirement or the fundamental flaw here. The given criteria are four independent checks; counting passes is a valid way to implement the typical rule (with an allowance for up to one violation). Saying you must count violations changes the framing but isn’t the specific bug explained in the prompt. Therefore, this option doesn’t accurately describe the methodological error in the code as written. Across the options, the most accurate diagnosis centers on Option 3: the code enforces four passing criteria, ignoring the standard allowance of up to one violation, which is the core mismatch with Lipinski’s rule of five.

2254 BIOSC 1544 SEC1000 Exam #2

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