. Author manuscript; available in PMC: 2026 Apr 15.

Published in final edited form as: J Comput Chem. 2026 Jan 15;47(2):e70312. doi: 10.1002/jcc.70312

Table 3.

Growth, pruning, and final outcomes for molecules constructed during de novo design.

	Growth outcomes ^a		Pruning outcomes ^b				Final outcomes ^c
Index	Type	Action	Lsize	MolProp	hRMSD	Rsize	Fate	Filename label
1	finalized	APs filled	n/a	pass	n/a	n/a	Retained	DN build (primary)
2	finalized	APs filled	n/a	fail	n/a	n/a	Pruned	filtered.i (aux^d)
3	root candidate	APs capped	fail	fail	n/a	n/a	Pruned	prune root.i (aux)
4	root candidate	APs capped	n/a	n/a	fail	n/a	Pruned	prune rmsd.i (aux)
5	root candidate	APs capped	n/a	n/a	n/a	fail	Pruned	root ignore.i (aux)
6	propagated	APs remain	pass	pass	pass	pass	Advanced	root.i (aux)

Growth outcome types include "finalized", "root candidate", or "propagated".

Pruning outcomes depend on growth outcome types and include removal when molecules fail to adhere to parameter values or ranges specified in the input file with regards to user-defined layer size (Lsize), molecular properties (MolProp), Hungarian-based RMSD (hRMSD), and root size (Rsize).

Final outcomes involve being "Retained" and written to the primary output file (multi-mol2 format), "Pruned" and written to one of several auxiliary output files (if desired) using a layer-based index i, or "Advanced" as roots for the next layer of growth.

Shorthand for auxiliary.