Glossary
- graph
A collection of nodes connected by edges.
- chemical graph
A graph where atoms are nodes and bonds are edges.
- molecular graph
A connected chemical graph representing a single molecule.
- complete chemical graph
- complete molecular graph
A chemical graph or molecular graph with all atoms and bonds present where all atoms have known elements and formal charges and all bonds have known bond orders. Contrast connectivity graph.
- connectivity graph
A chemical graph that includes all bonds and atoms, but not necessarily their formal charges or bond orders; ie, it defines the connectivity of a chemical system. Contrast molecular graph, chemical graph.
- connected
A connected graph is one in which for any two nodes \(a\) and \(b\) there exists some collection of edges that form a path from \(a\) to \(b\). That is, you can’t split the graph into subgraphs that have no edges between them.
- linking atom
An atom in a residue or residue definition that forms a bond with an atom in another residue.
- leaving atom
An atom in a residue or residue definition that is removed when a bond between linking atoms is formed.