Chemical Validity Checker

Validates that every atom in a generated structure adheres to standard valence rules. The filter parses the molecular graph and verifies that each atom's explicit bond count plus implicit hydrogen count matches its allowed valence states.

• Carbon must have exactly 4 bonds
• Nitrogen typically has 3 or 5 bonds
• Oxygen typically has 2 bonds
• Sulfur can have 2, 4, or 6 bonds

Example: A SMILES string like CC(C)(C)C is valid (quaternary carbon with 4 bonds), while CC(C)(C)(C)C would be rejected for pentavalent carbon.

Identifies and validates aromatic ring systems using Hückel's rule and electron counting algorithms. The checker detects conjugated cyclic systems and verifies they contain 4n+2 π electrons.

• Recognizes benzene, pyridine, pyrrole, furan, and fused polycyclic aromatics
• Distinguishes aromatic from anti-aromatic and non-aromatic rings
• Assigns correct aromatic bond types in Kekulé representations

Common failure mode: Generated SMILES with alternating single/double bonds in a 4-membered ring, which cannot sustain aromaticity.

Enforces physical distance constraints between bonded and non-bonded atoms. The filter calculates interatomic distances from 3D conformer generation or graph topology and flags violations of van der Waals radii.

• Rejects structures with overlapping atoms (steric clash)
• Validates that bond lengths fall within expected ranges for each bond type
• Detects impossibly strained small rings (e.g., cyclopropyne)

Example: A generated molecule with two methyl groups occupying the same spatial coordinates would be discarded as physically impossible.

Parses generated SMILES strings against a formal grammar to catch syntax errors before structural interpretation. This lightweight pre-check catches malformed outputs that would crash downstream cheminformatics toolkits.

• Validates matching parentheses for branches
• Checks correct ring closure digit pairing
• Verifies atom bracket syntax for isotopes and charges
• Rejects illegal characters and malformed tokens

Example: C1CCCCC (unclosed ring) and C(C(O (unmatched parenthesis) are caught at the syntax level before any chemical rule evaluation.

Ensures that the total formal charge and radical electron count of the molecule are chemically plausible. The checker sums formal charges across all atoms and flags structures with unreasonable net charges or unpaired electrons.

• Rejects molecules with net charges exceeding ±3 for drug-like compounds
• Flags persistent free radicals that would be unstable under physiological conditions
• Validates zwitterionic forms have balanced internal charges

Example: A generated carboxylate without a corresponding cation would be flagged for charge imbalance unless explicitly modeled as an ion.

Detects contradictory bond assignments where a single atom participates in more bonds than its valence permits. This checker operates on the molecular graph representation and catches errors that survive syntax parsing.

• Identifies atoms with bond order sum exceeding maximum valence
• Flags ambiguous bond types in resonance structures
• Validates that triple bonds are geometrically feasible

Example: A carbon atom with two double bonds and one single bond (bond order sum = 5) would be rejected, as carbon's maximum valence is 4.