Bonds between atoms are represented in the code by a Bond class, which defines the arity, optimal bond length, etc.
The Bond object also contains two Atom* members, named "atom" and (foolishly) "btom". These are supposed to point to the two atoms that share the particular bond represented by the Bond object.
Each Atom object has an array of Bonds called bonded_to. The way the code works is that every bond involving any given Atom will appear in that Atom's bonded_to. That means bonds are reciprocal; in an example C=O bond the C atom's bonded_to has a Bond with the "btom" pointing to the O, and the O has a bonded_to with the "btom" pointing to the C.
The bug is that some of the bonds are coming up as not reciprocal at runtime. The "btom" is variously either being overwritten with nonsense values or turning up null. This is causing all sorts of problems, one of which was incorrect clashes in the mol_assem_tests, for which the easy temporary solution was the following atrocity:
if (atoms[i]->is_bonded_to(atoms[j]) || atoms[j]->is_bonded_to(atoms[i]))
It will not be out of scope to this issue or its PR to change the name of "btom" to something less idiotic.
Bonds between atoms are represented in the code by a
Bondclass, which defines the arity, optimal bond length, etc.The
Bondobject also contains twoAtom*members, named "atom" and (foolishly) "btom". These are supposed to point to the two atoms that share the particular bond represented by theBondobject.Each
Atomobject has an array ofBonds calledbonded_to. The way the code works is that every bond involving any givenAtomwill appear in thatAtom'sbonded_to. That means bonds are reciprocal; in an example C=O bond the C atom'sbonded_tohas aBondwith the "btom" pointing to the O, and the O has abonded_towith the "btom" pointing to the C.The bug is that some of the bonds are coming up as not reciprocal at runtime. The "btom" is variously either being overwritten with nonsense values or turning up null. This is causing all sorts of problems, one of which was incorrect clashes in the
mol_assem_tests, for which the easy temporary solution was the following atrocity:It will not be out of scope to this issue or its PR to change the name of "btom" to something less idiotic.