Molecule.atomselect doesn't recognize numbonds. This is a deviation from the original VMD implementation (https://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node87.html)
from moleculekit.molecule import Molecule
mol = Molecule('3PTB')
mol.atomselect('numbonds = 2')
RuntimeError: Failed to parse selection numbonds = 2 with error Syntax error at ''numbonds''
Molecule.atomselectdoesn't recognizenumbonds. This is a deviation from the original VMD implementation (https://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node87.html)