Describe the bug
Because .connectivity only contains atoms with connections, unconnected atoms are omitted from .adjacency_dict. This revealed itself when I removed hydrogens from a protein structure and then had lots of floater O atoms that were missing from the adjacency_dict.
Fix
Need to add a key with an empty list of children to the adjacency dictionary for all indices not in the adjacency_dict after incorporating the .connectivity information.
.adjacency_matrix is OK because it is already has zeros for all elements.
Additional Context
Move these computational bits to qcinf? Annoying to need a third party library for this stuff. Mandates pynauty for qcio.
Describe the bug
Because
.connectivityonly contains atoms with connections, unconnected atoms are omitted from.adjacency_dict. This revealed itself when I removed hydrogens from a protein structure and then had lots of floaterOatoms that were missing from theadjacency_dict.Fix
Need to add a key with an empty list of children to the adjacency dictionary for all indices not in the adjacency_dict after incorporating the
.connectivityinformation..adjacency_matrixis OK because it is already has zeros for all elements.Additional Context
Move these computational bits to
qcinf? Annoying to need a third party library for this stuff. Mandatespynautyforqcio.