Fix incorrect comparison logic in operator< / difference_from#696
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lyskov-ai wants to merge 2 commits into
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Fix incorrect comparison logic in operator< / difference_from#696lyskov-ai wants to merge 2 commits into
lyskov-ai wants to merge 2 commits into
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Four independent classes had broken comparison logic that violated either the contract of `operator<` (strict weak ordering) or the intended semantics of `difference_from`: * `core/chemical/sdf/mol_util.cc`: `BondData::operator<` was `(lower < other.lower) || (upper < other.upper)`. This is not a strict weak ordering — for `(5,1)` vs `(3,7)`, both compare less than each other, breaking antisymmetry. `BondData` is used inside `std::set<BondData>` (see `parse_bond_type_data`), so the broken ordering directly affects the set. Replaced with a proper lexicographic compare via `std::tie`. * `core/scoring/motif/motif_hash_stuff.cc`: `ResPairMotif::operator<` returned `0 < memcmp(...)`, i.e. it reported "less than" exactly when memcmp said "greater than" — the comparison was inverted. Switched to `memcmp(...) < 0`, which matches the correct convention (and matches `MotifHit::operator<` in the same file). * `core/io/StructFileReaderOptions.cc`: `operator<` was using `==` instead of `!=` for the short-circuit "return false" lines. The intent of the pattern is "if a < b return true; if a != b return false; otherwise fall through to the next member" (this is exactly what the parent `StructFileRepOptions::operator<` does), but the `==` form returned false when members were equal — short-circuiting before the rest of the members were ever compared, *and* failed to return false when members satisfied `>`. Fixed every `==` to `!=` and added the missing `!=` follow-up after `glycam_pdb_format_`. * `core/chemical/gasteiger/GasteigerAtomTypeData.cc`: `difference_from` short-circuited "return Other" when `charge_ == OTHER.charge_ || element_type_ != ... || ...`. The first clause is inverted: the function should return Other when these fundamental properties *differ*, not when they match. Otherwise, two types with equal charge but otherwise comparable properties were misclassified as `Other` and the rest of the function (which uses `charge_` to compute lone-pair / s-orbital / p-orbital differences) was unreachable. Fixed `==` to `!=`.
Brief one-paragraph notes above each of the four sites describing the bug and why the corrected form is the right one, so a future reader doesn't accidentally revert to the simpler-looking but broken version.
roccomoretti
approved these changes
May 18, 2026
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Summary
Four independent classes had broken comparison logic that violated either the contract of `operator<` (strict weak ordering) or the intended semantics of `difference_from`. Each is a separate, surgical fix bundled into a single PR because they all share the same "comparison-operator misuse" theme.
`core/chemical/sdf/mol_util.cc` — `BondData::operator<` was `(lower < other.lower) || (upper < other.upper)`. This is not a strict weak ordering: for example, `(5, 1)` and `(3, 7)` each compare less than the other, breaking antisymmetry. `BondData` is held in `std::set` (see `parse_bond_type_data`), so the broken ordering directly affects the set. Replaced with a proper lexicographic compare via `std::tie`.
`core/scoring/motif/motif_hash_stuff.cc` — `ResPairMotif::operator<` returned `0 < memcmp(...)`, which is true exactly when `memcmp` says this > other; the comparison was inverted. Switched to `memcmp(...) < 0` (matches `MotifHit::operator<` in the same file).
`core/io/StructFileReaderOptions.cc` — `operator<` used `==` instead of `!=` for the short-circuit `return false` lines. The intended pattern (used correctly by the parent `StructFileRepOptions::operator<` and by `ImportPoseOptions::operator<`) is `if a < b return true; if a != b return false; // fall through`. The `==` form returns false when members are equal, short-circuiting before the rest of the members are compared, and falls through when one member is greater. Fixed every `==` to `!=` and added the missing `!=` follow-up after `glycam_pdb_format_`.
`core/chemical/gasteiger/GasteigerAtomTypeData.cc` — `difference_from` short-circuited `return Other` when `charge_ == OTHER.charge_ || element_type_ != ... || ...`. The first clause is inverted: the function should return `Other` when fundamental properties differ, not when they match. The bug also made the lone-pair / s-orbital / p-orbital classification logic below this check unreachable for any two types with equal charge. Fixed `==` to `!=`.